bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sequence variations of the locus‐specific 5′ untranslated regions of SLA class I genes and the development of a comprehensive genomic DNA‐based high‐resolution typing method for SLA‐2
Authors: Choi H. , Le M. T. , Lee H. , Choi M.‐K. , Cho H.‐S. , Nagasundarapandian S. , Kwon O.‐J. , Kim J.‐H. , Seo K. , Park J.‐K. , Lee J.‐H. , Ho C.‐S. , Park C. 
Published: September 2015

AbstractThe genetic diversity of the major histocompatibility complex (MHC) class I molecules of pigs has not been well characterized. Therefore, the influence of MHC genetic diversity on the immune‐related traits of pigs, including disease resistance and other MHC‐dependent traits, is not well understood. Here, we attempted to develop an efficient method for systemic analysis of the polymorphisms in the epitope‐binding region of swine leukocyte antigens (SLA) class I genes. We performed a comparative analysis of the last 92 bp of the 5′ untranslated region (UTR) to the beginning of exon 4 of six SLA classical class I‐related genes, SLA‐1, ‐2, ‐3, ‐4, ‐5, and ‐9, from 36 different sequences. Based on this information, we developed a genomic polymerase chain reaction (PCR) and direct sequencing‐based comprehensive typing method for SLA‐2. We successfully typed SLA‐2 from 400 pigs and 8 cell lines, consisting of 9 different pig breeds, and identified 49 SLA‐2 alleles, including 31 previously reported alleles and 18 new alleles. We observed differences in the composition of SLA‐2 alleles among different breeds. Our method can be used to study other SLA class I loci and to deepen our knowledge of MHC class I genes in pigs.
Characterization of a new human monoclonal antibody directed against the Vel antigen
Authors: Danger Y. , Danard S. , Gringoire V. , Peyrard T. , Riou P. , Semana G. , Vérité F. 
Published: September 2015

Background and ObjectivesThe Vel blood group antigen is a poorly characterized high‐prevalence antigen. Until now, anti‐Vel antibodies have been observed in only alloimmunized Vel‐negative individuals. In this study, we aimed to establish a human hybridoma cell line secreting the first anti‐Vel monoclonal antibody (mAb), clone SpG213Dc.Materials and MethodsPeripheral blood lymphocytes from a French Vel‐negative woman with anti‐Vel in her plasma were transformed with Epstein–Barr virus and then hybridized with the myeloma cell line Sp2/O‐Ag14 using the polyethylene glycol (PEG) method. A specific anti‐Vel mAb was successfully produced and was extensively characterized by serological, flow cytometry and Western blot analyses.ResultsOne human anti‐Vel‐secreting clone was produced and the secreted anti‐Vel mAb (SpG213Dc) was examined. The specificity of the SpG213Dc mAb was assessed by its reactivity against a panel of nine genotyped RBCs including, respectively, three Vel‐negative and six Vel‐positive (three wild‐type homozygous and three heterozygous) samples using flow cytometry method. Vel‐positive RBCs were specifically stained and were subsequently used to perform Western blot and immunoprecipitation analysis of the Vel antigen.ConclusionSerological characterization of the new monoclonal anti‐Vel SpG213Dc showed a heterogeneous level of expression of the Vel antigen on the different RBCs. Our results suggest that the mAb SpG213Dc can be reliably used as a blood grouping reagent, thus allowing the mass‐scale phenotyping of blood donors to strengthen rare blood banks with Vel‐negative RBC units.
Xenotransplantation and porcine cytomegalovirus
Authors: Denner Joachim 
Published: September 2015

AbstractPorcine microorganisms may be transmitted to the human recipient when xenotransplantation with pig cells, tissues, and organs will be performed. Most of such microorganisms can be eliminated from the donor pig by specified or designated pathogen‐free production of the animals. As human cytomegalovirus causes severe transplant rejection in allotransplantation, considerable concern is warranted on the potential pathogenicity of porcine cytomegalovirus (PCMV) in the setting of xenotransplantation. On the other hand, despite having a similar name, PCMV is different from HCMV. The impact of PCMV infection on pigs is known; however, the influence of PCMV on the human transplant recipient is unclear. However, first transplantations of pig organs infected with PCMV into non‐human primates were associated with a significant reduction of the survival time of the transplants. Sensitive detection methods and strategies for elimination of PCMV from donor herds are required.
Impact of donor age and weaning status on pancreatic exocrine and endocrine tissue maturation in pigs
Authors: Krishnan Rahul , Truong Nhat , Gerges Marina , Stiewig Miranda , Neel Nicholas , Ho‐Nguyen KhueTu , Kummerfeld Christina , Alexander Michael , Spizzo Tom , Martin Michael , Foster Clarence E. , Monuki Edwin S. , Lakey Jonathan R. T. 
Published: September 2015

