bluuebunny/crossref_metadata_2025_split huggingface dataset:
Model reconstruction from Small angle X-ray Scattering data using deep learning methods
Authors: He Hao , Liu Can , Liu Haiguang 
Published: July 2019

AbstractWe present an algorithm based on a deep learning method for model reconstruction from small angle X-ray scattering (SAXS) data. An auto-encoder for protein 3D models was trained to compress 3D shape information into vectors of a 200-dimensional latent space, and the vectors are optimized using genetic algorithms to build 3D models that are consistent with the scattering data. The algorithm was implemented using Python with the TensorFlow framework and tested with experimental data, demonstrating capacity and robustness of accurate model reconstruction even without using prior model size information.SynopsisA deep learning method based on the auto-encoder framework for model reconstruction from small angle scattering data
Diffuse retro-reflective imaging for improved video tracking of mosquitoes at human baited bednets
Authors: Voloshin Vitaly , Kröner Christian , Seniya Chandrabhan , Murray Gregory P. D. , Guy Amy , Towers Catherine E. , McCall Philip J. , Towers David P. 
Published: July 2019

AbstractRobust imaging techniques for tracking insects have been essential tools in numerous laboratory and field studies on pests, beneficial insects and model systems. Recent innovations in optical imaging systems and associated signal processing have enabled detailed characterisation of nocturnal mosquito behaviour around bednets and improvements in bednet design, a global essential for protecting populations against malaria. Nonetheless, there remain challenges around ease of use for large scale in situ recordings and extracting data reliably in the critical areas of the bednet where the optical signal is attenuated. Here we introduce a retro-reflective screen at the back of the measurement volume, which can simultaneously provide diffuse illumination, and remove optical alignment issues whilst requiring only one-sided access to the measurement space. The illumination becomes significantly more uniform, although, noise removal algorithms are needed to reduce the effects of shot noise particularly across low intensity bednet regions. By systematically introducing mosquitoes in front and behind the bednet in lab experiments we are able to demonstrate robust tracking in these challenging areas. Overall, the retro-reflective imaging setup delivers mosquito segmentation rates in excess of 90% compared to less than 70% with back-lit systems.
Meiosis-specific functions of kinesin motors in cohesin removal and maintenance of chromosome integrity in budding yeast
Authors: Mittal Priyanka , Prajapati Hemant Kumar , Ghule Komal , Ghosh Santanu K. 
Published: July 2019

AbstractKinesin motors provide the molecular forces at the kinetochore-microtubule interface and along the spindle to control chromosome segregation. During meiosis with the two rounds of microtubule assembly-disassembly, the roles of motor proteins remain unexplored. We observed that in contrast to mitosis Cin8 (kinesin 5) and Kip3 (kinesin 8) together are indispensable in meiosis. Examining the meiosis incin8∆kip3∆ cells, we detected chromosome breakage in the meiosis II cells. The double mutant exhibits delay in the cohesin removal and spindle elongation during anaphase I. Consequently, some cells abrogate meiosis II and form dyads while some, as they progress through meiosis II, cause defect in chromosome integrity. We believe that in the latter cells, an imbalance of spindle mediated force and simultaneous persistent cohesin on the chromosomes cause their breakage. We provide evidence that tension generated by Cin8 and Kip3 through microtubule cross-linking is essential for signaling efficient cohesin removal and maintenance of chromosome integrity during meiosis.SummaryMolecular motors generate forces that facilitate chromosome segregation. Unlike mitosis, in meiosis, two times chromosome segregation occur with twice microtubule assembly/disassembly. This work reports that the motor mediated forces are crucial for cohesin removal in meiosis and thus maintain genome integrity.
Estimating and testing the microbial causal mediation effect with high-dimensional and compositional microbiome data
Authors: Wang Chan , Hu Jiyuan , Blaser Martin J. , Li Huilin 
Published: July 2019

