bluuebunny/crossref_metadata_2025_split huggingface dataset:
massiR
: a method for predicting the sex of samples in gene expression microarray datasets
Authors: Buckberry Sam , Bent Stephen J. , Bianco-Miotto Tina , Roberts Claire T. 
Published: March 2014

Abstract
Summary: High-throughput gene expression microarrays are currently the most efficient method for transcriptome-wide expression analyses. Consequently, gene expression data available through public repositories have largely been obtained from microarray experiments. However, the metadata associated with many publicly available expression microarray datasets often lacks sample sex information, therefore limiting the reuse of these data in new analyses or larger meta-analyses where the effect of sex is to be considered. Here, we present the massiR package , which provides a method for researchers to predict the sex of samples in microarray datasets. Using information from microarray probes representing Y chromosome genes, this package implements unsupervised clustering methods to classify samples into male and female groups, providing an efficient way to identify or confirm the sex of samples in mammalian microarray datasets.
Availability and implementation: massiR is implemented as a Bioconductor package in R . The package and the vignette can be downloaded at bioconductor.org and are provided under a GPL-2 license.
Contact: sam.buckberry@adelaide.edu.au
Supplementary information: Supplementary data are available at Bioinformatics online
Response to a population bottleneck can be used to infer recessive selection
Authors: Balick Daniel J. , Do Ron , Reich David , Sunyaev Shamil R. 
Published: March 2014

AbstractHere we present the first genome wide statistical test for recessive selection. This test uses explicitly non-equilibrium demographic differences between populations to infer the mode of selection. By analyzing the transient response to a population bottleneck and subsequent re-expansion, we qualitatively distinguish between alleles under additive and recessive selection. We analyze the response of the average number of deleterious mutations per haploid individual and describe time dependence of this quantity. We introduce a statistic,BR, to compare the number of mutations in different populations and detail its functional dependence on the strength of selection and the intensity of the population bottleneck. This test can be used to detect the predominant mode of selection on the genome wide or regional level, as well as among a sufficiently large set of medically or functionally relevant alleles.
Towards a new history and geography of human genes informed by ancient DNA
Authors: Pickrell Joseph K. , Reich David 
Published: March 2014

AbstractGenetic information contains a record of the history of our species, and technological advances have transformed our ability to access this record. Many studies have used genome-wide data from populations today to learn about the peopling of the globe and subsequent adaptation to local conditions. Implicit in this research is the assumption that the geographic locations of people today are informative about the geographic locations of their ancestors in the distant past. However, it is now clear that long-range migration, admixture and population replacement have been the rule rather than the exception in human history. In light of this, we argue that it is time to critically re-evaluate current views of the peopling of the globe and the importance of natural selection in determining the geographic distribution of phenotypes. We specifically highlight the transformative potential of ancient DNA. By accessing the genetic make-up of populations living at archaeologically-known times and places, ancient DNA makes it possible to directly track migrations and responses to natural selection.
Genetic variants at 8q24 are associated with risk of esophageal squamous cell carcinoma in a Chinese population
Authors: Dai Ningbin , Zheng Mingfeng , Wang Cheng , Ji Yong , Du Jiangbo , Zhu Chen , He Yisha , Zhu Meng , Zhu Xun , Sun Min , Dai Juncheng , Ma Hongxia , Chen Jingyu , Hu Zhibin , Gu Haiyong , Jin Guangfu , Shen Hongbing 
Published: March 2014

