bluuebunny/crossref_metadata_2025_split huggingface dataset:
Angiotensin antagonist inhibits preferential negative memory encoding via decreasing hippocampus activation and its coupling with amygdala
Authors: Xu Ting , Zhou Xinqi , Jiao Guojuan , Zeng Yixu , Zhao Weihua , Li Jialin , Yu Fangwen , Zhou Feng , Yao Shuxia , Becker Benjamin 
Published: August 2021

AbstractExaggerated arousal and dysregulated emotion-memory interactions are key pathological dysregulations that accompany the development of post-traumatic stress disorder (PTSD). Current treatments for PTSD are of moderate efficacy and preventing the dysregulations already during exposure to threatening events may attenuate the development of PTSD-symptomatology. In a preregistered double-blind, between-subject, placebo-controlled pharmaco-fMRI design, the present proof-of-concept study examined the potential of a single dose of angiotensin II type 1 receptor (AT1R) antagonist losartan (LT) to attenuate the mnemonic advantage of threatening stimuli and the underlying neural mechanism via combining an emotional subsequent memory paradigm with LT (n=29) or placebo treatment (n=30) and a surprise memory test after 24h washout. LT generally improved memory performance and abolished emotional memory enhancement for negative yet not positive material while emotional experience during encoding remained intact. LT further suppressed hippocampus activity during encoding of subsequently remembered negative stimuli. On the network level LT reduced coupling between hippocampus and basolateral amygdala during successful memory formation of negative stimuli. Our findings suggest that LT may have the potential to attenuate memory formation for negative yet not positive information by decreasing hippocampus activity and its functional coupling strength with amygdala. These findings suggest a promising potential of LT to prevent preferential encoding and remembering of negative events, a mechanism that could prevent the emotion-memory dysregulations underlying the development of PTSD-symptomatology.
Scoring Protein Sequence Alignments Using Deep Learning
Authors: Shrestha Bikash , Adhikari Badri 
Published: August 2021

AbstractBackgroundA high-quality sequence alignment (SA) is the most important input feature for accurate protein structure prediction. For a protein sequence, there are many methods to generate a SA. However, when given a choice of more than one SA for a protein sequence, there are no methods to predict which SA may lead to more accurate models without actually building the models. In this work, we describe a method to predict the quality of a protein’s SA.MethodsWe created our own dataset by generating a variety of SAs for a set of 1,351 representative proteins and investigated various deep learning architectures to predict the local distance difference test (lDDT) scores of distance maps predicted with SAs as the input. These lDDT scores serve as indicators of the quality of the SAs.ResultsUsing two independent test datasets consisting of CASP13 and CASP14 targets, we show that our method is effective for scoring and ranking SAs when a pool of SAs is available for a protein sequence. With an example, we further discuss that SA selection using our method can lead to improved structure prediction.
Nanopore ion sources deliver single amino acid and peptide ions directly into high vacuum
Authors: Drachman Nicholas , LePoitevin Mathilde , Szapary Hannah , Wiener Benjamin , Maulbetsch William , Stein Derek 
Published: August 2021

AbstractWe report a nanopore ion source for mass spectrometry that delivers ions directly into high vacuum from aqueous solutions. The ion source comprises a pulled quartz pipette with a sub-100 nm opening. Ions escape an electrified meniscus by ion evaporation and travel along collisionless trajectories to the ion detector. We measure mass spectra of 16 different amino acid ions, post-translationally modified variants of glutathione, and the peptide angiotensin II, showing that these analytes can be emitted as desolvated ions. The emitted current is composed of ions rather than charged droplets, and more than 90% of the current can be recovered in a distant collector. By circumventing the sample loss mechanisms inherent to conventional electrospray ionization (ESI), where charged droplets are sprayed into a background gas that scatters ions and degrades their transmission, the nanopore ion source could enable more sensitive proteomic analyses.
Dynamics of transcription elongation are finely tuned by dozens of regulatory factors
Authors: Couvillion Mary , Harlen Kevin M. , Lachance Kate C. , Trotta Kristine L. , Smith Erin , Brion Christian , Smalec Brendan M. , Stirling Churchman L. 
Published: August 2021