AbstractBackgroundDuring the process of islet isolation, pancreatic enzymes are activated and released, adversely affecting islet survival and function. We hypothesize that the exocrine component of pancreases harvested from pre‐weaned juvenile pigs is immature and hence pancreatic tissue from these donors is protected from injury during isolation and prolonged tissue culture.MethodsBiopsy specimens taken from pancreases harvested from neonatal (5–10 days), pre‐weaned juvenile (18–22 days), weaned juvenile (45–60 days), and young adult pigs (>90 days) were fixed and stained with hematoxylin and eosin. Sections were examined under a fluorescent microscope to evaluate exocrine zymogen fluorescence intensity (ZFI) and under an electron microscope to evaluate exocrine zymogen granule density (ZGD).ResultsExocrine content estimation showed significantly lower ZFI and ZGD in juvenile pig pancreases (1.5 ± 0.04 U/μm2, ZFI; 1.03 ± 0.07 × 103/100 μm2, ZGD) compared to young adult pigs (2.4 ± 0.05U/μm2, ZFI; 1.53 ± 0.08 × 103/100 μm2 ZGD). Islets in juvenile pig pancreases were on average smaller (105.2 ± 11.2 μm) than islets in young adult pigs (192 ± 7.7 μm), but their insulin content was comparable (80.9 ± 2.2% juvenile; 84.2 ± 0.3% young adult, P > 0.05). All data expressed as mean ± SEM.ConclusionPorcine islet xenotransplantation continues to make strides toward utilization in clinical trials of type 1 diabetes. Porcine donor age and weaning status influence the extent of exocrine maturation of the pancreas. Juvenile porcine pancreases may represent an alternative donor source for islet xenotransplantation as their exocrine component is relatively immature; this preserves islet viability during extended tissue culture following isolation.
Interrater Reliability of the ENERGY Photo-Rating Instrument for School Environments Related to Physical Activity and Eating
Authors: Altenburg Teatske , Velde Saskia te , Chiu Kai-Jan , Moschonis George , Manios Yannis , De Bourdeaudhuij Ilse , Vik Frøydis N. , Lien Nanna , Brug Johannes , Chinapaw Mai 
Published: September 2015

Background:The school environment can play an important role in the prevention of childhood overweight and obesity. Photos of the school environment may contribute to more adequate measurement of the school environment, as photos can be rated by different assessors. We aimed to examine the interrater reliability for rating characteristics of primary school environments related to physical activity and eating.Methods:Photos taken at 172 primary schools in 7 European countries were rated according to a standardized protocol. Briefly, after categorizing all photos in subsections of physical activity or eating opportunities, 2 researchers independently rated aspects of safety, functionality, aesthetics, type of food/drinks advertised, type/variety of foods provided. Interrater reliability was assessed using the intraclass correlation coefficient (ICC) and Cohen’s kappa.Results:Six subsections of the photo-rating instrument showed excellent (ICC or Cohen’s kappa ≥0.81) or good (ICC or Cohen’s kappa 0.61 to 0.80) interrater reliability. Outdoor physical activity facilities (ICC = 0.54) showed moderate, and school canteens (Cohen’s kappa = 0.05) and vending machines showed poor (Cohen’s kappa = 0.16) interrater reliability.Conclusion:Interrater reliability of the ENERGY (EuropeaN Energy balance Research to prevent excessive weight Gain among Youth) photo-rating instrument was good-to-excellent for 6 out of 9 characteristics of primary school environment components related to physical activity and eating.
Changes in Leisure-Time Physical Activity From the Prepregnancy to the Postpartum Period: 2004 Pelotas (Brazil) Birth Cohort Study
Authors: Coll Carolina , Domingues Marlos , Santos Iná , Matijasevich Alicia , Horta Bernardo Lessa , Hallal Pedro C. 
Published: September 2015

