bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interoceptive sensitivity modulates heart rate and insula activity when listening to music
Authors: Maekawa Toru , Sasaoka Takafumi , Inui Toshio , Yamawaki Shigeto 
Published: December 2021

AbstractInteroception plays an important role in emotion processing, but the relationship between the physiological responses associated with emotional experience and interoception is unclear. In this study, we measured interoceptive sensitivity using the heartbeat discrimination task and investigated the effects of individual differences in interoceptive sensitivity on changes in heart rate and insula activity in response to music-induced emotions. We found that the heart rate increased when listening to the music pieces rated as emotionally high-touching in the high interoceptive sensitivity group only. Compared to the emotionally low-touching music, listening to the emotionally high-touching music was associated with higher insula activity. Furthermore, relative to individuals with low interoceptive sensitivity, the region of interest analysis of the insula subregions for individuals with high interoceptive sensitivity revealed significant activity in the bilateral dorsal granular insula, the right ventral dysgranular insula, and the right granular and dorsal dysgranular insula while listening to the high-touching music pieces. Our results suggest that individuals with high interoceptive sensitivity use their physical condition to assess their emotional level when listening to music. Furthermore, the insula activity may reflect the use of interoception to estimate emotions.
Tracing the genetics of neurological disease to the mutation-directed addition of single hydrogen bonds
Authors: Zhou Xiaoming , Tashiro Kyuto , Sumrow Lily , Sutherland Lillian , Liszczak Glen , McKnight Steven L. 
Published: December 2021

AbstractMutations causative of neurological and neurodegenerative disease can occur in coding regions that specify protein domains of low sequence complexity. These autosomal dominant mutations can be idiosyncratic in their recurrent appearance at the same amino acid. Here we report studies of recurrent mutations in proline residues located within low complexity (LC) domains associated with the neurofilament light chain protein, the microtubule-associated tau protein, and the heterogeneous nuclear RNPA2 protein. All such mutations manifest their effects by directing formation of variant proteins endowed with the addition of a single, main chain hydrogen bond specified by the variant amino acid replacing proline. Here we show that methylation of the peptide backbone nitrogen atom associated with these variant amino acids eliminates the aberrant hydrogen bond and restores normal protein function.
Relationships between pond water and tilapia skin microbiomes in aquaculture ponds in Malawi
Authors: McMurtrie Jamie , Alathari Shayma , Chaput Dominique L. , Bass David , Ghambi Camerson , Nagoli Joseph , Delamare-Deboutteville Jérôme , Mohan Chadag Vishnumurthy , Cable Joanne , Temperton Ben , Tyler Charles R. 
Published: December 2021

AbstractIntensification of fish farming practices is being driven by the demand for increased food production to support a rapidly growing global human population, particularly in lower-middle income countries. Intensification of production, however, increases the risk of disease outbreaks and thus the likelihood for crop losses. The microbial communities that colonise the skin mucosal surface of fish are poorly understood, but are important in maintaining fish health and resistance against disease. This skin microbial community is susceptible to disruption through stressors associated with transport, handling and the environment of intensive practices, and this risks the propagation of disease-causing pathogens. In this study, we characterised the microbial assemblages found on tilapia skin — the most widely farmed finfish globally — and in the surrounding water of seven earthen aquaculture ponds from two pond systems in distinct geographic regions in Malawi. Metabarcoding approaches were used to sequence the prokaryotic and microeukaryotic communities. We found 92% of prokaryotic amplicon sequence variants were common to both skin and water samples. Differentially enriched and core taxa, however, differed between the skin and water samples. In tilapia skin, Cetobacterium, Paucibacter, Pseudomonas and Comamonadaceae were enriched, whereas, the cyanobacteria Cyanobium, Microcystis and/or Synechocystis, and the diatom Cyclotella, were most prevalent in pond water. Ponds that clustered together according to their water prokaryotic communities also had similar microeukaryotic communities indicating strong environmental influences on prokaryotic and microeukaryotic community structures. While strong site-specific clustering was observed in pond water, the grouping of tilapia skin prokaryotes by pond site was less distinct, suggesting fish microbiota have a greater buffering capacity against environmental influences. The characterised diversity, structure and variance of microbial communities associated with tilapia culture in Malawi provide the baseline for studies on how future intensification practices may lead to microbial dysbiosis and disease onset.HighlightsFish skin and pond water communities differ structurally, but share common taxaPond locations have a stronger influence on water versus fish skin microbiome community structureSelected skin-associated taxa could be used to monitor dysbiotic events in aquacultureTaxa with opportunistic pathogen potential were identified at low abundance
THO and TRAMP complexes prevent transcription-replication conflicts, DNA breaks, and CAG repeat contractions
Authors: Brown Rebecca E. , Su Xiaofeng A. , Fair Stacey , Wu Katherine , Verra Lauren , Jong Robyn , Andrykovich Kristin , Freudenreich Catherine H. 
Published: December 2021