AbstractMotivationRecent microbiome association studies have revealed important associations between microbiome and disease/health status. Such findings encourage scientists to dive deeper to uncover the causal role of microbiome in the underlying biological mechanism, and have led to applying statistical models to quantify causal microbiome effects and to identify the specific microbial agents. However, there are no existing causal mediation methods specifically designed to handle high dimensional and compositional microbiome data.ResultsWe propose a rigorous Sparse Microbial Causal Mediation Model (SparseMCMM) specifically designed for the high dimensional and compositional microbiome data in a typical three-factor (treatment, microbiome and outcome) causal study design. In particular, linear log-contrast regression model and Dirichlet regression model are proposed to estimate the causal direct effect of treatment and the causal mediation effects of microbiome at both the community and individual taxon levels. Regularization techniques are used to perform the variable selection in the proposed model framework to identify signature causal microbes. Two hypothesis tests on the overall mediation effect are proposed and their statistical significance is estimated by permutation procedures. Extensive simulated scenarios show that SparseMCMM has excellent performance in estimation and hypothesis testing. Finally, we showcase the utility of the proposed SparseMCMM method in a study which the murine microbiome has been manipulated by providing a clear and sensible causal path among antibiotic treatment, microbiome composition and mouse weight.
Transcriptional and genomic parallels between the monoxenous parasiteHerpetomonas muscarumandLeishmania
Authors: Sloan Megan A. , Brooks Karen , Otto Thomas D. , Sanders Mandy J. , Cotton James A. , Ligoxygakis Petros 
Published: July 2019

AbstractTrypanosomatid parasites are causative agents of important human and animal diseases such as sleeping sickness and leishmaniasis. Most trypanosomatids are transmitted to their mammalian hosts by insects, often belonging to Diptera (or true flies). These are called dixenous trypanosomatids since they infect two different hosts, in contrast to those that infect just insects (monoxenous). However, it is still unclear whether dixenous and monoxenous trypanosomatids interact similarly with their insect host, as fly-monoxenous trypanosomatid interaction systems are rarely reported and under-studied – despite being common in nature. Here we present the genome of monoxenous trypanosomatidHerpetomonas muscarumand discuss its transcriptome duringin vitroculture and during infection of its natural insect hostDrosophila melanogaster. TheH. muscarumgenome is broadly syntenic with that of human parasiteLeishmania major. We also found strong similarities between theH. muscarumtranscriptome during fruit fly infection, and those ofLeishmaniaduring sand fly infections. Overall this suggestsDrosophila-Herpetomonasis a suitable model for less accessible insect-trypanosomatid host-parasite systems such as sandfly-Leishmania.Author SummaryTrypanosomes andLeishmaniaare parasites that cause serious Neglected Tropical Diseases (NTDs) in the world’s poorest people. Both of these are dixenous trypanosomatids, transmitted to humans and other mammals by biting flies. They are called dixenous as they can establish infections in two different types of hosts – insect vectors and mammals. In contrast, monoxenous trypanosomatids usually only infect insects. Despite establishment in the insect’s midgut being key to transmission of NTDs, events during early establishment inside the insect are still unclear in both dixenous and monoxenous parasites. Here, we study the interaction between a model insect – the fruit flyDrosophila melanogaster– and its natural monoxenous trypanosomatid parasiteHerpetomonas muscarum. We show that both the genome of this parasite, and gene regulation at early stages of infection have strong parallels withLeishmania. This work has begun to identify evolutionarily conserved aspects of the process by which trypanosomatids establish in insects, thus potentially highlighting key checkpoints necessary for transmission of dixenous parasites. In turn, this might inform new strategies to control trypanosomatid NTDs.
Molecular and structural mechanism of pan-genotypic HCV NS3/4A protease inhibition by glecaprevir
Authors: Timm Jennifer , Kosovrasti Klajdi , Henes Mina , Leidner Florian , Hou Shurong , Ali Akbar , Kurt-Yilmaz Nese , Schiffer Celia A. 
Published: July 2019

