Question:
You will be presented with the full text of a biomedical research paper. Please write an abstract for this paper. Your response should include the abstract and no additional text.

Paper text:
the chromosome number in the donkey ( equus asinus ) is 2n= 62 , but 2n= 64 in the horse ( equus caballus ) .
in fact , a certain level of bidirectional sex genome compatibility does exist : when a male donkey and a female horse mate , they produce a mule , and when a stallion mates with a female donkey , a hinny is produced .
both are usually sterile , but in some cases a certain level of genome compatibility is found and female mules get pregnant , although embryo loss is quite frequent . among the different dna sequences making up a eukaryotic genome , highly repetitive dna sequences are considered good evolutionary markers , due to their capacity to change rapidly as compared to single gene sequences . these dnas are commonly associated with satellite dna fractions ( sat - dna ) and are usually localized in constitutive heterochromatin regions . their ability to rapidly alter their base composition can produce rapid divergence in equivalent chromosome domains .
this divergence can easily be observed , both within species and among closely related species .
this is the case , for example , with alphoid dna sequences in humans and other primates . during the last few years
, our research group has developed a method , whole comparative genomic hybridization ( w - cgh ) , which allows the identification of chromosomal polymorphisms related to sat - dnas localized in constitutive heterochromatin .
w - cgh acts by detecting polymorphisms on the basis of competition between two different genomic dnas in the experimental conditions of in situ hybridization , without subtraction of highly repetitive dna sequences .
this technique has been used in several related species and/or individuals or populations belonging to the same species .
these differences are easily assessed when the y chromosome in boar is targeted . on the contrary , this differentiation was not noticeable when different ram breeds were compared . given the genetically - imposed lack of homologous recombination on y chromosomes , the rate of sequence evolution within these chromosomes is usually higher than that in autosomes .
furthermore , the y chromosome tends to be unusually rich in repetitive dnas , due to both transposable elements and tandem arrays of sat - dna sequences .
the aim of this preliminary work was to characterize donkey and horse y chromosome highly repetitive dna sequences , to understand resemblances and differences between the two y chromosomes isolated approximately 2 my ago .
whole genomic dna was obtained from the peripheral blood of one stallion and one male donkey .
the stallion was a pure spanish breed and the donkey a spanish breed ( zamorano - leons ) in danger of extinction .
peripheral blood lymphocytes were extracted and cultured for 72h in rpmi 1640 ( gibco , invitrogen corporation , carlsbad , ca , usa ) . this medium was supplemented with 1.5% phytohaemagglutinin , 10% fetal calf serum and antibiotics .
chromosomes were obtained using cells arrested at metaphase with colcemid ( 10 mg / ml ) for 90 minutes .
chromosome slides were prepared by exposing the cell suspension to 0.075 m kcl for 20 minutes and rapidly fixing it in fresh fixative ( methanol - acetic 3:1 ) . to obtain metaphase cells ,
fixed lymphocytes were spread onto clean slides and allowed to dry . for the w - cgh experiment , stallion and donkey dnas
the final concentration of each dna sample was carefully measured using a dna - spectrophotometer ( amersham - pharmacia biotech , piscataway , nj , usa ) .
two dna samples of equivalent concentration were labelled with biotin-14-dutp ( h : horse ) and digoxigenin-11-dutp ( d : donkey ) , employing a commercial nick translation kit ( roche diagnostics corporation , indianapolis , in , usa ) . after dna labelling ,
probe size fragments were tested to be in the range of 6002000 bp in a 1% agarose gel .
both dna probes were mixed at equal concentrations and the resulting mixed probe was precipitated with ethanol .
after air drying , the probe was dissolved in hybridization buffer ( 50% formamide-2xssc/10% dextran sulphate-2xssc , vol / vol ; ph 7 ) to a final concentration of 20 ng/l , denatured at 70c for 10 minutes and placed on ice for 5 minutes . for fish , metaphase slides
were incubated in 2xssc at 37c for 60 minutes and dehydrated in 70% , 85% and 100% ethanol .
after air drying , slides were denatured in 70% formamide/ 2xssc ph 7 at 70c for 2 minutes and dehydrated again . in this experimental approach ,
the dna probe was applied to the slides and hybridized at 37c in a moist chamber overnight .
after hybridization , slides were washed in 50% formamide at 42c for 15 minutes and in 2xssc at 37c for 8 minutes . a non - specific antibody blocking solution [ bsa 10% ( wt / vol)/tween 20 , 0.05% ( vol / vol)/ 2xssc , ph 7 ] was applied for 5 minutes at 37c .
slides were then incubated for 25 minutes at 37c in the antibody solution , with a single layer of fitc - avidin and rhodamine anti - digoxigenin antibodies ( appligene- oncor , illkirch , france ) , for simultaneous localization of the two probes in green ( g ) and red ( r ) , respectively ( stallion probe + donkey probe ) .
fish experiment samples were counterstained with dapi ( 4 , 6-diamidino-2-phenylindole ) ( 100 ng/l ) .
dapi counterstaining blocks yellow fluorescence produced by a similar contribution of both dna probes on the chromosome arms , but its use is advisable , as it enhances contrast with constitutive heterochromatin labelling .
slides were analyzed using a leica dmlb fluorescence microscope equipped with a charge - coupled device camera ( leica dfc350 fx , leica microsystems ) with three independent green , red and blue filters .
files were merged using using adobe - photoshop cs3 ( adobe systems incorporated , usa ) .
when w - cgh was carried out on stallion chromosomes using an equimolar genomic dna probe obtained from horse and donkey , all chromosomes showed varying quantities of green fluorescence in the constitutive heterochromatin of each autosome . this is the result expected , given that the chromosomal strip for dna probe landing was stallion chromosomes . in some autosomes , there was only a green signal ( arrows in figure 1a ) , while in others the green signal co - localized with a red signal ( contribution of expanded dna sequences in donkey ; arrowhead in figure 1a ) . interestingly , after w - cgh , the y chromosome split into three different chromosome domains ( figure 1a ) .
this region resembles the chromosome domain related to kinetochore activity , and for this reason was identified as the proper centromeric region ( h - cr ; figure 1b ) .
h - cr is small as compared to the rest of the y chromosome and , in this case , showed only intense green fluorescence . additionally , an interstitial , highly expanded and pericentromeric region ( h - pr ; figure 1b ) , showing red fluorescence , was present . finally , a distal region ( h - dr ; figure 1b ) which fluoresces in blue because of the counterstaining effect was observed .
h - dr before dapi counterstaining showed yellow fluorescence due to the equivalent contribution of both dna probes . in the w - cgh environment , this is the normal staining response in chromosomal arms . in short ,
the y chromosome in this stallion is principally compartmentalized in three different chromosome domains , where h - cr is mainly constructed with specific dna families from the horse , while h - pr reveals a massive presence of highly - expanded donkey dna sequences which are also present in the stallion , although at lower intensity .
this chromosome compartmentalization evident in the stallion chromosome is very similar to the gtg - banded y chromosome in donkey , as represented by raudsepp et al .

figure 1panel 1a shows metaphase chromosomes of stallion after hybridization with an equimolar genomic dna probe obtained using whole stallion ( labelled in green ) and donkey genomic dna ( labelled in red ) .
note that all autosomes reveal fish signal corresponding to the stallion dna labelling colour ( green , see standard arrows ) , while red ( donkey ) is present in some autosomes ( arrowhead ) and the y chromosome . a diagram showing the possible expansion and divergence among centromeric and pericentromeric dna subfamilies
panel 1a shows metaphase chromosomes of stallion after hybridization with an equimolar genomic dna probe obtained using whole stallion ( labelled in green ) and donkey genomic dna
note that all autosomes reveal fish signal corresponding to the stallion dna labelling colour ( green , see standard arrows ) , while red ( donkey ) is present in some autosomes ( arrowhead ) and the y chromosome . a diagram showing the possible expansion and divergence among centromeric and pericentromeric dna subfamilies
results obtained in the present preliminary study clearly show that the stallion and donkey still share some highly repetitive dna families , although the expansion level of specific sub - chromosomal domains varies and is characteristic for each species .
this tendency is observed in most autosomes , but in the particular case of the stallion y - chromosome , some peculiar dna arrangements ( h - pr ) are conserved , while appearing to have greatly expanded during the evolution of the donkey y - chromosome ( d - pr ; figure 1b ) .
an alternative explanation is that dna arrangements in h - pr , equivalent to those in d - pr , were partially lost during evolutionary processes regarding the y - chromosome . in both cases
, the absence of legitimate recombination would facilitate this process of differential dna expansion or contraction .
the results showing differential expansion of highly repetitive satellite dna families are congruent with the library hypothesis postulated by fry and salser , which suggested that major sat - dnas found in a group of extant species with any degree of phylogenetic relationship were already present in a common ancestor .
these dna sequences formed a pool of sat - dna sequences at low copy number , as a primordial sat - dna library .
this idea is depicted for the stallion and donkey y - chromosome in the diagram shown in figure 1b . in the case of the y chromosome in stallion and donkey ( sub - chromosomal regions h - cr or d - cr ) ,
however , in the case of h - pr and d - pr , these species - specific sat - dna profiles can be obtained by a change in the copy number of sat - dnas , without major variation in their sequence or obvious quantitative change .
alternatively , as in the majority of cases , the same situation can occur as a consequence of simultaneous change in both parameters .
for instance , w - cgh performed using two closely related grasshoppers , produces results on some autosomes similar to those reported here for the y chromosome .
the results obtained in grasshoppers were identical irrespective of the species employed as the chromosomal strip for probe landing .
this fact suggested that , in addition to heterochromatic compartmentalization on constitutive heterochromatin , variation in sat - dna family copy number , rather than sequence divergence , may account for the differential presence of dna families in the species compared .
in addition to the genome macro - variations concerning chromosome number and morphology described for horse and donkey , it is interesting to stress that eight centromere repositioning episodes occurred when the karyotypes of zebra , horse and stallion were compared .
this phenomenon presupposes the inactivation of old centromeric regions , accompanied by the rapid loss of centromeric satellite dna and by the dispersal of pericentromeric duplications over a relatively wide area of the chromosome .
this scheme of genome re - patterning is congruent with our observations regarding sat - dna expansion and contraction in the y , as well as other autosomes and the w - cgh , and could probably be used as a quick test to study this phenomenon .
finally , the differences in sat - dna found in some autosomes must be taken into account in explaining the sterility observed when hybrids are produced .
horse - donkey hybrids ( mules and hinnies ) exhibit massive meiotic dysfunction at the primary spermatocyte stage , and a large part of this dysfunction is caused by the incompatibility of synaptonemal pairing between paternal and maternal chromosomes , resulting in the total arrest of spermatogenesis .
this aspect is of interest , as it is known that differences in heterochromatin content in pericentromeric or distal chromosome regions , even within the same species , cause chiasma redistribution due to misleading chromosome pairing .