Esophageal cancer and gastric cancer have shared risk factors and inherited susceptibility. Recent genome‐wide association studies have identified multiple genetic loci associated with gastric cancer risk, which may also involve in the development of esophageal cancer. Herein, we evaluated the relationship of gastric cancer risk‐related variants at 1q22, 3q13.3, 5p13.1, and 8q24 with the risk of esophageal squamous cell carcinoma (ESCC) in a Chinese population with a case–control study (2139 cases and 2273 controls). We found that the T allele of rs2294008, an intronic variant of the PSCA gene at 8q24 that was previously associated with an increased risk of gastric cancer, was inversely associated with a decreased risk of ESCC (odds ratio = 0.90; 95% confidence interval, 0.81–0.99; P = 0.034). Of interest, the association of rs2294008 with ESCC was consistent with that observed in esophageal adenocarcinoma and ESCC in Caucasian populations. However, no significant associations were observed for the other three variants at 1q22 (rs4072037), 3q13.31 (rs9841504), and 5p13.1 (rs13361707). Our findings suggest that the susceptibility locus of PSCA at 8q24 may be a double‐edged sword, as modulator between the carcinogenesis processes of stomach and esophagus.
Risk factors for hepatitis B virus reactivation after conformal radiotherapy in patients with hepatocellular carcinoma
Authors: Huang Wei , Zhang Wei , Fan Min , Lu Yanda , Zhang Jian , Li Hongsheng , Li Baosheng 
Published: March 2014

This study investigated whether conformal radiotherapy affects hepatitis B virus (HBV) reactivation, and the risk factors for HBV reactivation in patients with HBV‐related hepatocellular carcinoma (HCC). Sixty‐nine patients with HCC were included in this retrospective study. Before radiotherapy (RT), all patients underwent imaging examinations and some baseline examinations, including CBC, liver function test, renal function test, α‐fetoprotein level, hepatitis B (HB) surface antigen, HB surface Ab, HB e antigen, HB e Ab, and serum HBV DNA quantification. During the period of RT and at least 16 weeks after the end of RT, CBCs were carried out weekly and the other tests were monitored monthly or more frequently if necessary. The clinical features and dosimetric parameters of RT were recorded. Univariate and multivariate logistic regression algorithms were used to analyze the risk factors of HBV reactivation. The incidence of complications in the study population was as follows: radiation‐induced liver disease, 17.4%; HBV reactivation, 24.6%; and HBV reactivation‐induced hepatitis, 21.7%. The HBV DNA level and dose volume parameters including normal liver volume, V20, and mean dose were associated with HBV reactivation. There was a relatively high incidence of HBV reactivation in HCC patients after the end of conformal RT. The serum HBV DNA level and some dosimetric parameters related to normal liver, including normal liver volume, V20, and mean dose, were the prognosis factors of HBV reactivation and should be carefully considered before conformal RT.
The child with difficult to control Congenital Adrenal Hyperplasia: is there a place for continuous subcutaneous hydrocortisone therapy
Authors: Hindmarsh Peter C. 
Published: March 2014

SummaryThe treatment of congenital adrenal hyperplasia requires administration of glucocorticoid and mineralocorticoid to replace the deficit resulting from the enzymatic block. During puberty, cortisol metabolism changes with an increase in clearance, which may lead to unstable control. This may require an increase in dosing frequency, and if this proves problematic, continuous subcutaneous hydrocortisone delivery using insulin pump technology can be valuable. The potential indications for such therapy along with some practical considerations are detailed in this Clinical Question report.
Preoperative risk factors for anastomotic leakage after resection for colorectal cancer: a systematic review and meta‐analysis
Authors: Pommergaard H.‐C. , Gessler B. , Burcharth J. , Angenete E. , Haglind E. , Rosenberg J. 
Published: March 2014

AbstractAimColorectal anastomotic leakage is a serious complication. Despite extensive research, no consensus on the most important preoperative risk factors exists. The aim of this systematic review and meta‐analysis was to evaluate risk factors for anastomotic leakage in patients operated with colorectal resection.MethodThe databases MEDLINE, Embase and CINAHL were searched for prospective observational studies on preoperative risk factors for anastomotic leakage. Meta‐analyses were performed on outcomes based on odds ratios (OR) from multivariate regression analyses. The Newcastle–Ottawa scale was used for bias assessment within studies, and the Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach was used for quality assessment of evidence on outcome levels.ResultsThis review included 23 studies evaluating 110 272 patients undergoing colorectal resection for cancer. The meta‐analyses found that a low rectal anastomosis [OR = 3.26 (95% CI: 2.31–4.62)], male gender [OR = 1.48 (95% CI: 1.37–1.60)] and preoperative radiotherapy [OR = 1.65 (95% CI: 1.06–2.56)] may be risk factors for anastomotic leakage. Primarily as a result of observational design, the quality of evidence was regarded as moderate or low for these risk factors according to the GRADE approach.ConclusionBased on the best available evidence, important preoperative risk factors for colorectal anastomotic leakage have been identified. Knowledge on risk factors may influence treatment and procedure‐related decisions, and possibly reduce the leakage rate.
Modified technique for aortic cross‐clamping during liver donor procurement
Authors: Desai Chirag S. , Girlanda Raffaele , Hawksworth Jason , Fishbein Thomas M. 
Published: March 2014