ABSTRACTUnderstanding the complex network and dynamics that regulate transcription elongation requires the quantitative analysis of RNA polymerase II (Pol II) activity in a wide variety of regulatory environments. We performed native elongating transcript sequencing (NET-seq) in 41 strains ofS. cerevisiaelacking known elongation regulators, including RNA processing factors, transcription elongation factors, chromatin modifiers, and remodelers. We found that the opposing effects of these factors balance transcription elongation dynamics. Different sets of factors tightly regulate Pol II progression across gene bodies so that Pol II density peaks at key points of RNA processing. These regulators control where Pol II pauses with each obscuring large numbers of potential pause sites that are primarily determined by DNA sequence and shape. Genes that are sensitive to disruptions in transcription elongation tend to couple changes in Pol II pausing and antisense transcription to transcription output. Our findings collectively show that the regulation of transcription elongation by a diverse array of factors affects gene expression levels and co-transcriptional processing by precisely balancing Pol II activity.
Deciphering Multi-way Interactions in the Human Genome
Authors: Dotson Gabrielle A. , Lindsly Stephen , Cicalo Anthony , Chen Can , Dilworth Sam , Ryan Charles , Jeyarajan Sivakumar , Meixner Walter , Beckloff Nicholas , Surana Amit , Wicha Max , Muir Lindsey A. , Rajapakse Indika 
Published: August 2021

AbstractChromatin architecture, a key regulator of gene expression, can be inferred using chromatin contact data from chromosome conformation capture, or Hi-C. However, classical Hi-C does not preserve multi-way contacts. Here we use long sequencing reads to map genome-wide multi-way contacts and investigate higher order chromatin organization in the human genome. We use hypergraph theory for data representation and analysis, and quantify higher order structures in neonatal fibroblasts, biopsied adult fibroblasts, and B lymphocytes. By integrating multi-way contacts with chromatin accessibility, gene expression, and transcription factor binding, we introduce a data-driven method to identify cell type-specific transcription clusters. We provide transcription factor-mediated functional building blocks for cell identity that serve as a global signature for cell types.
Soldier neural architecture is temporarily modality-specialized but poorly predicted by repertoire size in the stingless bee Tetragonisca angustula
Authors: Baudier Kaitlin M. , Bennett Meghan M. , Barrett Meghan , Cossio Frank J. , Wu Robert D. , O’Donnell Sean , Pavlic Theodore P. , Fewell Jennifer H. 
Published: August 2021

AbstractIndividual heterogeneity within societies provides opportunities to test hypotheses about adaptive neural investment in the context of group cooperation. Here we explore neural investment in defense specialist soldiers of the eusocial stingless bee (Tetragonisca angustula) which are age sub-specialized on distinct defense tasks, and have an overall higher lifetime task repertoire than other sterile workers within the colony. Consistent with predicted behavioral demands, soldiers had higher relative visual (optic lobe) investment than non-soldiers but only during the period when they were performing the most visually demanding defense task (hovering guarding). As soldiers aged into the less visually demanding task of standing guarding this difference disappeared. Neural investment was otherwise similar across all colony members. Despite having larger task repertoires, soldiers had similar absolute brain size and smaller relative brain size compared to other workers, meaning that lifetime task repertoire size was a poor predictor of brain size. Together, our results are consistent with the specialized but flexible defense strategies of this species, broadening our understanding of how neurobiology mediates age and morphological task specialization in highly cooperative societies.
Characteristic core voxels in normal individuals revealed by hyperbolic disc embedding and k-core percolation on resting state fMRI
Authors: Whi Wonseok , Huh Youngmin , Ha Seunggyun , Lee Hyekyoung , Kang Hyejin , Lee Dong Soo 
Published: August 2021

