bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diffuse Reflectance Spectroscopy reveals heat stress-induced changes in hemoglobin profile in chicken breast
Authors: Dadgar Sina , Greene Liz , Dhamad Ahmed , Mallmann Barbara , Dridi Sami , Rajaram Narasimhan 
Published: August 2019

AbstractGlobal rise in incidence of woody breast (WB) syndrome imposes a significant economic burden on the poultry industry. The increase in WB is due to the large increase in the weight of chickens these days within a very short period. An early determination of WB can significantly reduce losses to the poultry industry. Diffuse reflectance spectroscopy provides a noninvasive and rapid method to interrogate tissue function. The sensitivity of DRS to the distinct absorption spectra of oxygenated and deoxygenated hemoglobin allows accurate quantification of average hemoglobin concentration and vascular oxygenation within the sampled tissue. In this study, we used diffuse reflectance spectroscopy to monitor breast hemoglobin concentration (THb) and vascular oxygen saturation (sO2) of 16 chickens that were exposed to heat stress (HS). HS is an important cause of WB myopathy in chickens. Animals were exposed to heat-stress (HS) and optical data were acquired at three time points: at baseline prior to heat stress, 2 days, and 21 days after initiation of HS. Our results show that animals from control and HS groups had a steady decay in optically derived breast hemoglobin concentration consistent with independent i-STAT measurements made on blood sampled from the femoral artery and could provide a noninvasive technology for monitoring tissue function in the poultry industry.
First eight residues of apolipoprotein A-I mediate the C-terminus control of helical bundle unfolding and its lipidation
Authors: Brubaker Gregory , Lorkowski Shuhui W. , Gulshan Kailash , Hazen Stanley L. , Gogonea Valentin , Smith Jonathan D. 
Published: August 2019

AbstractThe crystal structure of a C-terminal deletion of apolipoprotein A-I (apoA1) shows a large helical bundle structure in the amino half of the protein, from residues 8 to 115. Using site directed mutagenesis, guanidine or thermal denaturation, cell free liposome clearance, and cellular ABCA1-mediated cholesterol efflux assays, we demonstrate that apoA1 lipidation can occur when the barrier to this bundle unfolding is lowered. The absence of the C-terminus renders the bundle harder to unfold resulting in loss of apoA1 lipidation that can be reversed by point mutations, such as Trp8Ala, and by truncations as short as 8 residues in the amino terminus, both of which lower the barrier to helical bundle unfolding. Locking the bundle via a disulfide bond leads to loss of apoA1 lipidation. We propose a model in which the C-terminus acts on the N-terminus to destabilize helical bundle. Upon lipid binding to the C-terminus, Trp8 is displaced from its interaction with Phe57, Arg61, Leu64, Val67, Phe71, and Trp72 to destabilize the bundle. However, when the C-terminus is deleted, Trp8 cannot be displaced, the bundle cannot unfold, and apoA1 cannot be lipidated.
First analysis of behavioural responses of humpback whales (Megaptera novaeangliae) to two acoustic alarms in a northern feeding ground off Iceland
Authors: Basran Charla J. , Woelfing Benno , Neumann Charlotte , Rasmussen Marianne H. 
Published: August 2019

AbstractMitigating cetacean entanglement in fishing industries is of global interest. Strategies include the use of acoustic alarms to warn whales of fishing gear. For baleen whales, responses to acoustic alarms are poorly understood. This behavioural response study compared the behaviour of humpback whales (Megaptera novaeangliae) in their feeding grounds off Iceland prior to, during, and after exposure to a low-frequency whale pinger (Future Oceans) and a high-frequency seal scarer (Lofitech ltd.). Linear mixed effects models and binary generalized linear mixed effects models were used to analyze the effect of the alarms on surface feeding, swimming speed, breathing rate, directness and dive time. We observed a significant decrease in surface feeding and a significant increase in swimming speed during exposure to the whale pinger. Changes in dive time between the phases of a trial differed significantly between individuals indicating that responses may depend on individual or behavioural state. We did not find any significant reactions in response to the seal scarer. In addition to the experimental exposures, a trial of whale pingers on a capelin purse seine net was conducted. Results from this trial showed that whales entered the net from the bottom while the pingers were attached at the top, but the encircled whales were able to locate an opening free of pingers and escape without damaging the net. Our results suggest that whale pingers may be a useful entanglement mitigation tool in humpback whale feeding grounds given that a reduction in feeding around nets likely reduces the risk of whales swimming through them. Pingers may also minimize net damage if whales are encircled by aiding the whales in finding their way out. However, given the uncertain long-term consequences of the behavioural changes reported here, whale pingers are most advisable for short-term use in conjunction with other entanglement mitigation measures.
GLAMbox: A Python toolbox for investigating the association between gaze allocation and decision behaviour
Authors: Molter Felix , Thomas Armin W. , Heekeren Hauke R. , Mohr Peter N. C. 
Published: August 2019

