bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clot retraction is mediated by factor XIII-dependent fibrin-αIIbβ3-myosin axis in platelet sphingomyelin-rich membrane rafts
Authors: Kasahara Kohji , Kaneda Mizuho , Miki Toshiaki , Iida Kazuko , Sekino-Suzuki Naoko , Kawashima Ikuo , Suzuki Hidenori , Shimonaka Motoyuki , Arai Morio , Ohno-Iwashita Yoshiko , Kojima Soichi , Abe Mitsuhiro , Kobayashi Toshihide , Okazaki Toshiro , Souri Masayoshi , Ichinose Akitada , Yamamoto Naomasa 
Published: September 2013

Key Points
Clot retraction of sphingomyelin-rich raft-depleted platelets from sphingomyelin synthase knockout mouse is delayed. Translocation of fibrin to sphingomyelin-rich rafts in platelet membrane is induced by thrombin in the presence of FXIII crosslinking activity.
Analysis of cattle olfactory subgenome: the first detail study on the characteristics of the complete olfactory receptor repertoire of a ruminant
Authors: Lee Kyooyeol , Nguyen Dinh Truong , Choi Minkyeung , Cha Se-Yeoun , Kim Jin-Hoi , Dadi Hailu , Seo Han Geuk , Seo Kunho , Chun Taehoon , Park Chankyu 
Published: September 2013

Abstract

Background
Mammalian olfactory receptors (ORs) are encoded by the largest mammalian multigene family. Understanding the OR gene repertoire in the cattle genome could lead to link the effects of genetic differences in these genes to variations in olfaction in cattle.

Results
We report here a whole genome analysis of the olfactory receptor genes of Bos taurus using conserved OR gene-specific motifs and known OR protein sequences from diverse species. Our analysis, using the current cattle genome assembly UMD 3.1 covering 99.9% of the cattle genome, shows that the cattle genome contains 1,071 OR-related sequences including 881 functional, 190 pseudo, and 352 partial OR sequences. The OR genes are located in 49 clusters on 26 cattle chromosomes. We classified them into 18 families consisting of 4 Class I and 14 Class II families and these were further grouped into 272 subfamilies. Comparative analyses of the OR genes of cattle, pigs, humans, mice, and dogs showed that 6.0% (n = 53) of functional OR cattle genes were species-specific. We also showed that significant copy number variations are present in the OR repertoire of the cattle from the analysis of 10 selected OR genes.

Conclusion
Our analysis revealed the almost complete OR gene repertoire from an individual cattle genome. Though the number of OR genes were lower than in pigs, the analysis of the genetic system of cattle ORs showed close similarities to that of the pig.
Guanylate cyclase C limits systemic dissemination of a murine enteric pathogen
Authors: Mann Elizabeth A , Harmel-Laws Eleana , Cohen Mitchell B , Steinbrecher Kris A 
Published: September 2013

Abstract

Background
Guanylate Cyclase C (GC-C) is an apically-oriented transmembrane receptor that is expressed on epithelial cells of the intestine. Activation of GC-C by the endogenous ligands guanylin or uroguanylin elevates intracellular cGMP and is implicated in intestinal ion secretion, cell proliferation, apoptosis, intestinal barrier function, as well as the susceptibility of the intestine to inflammation. Our aim was to determine if GC-C is required for host defense during infection by the murine enteric pathogen Citrobacter rodentium of the family Enterobacteriacea.

Methods
GC-C+/+ control mice or those having GC-C genetically ablated (GC-C−/−) were administered C. rodentium by orogastric gavage and analyzed at multiple time points up to post-infection day 20. Commensal bacteria were characterized in uninfected GC-C+/+ and GC-C−/− mice using 16S rRNA PCR analysis.

Results
GC-C−/− mice had an increase in C. rodentium bacterial load in stool relative to GC-C+/+. C. rodentium infection strongly decreased guanylin expression in GC-C+/+ mice and, to an even greater degree, in GC-C−/− animals. Fluorescent tracer studies indicated that mice lacking GC-C, unlike GC-C+/+ animals, had a substantial loss of intestinal barrier function early in the course of infection. Epithelial cell apoptosis was significantly increased in GC-C−/− mice following 10 days of infection and this was associated with increased frequency and numbers of C. rodentium translocation out of the intestine. Infection led to significant liver histopathology in GC-C−/− mice as well as lymphocyte infiltration and elevated cytokine and chemokine expression. Relative to naïve GC-C+/+ mice, the commensal microflora load in uninfected GC-C−/− mice was decreased and bacterial composition was imbalanced and included outgrowth of the Enterobacteriacea family.