AbstractUndue tension on the donor vessels during organ procurement is associated with intimal dissection, which can form the nidus for the thrombosis of the hepatic artery (HA) and graft loss. According to the US OPTN database, 143 grafts were discarded in the last 15 yr due to vascular damage during procurement. The most common technique to expose the supraceliac aorta is dissection between the left lateral segment of the liver and the esophagus–stomach. In obese donors, due to restricted space and in pediatric donors where the vessels are very delicate and this space is very small, the replaced or accessory left HA(R/A LHA) is prone to damage if approached conventionally. We describe a technique for the exposure of the supraceliac aorta in which the aorta is approached from the left side behind the gastroesophageal junction that does not require division of the gastrohepatic ligament. From May 2007 to May 2013, 104 liver procurements were performed. Eighty‐nine (85.6%) were adults, and 15 (14.4%) were pediatric donors. Twenty‐three (22.1%) had R/A LHA. No donor organ suffered any damage. One adult recipient with R/A LHA suffered HA thrombosis not related to it. In summary, this technical modification offers improved safety during cadaveric procurement and increases the ease.
Beyond survival: how well do transplanted livers work? A preliminary comparison of standard‐risk, high‐risk, and living donor recipients
Authors: Miller‐Matero Lisa R. , Eshelman Anne , Paulson Daniel , Armstrong Rachel , Brown Kimberly A. , Moonka Dilip , Abouljoud Marwan 
Published: March 2014

AbstractTo help decrease mortality on the liver transplant waitlist, transplant centers are using living donors (LD) and high‐risk donors (HRD) in addition to standard‐risk donors (SRD). HRD is defined as having a donor risk index score higher than 1.6, which suggests a great risk of graft failure. Recent studies have examined survival rates between HRD and SRD recipients; however, little is known about outcomes other than survival, specifically psychosocial outcomes. The purpose of this preliminary, prospective study was to compare post‐transplant psychosocial and recovery outcomes between SRD and LD and HRD liver recipients. These outcomes include cognitive functioning, psychological distress, quality of life, and self‐reported and objective measures of recovery. Eighty‐four patients provided baseline and six‐month post‐transplant data. There were generally no statistically significant differences at baseline or the six‐month follow‐up, suggesting that patients receiving HRD livers have similar outcomes to those who receive SRD livers. However, some effect sizes suggest potential advantages for LD recipients compared to SRD recipients. Transplant centers may be more willing to encourage patients to accept HRD or LD livers knowing that they may have comparable outcomes to SRD recipients, which also has implications for the transplant waitlist.
Current Opinions on the Control and Role of Vascular Smooth Muscle Cell Adhesion, Calcium Sensitization, and the Cytoskeleton in Vascular Structure and Function
Authors: Martinez‐Lemus Luis A. 
Published: March 2014

AbstractVascular smooth muscle contraction and relaxation play a preponderant role on the active (acute) and structural (long‐term) control of vascular diameter. This editorial overview summarizes and highlights the opinions expressed in seven reviews contained in this special topic issue of Microcirculation. The reviews address diverse aspects of the mechanisms that influence cell adhesion, calcium homeostasis, and cytoskeletal remodeling, and how these mechanisms affect vascular structure and function at different levels of the circulation.
Angiogenesis: Growth Points
Authors: Egginton Stuart , Birot Olivier 
Published: March 2014