AbstractRecent empirical findings have indicated that gaze allocation plays a crucial role in simple decision behaviour. Many of these findings point towards an influence of gaze allocation onto the speed of evidence accumulation in an accumulation-to-bound decision process (resulting in generally higher choice probabilities for items that have been looked at longer). Further, researchers have shown that the strength of the association between gaze and choice behaviour is highly variable between individuals, encouraging future work to study this association on the individual level. However, only few decision models exist that easily allow studying the gaze-choice association on the individual level, due to the high cost of developing and implementing them. The model space is particularly scarce for choice sets with more than two choice alternatives. Here, we present GLAMbox, a Python-based toolbox that is built upon PyMC3 and allows the easy application of the gaze-weighted linear accumulator model (GLAM) to experimental choice data. The GLAM assumes gaze-dependent evidence accumulation in a linear stochastic race that extends to decision scenarios with many choice alternatives. GLAMbox enables Bayesian parameter estimation of the GLAM for individual, pooled or hierarchical models, provides an easy-to-use interface to predict choice behaviour and visualize choice data, and benefits from all of PyMC3’s Bayesian statistical modeling functionality. Further documentation, resources and the toolbox itself are available athttps://github.com/glamlab/glambox.
HypercubeME: two hundred million combinatorially complete datasets from a single experiment
Authors: Esteban Laura Avino , Lonishin Lyubov R. , Bobrovskiy Daniil , Leleytner Gregory , Bogatyreva Natalya S. , Kondrashov Fyodor A. , Ivankov Dmitry N. 
Published: August 2019

AbstractMotivationEpistasis, the context-dependence of the contribution of an amino acid substitution to fitness, is common in evolution. To detect epistasis, fitness must be measured for at least four genotypes: the reference genotype, two different single mutants and a double mutant with both of the single mutations. For higher-order epistasis of the order n, fitness has to be measured for all 2n genotypes of an n-dimensional hypercube in genotype space forming a “combinatorially complete dataset”. So far, only a handful of such datasets have been produced by manual curation. Concurrently, random mutagenesis experiments have produced measurements of fitness and other phenotypes in a high-throughput manner, potentially containing a number of combinatorially complete datasets.ResultsWe present an effective recursive algorithm for finding all hypercube structures in random mutagenesis experimental data. To test the algorithm, we applied it to the data from a recent HIS3 protein dataset and found all 199,847,053 unique combinatorially complete genotype combinations of dimensionality ranging from two to twelve. The algorithm may be useful for researchers looking for higher-order epistasis in their high-throughput experimental data.Availabilityhttps://github.com/ivankovlab/HypercubeME.git.
Interactions between earliest Linearbandkeramik farmers and central European hunter gatherers at the dawn of European Neolithization
Authors: Nikitin Alexey G. , Stadler Peter , Kotova Nadezhda , Teschler-Nicola Maria , Price T. Douglas , Hoover Jessica , Kennett Douglas J. , Lazaridis Iosif , Rohland Nadin , Lipson Mark , Reich David 
Published: August 2019