Conclusions
This work demonstrates the novel finding that GC-C signaling is an essential component of host defense during murine enteric infection by reducing bacterial load and preventing systemic dissemination of attaching/effacing-lesion forming bacterial pathogens such as C. rodentium.
KIR3DS1/L1 and HLA-Bw4-80I are associated with HIV disease progression among HIV typical progressors and long-term nonprogressors
Authors: Jiang Yongjun , Chen Ou , Cui Chen , Zhao Bin , Han Xiaoxu , Zhang Zining , Liu Jing , Xu Junjie , Hu Qinghai , Liao Christina , Shang Hong 
Published: September 2013

AbstractBackgroundNatural killer (NK) cells have emerged as pivotal players in innate immunity, especially in the defense against viral infections and tumors. Killer immunoglobulin-like receptors (KIRs) – an important recognition receptor expressed on the surface of NK cells – regulate the inhibition and/or activation of NK cells after interacting with human leukocyte antigen (HLA) class I ligands. Various KIR genes might impact the prognosis of many different diseases. The implications of KIR-HLA interaction in HIV disease progression remains poorly understood.MethodsHere, we studied KIR genotypes, mRNA levels, HLA genotypes, CD4+T cell counts and viral loads in our cohort of Human Immunodeficiency Virus (HIV)-infected individuals, a group that includes HIV long-term nonprogressors (LTNPs) and typical progressors (TPs).ResultsWe found that the frequency of KIR3DS1/L1 heterozygotes with HLA-Bw4-80I gene was much higher in LTNPs than in TPs (P = 0.001) and that the KIR3DL1 homozygotes without HLA-Bw4-80I gene had higher viral loads and lower CD4+T cell counts (P = 0.014 andP = 0.021, respectively). Our study also confirmed that homozygosity for the HLA-Bw6 allele was associated with rapid disease progression. In addition to the aforementioned results on the DNA level, we observed that higher level expression of KIR3DS1 mRNA was in LTNP group, and that higher level expression of KIR3DL1 mRNA was in TP group.ConclusionsOur data suggest that different KIR-HLA genotypes and different levels of transcripts associate with HIV disease progression.
Pepsinogen I and II expressions in situ and their correlations with serum pesignogen levels in gastric cancer and its precancerous disease
Authors: Li Ping , He Caiyun , Sun Liping , Dong Nannan , Yuan Yuan 
Published: September 2013

Abstract

Background
Serum pepsinogen (PG) I/II ratio has been widely used as “serological biopsy” for the screening of gastric cancer (GC) and atrophic gastritis (GA). However, study concerning in situ expression of PGs is currently insufficient, particularly for their relationship with serum PGs levels. This study was designed to investigate in situ expression of PGI and PGII in subjects with normal mucosa (NOR), superficial gastritis (GS), GA and GC, and to evaluate the correlations between PGs expressions in situ and in serum.

Methods
185 subjects were enrolled for the study, including 30 NOR, 70 GS, 54 GA and 31 GC. PGI and PGII expressions in situ and in serum were detected by immunohistochemistry and enzyme-linked immunosorbent assay (ELISA) respectively. H. pylori immunoglobulin (Ig) G was also determined by ELISA.

Results
In situ expressions of PGI, PGII and PGI/II ratio consistently decreased in sequence of NOR/GS- > GA- > GC. The expressions of PGI, PGII and PGI/II ratio in situ were statistically higher in youngers than in olders (P < 0.05). In the NOR subjects, PGI staining was statistically higher in males than that in females (p = 0.02). For the correlations between in situ and serum expressions of PGI, PGII and PGI/II ratio, a borderline correlation in the total study sample (r = 0.131, P = 0.076) and a statistical correlation in GA cases (r = 0.307, P = 0.027) were observed for the PGI/II ratio. The PGI expression correlated well with that of PGII in situ and in serum.