AbstractExpansion of structure-forming CAG/CTG repetitive sequences is the cause of several neurodegenerative disorders and deletion of repeats is a potential therapeutic strategy. Transcription-associated mechanisms are known to cause CAG repeat instability. In this study, we discovered that Thp2, an RNA export factor and member of the THO complex, and Trf4, a key component of the TRAMP complex involved in nuclear RNA degradation, are necessary to prevent CAG fragility and repeat contractions in a S. cerevisiae model system. Depletion of both Thp2 and Trf4 proteins causes a highly synergistic increase in CAG repeat fragility, indicating a complementary role of the THO and TRAMP complexes in preventing genome instability. Loss of either Thp2 or Trf4 causes an increase in RNA polymerase stalling at the CAG repeats and genome-wide transcription-replication conflicts (TRCs), implicating impairment of transcription elongation as a cause of CAG fragility and instability in their absence. Analysis of the effect of RNase H1 overexpression on CAG fragility and TRCs suggests that co-transcriptional R-loops are the main cause of CAG fragility in the thp2Δ mutants. In contrast, CAG fragility and TRCs in the trf4Δ mutant can be compensated for by RPA overexpression, suggesting that excess unprocessed RNA in TRAMP4 mutants leads to reduced RPA availability and high levels of TRCs. Our results show the importance of RNA surveillance pathways in preventing RNAPII stalling, TRCs, and DNA breaks, and show that RNA export and RNA decay factors work collaboratively to maintain genome stability.
Chromatin accessibility differences between alpha, beta, and delta cells identifies common and cell type-specific enhancers
Authors: Mawla Alex M. , van der Meulen Talitha , Huising Mark O. 
Published: December 2021

AbstractHigh throughput sequencing has enabled the interrogation of the transcriptomic landscape of glucagon-secreting alpha cells, insulin-secreting beta cells, and somatostatin-secreting delta cells. These approaches have furthered our understanding of expression patterns that define healthy or diseased islet cell types and helped explicate some of the intricacies between major islet cell crosstalk and glucose regulation. All three endocrine cell types derive from a common pancreatic progenitor, yet alpha and beta cells have partially opposing functions, and delta cells modulate and control insulin and glucagon release. While gene signatures that define and maintain cellular identity have been widely explored, the underlying epigenetic components are incompletely characterized and understood. Chromatin accessibility and remodeling is a dynamic attribute that plays a critical role to determine and maintain cellular identity. Here, we compare and contrast the chromatin landscape between mouse alpha, beta, and delta cells using ATAC-Seq to evaluate the significant differences in chromatin accessibility. The similarities and differences in chromatin accessibility between these related islet endocrine cells help define their fate in support of their distinct functional roles. We identify patterns that suggest that both alpha and delta cells are poised, but repressed, from becoming beta-like. We also identify patterns in differentially enriched chromatin that have transcription factor motifs preferentially associated with different regions of the genome. Finally, we identify and visualize both novel and previously discovered common endocrine- and cell specific- enhancer regions across differentially enriched chromatin.
Disentangling hand and tool processing: distal effects of neuromodulation
Authors: Amaral L. , Donato R. , Valério D. , Caparelli-Dáquer E. , Almeida J. , Bergström F. 
Published: December 2021

