bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investigation of a bone lesion in a gorgonopsian (Synapsida) from the Permian of Zambia and periosteal reactions in fossil non-mammalian tetrapods
Authors: Kato Kyle M. , Rega Elizabeth A. , Sidor Christian A. , Huttenlocker Adam K. 
Published: January 2020

While only distantly related to mammals, the anatomy of Permian gorgonopsians has shed light on the functional biology of non-mammalian synapsids and on the origins of iconic ‘mammal-like’ anatomical traits. However, little is known of gorgonopsian behaviour or physiology, which would aid in reconstructing the paleobiological context in which familiar mammalian features arose. Using multi-modal imaging, we report a discrete osseous lesion in the forelimb of a late Permian-aged gorgonopsian synapsid, recording reactive periosteal bone deposition and providing insights into the origins and diversity of skeletal healing responses in premammalian synapsids. We suggest that the localized lesion on the anterolateral (preaxial) shaft of the left radius represents acute periostitis and, conservatively, most likely developed as a subperiosteal haematoma with subsequent bone deposition and limited internal remodelling. The site records an inner zone of reactive cortical bone forming irregular to radial bony spicules and an outer, denser zone of slowed subperiosteal bone apposition, all of which likely occurred within a single growing season. In surveys of modern reptiles—crocodylians, varanids—such haematomas are rare compared to other documented osteopathologies. The extent and rapidity of the healing response is reminiscent of mammalian and dinosaurian bone pathologies, and may indicate differing behaviour or bone physiology compared to non-dinosaurian reptiles. This report adds to a growing list of putative disease entities recognized in early synapsids and broadens comparative baselines for pathologies and the evolution of bone response to disease in mammalian forebears.This article is part of the theme issue ‘Vertebrate palaeophysiology’.
Inferring the physiological regimes of extinct vertebrates: methods, limits and framework
Authors: Padian Kevin , de Ricqlès Armand 
Published: January 2020

What can we know of the physiological regimes of ancient vertebrates? Essential to the exploration of this question are several epistemological tools: (i) a phylogenetic framework for interpreting whole animals and individual tissues, (ii) reliable knowledge of variation in populations and among climates and geographies, (iii) an understanding of phenotypic variation during ontogeny and between sexes, and (iv) a sense of the patterns of body size change, both phyletically and ontogenetically. Palaeobiologists are historically bound to a dichotomous set of terms developed long ago to describe the relatively depauperate living vertebrate fauna. This system sees only binary categories of five major groupings: the ‘cold-blooded’ fishes, amphibians, and reptiles, and the ‘warm-blooded’ birds and mammals. The integration of histoanatomical data with patterns of size, growth and phylogeny provides an opportunity to re-imagine not only vertebrate palaeophysiology, but vertebrate physiology in general. Here, we discuss how four ‘signals’ or ‘influences’ on bone tissues—phylogeny, ontogeny, mechanics and environment—can help to address these questions.
This article is part of the theme issue ‘Vertebrate palaeophysiology’.
Portable Objective Diagnostics using Visual Evoked Potentials for Age-related Macular Degeneration
Authors: Versek Craig , Banijamali S. Mohammad Ali , Bex Peter J. , Lashkari Kameran , Kamarthi Sagar V. , Sridhar Srinivas 
Published: January 2020

AbstractDelayed Dark Adapted vision Recovery (DAR) is a biomarker for Age-related Macular Degeneration (AMD), however its measurement is burdensome for patients and examiners. We developed a portable, wireless, quick-setup system that employs a headset with a smartphone to deliver controlled photobleach and monocular pattern reversal stimuli, while using custom electroencephalography (EEG) electrodes and electronics in order to measure objective Dark Adapted Visual Evoked Potentials (DAVEP) at multiple locations of the visual field - all in one comfortable 20-minute session, without requiring subject reporting. DAVEP responses post photobleach (up to 15 minutes), were measured concurrently in both eyes of 13 patients with AMD and 8 others not diagnosed with AMD. New, unexpected features at high latencies were observed in the DAVEP responses to scotopic stimulus intensities. The amplitude recovery of the DAVEP response was significantly delayed in AMD patients compared with controls. We developed DAVEP1 scores, a simple metric for DAR, using it to successfully identify all 100% of AMD subjects and classify 90% of subject eyes correctly. Deficits in DAR in patients with AMD can be identified using this objective VEP based system and the DAVEP1 metric, a promising new objective biomarker for this disease that can be easily tested in a clinic.
A Cross-Sectional Survey on Smartphone Usage Pattern, the Level of Mobile Phone Dependence and Psychosocial Effects among Undergraduate Students in a Malaysian University
Authors: Nasser Nisha Syed , Ling Loh Jia , Rashid Aida Abdul , Sharifat Hamed , Ahmad Umar , Ibrahim Buhari , Mustafa Salasiah , Kee Hoo Fan , Mooi Ching Siew , Suppiah Subapriya 
Published: January 2020