AbstractHepatitis C virus (HCV), causative agent of chronic viral hepatitis, infects 71 million people worldwide and is divided into seven genotypes and multiple subtypes with sequence identities between 68 to 82%. While older generation direct-acting antivirals (DAAs) had varying effectiveness against different genotypes, the newest NS3/4A protease inhibitors including glecaprevir (GLE) have pan-genotypic activity. The structural basis for pan-genotypic inhibition and effects of polymorphisms on inhibitor potency were not well known due to lack of crystal structures of GLE-bound NS3/4A or genotypes other than 1. In this study, we determined the crystal structures of NS3/4A from genotypes 1a, 3a, 4a and 5a in complex with GLE. Comparison with the highly similar grazoprevir (GZR) indicated the mechanism of GLE’s drastic improvement in potency. We found that while GLE is highly potent against wild type NS3/4A of all genotypes, specific resistance-associated substitutions (RASs) confer orders of magnitude loss in inhibition. Our crystal structures reveal molecular mechanisms behind pan-genotypic activity of GLE, including potency loss due to RASs at D168. Our structures permit for the first time analysis of changes due to polymorphisms among genotypes, providing insights into design principles that can aid future drug development and potentially can be extended to other proteins.
Compound stimuli reveal the structure of visual motion selectivity in macaque MT neurons
Authors: Zaharia Andrew D , Goris Robbe L T , Movshon J Anthony , Simoncelli Eero P 
Published: July 2019

AbstractMotion selectivity in primary visual cortex (V1) is approximately separable in orientation, spatial frequency, and temporal frequency (“frequency-separable”). Models for area MT neurons posit that their selectivity arises by combining direction-selective V1 afferents whose tuning is organized around a tilted plane in the frequency domain, specifying a particular direction and speed (“velocity-separable”). This construction explains “pattern direction selective” MT neurons, which are velocity-selective but relatively invariant to spatial structure, including spatial frequency, texture and shape. Surprisingly, when tested with single drifting gratings, most MT neurons’ responses are fit equally well by models with either form of separability. However, responses to plaids (sums of two moving gratings) tend to be better described as velocity-separable, especially for pattern neurons. We conclude that direction selectivity in MT is primarily computed by summing V1 afferents, but pattern-invariant velocity tuning for complex stimuli may arise from local, recurrent interactions.Significance StatementHow do sensory systems build representations of complex features from simpler ones? Visual motion representation in cortex is a well-studied example: the direction and speed of moving objects, regardless of shape or texture, is computed from the local motion of oriented edges. Here we quantify tuning properties based on single-unit recordings in primate area MT, then fit a novel, generalized model of motion computation. The model reveals two core properties of MT neurons — speed tuning and invariance to local edge orientation — result from a single organizing principle: each MT neuron combines afferents that represent edge motions consistent with a common velocity, much as V1 simple cells combine thalamic inputs consistent with a common orientation.
Diverse dynamics of glutamatergic input from sensory neurons underlie heterogeneous responses of olfactory bulb outputs in vivo
Authors: Moran Andrew K. , Eiting Thomas P. , Wachowiak Matt 
Published: July 2019

ABSTRACTMitral/tufted (MT) cells of the olfactory bulb (OB) show diverse temporal responses to odorant stimulation that are thought to encode odor information. To understand the role of sensory input dynamics versus OB circuit mechanisms in generating this diversity, we imaged glutamate signaling onto MT cell dendrites in anesthetized and awake mice. We found surprising diversity in the dynamics of these signals, including excitatory, suppressive, and biphasic responses as well as nonlinear changes in glutamate signaling across inhalations. Simultaneous imaging of glutamate and calcium signals from MT cell dendrites revealed highly correlated responses for both signals. Glutamate responses were only weakly impacted by blockade of postsynaptic activity, implicating sensory neurons as a primary source of glutamate signaling onto MT cells. Thus, the dynamics of sensory input alone, rather than emergent features of OB circuits, may account for much of the diversity in MT cell responses that underlies OB odor representations.
Stable and widespread structural heteroplasmy in chloroplast genomes revealed by a new long-read quantification method
Authors: Wang Weiwen , Lanfear Robert 
Published: July 2019