Answer:
the genome of stallion ( spanish breed ) and donkey ( spanish endemic zamorano - leons ) were compared using whole comparative genomic in situ hybridization ( w - cgh ) technique , with special reference to the variability observed in the y chromosome .
 results show that these diverging genomes still share some highly repetitive dna families localized in pericentromeric regions and , in the particular case of the y chromosome , a sub - family of highly repeated dna sequences , greatly expanded in the donkey genome , accounts for a large part of the chromatin in the stallion y chromosome .


Question:
You will be presented with the full text of a biomedical research paper. Please write an abstract for this paper. Your response should include the abstract and no additional text.

Paper text:
a 59-year - old man presented with a swelling of the left lower extremity that had begun two months earlier .
for further evaluation , we performed computed tomography ( ct ) venography and pelvic magnetic resonance imaging ( mri ) .
the ct venography axial images showed a 2.3 cm cystic mass compressing the left common femoral vein ( fig .
the mri images showed a cystic mass compressing the left common femoral vein as well ( fig .
we suspected adventitial cystic disease ( acd ) of the common femoral vein , and the patient underwent an operation . under general anesthesia in a supine position , the femoral artery and vein were dissected for about 5 cm with a longitudinal incision on the left inguinal area .
surgical exploration showed an approximately 2.0 cm sized cystic mass that originated from the adventitia of the common femoral artery and was compressing the common femoral vein .
the cyst that had adhered to the femoral artery was removed first , and the part of the wall that was attached to the cyst in the femoral artery was partially resected .
angioplasty was performed to repair the femoral artery whose wall was partially resected . because the patient had had a partial circulation problem in the vein before the surgery and thus venous obstruction was possible , a polytetrafluoroethylene ( ptfe ) patch was used for angioplasty instead of using an autologous vein graft . a cystic mass excision with ptfe roofing angioplasty
microscopically , the presence of a mucinous cyst and vessel wall degeneration confirmed cystic adventitial disease of the common femoral artery ( fig .
acd is an unusual cystic tumor of the blood vessels characterized by the accumulation of a mucinous substance in the adventitia .
acd is an uncommon disease that was first described in 1947 by atkins and key .
acd accounts for only 0.1% of cases of vascular disease , and among them , 85% of all cases of acd occur in the popliteal arteries , while fewer cases appear in the femoral arteries .
the first case of common femoral artery acd was reported by jaquet and meyer - burgdorff   in 1960 .
it was reported that the prevalence is 5 times higher in males than in females .
the age of occurrence ranges from 11 to 72 years , and the average age is 42 .
four theories have been proposed about the nature of acd : 1 ) the theory that it is a systemic disorder of the connective tissue ; 2 ) the theory that it is a chronic degenerative change due to repetitive trauma ; 3 ) the developmental theory , which maintains that a joint - related ganglion - like structure is incorporated into the vessels during embryologic development ; and 4 ) the ganglion theory that arterial adventitial cysts originate from joint capsular synovial structures .
thus continuous trauma from using fishing tools in contact with the thighs was suspected to have contributed to the lesion .
on the other hand , considering that the lesion occurred unilaterally and did not appear on the opposite thigh , repetitive trauma is not an obvious explanation for the lesion .
the symptoms of acd can include unilateral claudication of the lower extremity , and in rare cases it shows ischemic neuropathy such as paresthesia , pain , and rhigosis .
other possible symptoms include arterial obstruction that results in the pulse in the femoral , the popliteal , and the dorsal pedis arteries being weak or not palpable . however , the main symptom in our case was the uncommon occurrence of swelling that appeared due to the venous obstruction .
in addition , the pulse of the blood vessels of the lower extremities was fully palpable .
recently , it has been accepted that angiography using 3-dimensional ct alone is now considered sufficient for diagnosis .
ct angiography is considered to be an important test because it not only determines the site and extent of stenosis but is also useful in evaluating the entire circulation system .
aspiration of the cyst under ct or ultrasonography is a minimally invasive method , but it is difficult to perform and the cyst has a high recurrence rate .
this method also has a higher recurrence rate than complete resection involving the vessel with artificial material interposition .
interposition provides better long - term patency than the other methods . in this case , in the pre - surgical assessment the lesion was misdiagnosed as originating from the femoral vein instead of from the femoral artery .
in addition , recurrence will be minimized by our having performed the arterial repair and interposition as well as the cystic mass excision .
thus we report here a case of acd , a rare disease , with unusual symptoms , that was successfully treated with surgery .

Answer:
arterial adventitial cystic disease is an uncommon type of non - atherosclerotic peripheral vessel disease .
 most cases of arterial adventitial cystic disease occur in the popliteal arteries ; however , fewer cases have been reported in the femoral arteries .
 a 59-year - old male patient visited the hospital with a complaint of a swelling on the lower extremity that had begun two months earlier . suspecting deep vein thrombosis based on a physical examination and ultrasonography from another hospital , tests were performed . magnetic resonance imaging ( mri )
 was performed for exact diagnosis because venous adventitial cystic disease was suspected by computed tomography venography .
 the mri indicated venous adventitial cystic disease as well .
 thus , a cystic mass excision was performed . in the end , a cystic mass compressing the common femoral vein that originated from the common femoral artery was diagnosed based on the macroscopic findings .
 this case is reported because blood circulation in the vein was impeded due to arterial adventitial cystic disease , and the symptoms improved after the cystic mass excision and polytetrafluoroethylene roofing angioplasty .


Question:
You will be presented with the full text of a biomedical research paper. Please write an abstract for this paper. Your response should include the abstract and no additional text.