Conclusions
The in situ levels of PGI, PGII and PGI/II ratio sharply decreased in the GA and GC cases. The youngers exhibited higher levels of PGI, PGII and PGI/II ratios than the olders. The in situ PGI/II ratio rather than PGI and PGII alone showed certain correlation with that in serum, and the PGI expression correlated well with PGII expression. Further studies with large-scale samples are still required to validate our findings.
Benefits of a physician-facing tablet presentation of patient symptom data: comparing paper and electronic formats
Authors: Glaser Daniel , Jain Sanjula , Kortum Philip 
Published: September 2013

Abstract

Background
Providing patient information to physicians in usable form is of high importance. Electronic presentation of patient data may have benefits in efficiency and error rate reduction for these physician facing interfaces. Using a cancer symptom measurement tool (the MD Anderson Symptom Inventory (MDASI)) we assessed the usability of patient data in its raw paper form and compared that to presentation on two electronic presentation formats of different sizes.

Methods
In two separate experiments, undergraduates completed two identical six-part questionnaires on two twenty-patient MDASI data sets. In Experiment 1, participants completed one questionnaire using a paper packet and the other questionnaire using an in-house designed iPad application. In Experiment 2, MDASI data was evaluated using an iPad and iPod Touch. Participants assessed the usability of the devices directly after use. In a third experiment, medical professionals evaluated the paper and iPad interfaces in order to validate the findings from Experiment 1.

Results
Participants were faster and more accurate answering questions about patients when using the iPad. The results from the medical professionals were similar. No appreciable accuracy, task time, or usability differences were observed between the iPad and iPod Touch.

Conclusions
Overall, the use of our tablet interface increased the accuracy and speed that users could extract pertinent information from a multiple patient MDASI data set compared to paper. Reducing the size of the interface did not negatively affect accuracy, speed, or usability. Generalization of the results to other physician facing interfaces is discussed.
Event detection in consumer videos using GMM supervectors and SVMs
Authors: Kamishima Yusuke , Inoue Nakamasa , Shinoda Koichi 
Published: September 2013

Abstract
In large-scale multimedia event detection, complex target events are extracted from a large set of consumer-generated web videos taken in unconstrained environments. We devised a multimedia event detection method based on Gaussian mixture model (GMM) supervectors and support vector machines. A GMM supervector consists of the parameters of a GMM for the distribution of low-level features extracted from a video clip. A GMM is regarded as an extension of the bag-of-words framework to a probabilistic framework, and thus, it can be expected to be robust against the data insufficiency problem. We also propose a camera motion cancelled feature, which is a spatio-temporal feature robust against camera motions found in consumer-generated web videos. By combining these methods with the existing features, we aim to construct a high-performance event detection system. The effectiveness of our method is evaluated using TRECVID MED task benchmark.
What is next after the genes for autoimmunity?
Authors: Castiblanco John , Arcos-Burgos Mauricio , Anaya Juan-Manuel 
Published: September 2013

Abstract
Clinical pathologies draw us to envisage disease as either an independent entity or a diverse set of traits governed by common physiopathological mechanisms, prompted by environmental assaults throughout life. Autoimmune diseases are not an exception, given they represent a diverse collection of diseases in terms of their demographic profile and primary clinical manifestations. Although they are pleiotropic outcomes of non-specific disease genes underlying similar immunogenetic mechanisms, research generally focuses on a single disease. Drastic technologic advances are leading research to organize clinical genomic multidisciplinary approaches to decipher the nature of human biological systems. Once the currently costly omic-based technologies become universally accessible, the way will be paved for a cleaner picture to risk quantification, prevention, prognosis and diagnosis, allowing us to clearly define better phenotypes always ensuring the integrity of the individuals studied. However, making accurate predictions for most autoimmune diseases is an ambitious challenge, since the understanding of these pathologies is far from complete. Herein, some pitfalls and challenges of the genetics of autoimmune diseases are reviewed, and an approximation to the future of research in this field is presented.
Effect of beraprost sodium on arterial stiffness in patients with type 2 diabetic nephropathy
Authors: Na Ki Young , Kim Dong Ki , Kim Sung Gyun , Lee Young-Ki , Lim Chun Soo 
Published: September 2013

Abstract

Background
Diabetic nephropathy is the leading cause of end-stage renal disease (ESRD). Cardiovascular (CV) complications are the most common cause of death among ESRD patients. Beraprost sodium (BPS) is a prostacyclin analog with vasodilatory and antiplatelet effects.