Background:The aim of this study was to evaluate changes in leisure-time physical activity (LTPA) and its correlates from prepregnancy to the postpartum period in mothers enrolled in a Brazilian birth cohort study. Our hypothesis was that LTPA would decline considerably during pregnancy.Methods:Maternal LTPA in the 3 months before pregnancy and during each trimester of pregnancy was assessed soon after delivery. A follow-up visit was conducted 3 months later. Weekly frequency and duration of each session of LTPA in a typical week were assessed for each period and a cut-off point of 150 minutes per week was used to classify women as active or not.Results:The proportion of women active in leisure time declined from 11.3% in the prepregnancy to 2.3% in pregnancy and 0.1% in the postpartum period (P for trend <0.001). When considering any LTPA practice, the decline ranged from 15.4% to 4.4% and 7.5% (p for trend <0.001), respectively. Higher income, higher education and lower parity were the main predictors of LTPA practice.Conclusions:LTPA declined considerably during pregnancy and did not return to prepregnancy levels at 3 months postpartum. Mothers must be advised on the benefits of LTPA prepregnancy, during, and postpregnancy.
Genome Assemblies for 11 Yersinia pestis Strains Isolated in the Caucasus Region
Authors: Zhgenti Ekaterine , Johnson Shannon L. , Davenport Karen W. , Chanturia Gvantsa , Daligault Hajnalka E. , Chain Patrick S. , Nikolich Mikeljon P. 
Published: September 2015

ABSTRACT

Yersinia pestis
, the causative agent of plague, is endemic to the Caucasus region but few reference strain genome sequences from that region are available. Here, we present the improved draft or finished assembled genomes from 11 strains isolated in the nation of Georgia and surrounding countries.
De Novo
Genome Sequence of Yersinia aleksiciae Y159
T
Authors: Sprague Lisa D. , Neubauer Heinrich 
Published: September 2015

ABSTRACT

We report here on the genome sequence of
Yersinia aleksiciae
Y159
T
, isolated in Finland in 1981. The genome has a size of 4 Mb, a G+C content of 49%, and is predicted to contain 3,423 coding sequences.
Genome Sequence of Bradyrhizobium pachyrhizi Strain PAC48
T
, a Nitrogen-Fixing Symbiont of
Pachyrhizus erosus
(L.) Urb
Authors: Delamuta Jakeline Renata Marçon , Ribeiro Renan Augusto , Gomes Douglas Fabiano , Souza Renata Carolina , Chueire Ligia Maria Oliveira , Hungria Mariangela 
Published: September 2015

ABSTRACT

Bradyrhizobium pachyrhizi
PAC48
T
has been isolated from a jicama nodule in Costa Rica. The draft genome indicates high similarity with that of
Bradyrhizobium elkanii
. Several coding sequences (CDSs) of the stress response might help in survival in the tropics. PAC48
T
carries
nodD1
and
nodK
, similar to
Bradyrhizobium
(
Parasponia
) ANU 289 and a particular
nodD2
gene.
Draft Genome Sequences of Five Clinical Enterococcus cecorum Strains Isolated from Different Poultry Species in Poland
Authors: Dolka Beata , Heidemann Olsen Rikke , Naundrup Thøfner Ida Cecilie , Christensen Jens Peter 
Published: September 2015

ABSTRACT

Here, we report five draft genome sequences of
Enterococcus cecorum
strains that were isolated from different bird species of affected poultry flocks (commercial broilers [CB], broiler breeders [BB], commercial layers [CL], ducks [D], and geese [G]) in Poland.
Uterine size and ovarian size in adolescents with functional hypothalamic amenorrhoea
Authors: Bumbuliene Zana , Klimasenko Jelena , Sragyte Diana , Zakareviciene Jolita , Drasutiene Grazina 
Published: September 2015

IntroductionFunctional hypothalamic amenorrhoea (FHA) is a condition characterised by the absence of menses due to suppression of the hypothalamic-pituitary-ovarian axis.ObjectiveThe purpose of the study was to estimate uterine and ovarian sizes in adolescents with FHA and to compare these results with findings in peers having regular menstrual cycles.DesignProspective case-controlled study.SettingsVilnius University Hospital Santariskiu Klinikos, Lithuania.PatientsLithuanian adolescents—45 with FHA and 40 comparison group participants.Main outcome measuresWe assessed ultrasound measurements of internal reproductive organs, levels of luteinising hormone, follicle-stimulating hormone, prolactin, oestradiol and calculated body mass index (BMI).ResultsThe mean age of the participants was 16.3±1.2 years, the mean age after menarche—3.6 years. In adolescents with FHA the BMI was 17.8±1.8 kg/m2 and 20.4±1.4 kg/m2 in the comparison group, p<0.001. The uterine volume (14.7±6.3 cm3 vs 31.7±10.6 cm3, p<0.001), cervical length (2.3±0.4 cm vs 2.6±0.5 cm, p=0.03), volume of both ovaries (9.3±3.6 cm3 vs 13.8±4.3 cm3, p<0.001) and levels of LH (2.70±2.59 vs 6.01±2.44, p<0.001) were significantly lower in girls with FHA. A significantly positive correlation between volume of uterus and levels of LH (r=0.415; p<0.001) was found. We identified a positive correlation between uterine volume, uterine corpus length, cervical length, ovarian volume and weight, BMI.ConclusionsIn adolescents with FHA the dimensions of uterus and ovaries were smaller than in girls having regular menstrual cycles. Our study confirmed the influence of oestrogen on uterus size: oestrogen deficiency causes a reduction in uterine size. Uterine size and ovarian size correlate positively with BMI.
Multiplex H. pylori Serology and Risk of Gastric Cardia and Noncardia Adenocarcinomas
Authors: Shakeri Ramin , Malekzadeh Reza , Nasrollahzadeh Dariush , Pawilta Michael , Murphy Gwen , Islami Farhad , Sotoudeh Masoud , Michel Angelika , Etemadi Arash , Waterboer Tim , Poustchi Hossein , Brennan Paul , Boffetta Paolo , Dawsey Sanford M. , Kamangar Farin , Abnet Christian C. 
Published: September 2015