Paper text:
desmoid tumors ( dts ) , also called aggressive fibromatosis , are very rare with an estimated incidence of 25 cases per million of inhabitants in european countries [ 1 , 2 ] .
dts lack the capacity to metastasize but may behave in a locally aggressive fashion and possess a high risk of local recurrence despite adequate surgical resection with negative margins [ 1 , 3 ] .
dts can develop in any musculoaponeurotic structure and they may be located at virtually any anatomical site .
the principal sites of involvement for extra - abdominal fibromatosis are the shoulder , chest wall and back , thigh and head and neck region .
intra - abdominal fibromatosis arises in the mesentery or pelvis while abdominal tumors arise from musculoaponeurotic structures of the abdominal wall , especially the rectus and internal oblique muscles and their fascial coverings [ 4 , 5 ] . in the surgically treated patients who experience
recurrence of dt ( local recurrence rates are about 2565% ) a wide excision is needed in some cases .
synthetic meshes often used in extensive abdominal wall reconstruction may present with complications , including infection , bowel adhesion , extrusion , and fistula according to the prosthetic material used .
a prosthetic material with more favorable properties than traditional mesh could have a major effect on surgical practice and patient outcomes , avoiding chronic inflammation and resisting infection after implantation .
considering baumann 's description of the ideal biomaterial for abdominal wall repair , our choice was directed towards a not cross - linked acellular dermal matrix ( adm ) which remodels into host tissue .
the matrix serves as a scaffold and becomes rapidly revascularized and infiltrated with host cells , avoiding fibrotic reaction and encapsulation as well as seroma formation .
the revascularization of biological matrices is thought to promote access of host immune cells as well , thereby providing further resistance to future infections .
this is the first report about the use of the not cross - linked dermal matrix egis in a case of abdominal wall recostruction after extensive dt resection .
in 2008 , a 37-year - old woman underwent , in a different hospital , exeresis of a neoformation in the epigastric region of the abdominal wall and reinforcement with small prosthetic mesh .
she reported an appendectomy , two pregnancies with cesarean births and a voluntary interruption of pregnancy . in 2014 , a recurrence occurred in the context of the rectus abdominis in the left iliac fossa .
the patient therefore underwent tamoxifen therapy for 1 year followed by 3 months of neoadiuvant chemotherapy for progressive disease . in september 2015 , magnetic resonance imaging ( mri )
1a , c , e ) , which revealed a marked progression of the disease ( calculated size 18  10  6.4 cm ) .
after discussions at our multidisciplinary sarcoma meeting , the group decision was to treat the patient surgically .
one month later , the woman had a surgical resection through a suprapubic transverse incision .
the abdominal flap was cranially detached ; the neoformation invaded completely the left abdominal rectus muscle and partially oblique muscles with an extension of approximately 30  20 cm ( fig .
1a , 2a ) . the rectus muscle and a large portion of the oblique and transverse muscles were removed  en bloc  with 1 cm of healthy margin from the mass ( fig .
intraperitoneal drainage was placed , and a wide continuous solution was adopted in the left abdomen .
the not cross - linked porcine dermal matrix egis ( decomed , venice , italy ) 30  20 cm , 1.5 mm thick , was hydrated for 10 min in sterile saline solution and then secured with interrupted absorbable suture ( vicryl 2/0 ) to the fascia and abdominal wall muscles ( fig .
we performed caudal mobilization of the abdominal flap and then dermolipectomy of the superfluous integument .
the postoperative course was uneventful and the patient was discharged on the 8th postoperative day .
there was no evidence of recurrence of the tumor or incisional hernia at 12 months of follow - up ( fig .
1b , d , f ) and the membrane turned out to be completly incorporated with the sourrounding tissues .
histological examination of the resected specimen ( 17  10  6 cm ) revealed tumor - free margins and a whitish lesion with increased thickness and fibrous appearance , which had almost completely invaded the abdominal muscle .
the diagnosis was confirmed by the presence of spindle - cellular tumors which had immigrated through muscle tissues as shown by nuclear -catenin staining .
dfs are neoplasms with infiltrating growth and with a tendency toward local recurrences ; nevertheless , they lack metastatic potential .
although the morphologies of these tumors have been well characterized , their nature and pathogenesis have remained obscure for many years [ 6 , 9 ] . according to the literature
, the median age at the diagnosis of dfs is about 35 years , and the majority of patients are women . in particular , patients between puberty and the fourth decade of life tend to be female , and in these patients the abdominal wall is the preferred site of involvement . supposed risk factors of desmoids are previous surgical interventions , pregnancy , and hormonal treatment with estrogens . because the tumor biology is notoriously unpredictable , periods of rapid tumor growth can be followed by stability or even regression .
the treatment with tamoxifen , as well as chemotherapy and radiation , is controversial , since the long - term clinical improvement is minimal , while surgical excision should be performed only when absolutely necessary .
abdominal wall integrity after full - thickness surgery can be restored with direct suture , but the occurrence of postoperative incisional hernia is highly reported .
for this reason one - stage reconstruction with prosthetic abdominal wall reinforcement increases the chance of definitive cure , enhancing the patient 's perceived quality of treatment .
randomized controlled trial observed a double rate of hernia recurrence in the primary suture group compared with the mesh reinforcement group .
the meshes used are classified according to their gap size which defines the porosity of the mesh and consequently the behavior with surrounding tissue , but a common tendency to develop postoperative complications was reported with all these devices .
synthetic meshes are usually associated with an increased risk of extrusion , adhesion , and following obstruction and enterocutaneus fistula formation , especially when placed in an overlay fashion .
moreover , patients who have had radiation to the abdominal wall prior to reconstruction are at increased risk for wound healing complications and subsequent mesh exposure . for that reason , butler et al .   recommend avoiding synthetic meshes in patients with radiated abdominal walls .
the advent of biological matrices has added a valuable option to the field of abdominal wall reconstruction .
the inherent ability of biological matrix to turn into patient self - tissue , and therefore resist infection , allows to implant it in direct contact with the bowel , resulting in fewer adhesions than prosthetic mesh [ 8 , 12 ] .
these bioprosthetic devices , deriving from human or animal dermis , are chemically and enzymatically cleaned to remove all cellular components while maintaining the extracellular matrix , which can be cross - linked or not .
it is hypothesized that cross - linking treatment adds strength to the matrix , theoretically resulting in lower rates of hernia recurrence as compared to non - cross - linked products .
in contrast butler et al .   in a comparative study had not appreciated any mechanical differences between cross - linked and non - cross - linked matrices .
moreover cross - linked matrices revealed delayed revascularization and higher percentage of adhesions resulting in poor integration regarding non - cross - linked adms . despite the great advantages reported about the biological matrices , the high price that distinguishes them , ranging from usd 8.60/cm to usd 22.00/cm , remains a high deterrent to their use .
one variation of the biological materials , egis , has not been described yet in the literature for abdominal wall reconstruction after tumor excision .
egis ( decomed , venice , italy ) is a dry porcine adm , non - cross - linked , without any chemical preservative ; its very competitive price , about half of the aforementioned costs , allows us to choose the benefits of a biological matrix with the advantage of controlled expense .
we report for the first time the successful use of egis in a complex abdominal wall reconstruction following the resection of a large dt .
the matrix was well accepted without any postoperative complications and no evidence of recurrence of the tumor or incisional hernia has been reported 12 months later . in conclusion
, this single - case experience makes us to consider the biological matrix egis , as well as other adms , an ideal alternative to synthetic mesh , mainly in cases with a potential risk of infection .
the protocol for data collection of this case has been approved by the institute 's committee and complies with the helsinki guidelines for human studies .

Answer:
desmoid tumor is a rare monoclonal fibroblast proliferation that is regarded as benign .
 the clinical management of desmoid tumors is very complex and requires a multidisciplinary approach because of the unpredictable disease course . for those cases localized in the anterior abdominal wall , symptomatic and unresponsive to medical treatment , radical resection and reconstruction with a prosthetic device
 are indicated .
 we present here a case of desmoid fibromatosis of the left anterolateral abdominal wall with a marked increase of the mass that required a large excision followed by reconstruction with biological matrix .
 the fact that it can be incorporated in patient tissue without a fibrotic response and that it can resist future infections , together with a very competetive price , made the new collagen matrix egis our first choice .


Question:
You will be presented with the full text of a biomedical research paper. Please write an abstract for this paper. Your response should include the abstract and no additional text.