Methods
This is a multicenter prospective, randomized, double-blind, placebo-controlled trial to determine whether treatment with BPS improves arterial stiffness in patients with type 2 diabetic nephropathy. A total of 102 participants with type 2 diabetic nephropathy will be screened, enrolled, and randomly assigned to receive either 80 μg BPS or placebo daily for 12 weeks. The primary outcome is the change in brachial-ankle pulse wave velocity between baseline and after 12 weeks of medication use. The secondary outcomes will include changes in the ankle-brachial index, the urine albumin to creatinine ratio, the estimated glomerular filtration rate, lipid profiles, and blood pressure from baseline to after treatment.

Discussion
This clinical trial is the first to investigate the effects of BPS on changes in CV biomarkers, albuminuria, renal function, and lipid profiles in patients with diabetic nephropathy.

Trial registration
ClinicalTrials.gov number NCT01796418
Modularity and evolutionary constraints in a baculovirus gene regulatory network
Authors: Oliveira Juliana Velasco , de Brito Anderson Fernandes , Braconi Carla Torres , de Melo Freire Caio César , Iamarino Atila , de Andrade Zanotto Paolo Marinho 
Published: September 2013

AbstractBackgroundThe structure of regulatory networks remains an open question in our understanding of complex biological systems. Interactions during complete viral life cycles present unique opportunities to understand how host-parasite network take shape and behave. TheAnticarsia gemmatalismultiple nucleopolyhedrovirus (AgMNPV) is a large double-stranded DNA virus, whose genome may encode for 152 open reading frames (ORFs). Here we present the analysis of the ordered cascade of the AgMNPV gene expression.ResultsWe observed an earlier onset of the expression than previously reported for other baculoviruses, especially for genes involved in DNA replication. Most ORFs were expressed at higher levels in a more permissive host cell line. Genes with more than one copy in the genome had distinct expression profiles, which could indicate the acquisition of new functionalities. The transcription gene regulatory network (GRN) for 149 ORFs had a modular topology comprising five communities of highly interconnected nodes that separated key genes that are functionally related on different communities, possibly maximizing redundancy and GRN robustness by compartmentalization of important functions. Core conserved functions showed expression synchronicity, distinct GRN features and significantly less genetic diversity, consistent with evolutionary constraints imposed in key elements of biological systems. This reduced genetic diversity also had a positive correlation with the importance of the gene in our estimated GRN, supporting a relationship between phylogenetic data of baculovirus genes and network features inferred from expression data. We also observed that gene arrangement in overlapping transcripts was conserved among related baculoviruses, suggesting a principle of genome organization.ConclusionsAlbeit with a reduced number of nodes (149), the AgMNPV GRN had a topology and key characteristics similar to those observed in complex cellular organisms, which indicates that modularity may be a general feature of biological gene regulatory networks.
Target of rapamycin signaling regulates high mobility group protein association to chromatin, which functions to suppress necrotic cell death
Authors: Chen Hongfeng , Workman Jason J , Tenga Alexa , Laribee R Nicholas 
Published: September 2013

Abstract

Background
The target of rapamycin complex 1 (TORC1) is an evolutionarily conserved signal transduction pathway activated by environmental nutrients that regulates gene transcription to control cell growth and proliferation. How TORC1 modulates chromatin structure to control gene expression, however, is largely unknown. Because TORC1 is a major transducer of environmental information, defining this process has critical implications for both understanding environmental effects on epigenetic processes and the role of aberrant TORC1 signaling in many diseases, including cancer, diabetes, and cardiovascular disease.