AbstractThe chloroplast genome usually has a quadripartite structure consisting of a large single copy region and a small single copy region separated by two long inverted repeats. It has been known for some time that a single cell may contain at least two structural haplotypes of this structure, which differ in the relative orientation of the single copy regions. However, the methods required to detect and measure the abundance of the structural haplotypes are labour-intensive, and this phenomenon remains understudied. Here we develop a new method, Cp-hap, to detect all possible structural haplotypes of chloroplast genomes of quadripartite structure using long-read sequencing data. We use this method to conduct a systematic analysis and quantification of chloroplast structural haplotypes in 61 land plant species across 19 orders of Angiosperms, Gymnosperms and Pteridophytes. Our results show that there are two chloroplast structural haplotypes which occur with equal frequency in most land plant individuals. Nevertheless, species whose chloroplast genomes lack inverted repeats or have short inverted repeats have just a single structural haplotype. We also show that the relative abundance of the two structural haplotypes remains constant across multiple samples from a single individual plant, suggesting that the process which maintains equal frequency of the two haplotypes operates rapidly, consistent with the hypothesis that flip-flop recombination mediates chloroplast structural heteroplasmy. Our results suggest that previous claims of differences in chloroplast genome structure between species may need to be revisited.Significance StatementChloroplast genome consists of a large single copy region, a small single copy region, and two inverted repeats. Some decades ago, a discovery showed that there are two types chloroplast genome in some plants, which differ the way that the four regions are put together. However, this phenomenon has been shown in just a small number of species, and many open questions remain. Here, we develop a fast method to measure the chloroplast genome structures, based on long-reads. We show that almost all plants we analysed contain two possible genome structures, while a few plants contain only one structure. Our findings hint at the causes of the phenomenon, and provide a convenient new method with which to make rapid progress.
Regulating Soil Bacterial Diversity, Enzyme Activities and Community Composition Using Residues from Golden Apple Snails
Authors: Wang Jiaxin , Lu Xuening , Zhang Jiaen , Wei Guangchang , Xiong Yue 
Published: July 2019

AbstractGolden apple snails (GAS) have become a serious pest for agricultural production in Asia. A sustainable method for managing GAS is urgently needed, including potentially using them to produce commercial products. In this study, we evaluate the effects of GAS residues (shell and meat) on soil pH, bacterial diversity, enzyme activities, and other soil characteristics. Results showed that the amendment of GAS residues significantly elevated soil pH (to near-neutral), total organic carbon (TOC) (by 10-134%), NO3-N (by 46-912%), NH4-N (by 18-168%) and total nitrogen (TN) (by 12-132%). Bacterial diversity increased 13% at low levels of amendment and decreased 5% at high levels, because low-levels of GAS residues increased soil pH to near-neutral, while high-levels of amendment substantially increased soil nutrients and subsequently suppressed bacterial diversity. The dominant phyla of bacteria were: Proteobacteria (about 22%), Firmicutes (15-35%), Chloroflexi (12%-22%), Actinobacteria (8%-20%) Acidobacteria, Gemmatimonadetes, Cyanobacteria and Bacterioidetes. The amendment of GAS residues significantly increased the relative abundance of Firmicutes, Gemmatimonadetes, Bacterioidetes and Deinococcus-Thermus, but significantly decreased the relative abundance of Chloroflexi, Actinobacteria, Acidobacteria, Cyanobacteria and Planctomycetes. Our results suggest that GAS residues treatment induces a near-neutral and nutrient-rich soil. In this soil, soil pH may not be the best predictor of bacterial community composition or diversity; rather soil nutrients (ie., NH4-N and NO3-N) and soil TOC showed stronger correlations with bacterial community composition. Overall, GAS residues could replace lime for remediation of acidic and degraded soils, not only to remediate physical soil properties, but also microbial communities.ImportanceThe wide spreading golden apple snail (GAS) is a harmful pest to crop productions and could result in soil and air pollutions after death. In the previous study, we developed a biocontrol method: adding GAS residues to acidic soil to mitigate the living GAS invasion and spread, improve soil quality, and reduce soil and air pollution. However, the effects of GAS residues amendment on bacterial diversity and community still remain unclear. This study provided insights into bacterial diversity and community compositions to facilitate the evaluation of GAS residues application.
Novel genetic loci affecting facial shape variation in humans
Authors: Xiong Ziyi , Dankova Gabriela , Howe Laurence J. , Lee Myoung Keun , Hysi Pirro G. , de Jong Markus A. , Zhu Gu , Adhikari Kaustubh , Li Dan , Li Yi , Pan Bo , Feingold Eleanor , Marazita Mary L. , Shaffer John R. , McAloney Kerrie , Xu Shuhua , Jin Li , Wang Sijia , de Vrij Femke M. , Lendemeijer Bas , Richmond Stephen , Zhurov Alexei , Lewis Sarah , Sharp Gemma , Paternoster Lavinia , Thompson Holly , Gonzalez-Jose Rolando , Bortolini Maria Catira , Canizales-Quinteros Samuel , Gallo Carla , Poletti Giovanni , Bedoya Gabriel , Rothhammer Francisco , Uitterlinden André G. , Ikram M. Arfan , Wolvius Eppo B. , Kushner Steven A. , Nijsten Tamar , Palstra Robert-Jan , Boehringer Stefan , Medland Sarah E , Tang Kun , Ruiz-Linares Andrés , Martin Nicholas G. , Spector Timothy D. , Stergiakouli Evie , Weinberg Seth M. , Liu Fan , Kayser Manfred ,   on behalf of the International Visible Trait Genetics (VisiGen) Consortium
Published: July 2019

