bluuebunny/crossref_metadata_2025_split huggingface dataset:
FarmCPUpp: Efficient Large-Scale GWAS
Authors: Kusmec Aaron , Schnable Patrick S. 
Published: December 2017

AbstractGenome-wide association studies (GWAS) are computationally demanding analyses that use large sample sizes and dense marker sets to discover associations between quantitative trait variation and genetic variants. FarmCPU is a powerful new method for performing GWAS. However, its performance is hampered by details of its implementation and its reliance on the R programming language. In this paper we present an efficient implementation of FarmCPU, called FarmCPUpp, that retains the R user interface but improves memory management and speed through the use of C++ code and parallel computing.
A primate specific loss of function polymorphism in TLR2 gene decreases inflammation and protects humans from organ dysfunction in Malaria
Authors: K Panda Aditya , Mukherjee Ratnadeep , K Das Bidyut , Tripathy Rina , K Satapathy Ashok , Sharma Shobhona , Ravindran Balachandran 
Published: December 2017

AbstractPolymorphisms of TLR genes could regulate and contribute functionally to innate immunity and inflammation. TLR2, a promiscous receptor recognizes Pathogen Associated Molecular Patterns from several microbes, bacterial, viral, protozoan and helminths. We demonstrate that monocytes of humans with deletion polymorphism in TLR2 gene (a 23 bp deletion in 5’ UTR region) respond more vigorously in vitro to several TLR2 ligands in comparison to those with insertion allele. Lower primates such as Rhesus monkeys and Baboon display ‘deletion’ genotype while insertion is found in higher primates viz., Orangutan, Chimpanzees and Gorilla. Enhanced inflammation is a hallmark of pathogenesis in human severe malaria leading to bad prognosis and odds ratio of patients prone to develop severe malaira such as multi organ failure with del/del genotype was found to be very high. Based on induction of inflammatory cytokines by normal human PBMCs in vitro and circulating cytokine levels in cohorts of patients with severe P. falciparum malaria, we propose that ‘insertion’ of a 23bp sequence in 5’UTR region of TLR2 gene could have led to moderated TLR2 induced inflammation thus offering survival advantage to higher primates by rendering them relatively refractory to multi-organ dysfunction in severe malaria.One Sentence SummaryA 23bp deletion in TLR2 gene is associated with high inflammation and susceptibility to organ dysfunction in Plasmodium falciparum malaria.
Rotary jet-spun porous microfibers as scaffolds for stem cells delivery to central nervous system injury
Authors: Zamproni Laura N. , Grinet Marco A.V.M. , Mundim Mayara T.V.V. , Reis Marcella B.C. , Galindo Layla T. , Marciano Fernanda R. , Lobo Anderson O. , Porcionatto Marimelia 
Published: December 2017

AbstractTransplanting stem cells into the central nervous system is a promising therapeutic strategy. However, preclinical trials of cell-based therapies are limited by poor local cell engraftment and survival. Here, we present a polylactic acid (PLA) scaffold to support delivery of mesenchymal stem cells (MSCs) in a mouse model of stroke. We isolated bone marrow MSCs from adult C57/Bl6 mice, cultured them on PLA polymeric rough microfibrous (PLA-PRM) scaffolds obtained by rotary jet spinning, and transplanted into the brains of adult C57/Bl6 mice, carrying thermocoagulation-induced cortical stroke. Interleukins (IL4, IL6 and IL10) and tumor necrosis factor alfa (TNFα) expression levels in the brain of mice that received PRM were similar to untreated. MSCs transplantation significantly reduced the area of the lesion and PRM delivery increased MSCs retention at the injury site. We conclude that PLA-PRM scaffolds offer a promising new system to deliver stem cells to injured areas of the brain.GRAPHICAL ABSTRACTSynthetic scaffolds offer an alternative to optimize stem cell transplantation at sites of brain injury. Here, we present a rotary jet spun polylactic acid (PLA) polymer used as a scaffold to support delivery of mesenchymal stem cells (MSCs) in a mouse model of stroke. Transplantation of MSCs isolated or cultured on PRM significantly reduced the area of the lesion and PRM delivery increased MSCs retention at the injury site.
DeepMHC: Deep Convolutional Neural Networks for High-performance peptide-MHC Binding Affinity Prediction
Authors: Hu Jianjun , Liu Zhonghao 
Published: December 2017