Results
To elucidate the role of TORC1 signaling in chromatin regulation, we screened a budding yeast histone H3 and H4 mutant library using the selective TORC1 inhibitor rapamycin to identify histone residues functionally connected to TORC1. Intriguingly, we identified histone H3 lysine 37 (H3K37) as a residue that is essential during periods of limited TORC1 activity. An H3K37A mutation resulted in cell death by necrosis when TORC1 signaling was simultaneously impaired. The induction of necrosis was linked to alterations in high mobility group (HMG) protein binding to chromatin. Furthermore, the necrotic phenotype could be recapitulated in wild-type cells by deregulating the model HMG proteins, Hmo1 or Ixr1, thus implicating a direct role for HMG protein deregulation as a stimulus for inducing necrosis.

Conclusions
This study identifies histone H3 and H4 residues functionally required for TORC1-dependent cell growth and proliferation that are also candidate epigenetic pathways regulated by TORC1 signaling. It also demonstrates a novel role for H3K37 and TORC1 in regulating the binding of select HMG proteins to chromatin and that HMG protein deregulation can initiate a necrotic cell death response. Overall, the results from this study suggest a possible model by which chromatin anchors HMG proteins during periods of limited TORC1 signaling, such as that which occurs during conditions of nutrient stress, to suppress necrotic cell death.
Secondary cytoreduction surgery improves prognosis in platinum-sensitive recurrent ovarian cancer
Authors: Xu Xia , Chen Xiaoxiang , Dai Zhiqin , Deng Fei , Qu Junwei , Ni Jing 
Published: September 2013

AbstractBackgroundThere is no consensus regarding the secondary cytoreduction surgery (CRS) in recurrent ovarian cancer patients. The present study aims to determine the value of secondary CRS and the eligible subgroup for this procedure.Methods96 platinum-sensitive recurrent ovarian cancer patients were recruited from Jiangsu Institute of Cancer Research between 1992 and 2011. Follow-up was conducted based on the surveillance protocol of MD Anderson Cancer Center. Cox proportional hazards model and log-rank test were used to assess the associations between the survival durations and covariates. Logistic regression analysis was used to explore optimal secondary CRS related factors.ResultsOptimal secondary CRS was associated with time to progression (TTP) and overall survival (OS) in patients (p < 0.01 both). Optimal secondary CRS and asymptomatic recurrent were similarly associated with longer OS (median: 79.2vs.53.9 and 76.1vs.56.0 months with p = 0.02 and p = 0.04, respectively) and TTP (median: 13.9vs.10.5 and 19.3vs.9.0 months with p = 0.02 and p = 0.03, respectively) than counterparts. Optimal initial CRS (p = 0.01), asymptomatic recurrent (p = 0.02) and longer progression-free survival duration (p = 0.02) were the independent indicators of optimal secondary CRS.ConclusionsOptimal secondary CRS had survival benefit for platinum-sensitive epithelial ovarian cancer. Asymptomatic recurrent was one of the recruited factors for this procedure.
Differences in chemosensory response between eyed and eyeless Astyanax mexicanus of the Rio Subterráneo cave
Authors: Bibliowicz Jonathan , Alié Alexandre , Espinasa Luis , Yoshizawa Masato , Blin Maryline , Hinaux Hélène , Legendre Laurent , Père Stéphane , Rétaux Sylvie 
Published: September 2013

Abstract

Background
In blind cave-dwelling populations of Astyanax mexicanus, several morphological and behavioral shifts occurred during evolution in caves characterized by total and permanent darkness. Previous studies have shown that sensory systems such as the lateral line (mechanosensory) and taste buds (chemosensory) are modified in cavefish. It has long been hypothesized that another chemosensory modality, the olfactory system, might have evolved as well to provide an additional mechanism for food-searching in troglomorphic Astyanax populations.

Findings
During a March 2013 cave expedition to the Sierra de El Abra region of San Luís Potosi, Mexico, we tested chemosensory capabilities of the Astyanax mexicanus of the Rio Subterráneo cave. This cave hosts a hybrid population presenting a wide range of troglomorphic and epigean mixed phenotypes. During a behavioral test performed in situ in the cave, a striking correlation was observed between the absence of eyes and an increased attraction to food extract. In addition, eyeless troglomorphic fish possessed significantly larger naris size than their eyed, nontroglomorphic counterparts.

Conclusions
Our findings suggest that chemosensory capabilities might have evolved in cave-dwelling Astyanax mexicanus and that modulation of naris size might at least partially underlie this likely adaptive change.