Paper text:
morphine and codeine are naturally occurring alkaloids in opioid plants , have long been used as a drug , and are also abused . while the presence of illicit drugs or their metabolites in urine is an evidence of intake , their concentrations in blood are expected to correlate with their effects on the central nervous system .
codeine is a potent -opioid receptor agonist which is used for the treatment of adult cough .
simultaneously , there have been athletes in sports competitions who use a larger dose in order to improve performance .
this practice is contrary to the principle of fair competition and also harmful to the health of the athletes ' body .
heroin as one of the most widely abused drug , rapidly metabolized to 6-monoacetylmorphine ( 6-mam ) once inside the human body .
this specific heroin metabolite 6-mam is detected at a higher concentration usually within 2 to 4 hours , and after six hours , has not been detected in the urine .
the absence of 6-mam in urine , however , morphine is both a well - known pharmaceutical agent and an important metabolite of codeine and heroin which have relatively long a detection time .
morphine and codeine analysis of urine is used in forensic toxicology to study drug addiction .
there are numerous papers published about the simultaneous determination of morphine and codeine in human fluids , including the micellar electrokinetic chromatography ( mekc ) method , disposable pipette extraction ( dpx ) method , high performance liquid chromatography method , liquid chromatography - mass spectrometry , and liquid chromatography / triple quadrupole tandem mass spectrometry ( lc / ms / ms ) method [ 68 ] .
several gas chromatography - mass spectrometry ( gc - ms ) methods have been developed for the analysis of codeine , morphine , or other opiates .
much attention has been directed to the confirmation of morphine and codeine in urine by gc - ms .
a few methods have been developed specifically for the analysis of 6-acetylmorphine ( 6-am ) with morphine and codeine because all three drugs are often present after heroin use .
assays of morphine and codeine by gc - ms are capable of high sensitivity , specificity , and selectivity .
gc - ms is superior to other analytical methods which provide important diagnostic value to study the drug abuse .
the aim of this study was to establish methods and seek out more reliable identification and quantitation of morphine and codeine for detection addicts sample .
although through in saliva is another approach ; the reliability of saliva analysis is limited by the fact that analyte levels , and even the availability of required sample volume , are again dependent on several physiological factors , nutrition and fluid intake , while the biological effects of the consumed illicit substance may also be a significant factor .
the identification of chronic consumers or the late verification of a single intake is feasible using hair as a matrix , but it is not suitable for the early verification of consumption .
urine is a preferable matrix for analytical purposes in comparison with saliva because of the minimal discomfort caused to sampled individuals , so it is widely available .
the simple and effective ethyl acetate extraction was employed in our work , and ethyl acetate was adopted because of its high extraction efficiency .
propionic anhydride was chosen as the derivatization reagent because it exhibited better effect than acetic anhydride or trifluoroacetic acid anhydride , which could provide preferable stability , and the disadvantage of acetyl derivatives indistinguishable from morphine and the 6-am can be avoided .
.   evaluated propionic anhydride , mbtfa , hfaa , and bstfa for gc - ms analysis of 6-am .
they concluded that propionic anhydride gave accurate , precise , and sensitive results while providing compatibility with other methods on the same gc - ms instrument .
residual derivatization reagent in the injector will react with drugs in other methods not intended for derivatization .
the derivatization procedure accommodates the analysis of opioids commonly requiring gc - ms confirmation in urine .
concentrations of the analytes in the samples were expected to be smaller than the low end of the therapeutic range ( 25  ng / ml ) , which highlighted the importance of efforts aimed at increasing the sensitivity of detection .
the relative standard deviation of the retention parameters of the target compound was required not to exceed 5% relative standard deviation .
morphine [ 10  g / ml in methanol ] and codeine [ 10  g / ml in methanol ] solutions were obtained from the institute of forensic science under the ministry of justice ( shanghai , china ) .
sodium hydroxide ( purity > 98.0% ) was purchased from sigma - aldrich trading co ( shanghai , p.r . ,
china ) , and ethyl acetate ( purity > 98.0% ) was purchased from siyou chemical reagent co. , ltd ( tianjin , china ) , and propionic acid anhydride ( purity > 98.0% ) was purchased from sinopharm chemical reagent co. , ltd ( beijing , china ) .
pyridine was from shenbo chemical co. , ltd ( shanghai , china ) . while methanol was obtained from siyou chemical reagent co. , ltd ( tianjin , china ) .
ultrapure water was prepared by a milli - q purification system from millipore ( bedford , usa ) .
analysis was performed on an agilent 6890n gas chromatograph ( gc ) coupled with an agilent 5975b mass spectrometer ( ms , agilent technologies , wilmington , de , usa ) .
the capillary column used was a hp-1ms [ 30  m  0.25  mm , 0.25  m ] .
helium was the carrier gas at a flow rate of 1.0  ml / min .
the temperature program was : initial temperature , 100c for 1.5  min ; ramp at 25c / min to 280c and held for 15  min ; injection temperature , 250c ; and transfer line , 280c .
electron impact ionization was performed at 70  ev energy and at a 230c ion source temperature .
sim mode was applied to quantify analyzes using target ions at m / z 341 , 397 , and 268 for morphine propionyl compound and m / z 229 , 355 , and 282 for codeine propionyl compound ( figure 1 ) .
the primary standard stock solutions of morphine ( 100  g / ml ) and codeine ( 100  g / ml ) were separately prepared in 10  ml volumetric flasks with urine ; 10% naoh was added dropwise until ph 9.09.2 was reached , and 1.0  ml of borax buffer solution was added . to this , 3  ml of extraction solvent ( ethyl acetate ) was added and vortex - mixed on a vortexer for 2.0  min , followed by centrifugation at 3000  r / min for 5 min .
the supernatant organic layer was transferred into a 5  ml glass test tube and dried under air stream at 60c .
the dried residue was reconstituted in 50  l of propionic anhydride and 20  l of pyridine .
all reagents were vortex - mixed , then heating for 3  min at 80c and dried under air stream at 60c . the dried residue was reconstituted in 50  l of methanol , and 1  l of this solution was injected into gc - ms .
specificity was determined by analysis of blank urine , without addition of morphine and codeine to determine possible interference with these compounds . to evaluate the linearity ,
the calibration curves were generated using the analyte peak area by linear regression on three consecutive days .
the lloq was estimated in the process of calibration curve construction and was defined as the lowest concentration for which precision ( rsd ) was better than 20% .
qc samples at three concentration levels ( 50 , 200 , and 1600  ng / ml for morphine and codeine ) were analyzed to assess the accuracy and precision of the method .
again , the assays were performed on three separate days , and on each day six replicates of the qc samples at each concentration level were analyzed .
the assay precision for each qc level was determined as the relative standard deviation ( rsd ) of the measured concentrations .
the intra- and interday precisions were required to be below 15% , and the accuracy was required to be within 15% .
stability in urine was assessed in the autosampler at room temperature for 12  h. the effect of three freeze - thaw cycles was also investigated .

 figure 2 shows the typical chromatograms of a blank urine sample spiked with morphine and codeine .
no interfering endogenous substances were observed at the retention times of the morphine and codeine .
calibration curves for morphine and codeine were generated by linear regression of peak area ratios against concentrations , respectively .
the regression equation for the calibration plot were y = 2270.9c + 202.3 with r = 0.9974 for morphine , and y = 3099.0c + 31625.7 with r = 0.9958 for codeine ( y is the peak area of analyte , and c is the concentration of analyte in human urine ) , and concentrations are in the range 252000  ng / ml for morphine and codeine , respectively .
the lloq for morphine in human urine was 25  ng / ml and the precision and accuracy at lloq were 10.5% and 87.6% , respectively .
the lloq for codeine in human urine was 25  ng / ml and the precision and accuracy at lloq were 13.8% and 88.9% , respectively .
the precision of the method was determined by calculating rsd for qcs at three concentration levels over three validation days .
intraday precision was 12% or less and the interday precision was 13% or less at each qc level .
the aforementioned results demonstrate that the values are within the acceptable range and the method is accurate and precise .
the recovery of morphine and codeine was evaluated by comparing peak area ratios of extracted qc samples with those of reference qc solutions reconstituted in blank urine extracts .
all the stability studies of morphine and codeine in human urine were conducted at three concentration levels ( 50 , 200 , and 1600  ng / ml for morphine and codeine ) with three replicates for each concentration .
the stability results showed that morphine and codeine in human urine were stable during three freeze - thaw cycles .
stability of morphine and codeine extracts in the sample solvent on autosampler was also observed over a 12  h period .
a stable , selective , and sensitive gc - ms method has been developed for the simultaneous determination of codeine and its metabolite morphine in human urine .
this developed method with derivatization for sample preparation was successfully applied for the determination of morphine and codeine in human urine for methodological study .

Answer:
a sensitive and selective gas chromatography - mass spectrometry ( gc - ms ) method was developed and validated for the determination of morphine and codeine in human urine .
 the gc - ms conditions were developed .
 the analysis was carried out on a hp-1ms column ( 30  m  0.25  mm , 0.25  m ) with temperature programming , and helium was used as the carrier gas with a flow rate of 1.0  ml / min .
 selected ion monitoring ( sim ) mode was used to quantify morphine and codeine .
 the derivation solvent , temperature , and time were optimized .
 a mixed solvent of propionic anhydride and pyridine ( 5  :  2 ) was finally used for the derivation at 80c for 3  min .
 linear calibration curves were obtained in the concentration range of 252000.0  ng / ml , with a lower limit of quantification of 25  ng / ml . the intra- and interday precision ( rsd ) values were below 13% , and the accuracy was in the range 87.2108.5% .
 this developed method was successfully used for the determination of morphine and codeine in human urine for forensic identification study .


Question:
You will be presented with the full text of a biomedical research paper. Please write an abstract for this paper. Your response should include the abstract and no additional text.