ABSTRACTObjectiveProblematic smartphone use (PSU) is the development of pathological dependence at the expense of performing activities of daily living, thus having a negative health and psychosocial impact on the users. Previous PSU studies focused on medical students and little is known regarding its effect on students undergoing other fields of study. The objective of this study is to identify the pattern of smartphone usage and determine the psychosocial factors affecting PSU among undergraduate students in Malaysia and compare the pattern among different fields of study.MethodA prospective cross-sectional study was conducted using validated Smartphone Addiction Scale–Malay version (SAS-M) questionnaire. One-way ANOVA was used to determine the correlation between the patterns of smartphone usage among the students categorised by their ethnic groups, hand dominance and by their field of study. MLR analysis was applied to predict PSU based on socio-demographic data, smartphone usage patterns, psychosocial factors and field of study.ResultsA total of 1060 students completed the questionnaire. The majority of students had PSU (60.7%). Students used smartphones predominantly to access SNAs, namely Instagram. Longer duration on the smartphone per day (≥ 9 hours), age at first using a smartphone and depression carried higher risk of developing PSU, whereas the field of study (science vs. arts based) did not contribute to an increased risk of developing PSU.ConclusionFindings from this study can help better inform university administrators about at-risk groups of undergraduate students who may benefit from targeted intervention designed to reduce their addictive behavior patterns.
A Combined HLA Molecular Mismatch and Expression Analysis for Evaluating HLA-DPB1 de novo Donor-Specific Antibody Risk in Pediatric Solid Organ Transplantation: Implications for Solid Organ & Hematopoietic Stem Cell Transplantation
Authors: Shieh Mengkai , Hayeck Tristan J. , Dinh Anh , Duke Jamie L. , Chitnis Nilesh , Mosbruger Timothy , Morlen Ryan P. , Ferriola Deborah , Kneib Carolina , Hu Taishan , Huang Yanping , Monos Dimitri S. 
Published: January 2020

ABSTRACTBackgroundHLA molecular mismatch (MM) has been shown to be a risk factor for de novo donor-specific antibody (dnDSA) development in solid organ transplantation (SOT). HLA expression differences have also been associated with adverse outcomes in hematopoietic cell transplantation. We sought to study both MM and expression in assessing dnDSA risk.MethodsOne-hundred-and-three HLA-DP-mismatched SOT pairs were retrospectively analysed. MM was computed using amino acids (aa), eplets and, supplementarily, Grantham/Epstein scores. DPB1 alleles were classified as rs9277534-A (low-expression) or -G (high-expression)–linked. To determine the associations between risk factors and dnDSA, logistic regression, linkage disequilibrium (LD) and population-based analyses were performed.ResultsA high-risk AA:GX (recipient:donor) expression combination (X=A or G) demonstrated strong association with DP-dnDSA (p=0.001). MM was also associated with DP-dnDSA when evaluated by itself (eplet_p=0.007, aa_p=0.003, Grantham_p=0.005, Epstein_p=0.004). When attempting to determine the relative individual effects of the risk factors in multivariable analysis, only AA:GX expression status retained a strong association (RR=18.6, p=0.007 with eplet; RR=15.8, p=0.02 with aa), while MM was no longer significant (eplet_p=0.56, aa_p=0.51). Importantly, these risk factors are correlated, due to LD between the expression-tagging SNP and polymorphisms along HLA-DPB1.ConclusionsThe MM and expression risk factors each appear to be strong predictors of DP-dnDSA and to possess clinical utility; however, the two risk factors are closely correlated. These metrics may represent distinct ways of characterizing a common overlapping dnDSA risk profile, but they are not independent. Further, we demonstrate the importance and detailed implications of LD effects in risk assessment of dnDSA and possibly transplantation overall.
Geographical and environmental contributions to genomic divergence in mangrove forests
Authors: da Silva Michele Fernandes , Cruz Mariana Vargas , de Deus Vidal Júnior João , Zucchi Maria Imaculada , Mori Gustavo Maruyama , de Souza Anete Pereira 
Published: January 2020