AbstractConvolutional neural networks (CNN) have been shown to outperform conventional methods in DNA-protien binding specificity prediction. However, whether we can transfer this success to protien-peptide binding affinity prediction depends on appropriate design of the CNN architectue that calls for thorough understanding how to match the architecture to the problem. Here we propose DeepMHC, a deep convolutional neural network (CNN) based protein-peptide binding prediction algorithm for achieving better performance in MHC-I peptide binding affinity prediction than conventional algorithms. Our model takes only raw binding peptide sequences as input without needing any human-designed features and othe physichochemical or evolutionary information of the amino acids. Our CNN models are shown to be able to learn non-linear relationships among the amino acid positions of the peptides to achieve highly competitive performance on most of the IEDB benchmark datasets with a single model architecture and without using any consensus or composite ensemble classifier models. By systematically exploring the best CNN architecture, we identified critical design considerations in CNN architecture development for peptide-MHC binding prediction.
Competitive release from native range does not predict invasive success of a globally dominant exotic ant species
Authors: Yitbarek Senay , Perfecto Ivette , Vandermeer John H. 
Published: December 2017

AbstractA major goal of invasion biology is to understand under what conditions exotic species thrive in the introduced range. High competitive abilities are thought to be an important characteristic of exotic species. Most invasion studies focus on the competitive ability of exotic species in the introduced range and attribute their ecological success to competitive release, but fewer studies have compared the relative competitive differences within the native range. These comparative studies are important in order to determine if competitive abilities of exotic species are strong predictors of invasion success. The little fire ant Wasmmnia auropunctata is a highly invasive species that has spread from its original range (Central and South America) to becoming a globally distributed exotic species in recent decades. It is generally accepted that island ecosystems offer weak biotic resistance to exotic species as compared to their native range. Here, we examined this empirically by comparing the relative competitive difference of W. auropunctata and locally dominant ants, between its native range of Mexico and introduced range of Puerto Rico. Resource competition was assessed between W. auropunctata and native ants under field conditions and in the laboratory. Furthermore, we compared resource competition at different temporal intervals ranging from short-term (< 2 hours) to long-term (14-days) dynamics. Our results are in contrast to common invasion predictions on island communities because we show that native species were resistant to W. auropunctata in its introduced range of Puerto Rico. We observed that the ground-foraging ant Solenopsis invicta competitive displaced W. auropunctata in Puerto Rico during short-term experiments. Meanwhile, the native arboreal ant Linepithema iniquum withstood competitive pressure from W. auropunctata. In the native range of Mexico, W. auropunctata was superior against Solenopsis Picea and Pheidole protensa species, but was outcompeted by dominant ants Solenopsis geminata and Pheidole synanthropica. This study challenges the relative importance of competitive ability in predicting invasion success. This is one of the few detailed comparative studies that examines exotic species performance between native and introduced habitats.
Caring for parents: an evolutionary rationale
Authors: Garay J. , Számadó S. , Varga Z. , Szathmáry E. 
Published: December 2017

AbstractThe evolutionary roots of human moral behavior are a key precondition to understand human nature. Here we investigate whether a biological version of Fifth Commandment (“Honor your father and your mother, that your days may be long”), respected in different variants across cultures, can spread through Darwinian competition. We show by a novel demographic model that a corresponding Fifth Rule (“During your reproductive period, give away from your resources to your post-fertile parents”) will spread even if the cost of support to post-fertile grandmothers considerably decreases the demographic parameters of fertile parents but radically increases the survival rate of grandchildren. Teaching vital cultural content is likely to have been critical for the value of grandparental service. Selection on such behavior may have produced an innate moral tendency to honor parents even in situations, such as experienced today, when the quantitative conditions would not necessarily favor the maintenance of this trait.
Brain, immune system and selenium: a starting point for a new diagnostic marker for Alzheimer’s disease?
Authors: Achilli Cesare , Ciana Annarita , Minetti Giampaolo 
Published: December 2017