Abstract
The reported associations with gastric adenocarcinoma and seropositivity to different Helicobacter pylori antigens using multiplex serology have not been consistent across studies. We aimed to investigate the association between 15 different multiplex serology antigens and the risk of gastric cardia (GCA) and gastric noncardia (GNCA) adenocarcinomas in northeastern Iran, a population with high rates of gastric adenocarcinoma. We included 272 cases of gastric adenocarcinoma (142 GCA, 103 GNCA, and 27 unspecified) and 524 controls who were individually matched to cases for age, sex, and place of residence in a population-based case–control study. Seropositivity to H. pylori was assessed using both multiplex serology and H. pylori IgG ELISA. Ninety-five percent of controls were seropositive to H. pylori. Of the 15 antibodies in the multiplex assay, 11 showed no significant association with gastric adenocarcinomas. CagA and VacA were associated with a significantly increased risk of all gastric adenocarcinoma and GNCA in multivariate models. Surprisingly, GroEL and NapA were significantly associated with a reduced risk of these tumors. Only CagA antigen was associated with significantly elevated risk of GCA. We found no associations between H. pylori seropositivity overall either by whole-cell ELISA test or multiplex serology, likely due to the high prevalence of seropositivity. Individual antigen testing showed that CagA positivity was associated with increased risk of both noncardia and cardia adenocarcinoma, which is similar to some other Asian populations, whereas two antigens were associated with lower risk of gastric cancer. This latter result was unexpected and should be retested in other populations. Cancer Res; 75(22); 4876–83. ©2015 AACR.
Low-Coverage Exome Sequencing Screen in Formalin-Fixed Paraffin-Embedded Tumors Reveals Evidence of Exposure to Carcinogenic Aristolochic Acid
Authors: Castells Xavier , Karanović Sandra , Ardin Maude , Tomić Karla , Xylinas Evanguelos , Durand Geoffroy , Villar Stephanie , Forey Nathalie , Le Calvez-Kelm Florence , Voegele Catherine , Karlović Krešimir , Mišić Maja , Dittrich Damir , Dolgalev Igor , McKay James , Shariat Shahrokh F. , Sidorenko Viktoria S. , Fernandes Andrea , Heguy Adriana , Dickman Kathleen G. , Olivier Magali , Grollman Arthur P. , Jelaković Bojan , Zavadil Jiri 
Published: September 2015

Abstract
Background: Dietary exposure to cytotoxic and carcinogenic aristolochic acid (AA) causes severe nephropathy typically associated with urologic cancers. Monitoring of AA exposure uses biomarkers such as aristolactam-DNA adducts, detected by mass spectrometry in the kidney cortex, or the somatic A&gt;T transversion pattern characteristic of exposure to AA, as revealed by previous DNA-sequencing studies using fresh-frozen tumors.
Methods: Here, we report a low-coverage whole-exome sequencing method (LC-WES) optimized for multisample detection of the AA mutational signature, and demonstrate its utility in 17 formalin-fixed paraffin-embedded urothelial tumors obtained from 15 patients with endemic nephropathy, an environmental form of AA nephropathy.
Results: LC-WES identified the AA signature, alongside signatures of age and APOBEC enzyme activity, in 15 samples sequenced at the average per-base coverage of approximately 10×. Analysis at 3 to 9× coverage revealed the signature in 91% of the positive samples. The exome-wide distribution of the predominant A&gt;T transversions exhibited a stochastic pattern, whereas 83 cancer driver genes were enriched for recurrent nonsynonymous A&gt;T mutations. In two patients, pairs of tumors from different parts of the urinary tract, including the bladder, harbored overlapping mutation patterns, suggesting tumor dissemination via cell seeding.
Conclusions: LC-WES analysis of archived tumor tissues is a reliable method applicable to investigations of both the exposure to AA and its biologic effects in human carcinomas.
Impact: By detecting cancers associated with AA exposure in high-risk populations, LC-WES can support future molecular epidemiology studies and provide evidence-base for relevant preventive measures. Cancer Epidemiol Biomarkers Prev; 24(12); 1873–81. ©2015 AACR.
Prediagnostic Plasma Adiponectin and Survival among Patients with Colorectal Cancer
Authors: Chong Dawn Q. , Mehta Raaj S. , Song Mingyang , Kedrin Dmitriy , Meyerhardt Jeffrey A. , Ng Kimmie , Wu Kana , Fuchs Charles S. , Giovannucci Edward L. , Ogino Shuji , Chan Andrew T. 
Published: September 2015