AbstractHyperbolic disc embedding and k-core percolation reveal the core structure of the functional connectivity on resting-state fMRI (rsfMRI). Inter-voxel relations were visualized on embedded hyperbolic discs, and their core composition was traced using k-core percolation. Using 180 normal adults’ rsfMRI data from the Human Connectome Project database, scale- free intervoxel connectivity represented by IC-voxels composition, while visualized on hyperbolic discs using model, showed the expected change of the largest component decreasing its size on k-core percolation eventually yielding the core structures of individuals. This kmax-core voxels-ICs composition revealed such stereotypes of individuals as visual network dominant, default mode network dominant, and distributed patterns. Characteristic core structures of resting-state brain connectivity of normal subjects disclosed the distributed or asymmetric contribution of voxels to the kmax-core, which suggests the hierarchical dominance of certain IC subnetworks characteristic to subgroups of individuals at rest.
Insights into the nutritional properties and microbiome diversity in sweet and sour yogurt manufactured in Bangladesh
Authors: Islam S. M. Rafiqul , Tanzina Afsana Yeasmin , Foysal Md Javed , Hoque M. Nazmul , Siddiki AMAM Zonaed , Tay Alfred , Hossain S. M. Jakir , Bakar Muhammad Abu , Mostafa Mohammad , Rumi Meheadi Hasan , Mannan Adnan 
Published: August 2021

AbstractYogurt quality mainly depends on nutritional properties, microbial diversity and purity of starter culture. This study aimed to assess the nutritional composition and microbiome diversity in yogurt. Microbial diversity was analyzed by 16S and 18S rRNA based high-throughput sequencing. Significantly (P<0.05) higher pH, fat, moisture, total solid and solid-non-fat contents (%) were observed in sweet yogurt whereas sour varieties had significantly higher ash and minerals. Metagenomic investigation showed that 44.86% and 55.14% reads were assigned to bacterial and fungal taxa, respectively, with significantly higher taxonomic richness in sour yogurt. A significant difference in bacterial (Ppermanova=0.001) and fungal (Ppermanova=0.013) diversity between sweet and sour yogurt was recorded. We detected 76 bacterial and 70 fungal genera across these samples which were mostly represented by Firmicutes (>92%) and Ascomycota (98%) phyla, respectively. Among the detected genera, 36.84% bacterial and 22.86% fungal genera were found in both yogurt types. Our results suggest that Streptococcus (50.82%), Lactobacillus (39.92%), Enterobacter (4.85%), Lactococcus (2.84%) and Aeromonas (0.65%) are the most abundant bacterial genera, while Kluyveromyces (65.75%), Trichosporon (8.21%), Clavispora (7.19%), Candida (6.71%), Iodophanus (2.22%), Apiotrichum (1.94%), and Issatchenkia (1.35%) are the most abundant fungal genera in yogurt metagenomes. This is the first study on nutritional properties and microbiome diversity of Bangladeshi yogurt that would be a benchmark for safe production of quality yogurt by commercial manufacturers.
ColabFold - Making protein folding accessible to all
Authors: Mirdita Milot , Schütze Konstantin , Moriwaki Yoshitaka , Heo Lim , Ovchinnikov Sergey , Steinegger Martin 
Published: August 2021

ColabFold offers accelerated protein structure and complex predictions by combining the fast homology search of MMseqs2 with AlphaFold2 or RoseTTAFold. ColabFold’s 40 - 60× faster search and optimized model use allows predicting close to a thousand structures per day on a server with one GPU. Coupled with Google Colaboratory, ColabFold becomes a free and accessible platform for protein folding. ColabFold is open-source software available at github.com/sokrypton/ColabFold. Its novel environmental databases are available at colabfold.mmseqs.comContactmilot.mirdita@mpibpc.mpg.de, so@fas.harvard.edu, martin.steinegger@snu.ac.kr
Diversity and evolution of amphibian pupil shapes
Authors: Thomas Kate N. , Rich Caitlyn , Quock Rachel , Streicher Jeffrey W. , Gower David J. , Schott Ryan K. , Fujita Matthew K. , Bell Rayna C. 
Published: August 2021