ABSTRACTAssessing the relative importance of geographical and environmental factors to the spatial distribution of genetic variation can provide information about the processes that maintain genetic variation in natural populations. With a globally wide but very restricted habitat distribution, mangrove trees are a useful model for studies aiming to understand the contributions of these factors. Mangroves occur along the continent–ocean interface of tropical and subtropical latitudes, regions considered inhospitable to many other types of plants. Here, we used landscape genomics approaches to investigate the relative contributions of geographical and environmental variables to the genetic variation of two black mangrove species,Avicennia schauerianaandAvicennia germinans, along the South American coast. Using single nucleotide polymorphisms, our results revealed an important role of ocean currents and geographical distance in the gene flow ofA. schauerianaand an isolation-by-environment pattern in the organization of the genetic diversity ofA. germinans. Additionally, forA. germinans, we observed significant correlations between genetic variation with evidence of selection and the influence of precipitation regimens, solar radiation and temperature patterns. These discoveries expand our knowledge about the evolution of mangrove trees and provide important information to predict future responses of coastal species to the expected global changes during this century.
On mechanisms of light-induced deformations in photoreceptors
Authors: Boyle Kevin C. , Chen Zhijie Charles , Ling Tong , Pandiyan Vimal Prabhu , Kuchenbecker James , Sabesan Ramkumar , Palanker Daniel 
Published: January 2020

AbstractPhotoreceptors in the retina convert light into electrical signals through a phototransduction cycle that consists of multiple electrical and biochemical events. Phase-resolved optical coherence tomography (pOCT) measurements of the optical path length (OPL) change in the cone photoreceptor outer segments after a light stimulus (optoretinogram) reveal a fast, ms-scale contraction by tens of nm, followed by a slow (hundreds of ms) elongation reaching hundreds of nm. Ultrafast measurements with a line-scan pOCT system show that the contractile response amplitude increases logarithmically with the number of incident photons, and its peak shifts earlier at higher stimulus intensities.We present a model that accounts for these features of the contractile response. Conformational changes in opsins after photoisomerization result in the fractional shift of charge across the disk membrane, leading to a transmembrane voltage change, known as the early receptor potential (ERP). Lateral repulsion of the ions on both sides of the membrane affects its surface tension and leads to its lateral expansion. Since the volume of the disks does not change much on a ms time scale, their lateral expansion leads to an axial contraction of the outer segment. With increasing stimulus intensity and resulting tension, the area expansion coefficient of the disk membrane also increases as thermally-induced fluctuations are pulled flat, resisting further expansion. This results in a logarithmic saturation of the deformation and a peak shift to earlier with brighter stimuli. Slow expansion of the photoreceptors is explained by the influx of water due to osmotic changes during phototransduction. Both effects closely match measurements in healthy human volunteers.
TarDict: RandomForestClassifier-based software predict Drug-Tartget interaction
Authors: Habib Peter T. , Alsamman Alsamman M. , Hassanein Sameh E. , Hamwieh Aladdin 
Published: January 2020

AbstractPredicting the target of unknown or/and drugs under investigation from data of already identified drugs is very important not only for the understanding of various drug and molecular interaction processes but also for the development of novel drugs. Here we introduce TarDict, a RandomForestClassifier based-software predict the target pathway or protein based on SMILES of chemical. TarDict receives SMILES and returns a list of the possible similar drug, then export list to the user the target that drug contribute in. Training data set of 20442 entry and testing reveal %95 accuracy.
A critical re-evaluation of fMRI signatures of motor sequence learning
Authors: Berlot Eva , Popp Nicola J. , Diedrichsen Jörn 
Published: January 2020

AbstractDespite numerous studies, there is little agreement about what brain changes accompany motor sequence learning, partly because of a general publication bias that favors novel results. We therefore decided to systematically reinvestigate proposed functional magnetic resonance imaging correlates of motor learning in a preregistered longitudinal study with four scanning sessions over 5 weeks of training. Activation decreased more for trained than untrained sequences in premotor and parietal areas, without any evidence of learning-related activation increases. Premotor and parietal regions also exhibited changes in the fine-grained, sequence-specific activation patterns early in learning, which stabilized later. No changes were observed in the primary motor cortex (M1). Overall, our study provides evidence that human motor sequence learning occurs outside of M1. Furthermore, it shows that we cannot expect to find activity increases as an indicator for learning, making subtle changes in activity patterns across weeks the most promising fMRI correlate of training-induced plasticity.
Molecular profiling of innate immune response mechanisms in ventilator-associated pneumonia
Authors: Pathak Khyatiben V. , McGilvrey Marissa I. , Hu Charles K. , Mansfield Krystine Garcia- , Lewandoski Karen , Eftekhari Zahra , Yuan Yate-Ching , Zenhausern Frederic , Menashi Emmanuel , Pirrotte Patrick 
Published: January 2020