AbstractThe neural processing within a brain region that responds to more than one object category can be separated by looking at the horizontal modulations established by that region, which suggests that local representations can be affected by connections to distal areas, in a category-specific way. Here we first wanted to test whether by applying transcranial direct current stimulation (tDCS) to a region thatre sponds both to hands and tools (posterior middle temporal gyrus; pMTG), while participants performed either a hand- or tool-related training task, we would be able to specifically target the trained category, and thereby dissociate the overlapping neural processing. Second, we wanted to see if these effects were limited to the target area or extended to distal but functionally connected brain areas. After each combined tDCS and training session, participants therefore viewed images of tools, hands, and animals, in an fMRI scanner. Using multivoxel pattern analysis, we found that tDCS stimulation to pMTG indeed improved the classification accuracy between tools vs. animals, but only when combined with a tool training task (not a hand training task). However, surprisingly, tDCS stimulation to pMTG also improved the classification accuracy between hands vs. animals when combined with a tool training task (not a hand training task). Our findings suggest that overlapping but functionally-specific networks can be separated by using a category-specific training task together with tDCS - a strategy that can be applied more broadly to other cognitive domains using tDCS - and demonstrates the importance of horizontal modulations in objectcategory representations.
Short latency stretch reflexes depend on the balance of activity in agonist and antagonist muscles during ballistic elbow movements
Authors: Villamar Zoe , Ludvig Daniel , Perreault Eric J 
Published: December 2021

AbstractThe spinal stretch reflex is a fundamental building block of motor function, with a sensitivity that varies continuously during movement and when changing between movement and posture. Many have investigated task-dependent reflex sensitivity, but few have provided simple, quantitative analyses of the relationship between the volitional control and stretch reflex sensitivity throughout tasks that require coordinated activity of several muscles. Here we develop such an analysis and use it to test the hypothesis that modulation of reflex sensitivity during movement can be explained by the balance of activity within agonist and antagonist muscles better than by activity only in the muscle homonymous with the reflex. Subjects completed hundreds of flexion and extension movements as small, pseudo-random perturbations of elbow angle were applied to obtain estimates of stretch reflex amplitude throughout the movement. A subset of subjects performed a postural control task at muscle activities matched to those during movement. We found that reflex modulation during movement can be described by background activity in antagonist muscles about the elbow much better than by activity only in the muscle homonymous to the reflex (p<0.001). Agonist muscle activity enhanced reflex sensitivity whereas antagonist activity suppressed it. Surprisingly, the magnitude of these effects was similar, suggesting a balance of control between agonists and antagonists very different from the dominance of sensitivity to homonymous activity during posture. This balance is due to a large decrease in sensitivity to homonymous muscle activity during movement rather than substantial changes in the influence of antagonistic muscle activity.New and NoteworthyThis study examined the sensitivity of the stretch reflexes elicited in elbow muscles to the background activity in these same muscles during movement and postural tasks. We found a heightened reciprocal control of reflex sensitivity during movement that was not present during maintenance of posture. These results help explain previous discrepancies in reflex sensitivity measured during movement and posture and provide a simple model for assessing their contributions to muscle activity in both tasks.
The accuracy of absolute differential abundance analysis from relative count data
Authors: Roche Kimberly E. , Mukherjee Sayan 
Published: December 2021

AbstractConcerns have been raised about the use of relative abundance data derived from next generation sequencing as a proxy for absolute abundances. For example, in the differential abundance setting, compositional effects in relative abundance data may give rise to spurious differences (false positives) when considered from the absolute perspective. In practice however, relative abundances are often transformed by renormalization strategies intended to compensate for these effects and the scope of the practical problem remains unclear. We used simulated data to explore the consistency of differential abundance calling on renormalized relative abundances versus absolute abundances and find that, while overall consistency is high, with a median sensitivity (true positive rates) of 0.91 and specificity (1 - false positive rates) of 0.89, consistency can be much lower where there is widespread change in the abundance of features across conditions. We confirm these findings on a large number of real data sets drawn from 16S metabarcoding, expression array, bulk RNA-seq, and single-cell RNA-seq experiments, where data sets with the greatest change between experimental conditions are also those with the highest false positive rates. Finally, we evaluate the predictive utility of summary features of relative abundance data themselves. Estimates of sparsity and the prevalence of feature-level change in relative abundance data give reasonable predictions of discrepancy in differential abundance calling in simulated data and can provide useful bounds for worst-case outcomes in real data.
ARBRE: Computational resource to predict pathways towards industrially important aromatic compounds
Authors: Sveshnikova Anastasia , MohammadiPeyhani Homa , Hatzimanikatis Vassily 
Published: December 2021