AbstractThe clinical diagnosis of Alzheimer’s disease (AD) is based primarily on neuropsychological tests, which assess the involutive damage, and imaging techniques that evaluate morphologic changes in the brain. The currently available diagnostic tests do not show complete specificity and do not permit an accurate differentiation between AD and other forms of senile dementia. The correlation of these tests with laboratory investigations based on biochemical parameters could increase the certainty of the diagnosis. In recent years, several biochemical markers for the diagnosis of AD have been proposed, but in most cases they show a limited specificity and their application is invasive, because it generally requires the sampling of cerebrospinal fluid. Therefore, the use of a peripheral biochemical marker could represent a valuable complement for the diagnosis of this disease.Several studies have shown a relationship between the neurodegenerative disorders typical of the ageing process, the weakening of the immune system, alterations in the levels of selenium and of the antioxidant selenoenzymes in brain tissues and blood cells, particularly in neutrophil granulocytes. The levels of peripheral selenoenzymes may reveal a promising clinical parameter for helping in the assessment of the pathological condition in AD.HighlightsMsrBl is one of the 25 selenoenzymes expressed in the humansMsrBl is highly expressed in human circulating neutrophilsThe diagnostic markers for Alzheimer’s disease are still insufficiently validatedThe impairment of some selenoenzymes is associated with Alzheimer’s diseaseNeutrophil MsrBl can be a peripheral marker for the diagnosis of Alzheimer’s disease
Chromatin interaction data visualization in the WashU Epigenome Browser
Authors: Li Daofeng , Hsu Silas , Purushotham Deepak , Wang Ting 
Published: December 2017

AbstractMotivationLong-range chromatin interactions are critical for gene regulations and genome maintenance. HiC and Cool are the two most common data formats used by the community, including the 4D Nucleome Consortium (4DN), to represent chromatin interaction data from a variety of chromatin conformation capture experiments, and specialized tools were developed for their analysis, visualization, and conversion. However, there does not exist a tool that can support visualization of both data formats simultaneously.ResultsThe WashU Epigenome Browser has integrated both HiC and Cool data formats into its visualization platform. Investigators can seamlessly explore chromatin interaction data regardless of their underlying data format. For developers it is straightforward to benchmark the differences in rendering speed and computational resource usage between the two data formats.Availabilityhttp://epigenomegateway.wustl.edu/browser/.
Modeling Spatio-temporal Dynamics of Chromatin Marks
Authors: Fiziev Petko , Ernst Jason 
Published: December 2017

ABSTRACTTo model spatial changes of chromatin mark peaks over time we developed and applied ChromTime, a computational method that predicts regions for which peaks either expand or contract significantly or hold steady between time points. Predicted expanding and contracting peaks can mark regulatory regions associated with transcription factor binding and gene expression changes. Spatial dynamics of peaks provided information about gene expression changes beyond localized signal density changes. ChromTime detected asymmetric expansions and contractions, which for some marks associated with the direction of transcription. ChromTime facilitates the analysis of time course chromatin data in a range of biological systems.
MAPLE: a Modular Automated Platform for Large-scale Experiments, a low-cost robot for integrated animal-handling and phenotyping
Authors: Alisch Tom , Crall James D. , Zucker Dave , de Bivort Ben 
Published: December 2017

AbstractGenetic model system animals have significant scientific value in part because of large-scale experiments like screens, but performing such experiments over long time periods by hand is arduous and risks errors. Thus the field is poised to benefit from automation, just as molecular biology did from liquid-handling robots. We developed a Modular Automated Platform for Large-scale Experiments (MAPLE), a Drosophila-handling robot capable of conducting lab tasks and experiments. We demonstrate MAPLE’s ability to accelerate the collection of virgin female flies (a pervasive experimental chore in fly genetics) and assist high-throughput phenotyping assays. Using MAPLE to autonomously run a novel social interaction experiment, we found that 1) pairs of flies exhibit persistent idiosyncrasies in affiliative behavior, 2) these dyad-specific interactions require olfactory and visual cues, and 3) social interaction network structure is topologically stable over time. These diverse examples demonstrate MAPLE’s versatility as a general platform for conducting fly science automatically.
Increased (pro)renin receptor expression in the subfornical organ of hypertensive humans
Authors: Cooper Silvana G. , Trivedi Darshan P. , Yamamoto Rieko , Worker Caleb J. , Feng Cheng-Yuan , Sorensen Jacob T. , Yang Wei , Xiong Zhenggang , Feng Yumei 
Published: December 2017