AbstractPupil constriction has important functional consequences for animal vision, yet the evolutionary mechanisms underlying diverse pupil sizes and shapes, often among animals that occupy optically similar environments, are poorly understood. We aimed to quantify the diversity and evolution of pupil shapes among amphibians and test for potential correlations to ecology based on functional hypotheses. Using photographs, we surveyed pupil shape and the orientation of the constricted pupil across adults of 1293 amphibian species, 72 families, and 3 orders, and additionally for larval life stages for all families of frogs and salamanders with a biphasic ontogeny. Pupil shape is exceptionally diverse in amphibians with evolutionary transitions throughout the amphibian tree of life. For amphibians with a biphasic life history, we found that pupils change in many species that occupy distinct habitats before and after metamorphosis. Finally, we found that non-elongated (round or diamond) constricted pupils were correlated with species inhabiting consistently dim light environments (burrowing and aquatic species) and that elongated pupils (vertical and horizontal) were more common in species with larger absolute eye sizes. We propose that amphibians provide a valuable group within which to explore the anatomical, physiological, optical, and ecological mechanisms underlying the evolution of pupil shape.
On-chip light diffraction imaging of nano structures in the guanine platelet
Authors: Iwasaka Masakazu 
Published: August 2021

AbstractLight projection over short distances can minimize the size of photonic devices, e.g., head-mounted displays and lens-free microscopes. Small lenses or light condensers without typical lenses are essential for light control in micron-scale spaces. In this work, micro-platelets floating in water are used for light projection near the image sensor. These platelets, which are made from guanine, have nanohole gratings and demonstrate light diffraction toward specific directions. By setting a thin water layer on the image sensor’s cover glass, each platelet in water forms column-or bar-code-shaped images on the screen. The projected image shapes and colors are inferred to contain information about nano-structures present in the guanine platelet. The proposed down-sized imaging technique can realize extremely compact and portable imagers for nanoscale object detection.
Structures of Tweety Homolog Proteins TTYH2 and TTYH3 reveal a Ca2+-dependent switch from intra- to inter-membrane dimerization
Authors: Li Baobin , Hoel Christopher M. , Brohawn Stephen G. 
Published: August 2021

AbstractTweety homologs (TTYHs) comprise a conserved family of transmembrane proteins found in eukaryotes with three members (TTYH1-3) in vertebrates. They are widely expressed in mammals including at high levels in the nervous system and have been implicated in cancers and other diseases including epilepsy, chronic pain, and viral infections. TTYHs have been reported to form Ca2+- and cell volume-regulated anion channels structurally distinct from any characterized protein family with potential roles in cell adhesion, migration, and developmental signaling. To provide insight into TTYH family structure and function, we determined cryo-EM structures of Mus musculus TTYH2 and TTYH3 in lipid nanodiscs. TTYH2 and TTYH3 adopt a novel fold which includes an extended extracellular domain with a partially solvent exposed pocket that may be an interaction site for hydrophobic molecules. In the presence of Ca2+, TTYH2 and TTYH3 form homomeric cis-dimers bridged by extracellularly coordinated Ca2+. Strikingly, in the absence of Ca2+, TTYH2 forms trans-dimers that span opposing membranes across a ~130 Å intermembrane space as well as a monomeric state. All TTYH structures lack ion conducting pathways and we do not observe TTYH2-dependent channel activity in cells. We conclude TTYHs are not pore forming subunits of anion channels and their function may involve Ca2+-dependent changes in quaternary structure, interactions with hydrophobic molecules near the extracellular membrane surface, and/or association with additional protein partners.
Genetic analysis of early phenology in lentil identifies distinct loci controlling component traits
Authors: Rajandran Vinodan , Ortega Raul , Vander Schoor Jacqueline K. , Butler Jakob B. , Freeman Jules S. , Hecht Valerie F.G. , Erskine Willie , Murfet Ian C. , Bett Kirstin E. , Weller James L. 
Published: August 2021