ABSTRACTArchaeogenetic research over the last decade has demonstrated that European Neolithic farmers (ENFs) were descended primarily from Anatolian Neolithic farmers (ANFs). ENFs, including early Neolithic central European Linearbandkeramik (LBK) farming communities, also harbored ancestry from European Mesolithic hunter gatherers (WHGs) to varying extents, reflecting admixture between ENFs and WHGs. However, the timing and other details of this process are still imperfectly understood. In this report, we provide a bioarchaeological analysis of three individuals interred at the Brunn 2 site of the Brunn am Gebirge-Wolfholz archeological complex, one of the oldest LBK sites in central Europe. Two of the individuals had a mixture of WHG-related and ANF-related ancestry, one of them with approximately 50% of each, while the third individual had approximately all ANF-related ancestry. Stable carbon and nitrogen isotope ratios for all three individuals were within the range of variation reflecting diets of other Neolithic agrarian populations. Strontium isotope analysis revealed that the ~50% WHG-ANF individual was non-local to the Brunn 2 area. Overall, our data indicate interbreeding between incoming farmers, whose ancestors ultimately came from western Anatolia, and local HGs, starting within the first few generations of the arrival of the former in central Europe, as well as highlighting the integrative nature and composition of the early LBK communities.
The Interaction of LILRB2 with HLA-B is Associated with Psoriasis Susceptibility
Authors: Yanovsky Rebecca L. , Chen Haoyan , Leslie Stephen , Carrington Mary , Liao Wilson 
Published: August 2019

ABSTRACTGenetic variation within the major histocompatibility complex (MHC) class I is a well-known risk factor for psoriasis. While the mechanisms behind this variation are still being fully elucidated, human leukocyte antigen (HLA) presentation of auto-antigens as well as the interaction of HLA-B with killer cell immunoglobulin-like receptors (KIRs) have been shown to contribute to psoriasis susceptibility. Here we demonstrate that the interaction of HLA class I molecules with leukocyte immunoglobulin-like receptors (LILR), a related group of immunomodulatory receptors primarily found on antigen presenting cells, also contributes to psoriasis susceptibility. We used previously characterized binding capacities of HLA-A, HLA-B, and HLA-C allotypes to two inhibitory LILRs, LILRB1 and LILRB2, to investigate the effect of LILRB1/2 binding in two large genome wide association study cohorts of psoriasis patients and controls (N = 10,069). We found that the strength of binding of LILRB2 to HLA-B was inversely associated with psoriasis risk (p = 2.34E-09, OR [95% CI], 0.41 [0.30−0.55]) independent of individual class I or II allelic effects. We thus propose that weak binding of inhibitory LILRB2 to HLA-B may play a role in patient susceptibility to psoriasis via increased activity of antigen presenting cells.
Cross-compatibility of five highbush blueberry varieties and ideal crossing combinations
Authors: Martin Keanu , Minnaar Corneile , Jager Marinus de , Anderson Bruce 
Published: August 2019

AbstractBlueberry plants require large quantities of pollen deposited on stigmas to produce commercial-quality fruit. Like many agricultural crops, the interaction between pollen-source variety and pollen-recipient variety can be a major determinant of fruit quality in blueberries. However, little information exists to guide growers in optimising fruit set and quality. Using five commonly grown blueberry varieties, I determined whether crossing between varieties (inter-varietal) increased fruit mass and decreased developmental time relative to crossing within a variety (intra-varietal), and if so, what the best crossing combinations are. While intra-varietal pollination often produced fruit, for certain varieties the fruit set and fruit mass were highly reduced compared to inter-varietal pollination. Furthermore, intra-varietal pollination resulted in longer fruit developmental time in comparison to pollination between varieties. For the same pollen-recipient variety, inter-varietal crosses typically outperformed intra-varietal crosses in fruit mass and developmental time; however, the extent to which inter-varietal crosses outperformed intra-varietal crosses differed between pollen-donor varieties. This result suggests that combinations of varieties are not trivial as some inter-varietal combinations may outperform others. Furthermore, some varieties appear to be more susceptible to the negative effects of intra-varietal crosses than others and that less susceptible varieties may be better suited to conditions where pollinator movement is poor. While our study can guide growers in determining optimal co-planting schemes for the varieties tested, for example in South Africa where these varieties are frequently grown. It also serves as a blueprint for similar compatibility studies that can easily be performed prior to planting to determine the best inter-varietal combinations.
Accurate and Efficient Cell Lineage Tree Inference from Noisy Single Cell Data: the Maximum Likelihood Perfect Phylogeny Approach
Authors: Wu Yufeng 
Published: August 2019