The central nervous system plays an important role in essential hypertension in humans and in animal models of hypertension through modulation of sympathetic activity and Na+and body fluid homeostasis. Data from animal models of hypertension suggest that the renin-angiotensin system in the subfornical organ (SFO) of the brain is critical for hypertension development. We recently reported that the brain (pro)renin receptor (PRR) is a novel component of the brain renin-angiotensin system and could be a key initiator of the pathogenesis of hypertension. Here, we examined the expression level and cellular distribution of PRR in the SFO of postmortem human brains to assess its association with the pathogenesis of human hypertension. Postmortem SFO tissues were collected from hypertensive and normotensive human subjects. Immunolabeling for the PRR and a retrospective analysis of clinical data were performed. We found that human PRR was prominently expressed in most neurons and microglia, but not in astrocytes, in the SFO. Importantly, PRR levels in the SFO were elevated in hypertensive subjects. Moreover, PRR immunoreactivity was significantly correlated with systolic blood pressure but not body weight, age, or diastolic blood pressure. Interestingly, this correlation was independent of antihypertensive drug therapy. Our data indicate that PRR in the SFO may be a key molecular player in the pathogenesis of human hypertension and, as such, could be an important focus of efforts to understand the neurogenic origin of hypertension.NEW & NOTEWORTHY This study provides evidence that, in the subfornical organ of the human brain, the (pro)renin receptor is expressed in neurons and microglia cells but not in astrocytes. More importantly, (pro)renin receptor immunoreactivity in the subfornical organ is increased in hypertensive humans and is significantly correlated with systolic blood pressure.
Transthoracic defibrillation in 100-kg calves with sequentially applied pulses
Authors: Gold Jerry H. , Schuder John C. , Stoeckle Harry , McDaniel Wayne C. , Moellinger Duane W. , Roberts Stephanie A. 
Published: December 2017

The effectiveness of up to five 50-A, 4-ms rectangular pulses (each nominally 50% successful) followed, when required, by up to six 70-A, 6-ms pulses applied at 15-s intervals in reversing ventricular fibrillation in 100-kg calves was studied in 600 episodes in which 50-A, 6-ms; 70-A, 3-ms; 70-A, 6-ms; 70-A, 12-ms; or 100-A, 6-ms prefibrillation shocks had been delivered 5 s before the induction of fibrillation and in another 600 episodes in which the prefibrillation shock was omitted. We found that 1) there was a modest adverse influence of the prefibrillation shock upon the outcome of the 50-A, 4-ms portion of the sequential shock effort; 2) the 50-A, 4-ms shocks remained reasonably successful throughout the five-shock sequence; 3) when the prefibrillation shock was omitted, the time intervals for a return of a ventricular complex and normal sinus rhythm in the postdefibrillation electrocardiogram increased rapidly with the number of shocks required for defibrillation; and 4) if defibrillation was not achieved with the five-shock sequence, a single 70-A, 6-ms shock was about 94% successful and the sequence of up to six shocks was 100% successful. ventricular defibrillation; large-animal defibrillation; postdefibrillation arrhythmias; strength-duration success contours; sequential-shock strategy; single-shock strategy Submitted on March 31, 1982 Accepted on July 23, 1982
Effect of sodium on calcium-dependent force in unstimulated rat cardiac muscle
Authors: Walford Gary D. , Gerstenblith Gary , Lakatta Edward G. 
Published: December 2017

Page H222: Gary D. Walford, Gary Gerstenblith, and Edward G. Lakatta. “Effect of sodium on calcium-dependent force in unstimulated rat cardiac muscle.” Page H228: the equation should read (See PDF)
Human immunodeficiency virus envelope glycoprotein 120 alters sleep and induces cytokine mRNA expression in rats
Authors: Opp M. R. , Rady P. L. , Hughes T. K. , Cadet P. , Tyring S. K. , Smith E. M. 
Published: December 2017