ABSTRACTReproductive phenology is well known to be a key feature of crop adaptation to diverse ecogeographic variation and management practices. Lentil is one of the founder pulse crops of middle-eastern Neolithic agriculture, and the modern-day domesticated lentil germplasm is generally considered to form three broad adaptation groups: Mediterranean, South Asian and northern temperate, which correspond approximately to the major global production environments. Understanding the molecular basis of these adaptations is crucial to maximise efficiency of breeding programs. Here, we use a QTL approach to dissect the earliness that is characteristic of the South Asian pilosae ecotype, and that suits it to the typically short winter cropping season. We identified two loci, DTF6a and DTF6b, at which dominant alleles confer early flowering. We show that, although these loci can interact in an additive manner, DTF6a alone is sufficient to confer early flowering even in extremely short photoperiods. Comparisons with closely related legume species confirmed the presence of a conserved cluster of three FT orthologs among potential candidate genes in the region, and expression analysis in near-isogenic material showed that the early dtf6a allele is associated with a strong derepression of the FTa1 gene in particular. Analysis of sequence variation revealed the presence of a 7.4 kb deletion in the FTa1-FTa2 intergenic region in the pilosae parent, and a wide survey of over 400 accessions with diverse origin showed that the dtf6a allele is dominant in South Asia material. Collectively, these results contribute to understanding the molecular basis of global adaptation in lentil, and further emphasize the importance of this conserved genomic region for adaptation in temperate legumes generally.
Peptide Scanning of SARS-CoV and SARS-CoV-2 Spike Protein Subunit 1 Reveals Potential Additional Receptor Binding Sites
Authors: Lin Weilin , Rafeya Jannatul , Roschewitz Vanessa , Smith David , Keller Adrian , Zhang Yixin 
Published: August 2021

AbstractThe binding of SARS-CoV and SARS-CoV-2 to the ACE2 receptor on human cells is mediated by the spike protein subunit 1 (S1) on the virus surfaces, while the receptor binding domains (RBDs) of S1 are the major determinants for the interaction with ACE2 and dominant targets of neutralizing antibodies. However, at the virus-host interface, additional biomolecular interactions, although being relatively weak in affinity and low in specificity, could also contribute to viral attachment and play important roles in gain- or loss-of-function mutations. In this work, we performed a peptide scanning of the S1 domains of SARS-CoV and SARS-CoV-2 by synthesizing 972 16-mer native and mutated peptide fragments using a high throughput in situ array synthesis technology. By probing the array using fluorescently labelled ACE2, a number of previously unknown potential receptor binding sites of S1 have been revealed. 20 peptides were synthesized using solid phase peptide synthesis, in order to validate and quantify their binding to ACE2. Four ACE2-binding peptides were selected, to investigate whether they can be assembled through a biotinylated peptide/neutravidin system to achieve high affinity to ACE2. A number of constructs exhibited high affinity to ACE2 with Kd values of pM to low nM.
Fuzzy robust fault estimation scheme for fault tolerant flight control systems based on unknown input observer
Authors: Unal Gulay 
Published: August 2021

Purpose
The purpose of this study is to present a new integrated structure for a fault tolerant aircraft control system because fault diagnosis of flight control systems is extremely important in obtaining healthy flight. An approach to detect and isolate aircraft sensor faults is proposed, and a new integrated structure for a fault tolerant aircraft control system is presented.

Design/methodology/approach
As disturbance and sensor faults are mixed together in a flight control system, it is difficult to isolate any fault from the disturbance. This paper proposes a robust unknown input observer for state estimation and fault detection as well as isolation using fuzzy logic.

Findings
The dedicated observer scheme (DOS) and generalized observer scheme (GOS) are used for fault detection and isolation in an observer-based approach. Using the DOS, it has been shown through simulation that sensor fault detection and isolation can be made, but here the threshold value must be well chosen; if not, the faulty sensor cannot be correctly isolated. On the other hand, the GOS is more usable and flexible than the DOS and allows isolation of faults more correctly and for a fuzzy logic-based controller to be used to realize fault isolation completely.

Originality/value
The fuzzy logic approach applied to the flight control system adds an important key for sensor fault isolation because it reduces the effect of false alarms and allows the identification of different kinds of sensor faults. The proposed approach can be used for similar systems.