Paper text:
the national cooperative dialysis study , the first randomised controlled study of dialysis dose , defined an
adequacy threshold for end - stage chronic kidney disease patients receiving chronic haemodialysis   based on the dialyser clearance of urea , a small solute marker of nitrogen turnover , which was defined in terms of a dimensionless parameter known as the normalised urea clearance , or kt / v ( k , dialyzer urea clearance ; t , dialysis session duration ; and v , urea volume distribution ) . below a sessional threshold kt / v of 0.9 for standard thrice - weekly schedules , complication - free survival was compromised within months .
subsequent observational studies suggested that higher doses resulted in improved longer - term outcomes , and by consensus the minimum target kt / v was raised to 1.2 .
a subsequent prospective randomised controlled study , the hemodialysis ( hemo ) study , reported that higher doses did not appear to further improve outcome .
however , subgroup analysis suggested that women may benefit from higher kt / v doses , fuelling suggestions that using standard kt / v targets to prescribe dialysis may lead to under - dosing in women and small men .
these studies suggest that , for standard thrice - weekly therapy , medium - term survival ( measured in months ) is dependent on achieving a minimum level of small solute removal , as defined by the national cooperative dialysis study .
just as the amount of dialysis delivered to patients with end - stage chronic kidney disease is important in determining survival , it was reported that the dose of intermittent haemodialysis or continuous renal replacement therapy ( crrt ) was also important in determining survival in patients with acute kidney injury ( aki ) [ 8 - 10 ] , although this was not a universal finding . as patients with aki continue to have high mortality , and evidence
- based clinical management is somewhat limited , two prospective multicentre trials were designed to investigate the effect of dose of renal replacement therapy on outcome in patients with aki .
the veterans affairs / national institutes of health ( va / nih ) study essentially randomised patients to initially receive either an intensive or less intensive dose of intermittent haemodialysis , or an intensive or less intensive dose of crrt , depending upon severity of illness at the time of randomisation .
( during the course of the study patients were switched between treatment modalities according to haemodynamic stability . ) during haemofiltration , it is assumed that urea is effectively cleared ( to the extent that the concentration in the effluent ultrafiltrate is equal to that of plasma water ) so that urea clearance can simply be assessed by the total ultrafiltration volume achieved . in this study
, more intensive renal replacement therapy did not show any survival advantage for either the intermittent haemodialysis or crrt groups .
however , the minimum haemodialysis target kt / v of 1.2 was somewhat higher than that typically prescribed for patients with aki by the recruiting centres .
in addition , there was no survival advantage for the haemofiltration cohort compared to those treated by dialysis .
haemofiltration clears solutes primarily by convection , thus removing a larger spectrum of solutes than haemodialysis , which predominantly clears small water soluble solutes by diffusion .
the second study , the renal ( randomised evaluation of normal versus augmented level of renal replacement therapy in icu ) study , assessed the effect of an augmented dose of crrt ( an ultrafiltration rate of 40 ml / kg / h versus 25 ml / kg / h ) . once again
, this study failed to show any significant effect of dose of convective renal replacement therapy on patient outcomes , although the delivered dosages were less than that prescribed and both small patients ( < 60 kg ) and very heavy patients ( > 120 kg ) were excluded .
although urea can dissociate to cyanate in plasma water and then form carbamylated products in a reversible fashion , with some analogy to glycosylation , it would appear that toxicity from the accumulation of small nitrogenous solutes is not the major determinant of short - term outcome ( days to weeks ) in patients with aki .
aki frequently occurs in the setting of multiple organ failure , and mortality remains high , with patient outcome typically dependent upon the severity of the underlying condition and associated co - morbidities .
the replacement of organ function may play a critical short - term role in maintaining life in patients already destined by other factors to have the potential to recover . however , urea clearance is only one component of renal replacement therapies .
for example , failure to correct persistent volume overload is associated with not only increased post - surgical morbidity , but also increased risk of aki   and mortality .
thus , for patients with aki , the adequate removal of even smaller moieties than urea is the principal determinant of the  adequacy of renal replacement . these moieties are the neglected
uraemic toxins , including potassium , sodium , hydrogen ions and water   ( figure 1 ) .
the consequences of the accumulation of these moieties , hyperkalaemia , pulmonary oedema , and acidosis , may be lethal in minutes .
toxins play a role over time , and as such may require different clinical management strategies .
hemo , hemodialysis ; ncds , national cooperative dialysis study ; renal , randomised evaluation of normal versus augmented level of renal replacement therapy in icu ; va / nih , veterans affairs / national institutes of health .
although the delivery of higher doses of haemofiltration or more frequent haemodialysis did not improve overall outcome , higher volume crrt exchange cycles and more frequent haemodialysis treatments will help correct acidosis , and may be appropriate during the initial resuscitation phase of aki .
correction of volume overload may help explain the positive findings and improved clinical outcomes reported from some of the earlier trials of increased dose of renal support , compared to the more recent va / nih and renal studies , which had similar fluid balance targets .

Answer:
traditionally , the dose of haemodialysis or haemofiltration delivered to patients with kidney failure is assessed by urea clearance . for patients with chronic kidney disease below a critical urea clearance threshold ,
 patient wellbeing is compromised .
 it was suggested , therefore , that the dose of dialysis or haemofiltration delivered could also affect outcomes for patients with acute kidney injury .
 two major prospective multicentre clinical trials have recently reported that a higher intensity of renal support , by either intermittent haemodialysis or continuous renal replacement therapy , did not improve patient survival or recovery from dialysis .
 it must be recognised , however , that urea clearance is only one component of renal supportive therapy , and other aspects , including volume control , electrolyte homeostasis and acid - base balance , may be equally important targets for patients with acute kidney injury .


Question:
You will be presented with the full text of a biomedical research paper. Please write an abstract for this paper. Your response should include the abstract and no additional text.

Paper text:
a 22-year - old - male patient presented with a painless swelling over the left eye along with mechanical ptosis of the upper lid .
the mass was located anterior to the orbital rim in the superolateral part of the orbit ; with the posterior edge not palpable as it was within the orbit .
anterior segment evaluation , intraocular pressure , and fundus examination of both eyes were normal .
a computed tomography showed an iso - to - hypodense mass lesion in the superotemporal aspect of the left orbit , arising possibly from the lacrimal gland since the gland could not be clearly delineated from the mass .
no obvious changed to the bony orbit could be noted on the scans [ fig .
fine needle aspiration cytology smears drawn showed no malignant cells ; however , a conclusive diagnosis could not be made .
a working diagnosis of a pleomorphic adenoma of the lacrimal gland was made , and an excision biopsy was performed .
intraoperatively , the mass was pink , vascular , and well circumscribed but not encapsulated .
the lacrimal gland was seen in close relation to the mass , compressed between the mass and the superolateral orbital bony rim .
( a ) external clinical photograph shows the mass located in the superolateral quadrant of the orbit .
( b ) axial slice of the computed tomography scan showing the mass in the vicinity of the lacrimal gland ( yellow arrow ) the cut surface was homogeneous and did not have any distended vascular channels , lacrimal tissue , or cystic dilatations . on microscopic examination ,
spindle cells in compact sheaves closely opposed to thin walled vessels were seen in a fibrocollagenous background [ fig .
the nuclei were open , oval , and contained small , uniform nucleoli [ fig .
. no necrosis was noted , and a few engorged vessels were seen in the outlying area .
immunohistochemical studies showed that the tumor cells stained positive for cd 34 and cd 31 , which are markers for endothelium [ fig .
furthermore , the tumor stained positive for smooth muscle actin and negative for cd68 [ fig .
immunostaining was negative , and the ki-67 proliferation index was low with < 5% of the cells staining positive [ fig .
thus , the tumor had no conclusive features of a malignancy and the final diagnosis based on its microscopic appearance , and immunohistochemical characteristics was that of a solid variant of angioleiomyoma of the orbit . as it had been excised completely , no further treatment was warranted . at 1-year follow - up , no recurrence was observed .
( a ) low power view showing spindle cells in a background of fibrocollagenous tissue ( h and e , 10 ) .
( b ) high power view demonstrating uniform oval nuclei ( h and e , 40 ) ( a and b ) immunohistochemical studies showed that the tumor cells stained positive for cd 34 ( endothelium ) and cd 31 ( 10 ) ( a and b ) immunohistochemical studies positivity for smooth muscle actin and immunonegativity for cd68 ( 10 ) .
( c ) the ki-67 proliferation index was low with < 5% of the cells staining positive ( 10 )
the differentials for such an orbital tumor could be cavernous hemangioma , angiomyofibroma , or complex orbital angiomyoma . the tissue of origin of angioleiomyoma is considered to be smooth muscle ; so the possible native tissues from which the tumor could have arisen include blood vessels , pericytes , mller 's muscle or the capsulopalpebral muscle of hessar .
angioleiomyoma is well recognized within the spectrum of vascular lesions of the soft tissues and has been subdivided into three types  solid , venous , and cavernous .
since there were no dilated cavernous spaces within our tumor , we consider our case to be a solid variant .
morimoto , who classified angioleiomyomas , observed that solid variants are often painful and seen in the extremities .
in contrast to his comments , our case was a solid variant which was painless .
described an angiomyofibroma of the orbit as a hybrid tumor exhibiting characteristics of a vascular leiomyoma and cavernous hemangioma .
the lack of the cavernous venous channels , the unusual location , and absence of the classical purplish hue rule out cavernous hemangioma and angiofibroma in our case .
jakobiec has also described in detail the characteristics of a complex orbital angiomyoma , which had features of a lymphangiohemangioma .
three of them were located in the muscle cone , two of them were located in the superotemporal orbit , and one was located in the inferior orbit .
two other eyelid angioleiomyomas were also described in the same series . of these eight cases ,
based on their histological classification , however , only one case was the same type as our case : the solid variant ; five cases were of the cavernous type and two cases were venous type .
alam et al . , have also reported a similar tumor from the anterior orbit , which was found to be of the cavernous subtype .
preoperative magnetic resonance imaging may provide some clues : magnetic resonance findings of peripheral angioleiomyomas were relatively nonspecific , but t2-weighted images show a mass with mixed areas that are both hyper- and iso - intense relative to the skeletal muscle and a hypointense rim .
angioleiomyomas of the orbit are rare tumors with good prognosis , and the treatment of choice remains complete surgical excision .

Answer:
we describe the clinicopathological features of a solid variant of orbital angioleiomyoma .
 a review of clinical records , diagnostic , and radiographic studies combined with histopathological evaluation with standard histochemical staining and immunohistochemistry was conducted . a 22-year - old male patient presented with a mass in the region of the left lacrimal gland that was gradually increasing over the past 2 years .
 radiological and clinical examinations showed no signs suspicious of a malignancy and fine needle aspiration cytology was inconclusive . therefore
 , an excision biopsy was performed .
 on histopathological examination , the picture was consistent with a benign spindle cell tumor . immunohistochemistry showed positivity for cd 34 and cd 31 ( markers for vascular endothelium ) .
 the tumor also showed positivity for smooth muscle actin and ki-67 proliferative index was low .
 angioleiomyomas are rarely encountered in the orbit and has features seen in leiomyoma as well as some vascular tumor elements . in most cases , surgical excision is usually curative .