AbstractCells in an organism share a common evolutionary history, called cell lineage tree. Cell lineage tree can be inferred from single cell genotypes at genomic variation sites. Cell lineage tree inference from noisy single cell data is a challenging computational problem. Most existing methods for cell lineage tree inference assume uniform uncertainty in genotypes. A key missing aspect is that real single cell data usually has non-uniform uncertainty in individual genotypes. Moreover, existing methods are often sampling-based and can be very slow for large data.In this paper, we propose a new method called ScisTree, which infers cell lineage tree and calls genotypes from noisy single cell genotype data. Different from most existing approaches, ScisTree works with genotype probabilities of individual genotypes (which can be computed by existing single cell genotype callers). ScisTree assumes the infinite sites model. Given uncertain genotypes with individualized probabilities, ScisTree implements a fast heuristic for inferring cell lineage tree and calling the genotypes that allow the so-called perfect phylogeny and maximize the likelihood of the genotypes. Through simulation, we show that ScisTree performs well on the accuracy of inferred trees, and is much more efficient than existing methods. The efficiency of ScisTree enables new applications including imputation of the so-called doublets.AvailabilityThe program ScisTree is available for download at: https://github.com/yufengwudcs/ScisTreeContactyufeng.wu@uconn.edu
Simplified Methodology for a Modular and Genetically Expanded Protein Synthesis in Cell-Free Systems
Authors: Chemla Yonatan , Ozer Eden , Shaferman Michael , Zaad Ben , Dandela Rambabu , Alfonta Lital 
Published: August 2019

ABSTRACTGenetic code expansion, which enables the site-specific incorporation of unnatural amino acids into proteins, has emerged as a new and powerful tool for protein engineering. Currently, it is mainly utilized inside living cells for a myriad of applications. However, utilization of this technology in a cell-free, reconstituted platform has several advantages over living systems. The common limitations to the employment of these systems are the laborious and complex nature of its preparation and utilization. Herein, we describe a simplified method for the preparation of this system from Escherichia coli cells, which is specifically adapted for the expression of the components needed for cell-free genetic code expansion. In addition, we propose and demonstrate a modular approach to its utilization. By this approach, it is possible to prepare and store different extracts, harboring various translational components, and mix and match them as needed for more than four years retaining its high efficiency. We demonstrate this with the simultaneous incorporation of two different unnatural amino acids into a reporter protein. Finally, we demonstrate the advantage of cell-free systems over living cells for the incorporation of δ-thio-boc-lysine into ubiquitin by using the methanosarcina mazei wild-type pyrrolysyl tRNACUA and tRNA-synthetase pair, which can not be achieved in a living cell.
Distinct structure-function relationships across cortical regions and connectivity scales in the rat brain
Authors: Straathof Milou , Sinke Michel R.T. , Roelofs Theresia J.M. , Blezer Erwin L.A. , Sarabdjitsingh R. Angela , van der Toorn Annette , Schmitt Oliver , Otte Willem M. , Dijkhuizen Rick M. 
Published: August 2019