Pages R963–R970: M. R. Opp, P L. Rady, T. K. Hughes, Jr., P. Cadet, S. K. Tyring, and E. M. Smith. “Human immunodeficiency virus envelope glycoprotein 120 alters sleep and induces cytokine mRNA expression in rats.” On p. R968, Fig. 3 should appear as below. (See PDF)
Vasopressin pressor receptor-mediated activation of HPA axis by acute ethanol stress in rats
Authors: László Ferenc A. , Varga Csaba , Pávó Imre , Gardi János , Vecsernyés Miklós , Gálfi Márta , Morschl Éva , László Ferenc , Makara Gábor B. 
Published: December 2017

The plasma arginine vasopressin (AVP), ACTH, and corticosterone levels and the hypothalamic corticotropin-releasing hormone (CRH) content were measured after oral administration of 1 ml of 75% ethanol to rats, a model known to induce acute gastric erosions and stress.Elevated plasma AVP, ACTH, and corticosterone levels were detected 1 h after ethanol administration. Treatment with the vasopressin pressor (V1) receptor antagonist [d(CH2)5Tyr(Me)-AVP] before ethanol administration significantly reduced the ACTH and corticosterone level increases. A higher hypothalamic CRH content was measured at 30 or 60 min after ethanol administration. V1receptor antagonist injection, 5 min before ethanol administration, inhibited the rise in hypothalamic CRH content. The protein synthesis blocker cycloheximide prevented the hypothalamic CRH content elevation after stress. The AVP-, CRH-, and AVP + CRH-induced in vitro ACTH release in normal anterior pituitary tissue cultures was also prevented by pretreatment with the V1receptor antagonist.The results support the hypothesis that stress-induced AVP may not only act directly on the ACTH producing anterior pituitary cells but also indirectly at the hypothalamic level via the synthesis and release of CRH.
Response of alveolar epithelial solute permeability to changes in lung inflation
Authors: Egan E. A. 
Published: December 2017

The relation between the solute permeability of th alveolar epithelium, characterized as a pore radius, and lung inflation was studied in anesthetized dogs. Pore radius was calculated from measurements of the rate of efflux of several radiolabeled solutes of known molecular size from alveolar saline. Individual animals were studied at two or more separate inflation volumes. The pore radius during the first volume studied averaged 20 A in high-volume animals (mean inflation 82% of capacity) and 15 A at lower volume (mean inflation, 47% of capacity). The difference was significantly P < 0.05. Lungs inflated to total capacity showed free solute movement across the lung epithelium. Increasing inflation volume in an animal always produced a larger pore radius. Decreasing the inflation volume did not produce a smaller pore radius; it remained the same or became larger. Volume induced increases in lung epithelial solute permeability do not reverse immediately at lower volumes, suggesting this phenomenon represents lung injury.
Ergometric evaluation of pathological gait
Authors: Cavagna G. A. , Tesio L. , Fuchimoto T. , Heglund N. C. 
Published: December 2017

At each step of walking, the center of gravity of the body moves up and down and accelerates and decelerates forward with a combined movement that allows an appreciable transfer (R) between gravitational potential energy and kinetic energy, as occurs in a pendulum. The positive work and power to lift the center of gravity, to accelerate it forward, and to maintain its motion in a sagittal plane, the amount of R, the maximal height reached during each step by the center of gravity, and the step length and frequency are all determined by a microcomputer a few minutes after a subject walks on a force platform. This method is applied to the analysis of pathological gait in the attempt to measure quantitatively the alteration of the normal locomotory movement of the center of gravity. The strides of the patient are compared with the strides of normal subjects; in addition, the movement of the center of gravity of the patient during the stance on the affected limb is compared with the movement of the center of gravity during the stance on the unaffected limb, thus giving an index of the asymmetry of locomotion. biomechanics; locomotion; walking; mechanical work Submitted on January 21, 1982 Accepted on March 3, 1983