Question:
You will be presented with the full text of a biomedical research paper. Please write an abstract for this paper. Your response should include the abstract and no additional text.

Paper text:
to study the short - term effects of waterborne depleted uranium ( du ) , atlantic salmon parr ( n  =  6 ) were exposed for 48  h to 0 , 0.25 , 0.5 and 1.0  mg / l uranyl acetate ( uo2(ch3coo)22h2o , purity    98.0% , specific activity 1.459    10  bq / g , fluka , sigma - aldrich , buchs , switzerland ) dissolved in lake water collected from lake maridalsvannet , oslo , norway .
fish experiments were approved by the norwegian animal research authority ( nara i d : 3026 ) and conducted at the figaro facility for environmental radioactivity studies ( norwegian university of life sciences , s , norway ) .
all operations strictly followed the norwegian welfare act and research animal legislation . immediately after the exposure
samples were then stored in ultrafreezer (   80  c ) until further analysis . for rna isolation ,
the rneasy plus mini kit ( qiagen , hilden , germany ) was used to extract total rna from 20 to 30  mg frozen liver .
the procedures have been previously described in detail , . the rna yield and purity ( yield  >  200  ng/l , 260/230  >  2.0 , 260/280  >  1.8 ) were determined using nanodrop spectrophotometer ( nd-1000 , nanodrop technologies , wilminton , delaware , usa ) .
the rna integrity ( rin  >  9.0 ) was determined using bioanalyzer rna 6000 nano chips ( agilent technologies , santa clara , california , usa ) following the manufacturer 's manual .
the microarray probes ( totally 55,418 features ) were designed using the consensus sequences of two salmonid fish , salmo salar and oncorhynchus mykiss from the cgrasp 44  k salmonid oligoarray ( 35,920 sequences ) , release 11/09   complimented by ncbi unigenes ( 2995 sequences from s. salar , build 31 and 16503 sequences from o. mykiss , build 27 ) .
the cross - hybridization potential of the array probes was predicted to be less than 7% ( 3587 probes ) .
a high density 60,000-feature ( 60  k ) custom salmonid oligonucleotide array was then manufactured by agilent technologies ( santa clara , ca , usa ) .
the custom salmonid array platform is currently available in gene expression omnibus ( geo i d : gpl18864 ) .
the agilent  one - color microarray - based gene expression analysis ( v6.5 )  protocol ( agilent technologies ) was used in the microarray analysis with small modifications .
two hundred nanogram of liver total rna was used as input material for array experiment ( n  =  3 ) .
the hybridized array slides were scanned using agilent microarray c scanner ( agilent technologies , scan region : 61    21.6  mm , resolution : 3  m , output tiff image : 20 bit ) .
the agilent feature extraction ( fe ) software ( v10.7 ) was used to extract raw data from scanned array images . the quality assessment for extracted data
was based on the quality control ( qc ) files generated by the fe software ( table  1 ) and correlations of signal intensity of control probes between different arrays .
high quality raw data ( signal intensity values ) was further processed using genespring software ( v11.0 , agilent technologies ) .
briefly , raw data were first corrected for background signals , flagged for low quality and missing features and then normalized within- and between - array using 75% quantile method .
values from replicate features were computed for median and merged to a single normalized signal intensity value for each rna source sequence .
after raw data processing , in total 40,267 features were log-2 transformed and used for downstream statistical analysis to determine differentially expressed gene transcripts ( degs ) .
to study the short - term effects of waterborne depleted uranium ( du ) , atlantic salmon parr ( n  =  6 ) were exposed for 48  h to 0 , 0.25 , 0.5 and 1.0  mg / l uranyl acetate ( uo2(ch3coo)22h2o , purity    98.0% , specific activity 1.459    10  bq / g , fluka , sigma - aldrich , buchs , switzerland ) dissolved in lake water collected from lake maridalsvannet , oslo , norway .
fish experiments were approved by the norwegian animal research authority ( nara i d : 3026 ) and conducted at the figaro facility for environmental radioactivity studies ( norwegian university of life sciences , s , norway ) .
samples were then stored in ultrafreezer (   80  c ) until further analysis . for rna isolation ,
the rneasy plus mini kit ( qiagen , hilden , germany ) was used to extract total rna from 20 to 30  mg frozen liver .
the procedures have been previously described in detail , . the rna yield and purity ( yield  >  200  ng/l , 260/230  >  2.0 , 260/280  >  1.8 ) were determined using nanodrop spectrophotometer ( nd-1000 , nanodrop technologies , wilminton , delaware , usa ) .
the rna integrity ( rin  >  9.0 ) was determined using bioanalyzer rna 6000 nano chips ( agilent technologies , santa clara , california , usa ) following the manufacturer 's manual .
the microarray probes ( totally 55,418 features ) were designed using the consensus sequences of two salmonid fish , salmo salar and oncorhynchus mykiss from the cgrasp 44  k salmonid oligoarray ( 35,920 sequences ) , release 11/09   complimented by ncbi unigenes ( 2995 sequences from s. salar , build 31 and 16503 sequences from o. mykiss , build 27 ) .
the cross - hybridization potential of the array probes was predicted to be less than 7% ( 3587 probes )
. a high density 60,000-feature ( 60  k ) custom salmonid oligonucleotide array was then manufactured by agilent technologies ( santa clara , ca , usa ) .
the custom salmonid array platform is currently available in gene expression omnibus ( geo i d : gpl18864 ) .
the agilent  one - color microarray - based gene expression analysis ( v6.5 )  protocol ( agilent technologies ) was used in the microarray analysis with small modifications .
two hundred nanogram of liver total rna was used as input material for array experiment ( n  =  3 ) .
the hybridized array slides were scanned using agilent microarray c scanner ( agilent technologies , scan region : 61    21.6  mm , resolution : 3  m , output tiff image : 20 bit ) .
the agilent feature extraction ( fe ) software ( v10.7 ) was used to extract raw data from scanned array images . the quality assessment for extracted data
was based on the quality control ( qc ) files generated by the fe software ( table  1 ) and correlations of signal intensity of control probes between different arrays .
high quality raw data ( signal intensity values ) was further processed using genespring software ( v11.0 , agilent technologies ) .
briefly , raw data were first corrected for background signals , flagged for low quality and missing features and then normalized within- and between - array using 75% quantile method .
values from replicate features were computed for median and merged to a single normalized signal intensity value for each rna source sequence .
after raw data processing , in total 40,267 features were log-2 transformed and used for downstream statistical analysis to determine differentially expressed gene transcripts ( degs ) .
this article describes high quality transcriptomic datasets generated from an ecotoxicological study on the early stress responses in atlantic salmon after short - term ( 48  h ) exposure to waterborne depleted uranium ( du ) using a custom microarray for salmonid fish .
the full study has recently been published   and these datasets may serve as a platform to understand the toxic mechanisms and ecological hazard of environmental radionuclides such as du in fish .

Answer:
potential environmental hazards of radionuclides are often studied at the individual level .
 sufficient toxicogenomics data at the molecular / cellular level for understanding the effects and modes of toxic action ( moas ) of radionuclide is still lacking .
 the current article introduces transcriptomic data generated from a recent ecotoxicological study , with the aims to characterize the moas of a metallic radionuclide , deplete uranium ( du ) in an ecologically and commercially important fish species , atlantic salmon ( salmo salar ) .
 salmon were exposed to three concentrations ( 0.25 , 0.5 and 1.0  mg / l ) of du for 48  h. short - term global transcriptional responses were studied using agilent custom - designed high density 60,000-feature ( 60  k ) salmonid oligonucleotide microarrays ( oligoarray ) .
 the microarray datasets deposited at gene expression omnibus ( geo i d : gse58824 ) were associated with a recently published study by song et al .
 ( 2014 ) in bmc genomics .
 the authors describe the experimental data herein to build a platform for better understanding the toxic mechanisms and ecological hazard of radionuclides such as du in fish .


Question:
You will be presented with the full text of a biomedical research paper. Please write an abstract for this paper. Your response should include the abstract and no additional text.