AbstractVentilator-associated pneumonia (VAP) is a common hospital-acquired infection, leading to high morbidity and mortality. Currently, bronchoalveolar lavage (BAL) is utilized in hospitals for VAP diagnosis and guiding treatment options. While BAL collection procedures are invasive, alternatives such as endotracheal aspirates (ETA) may be of diagnostic value, however, their utility has not been thoroughly explored. Longitudinal ETA and BAL were collected from 16 intubated patients up to 15 days, of which 11 developed VAP. We conducted a comprehensive LC-MS/MS based proteome and metabolome characterization of longitudinal ETA and BAL to detect host and pathogen responses to VAP infection. We discovered a diverse ETA proteome of the upper airways reflective of a rich and dynamic host-microbe interface. Prior to VAP diagnosis by microbial cultures from BAL, patient ETA presented characteristic signatures of reactive oxygen species and neutrophil degranulation, indicative of neutrophil mediated pathogen processing as a key host response to the VAP infection. Along with an increase in amino acids, this is suggestive of extracellular membrane degradation resulting from proteolytic activity of neutrophil proteases. Days prior to VAP diagnosis, detection of pathogen peptides with species level specificity in ETA may increase specificity over culture-based diagnosis. Our findings suggest that ETA may provide early mechanistic insights into host-pathogen interactions associated with VAP infection and therefore facilitate its diagnosis and treatment.Graphical abstract
C-terminal eYFP fusion impairsEscherichia coliMinE function
Authors: Palanisamy Navaneethan , Öztürk Mehmet Ali , Di Ventura Barbara 
Published: January 2020

AbstractTheEscherichia coliMin system plays an important role in the proper placement of the septum ring (Z-ring) at mid-cell during cell division. MinE forms a pole-to-pole spatial oscillator together with the membrane-bound ATPase MinD, which results in MinD having a concentration gradient with maxima at the poles and minimum at mid-cell. MinC, the direct inhibitor of the Z-ring initiator protein FtsZ, forms a complex with MinD at the membrane, thus mirroring MinD polar gradients. Therefore, MinC-mediated FtsZ inhibition occurs away from mid-cell. The existence of the oscillations was revealed by performing time-lapse microscopy with fluorescently-labeled Min proteins. These fusion proteins have been since then widely used to study properties of the Min system. Here we show that, despite permitting oscillations to occur in a range of protein concentrations, the enhanced yellow fluorescent protein (eYFP) C-terminally fused to MinE impairs its function. Combiningin vivo, in vitroandin silicoapproaches, we demonstrate that the eYFP compromises MinE ability to displace MinC from MinD, to stimulate MinD ATPase activity and to directly bind to the membrane. Moreover, we reveal that MinE-eYFP is prone to aggregation. Taken together, our results indicate that this fusion is functionally impaired and should be used with caution in cell biological studies.
Polymorphism of fecundity genes (BMP15andGDF9) and their association with litter size in Bangladeshi prolific Black Bengal goat
Authors: Das A. , Shaha M. , Gupta M. Das , Dutta Avijit , Miazi O. F. 
Published: January 2020

AbstractIdentification of prolificacy associated genetic markers remains vital in goat breeding industry since an increase in litter size can generate significant profit. Black Bengal is a prolific goat breed in Bangladesh. There are no inland reports on polymorphisms associated with fertility of Black Bengal goats in Bangladesh. In this study, we investigated two major fecundity genes-bone morphogenetic protein 15 (BMP15) and growth differentiation factor 9 (GDF9) in order to detect any possible mutations in these two genes in Bangladeshi Black Bengal goats. We identified six single nucleotide polymorphisms (SNP), of which five (C735A, C743A, G754T, C781A, and C808G) inBMP15exon 2 and one (T1173A) inGDF9exon 2. We also studied their association with litter size. Association analysis results show that polymorphism at the 735, 754 and 781 nucleotide positions ofBMP15exon 2 had significant association with litter size in Black Bengal goat. The effect of parity was also highly significant (p <0.001) on litter size. This study explored, for the first time, SNP loci in fecundity genes in Bangladeshi prolific Black Bengal goats. Further studies with a high number of genetically unrelated animals for assessing the association of these loci and others in the fecundity genes with litter size may be useful.
Cannabis use is associated with sexually dimorphic changes in executive control of visuospatial decision-making
Authors: Banks Parker J. , Bennett Patrick J. , Sekuler Allison B. , Gruber Aaron J. 
Published: January 2020

AbstractWhen the outcome of a choice is less favourable than expected, humans and animals typically shift to an alternate choice option. Several lines of evidence indicate that this “lose-shift” responding is an innate sensorimotor response strategy that is normally suppressed by executive function. Therefore, the lose-shift response provides a covert gauge of cognitive control over choice mechanisms. We report here that the spatial position, rather than visual features, of choice targets drives the lose-shift effect. Furthermore, the ability to inhibit lose-shift responding to gain reward is different among male and female habitual cannabis users. Increased self-reported cannabis use was concordant with suppressed response flexibility and an increased tendency to lose-shift in women, which reduced performance in a choice task in which random responding is the optimal strategy. On the other hand, increased cannabis use in men was concordant with reduced reliance on spatial cues during decision-making, and had no impact on the number of correct responses. These data (63,600 trials from 106 participants) provide strong evidence that spatial-motor processing is an important component of economic decision-making, and that its governance by executive systems is different in men and women who use cannabis frequently.