AbstractThis collection of papers is based on talks presented at the IUPS meeting in Birmingham, UK last summer, in a symposium as part of the ESM & EVBO program, sponsored by the British Microcirculation Society and Microcirculation. In this issue we discuss new insights into the control of angiogenesis, including regulation of different aspects of endothelial cell biology by the tissue stroma, during inflammatory disease, and active remodelling of the microcirculation. We address a variety of signalling modes that determine the endothelial responses to pro‐angiogenic stimuli, including necessary synergy among different pathways and processes. We present an update of recent developments, and identify some areas where significant progress will likely occur.
Homocysteine Disrupts Outgrowth of Microvascular Endothelium by an iNOS‐Dependent Mechanism
Authors: Mayo Jamie N. , Chen Cheng‐Hung , Liao Francesca‐Fang , Bearden Shawn E. 
Published: March 2014

AbstractObjectiveTo test the hypothesis that Hcy impairs angiogenic outgrowth through an iNOS‐dependent mechanism.MethodsAdult C57Bl/6 mouse choroid explants were used in angiogenic outgrowth assays. Mouse microvascular endothelial cells were studied in culture during scrape‐induced migration and dispersed cell locomotion experiments. Activity of iNOS was manipulated with pharmacology (1400W), siRNA, and by use of choroid explants from iNOS knockout mice (iNOS−/−).ResultsHcy (20 μM) significantly decreased the area of endothelial outgrowth without altering the number of cells in the choroid explant angiogenic assay, resulting in more densely packed outgrowth. Hcy prevented the outward orientation of actin filaments and decreased the number of actin projections along the leading edge of outgrowth. Hcy also slowed outgrowth from the edge of a scraped endothelial monolayer and in cultures of dispersed cells, Hcy impaired cell locomotion without affecting proliferation. Inhibition of iNOS activity rescued the effect of Hcy on area of explant outgrowth, cell density, number of projections, cell locomotion, and rate of outgrowth following scraping.ConclusionsHcy impairs microvascular endothelial outgrowth, but not proliferation, by disrupting cell locomotion through an iNOS‐dependent mechanism.
Differential dendritic cell‐mediated activation and functions of invariant NKT‐cell subsets in oral cancer
Authors: Singh AK , Gaur P , Shukla NK , Das SN 
Published: March 2014

ObjectivesInvariant natural killer T (iNKT) cells are unique subset of glycolipid‐reactive T lymphocytes with potent antitumour characteristics. This study was planned to understand Th‐like cytokine profiles of iNKT‐cell subsets and modulation of their functions in response to glycolipid ligand and tumour cell lysate (TL).Subjects and MethodsCytokine profile of iNKT‐cell subsets was evaluated from the peripheral blood of eight oral squamous cell carcinoma (OSCC) patients by flow cytometry and enzyme‐linked immunosorbent assay (ELISA), while antitumour activity of iNKT cells was measured by methyl tetrazolium salt assay.ResultsCD4+ (CD4+CD8−) iNKT subset from OSCC patients showed significant (P < 0.01) expansion and higher IL‐4 production following activation with α‐GalCer‐pulsed DCs, while CD4−CD8− double negative (DN) and CD8+ (CD4−CD8+) iNKT subsets produced IFN‐γ predominantly. iNKT cells showed significantly (P = 0.02) increased secretion of IFN‐γ and enhanced cytotoxicity to KB and SCC‐4 tumour cells in response to α‐GalCer and TL‐pulsed DCs.ConclusionIt appears that mutual balance/ratio of iNKT subsets may be important for their effector functions. Selectively expanded DN and CD8+ iNKT cells with α‐GalCer and TL may be a better candidate vaccine for iNKT‐cell‐based adoptive cancer immunotherapy.
Neural control of blood flow during exercise in human metabolic syndrome
Authors: Limberg Jacqueline K. , Morgan Barbara J. , Sebranek Joshua J. , Proctor Lester T. , Eldridge Marlowe W. , Schrage William G. 
Published: March 2014