Paper text:
in modern society , the fashion of wearing tight clothes for stylish dressed states or
 comeliness is getting very popular1 .

however , specialists reported that excessively pressing certain areas of the human body
 could cause many problems in the cardiovascular systems and visceral organs1 .
in addition to this pressure inflicted on
 the human body may deform muscles , the skeletal system , and even the overall body type2 , 3 .

jeans that are too tight compress a nerve that cuts off sensation to the thighs , and this is
 consistent with human anatomy and physiology4 .
trousers that are too tight can squeeze a sensory nerve under the
 hip bone , causing a tingling , burning sensation called paresthesia1 , 4 , 5 . with this as the background , the present study aimed to understand
 the hazards of the habit of wearing tightly fitting clothes in relation to deformations of
 the musculoskeletal system and the movement of the lumbar spine and pelvis for the purpose
 of providing basic data regarding proper habits in wearing clothes for the prevention of
 pain in the musculoskeletal systems2 , 3 .
so the present study evaluated the effect
 of wearing tight pants on the trunk flexion and pelvic tilting angles in stand - to - sit
 movement and in a seated posture .
this study was performed on nine males aged 2027  years ( 23.22.0  years , meansd ) whose
 height and weight were 175.13.2  cm and 62.13.4  kg , respectively .
subjects with conditions
 that might affect trunk mobility , such as injury or neurologic deficits of the hip and lower
 extremities during the past year , were excluded from study . the study purpose and methods
 were explained to all the subjects , who provided informed consent according to the
 principles of the declaration of helsinki before participating .
data were collected at a sampling rate of 100  hz with a motion capture system
 ( vicon mx , oxford metrics , oxford , uk ) that consisted of eight infrared cameras .
sixteen reflective markers were
 attached to the lower body according to the plug - in - gait marker set ( oxford metrics ) using
 double - sided tape .
the software used for kinematic data collection was nexus 1.4.1 ( oxford
 metrics ) , and the data were analyzed with the polygon 3.1 software ( oxford metrics ) .
the
 experimental protocol required the completion of two stand - to - sit trials for each of the two
 pants conditions .
the worn pants were made from the same material , cotton , woven into a
 rugged cotton textile .
we used general and tight pants from the same company ( g company ) .

the pants were worn under two conditions in this study : ( 1 ) general pants , worn with sizes
 equivalent to 105110% of the subjects hip , thigh , and calf circumferences , and ( 2 ) tight
 pants , worn with sizes equivalent to 9095% of the subjects hip , thigh , and calf
 circumferences .
each subject was asked to stand up at a
 self - selected speed from a seated posture and to stand in an erect spine posture . for time
 normalization , the time required for a complete stand - to - sit movement cycle ,
that is , from
 movement onset to completion , was considered to be 100% ; values were determined for each 2%
 of the movement , beginning at 0% .
the changes in trunk flexion and pelvic posterior tilting
 angles were calculated based on the difference between the maximal and initial angles . as
 the analysis was performed with a withwn - subject design ,
the paired t - test was conducted to
 test for differences in pelvic and trunk kinematics values during the maneuver .
all
 significance levels were set at p<0.05 , and spss version 12.0 ( spss , chicago , il , usa )
 was used for statistical analyses .
the change in the posterior pelvic tilting angle ( 9.3 4.1 ) during the stand - to - sit
 movement when wearing the tight pants increased significantly compared with that when
 wearing the general pants ( 7.0 3.3 ) ( p<0.05 ) .
the change of the trunk flexion angle
 ( 19.3 5.4 ) during the stand - to - sit movement when wearing the tight pants increased
 significantly compared with that when wearing the general pants ( 12.0 3.8 ) ( p<0.05 ) .
 the change in the posterior pelvic tilting angle ( 13.3 3.2 ) in the seated posture when
 wearing the tight pants increased significantly compared with that when wearing of the
 general pants ( 10.3 2.9 ) ( p<0.05 ) .
the change in the trunk flexion angle ( 25.3 6.1 )
 in the seated posture when wearing the tight pants increased significantly compared with
 that when wearing of the general pants ( 20.1 5.4 ) ( p<0.05 ) .
park and yoo reported that the tightness of a waist belt might restricts forward movement
 of the center of mass and that pelvic inclination might be increased as a compensatory
 mechanism2 .
they showed that the wearing
 a tight belt could interrupt normal lumbo - pelvic coordination , which might contribute to
 muscle imbalance2 .
elevated abdominal
 pressure has been shown to cause multidirectional stiffness of the spine5 , 6 .
a
 previous study that used a wide belt reported that the intramuscular pressure on the erector
 spinae could influence spinal stiffness separately from muscle7 .
the results of the present study showed that the trunk flexion and
 posterior pelvic tilting angles during the stand - to - sit movement when wearing tight pants
 significantly increased when compared with wearing general pants .
also , the trunk flexion
 and posterior pelvic tilting angles in the seated posture when wearing tight pants
 significantly increased when compared with those when wearing of general pants .
the lumbar
 and hip rhythm and interaction between the lumbar spine and hip are important kinematic
 factors that are used not only in experimental research but also in clinical
 examination8 , 9 . wearing tight jeans induced excessive lumbar flexion during stand
 to sit movement and in the seated posture .
the exaggerated lumbar flexion may overstretch
 posterior connective tissues , such as the interspinous ligament , apophyseal joint capsule ,
 and thoracolumbar fascia , or increase stress on discs and apophyseal joints5 .
posterior pelvic tilt decreases lordosis
 via flexion of the lumbar spine , causes posterior movement of the nucleus pulposus , and
 increases the diameter of the intervertebral foramina5 , 8 .
slump sitting reduces the
 activation of the spinal stabilizing muscles and is associated with increases in loading on
 the intervertebral disc and connective tissue8 , 9 .
therefore , wearing tight pants could
 produce musculoskeletal disorders via abnormal movement and posture in the lumbar spine and
 pelvis .
so the effects of wearing tight pants need to be investigated in further studies to
 reveal their direct relationship to musculoskeletal problems .
the effects of tight clothes
 and accessory items on the human body should also be investigated in order to provide basic
 data for proper use .
further studies will become the starting point for studies regarding
 the effects of wearing tight clothes and tight fashion accessories on the musculoskeletal
 system .

Answer:
[ purpose ] the purpose of this study was to evaluate the effect of wearing the tight pants
 on the trunk flexion and pelvic tilting angles in the stand - to - sit movement and a seated
 posture .
 [ subjects ] nine male subjects were recruited .
 [ methods ] the trunk flexion angle
 and pelvic posterior tilting angle were measured using a motion - capture system during the
 stand - to - sit movement and in a seated posture . [ results ] the trunk flexion and the
 posterior pelvic tilting angles during the stand - to - sit movement and in the seated posture
 when wearing tight pants significantly increased compared with those when wearing of
 general pants .
 [ conclusion ] therefore , wearing tight pants could produce musculoskeletal
 disorders via abnormal movement and posture in the lumbar spine and pelvis .
 so the effects
 of wearing tight pants need to be investigated in further studies to reveal their direct
 relationship to musculoskeletal problems .


Question:
You will be presented with the full text of a biomedical research paper. Please write an abstract for this paper. Your response should include the abstract and no additional text.