AbstractAn improved understanding of the structure-function relationship in the brain is necessary to know to what degree structural connectivity underpins abnormal functional connectivity seen in many disorders. We integrated high-field resting-state fMRI-based functional connectivity with high-resolution macro-scale diffusion-based and meso-scale neuronal tracer-based structural connectivity, to obtain an accurate depiction of the structure-function relationship in the rat brain. Our main goal was to identify to what extent structural and functional connectivity strengths are correlated, macro- and meso-scopically, across the cortex. Correlation analyses revealed a positive correspondence between functional connectivity and macro-scale diffusion-based structural connectivity, but no correspondence between functional connectivity and meso-scale neuronal tracer-based structural connectivity. Locally, strong functional connectivity was found in two well-known resting-state networks: the sensorimotor and default mode network. Strong functional connectivity within these networks coincided with strong short-range intrahemispheric structural connectivity, but with weak heterotopic interhemispheric and long-range intrahemispheric structural connectivity. Our study indicates the importance of combining measures of connectivity at distinct hierarchical levels to accurately determine connectivity across networks in the healthy and diseased brain. Distinct structure-function relationships across the brain can explain the organization of networks and may underlie variations in the impact of structural damage on functional networks and behavior.
ER stress-linked autophagy stabilizes apoptosis effector PERP and triggers its co-localization with SERCA2b at ER-plasma membrane junctions
Authors: McDonnell Samantha J. , Spiller David G. , White Michael R. H. , Prior Ian A. , Paraoan Luminita 
Published: August 2019

AbstractSpecific molecular interactions that underpin the switch between ER stress-triggered autophagy-mediated cellular repair and cellular death by apoptosis are not characterized. This study reports the unexpected interaction elicited by ER stress between the plasma membrane (PM)-localized apoptosis effector PERP and the ER Ca2+ pump SERCA2b. We show that the p53 effector PERP, which specifically induces apoptosis when expressed above a threshold level, has a heterogeneous distribution across the PM of un-stressed cells and is actively turned over by the lysosome. PERP is upregulated following sustained starvation-induced autophagy, which precedes the onset of apoptosis indicating that PERP protein levels are controlled by a lysosomal pathway that is sensitive to cellular physiological state. Furthermore, ER stress stabilizes PERP at the PM and induces its increasing co-localization with SERCA2b at ER-PM junctions. The findings highlight a novel crosstalk between pro-survival autophagy and pro-death apoptosis pathways and identify, for the first time, accumulation of an apoptosis effector to ER-PM junctions in response to ER stress.
Mg2+Impacts the Twister Ribozyme through Push-Pull Stabilization of Non-Sequential Phosphate Pairs
Authors: Kognole A. A. , MacKerell A. D. 
Published: August 2019

AbstractRNA molecules perform a variety of biological functions for which the correct three-dimensional structure is essential, including as ribozymes where they catalyze chemical reactions. Metal ions, especially Mg2+, neutralize these negatively charged nucleic acids and specifically stabilize RNA tertiary structures as well as impact the folding landscape of RNAs as they assume their tertiary structures. Specific binding sites of Mg2+in folded conformations of RNA have been studied extensively, however, the full range of interactions of the ion with compact intermediates and unfolded states of RNA is challenging to investigate and the atomic details of the mechanism by which the ion facilitates tertiary structure formation is not fully known. Here, umbrella sampling combined with oscillating chemical potential Grand Canonical Monte Carlo/Molecular Dynamics (GCMC/MD) simulations are used to capture the energetics and atomic-level details of Mg2+-RNA interactions that occur along an unfolding pathway of the Twister ribozyme. The free energy profiles reveal stabilization of partially unfolded states by Mg2+, as observed in unfolding experiments, with this stabilization being due to increased sampling of simultaneous interactions of Mg2+with two or more non-sequential phosphate groups. Notably, the present results indicate a push-pull mechanism where the Mg2+-RNA interactions actually lead to destabilization of specific non-sequential phosphate-phosphate interactions while other interactions are stabilized, a balance that facilitates the folding and stabilization of Twister including formation hydrogen bonds associated with the tertiary structure. The present study establishes a better understanding of how Mg2+ion-interactions contribute to RNA structural properties and stability.Statement of SignificanceRNAs are biologically and therapeutically of great emerging interest such that it is critical to understand how RNA molecules fold into complex structures. While experiments yield information on the stabilization of RNA by ions they are limited in the atomic-level insights they can provide. A combination of enhanced sampling methods is applied to explore the compact intermediate states of RNA and their interactions with Mg2+ions. Results reveal a picture of how Mg2+overall stabilizes short phosphate-phosphate interactions thereby facilitating the stabilization of RNA, though doing so by both the stabilization and destabilization of specific interactions. The applied method will be applicable to exploring the impact of divalent ions on the conformational heterogeneity of a range of macromolecules.