AbstractThe human face represents a combined set of highly heritable phenotypes, but knowledge on its genetic architecture remains limited despite the relevance for various fields of science and application. A series of genome-wide association studies on 78 facial shape phenotypes quantified from 3-dimensional facial images of 10,115 Europeans identified 24 genetic loci reaching genome-wide significant association, among which 17 were previously unreported. A multi-ethnic study in additional 7,917 individuals confirmed 13 loci including 8 unreported ones. A global map of polygenic face scores assembled facial features in major continental groups consistent with anthropological knowledge. Analyses of epigenomic datasets from cranial neural crest cells revealed abundant cis-regulatory activities at the face-associated genetic loci. Luciferase reporter assays in neural crest progenitor cells highlighted enhancer activities of several face-associated DNA variants. These results substantially advance our understanding of the genetic basis underlying human facial variation and provide candidates for future in-vivo functional studies.
YAP nuclear translocation through dynein and acetylated microtubule controls fibroblast activation
Authors: You Eunae , Ko Panseon , Jeong Jangho , Keum Seula , Kim Jung-Woong , Seo Young-Jin , Song Woo Keun , Rhee Sangmyung 
Published: July 2019

AbstractMyofibroblasts are the major cell type that are responsible for increase the mechanical stiffness in fibrotic tissues. It has well documented that the TGF-β/Smad axis is required for myofibroblast differentiation under the rigid substrate condition. However, the mechanism driving myofibroblast differentiation in soft substrates remains unknown. In this research, we demonstrated that interaction of yes-associated protein (YAP) and acetylated microtubule via dynein, a microtubule motor protein drives nuclear localization of YAP in soft matrix, which in turn increased TGF-β1 induced transcriptional activity of Smad for myofibroblast differentiation. Pharmacological and genetical disruption of dynein impaired the nuclear translocation of YAP and decreased the TGF-β1 induced Smad activity even though phosphorylation and nuclear localization of Smad occurred normally in α-tubulin acetyltransferase (α-TAT1) knockout cell. Moreover, microtubule acetylation prominently appeared in the fibroblast-like cells nearby the blood vessel in the fibrotic liver induced by CCl4 administration which were conversely decreased by TGF-β receptor inhibitor. As a result, quantitative inhibition of microtubule acetylation may be suggested as a new target for overcome the fibrotic diseases.