Paper text:
the online version of this article ( doi:10.1007/s00227 - 011 - 1643 - 5 ) contains supplementary material , which is available to authorized users .
white sharks , carcharodon carcharias , observed off the coast of california belong to a genetically distinct population unique to the eastern pacific ( jorgensen et al . 2010 ) .
subadult and adults travel long distances offshore from california and northern mexico during yearly migrations ( boustany et al . 2002 ; weng et al . 2007 ; domeier and nasby - lucas 2008 ; jorgensen et al .
these offshore movements traverse international waters where individuals are susceptible to fishing mortality , yet few data are available from potential offshore fisheries , confounding efforts to determine white shark population status .
therefore , fishery - independent methods must be employed to begin to estimate their population size .
mark - recapture methods have been used to estimate white shark population sizes in south africa ( cliff et al .
1996 ) , australia ( strong et al . 1996 ) and the northeast pacific ( chapple et al . 2011 ) .
these studies are dependent on the assumption that white sharks return to the same location over multiple sampling periods .
recent work has illustrated the short - term [ e.g. , < 8  years or 25% of estimated lifespan ( cailliet et al . 1985 ) ] seasonal site fidelity of sharks to coastal aggregation sites .
white sharks tagged off coastal california and guadalupe island , mexico returned to their tagging location following offshore movements ( domeier and nasby - lucas 2008 ; jorgensen et al .
similarly , a combination of a satellite tag and dorsal fin identification described the movement of a shark in south africa to australia and back in 9  months ( bonfil et al . 2005 ) .
however , no studies have tested the long - term [ e.g. , > 14  years or 50% estimated lifespan ( cailliet et al .
these mark - recapture frameworks also assume external identification tags or unique markings are conserved and identifiable throughout the study . shedding and
therefore , current research on white sharks has focused on the use of distinctive natural markings as individual identifiers ( klimley and anderson 1996 ; strong et al . 1996 ; bonfil et al . 2005 ; domeier and nasby - lucas 2007 ; gubili et al .
one method proposed for individual identification in white sharks at guadalupe island utilizes pigmentation patterns ( domeier and nasby - lucas 2007 ) .
though resighting requires only one photograph of the gill flaps , pelvic fin or caudal fin on either side , initial identification requires photographs of all three of these locations on both sides of the animal .
in addition , the conditions necessary to support this type of identification , superb water visibility and high recreational diving effort , are unique to only guadalupe island .
collecting these data is likely to be too labor intensive and impractical in areas outside of guadalupe island with low water visibility ( e.g. , south africa ) and/or limited diving effort ( e.g. , california ) .
additionally , pigmentation patterns in several sharks were shown to naturally change in shape and/or size from year to year ( domeier and nasby - lucas 2007 ) .
alternately , dorsal fins can be photographed from either side and are often observed out of the water , precluding issues with water clarity or the need for divers .
dorsal fin identification , requiring limited effort , is possible at all white shark aggregation sites globally .
a comparison of matched individuals using genetic markers and dorsal fin photographs showed a high degree of concordance ( 85% ) between the two techniques over short ( 5  year ) time periods ( gubili et al .
white sharks have been shown to exhibit short - term site fidelity and repeatable individual identification through dorsal fin photographs ( klimley and anderson 1996 ; strong et al .
2009 ) and body pigmentation ( klimley and anderson 1996 ; domeier and nasby - lucas 2007 ) ; however , in order to understand the long - term status of white sharks , mark - recapture studies must be expanded out to longer time series .
therefore , it is imperative to determine whether assumptions regarding site fidelity and identification are valid across these longer time periods ( e.g. , > 14  years ) .
here , we aimed to determine ( 1 ) the stability of posterior edge dorsal fin morphology as individual identifiers over long time periods and ( 2 ) use this information to illustrate the long - term site fidelity of individual mature and subadult white sharks at coastal aggregation sites .
this study began at the south farallon islands in 1987 ( see anderson et al .
, the study was expanded to include coastal areas near tomales bay , california and beginning in 2005 , a small amount of marine mammal blubber was used as bait to increase encounter rates and duration .
high - resolution photographs and video were taken of each shark when they came near the surface to investigate a seal - shaped decoy .
we extracted dorsal fin images from these photographs and , if above water photographs were not available and water clarity permitted , from underwater video .
estimates of total length ( tl ) were also made when possible as sharks swam alongside a research skiff of known length .
images were assessed for quality based on four criteria : angle , size , focus , and contrast .
images of insufficient quality were removed ( see online resources 1 for discussion of photograph processing methods ) .
experts ( individuals with demonstrated expertise matching dorsal fin photographs ) then matched the remaining accepted fin photographs within and across all years simultaneously . if individuals were identified multiple times over the study period , we compared the earliest and latest photographs to determine long - term stability of dorsal fin morphology . when possible , secondary characteristics ( e.g. , tags , permanent scars , mutilations , etc . ) were used to validate these matches .
. experts matched 20 randomly chosen photographs from 12 sharks , which had obvious secondary characteristics ( not evident in the fin photographs ) .
matching results from each expert were compared to the true matches based on these known secondary characteristics .
confirmed males were sighted nearly twice as often as confirmed females ( 1.8:1 ) , though this ratio may be biased because it is easier to confirm the presence of claspers than the absence .
if the sex could not be confirmed , the animal was labeled  unknown .
four experts accurately identified individuals and matches 98% of the time with no false positives and only one false negative .
similarly , gubili et al . ( 2009 ) used genetic data to show nearly 85% accuracy in experts matching dorsal fin photographs .
annually , limited effort and photograph quality resulted in the identification of few sharks before 2006 when effort increased and digital slrs were used . prior to 2006 , over 60% of sharks were resighted ( 29 of 48 ) . in 2006 and 2007 , significantly more new sharks were recorded ( 76 ) , but by 2008 , 35% ( 27 ) of these new sharks had been resighted at least once .
twenty - one individuals were repeatedly identified over periods 5  year , ten individuals 10  years , and five individuals 15  years ( fig .  1 ) .
to illustrate the stability of markers and the empirical evidence of longevity , we describe five individuals resighted over periods 15  years at south farallon islands ( fig .
1cumulative number of individuals identified repeatedly over time periods ranging from one to twenty - two yearsfig .
2individuals a tj , b ct , c ft , d bh , and e rf repeatedly identified by dorsal fin morphology over periods > 15  years . the year indicates the date the photograph was takentable  1yearly identification of five white sharks resighted between 1987 and 20081987198819891990199119921993199419951996199719981999200020012002200320042005200620072008bhxxxxx
 xxxxct  x  x  xxx  x  xxxxxxxx  ftx  xxxxxxrfxxx  xtjxx  xxxxxxx depicts when an animal was sighted .
all individuals were identified in 1993 when effort was increased cumulative number of individuals identified repeatedly over time periods ranging from one to twenty - two years individuals a tj , b ct , c ft , d bh , and e rf repeatedly identified by dorsal fin morphology over periods > 15  years .
the year indicates the date the photograph was taken yearly identification of five white sharks resighted between 1987 and 2008 x depicts when an animal was sighted .
all individuals were identified in 1993 when effort was increased the longest record was shark tj , a 4.5-m - tl male .
tj was sighted 8 times over 22  years , initially in 1987 and most recently in 2008 ( fig  2a ) .
shark ct , a 3.5-m - tl male was sighted on 14 occasions over 20  years ( fig .
ft , a 4-m - tl male , was sighted 7 times in 19  years ( fig .
bh and rf , a 4-m - tl male sighted 9 times ( fig .
all tl estimates given refer to the size at the most recent sighting of each shark .
our findings support the use of the trailing edge of the dorsal fin for long - term photo - identification studies at coastal aggregation sites .
we photographically identified five white sharks repeatedly over a period of 1622  years . through the use of secondary characteristics and comparisons of first and last photographs of these five sharks
, we found no evidence of changes in the size , shape , or arrangement of existing notches on these fins .
we did , however , identify two sharks that incurred changes to their dorsal fins within the study period .
these two sharks , a 4.9-m - tl female photographed each year from 2004 to 2008 ( fig .
3a ) and a 4.3-m - tl male sighted november 07 , 2008 , and again 11  days later on november 18 ( fig .
3b ) , were shown to incur damage to their dorsal fins over the periods sighted . though the trailing edge of the dorsal fin was damaged , creating a new notch , identifiable markings above and below this notch remained unchanged and sufficient for identification , illustrating how even relatively major fin trauma may results in the addition of a notch while leaving ample morphologic information for a positive identification .
it is possible that the entire fin edge could be removed or altered due to major trauma preventing matching to previous sightings , but we saw no indication of this type of trauma during the 22  years of this study , which suggests this would be an extremely rare occurrence.fig .
3identification of fins after observations of fin damage . a a female shark photographed in 2004 with a complete fin , in 2005 with large lacerations on the fin , and in 2008 with scars from the damage , but all other distinguishing markings intact .
b a second shark showing new damage over a two - month period in 2008 identification of fins after observations of fin damage . a a female shark photographed in 2004 with a complete fin , in 2005 with large lacerations on the fin , and in 2008 with scars from the damage , but all other distinguishing markings intact .
b a second shark showing new damage over a two - month period in 2008 dorsal fin identification also supports the long - term ( 15  years ) site fidelity of white sharks at coastal aggregation sites and provides the longest empirical documentation of white shark longevity to date , > 22  years .
individual identification illustrated that animals returned to these sites consistently throughout the study period and potentially during their entire adult life span .
each animal was not necessarily seen every year , but unequal effort across both spatial and temporal scales most likely contributed greatly to such gaps in identification .
additionally , the prevalence of short - term resights ( < 5  years ) is also largely attributed to increased effort during the last 3  years of the study ( fig .  1 ) .
this methodology , obtaining one photograph of the dorsal fin , requires far less effort than methods to document body pigmentation patterns and does not suffer from large rates of tag shedding or biofouling as traditional tagging methods do .
many of the white sharks in this study have been tagged with ( on occasion multiple ) pop - off archival tags , ultrasonic transmitters and/or floy tags , which have the potential to shed within a short time span ( < 1  year ) ( jorgensen et al . 2010 ) , precluding their use in long - term mark - recapture studies .
in addition , further effort to automate the matching process will make the process more feasible with large datasets , allowing for the universal comparison of animals across different geographic regions regardless of diving effort or water clarity conditions .
dorsal fin identification offers the foundation for mark - recapture studies to quantify the population size and trends of white sharks . if possible , we suggest all available data be recorded ( e.g. , fin photographs and body pigments )
therefore , we propose that dorsal fins , because of their ease in recording , illustrated longevity and potential for universal application , be prioritized as a method to document individual white sharks . this methodology can not only be used to monitor the status of the white shark population in the northeast pacific , but unlike other photo - identification methods , it can be more uniformly applied to archive white sharks worldwide , standardizing documentation of individuals across vast spatial and temporal scales .
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Answer:
mark - recapture techniques can be used to estimate white shark ( carcharodon carcharias ) population abundance .
 these frameworks are based on assumptions that marks are conserved and animals are present at the sampling location over the entire duration of the study . though these assumptions have been validated across short - time scales for white sharks , long - term studies of population trends are dependent on these assumptions being valid across longer periods .
 we use 22  years of photographic data from aggregation sites in central california to support the use of dorsal fin morphology as long - term individual identifiers .
 we identified five individuals over 1622  years , which support the use of dorsal fins as long - time individual identifiers , illustrate strong yearly site fidelity to coastal aggregation sites across extended time periods ( decades ) , and provide the first empirical validation of white shark longevity > 22  years .
 these findings support the use of fin morphology in mark - recapture frameworks for white sharks.electronic supplementary materialthe online version of this article ( doi:10.1007/s00227 - 011 - 1643 - 5 ) contains supplementary material , which is available to authorized users .