Abstract
Circulating adiponectin is inversely related to the risk of colorectal cancer. However, its influence on colorectal cancer survival is unclear. We conducted a prospective study to evaluate the association between prediagnostic plasma levels of adiponectin and mortality in patients with colorectal cancer. We identified 621 incident colorectal cancer cases who provided blood specimens prior to diagnosis within the Nurses' Health Study (NHS) and Health Professionals Follow-up Study (HPFS). Cox proportional hazards models were used to calculate HRs and 95% confidence intervals (CI). After a median follow-up of 9 years, there were 269 (43%) total deaths, of which 181 (67%) were due to colorectal cancer. Compared with participants in the lowest quartile of adiponectin, those in the highest quartile had multivariate HRs of 1.89 (95% CI, 1.21–2.97; Ptrend = 0.01) for colorectal cancer–specific mortality and 1.66 (95% CI, 1.15–2.39; Ptrend = 0.009) for overall mortality. The apparent increased risk in colorectal cancer–specific mortality was more pronounced in patients with metastatic disease (HR, 3.02: 95% CI, 1.50–6.08). Among patients with colorectal cancer, prediagnostic plasma adiponectin is associated with an increased risk of colorectal cancer–specific and overall mortality and is more apparent in patients with metastatic disease. Adiponectin may be a marker for cancers which develop through specific pathways that may be associated with worsened prognosis. Further studies are needed to validate these findings. Cancer Prev Res; 8(12); 1138–45. ©2015 AACR.
Influence of Amyloid-β on Cognitive Decline After Stroke/Transient Ischemic Attack
Authors: Liu Wenyan , Wong Adrian , Au Lisa , Yang Jie , Wang Zhaolu , Leung Eric Y.L. , Chen Sirong , Ho Chi L. , Mok Vincent C.T. 
Published: September 2015

Background and Purpose—
We hypothesized that comorbid amyloid-beta (Aβ) deposition played a key role in long-term cognitive decline in subjects with stroke/transient ischemic attack.

Methods—
We recruited 72 subjects with cognitive impairment after stroke/transient ischemic attack to receive Carbon-11-labeled Pittsburgh compound B positron emission tomography. We excluded subjects with known clinical Alzheimer’s disease. Those with and without Alzheimer’s disease–like Aβ deposition were classified as mixed vascular cognitive impairment (mVCI, n=14) and pure VCI (pVCI, n=58), respectively. We performed Mini-Mental State Examination (MMSE) and Montreal Cognitive Assessment to evaluate global cognition and cognitive domains (memory, visuospatial function, language, attention, and executive function) at 3 to 6 months (baseline) and annually for 3 years after the index event. We compared cognitive changes between mVCI and pVCI using linear mixed models and analysis of covariance adjusted for age and education.

Results—

Over 3 years, there were significant differences between mVCI and pVCI on change of MMSE score over time (group×time interaction,
P
=0.007). We observed a significant decline on MMSE score (
P
=0.020) in the mVCI group but not in the pVCI group (
P
=0.208). The annual rates of decline on MMSE (
P
=0.023) and Montreal Cognitive Assessment score (
P
=0.003) were greater in the mVCI group than in the pVCI group. Memory, visuospatial, and executive function domain scores on the Montreal Cognitive Assessment were related to Aβ deposition.

Conclusions—
Compared with subjects without Alzheimer’s disease–like Aβ deposition, those with Aβ deposition experienced a more severe and rapid cognitive decline over 3 years after stroke/transient ischemic attack. Aβ was associated with changes in multiple cognitive domains.