New Findings
What is the central question of this study?
α‐Adrenergic‐mediated vasoconstriction is greater during simulated exercise in animal models of metabolic syndrome when compared with control animals. Whether such findings can be translated to humans was previously unexamined.
What is the main finding and its importance?
We observed greater muscle sympathetic nerve activity and clonidine‐mediated vasoconstriction in adults with metabolic syndrome, yet preserved exercise blood flow when compared with age‐matched healthy control subjects. These results suggest that adults with metabolic syndrome exhibit compensatory vascular control mechanisms capable of counteracting altered adrenergic responsiveness, thus preserving blood flow responses to low‐intensity, dynamic hand‐grip exercise.
α‐Adrenergic‐mediated vasoconstriction is greater during simulated exercise in animal models of metabolic syndrome (MetSyn) when compared with control animals. In an attempt to translate such findings to humans, we hypothesized that adults with MetSyn (n = 14, 35 ± 3 years old) would exhibit greater α‐adrenergic responsiveness during exercise when compared with age‐matched healthy control subjects (n = 16, 31 ± 3 years old). We measured muscle sympathetic nerve activity (MSNA; microneurography) and forearm blood flow (Doppler ultrasound) during dynamic forearm exercise (15% of maximal voluntary contraction). α‐Adrenergic agonists (phenylephrine and clonidine) and an antagonist (phentolamine) were infused intra‐arterially to assess α‐adrenergic receptor responsiveness and restraint, respectively. Resting MSNA was ∼35% higher in adults with MetSyn (P < 0.05), but did not change in either group with dynamic exercise. Clonidine‐mediated vasoconstriction was greater in adults with MetSyn (P < 0.01). Group differences in vascular responses to phenylephrine and phentolamine were not detected (P > 0.05). Interestingly, exercise‐mediated vasodilatation was greater in MetSyn (P < 0.05). Adults with MetSyn exhibit greater resting MSNA and clonidine‐mediated vasoconstriction, yet preserved functional sympatholysis and higher exercise blood flow during low‐intensity hand‐grip exercise when compared with age‐matched healthy control subjects. These results suggest that adults with MetSyn exhibit compensatory vascular control mechanisms capable of preserving blood flow responses to exercise in the face of augmented sympathetic adrenergic activity.
Microbial Community Dynamics and Stability during an Ammonia-Induced Shift to Syntrophic Acetate Oxidation
Authors: Werner Jeffrey J. , Garcia Marcelo L. , Perkins Sarah D. , Yarasheski Kevin E. , Smith Samuel R. , Muegge Brian D. , Stadermann Frank J. , DeRito Christopher M. , Floss Christine , Madsen Eugene L. , Gordon Jeffrey I. , Angenent Largus T. 
Published: March 2014

ABSTRACT
Anaerobic digesters rely on the diversity and distribution of parallel metabolic pathways mediated by complex syntrophic microbial communities to maintain robust and optimal performance. Using mesophilic swine waste digesters, we experimented with increased ammonia loading to induce a shift from aceticlastic methanogenesis to an alternative acetate-consuming pathway of syntrophic acetate oxidation. In comparison with control digesters, we observed shifts in bacterial 16S rRNA gene content and in functional gene repertoires over the course of the digesters' 3-year operating period. During the first year, under identical startup conditions, all bioreactors mirrored each other closely in terms of bacterial phylotype content, phylogenetic structure, and evenness. When we perturbed the digesters by increasing the ammonia concentration or temperature, the distribution of bacterial phylotypes became more uneven, followed by a return to more even communities once syntrophic acetate oxidation had allowed the experimental bioreactors to regain stable operation. The emergence of syntrophic acetate oxidation coincided with a partial shift from aceticlastic to hydrogenotrophic methanogens. Our 16S rRNA gene analysis also revealed that acetate-fed enrichment experiments resulted in communities that did not represent the bioreactor community. Analysis of shotgun sequencing of community DNA suggests that syntrophic acetate oxidation was carried out by a heterogeneous community rather than by a specific keystone population with representatives of enriched cultures with this metabolic capacity.