AbstractSynthetic biology and metabolic engineering rely on computational search tools for predictions of novel biosynthetic pathways to industrially important compounds, many of which are derived from aromatic amino acids. Pathway search tools vary in their scope of covered reactions and compounds, as well as in metrics for ranking and evaluation. In this work, we present a new computational resource called ARBRE: Aromatic compounds RetroBiosynthesis Repository and Explorer. It consists of a comprehensive biochemical reaction network centered around aromatic amino acid biosynthesis and a computational toolbox for navigating this network. ARBRE encompasses over 28’000 known and 100’000 novel reactions predicted with generalized enzymatic reactions rules and over 70’000 compounds, of which 22’000 are known to biochemical databases and 48’000 only to PubChem. Over 1,000 molecules that were solely part of the PubChem database before and were previously impossible to integrate into a biochemical network are included into the ARBRE reaction network by assigning enzymatic reactions. ARBRE can be applied for pathway search, enzyme annotation, pathway ranking, visualization, and network expansion around known biochemical pathways to predict valuable compound derivations. In line with the standards of open science, we have made the toolbox freely available to the scientific community athttp://lcsb-databases.epfl.ch/arbre/. We envision that ARBRE will provide the community with a new computational toolbox and comprehensive search tool to predict and rank pathways towards industrially important aromatic compounds.
Through-plane super-resolution with autoencoders in diffusion magnetic resonance imaging of the developing human brain
Authors: Kebiri Hamza , Canales Rodríguez Erick J. , Lajous Hélène , de Dumast Priscille , Girard Gabriel , Alemán-Gómez Yasser , Koob Mériam , Jakab András , Cuadra Meritxell Bach 
Published: December 2021

ABSTRACTFetal brain diffusion magnetic resonance images are often acquired with a lower through-plane than in-plane resolution. This anisotropy is often overcome by classical upsampling methods such as linear or cubic interpolation. In this work, we employ an unsupervised learning algorithm using an autoencoder neural network to enhance the through-plane resolution by leveraging a large amount of data. Our framework, which can also be used for slice outliers replacement, overperformed conventional interpolations quantitatively and qualitatively on pre-term newborns of the developing Human Connectome Project. The evaluation was performed on both the original diffusion-weighted signal and on the estimated diffusion tensor maps. A byproduct of our autoencoder was its ability to act as a denoiser. The network was able to generalize to fetal data with different levels of motion and we qualitatively showed its consistency, hence supporting the relevance of pre-term datasets to improve the processing of fetal brain images.
Degradation of lactoferrin caused by droplet atomization process via two-fluid nozzle: The detrimental effect of air–water interfaces
Authors: Dao Huy M. , Sahakijpijarn Sawittree , Chrostowski Robert R. , Moon Chaeho , Mangolini Filippo , Cui Zhengrong , Williams Robert O. 
Published: December 2021

ABSTRACTBiological macromolecules, especially therapeutic proteins, are delicate and highly sensitive to degradation from stresses encountered during the manufacture of dosage forms. Thin-film freeze-drying (TFFD) and spray freeze-drying (SFD) are two processes used to convert liquid forms of protein into dry powders. In the production of inhalable dry powders that contain proteins, these potential stressors fall into three categories based on their occurrence during the primary steps of the process: (1) droplet formation (e.g., the mechanism of droplet formation, including spray atomization), (2) freezing, and (3) frozen water removal (e.g., sublimation). This study compares the droplet formation mechanism used in TFFD and SFD by investigating the effects of spraying on the stability of proteins, using lactoferrin as a model. This study considers various perspectives on the degradation (e.g., conformation) of lactoferrin after subjecting the protein solution to the atomization process using a pneumatic two-fluid nozzle (employed in SFD) or a low-shear drop application through the nozzle. The surface activity of lactoferrin was examined to explore the interfacial adsorption tendency, diffusion, and denaturation process. Subsequently, this study also investigates the secondary and tertiary structure of lactoferrin, the quantification of monomers, oligomers, and ultimately, aggregates. The spraying process affected the tertiary structure more negatively than the tightly woven secondary structure, resulting in a 1.5 nm red shift in peak position corresponding to the Tryptophan (Trp) residues. This conformational change can either (a) be reversed at low concentrations via relaxation or (b) proceed to form irreversible aggregates at higher concentrations. Interestingly, when the sample was allowed to progress into micron-sized aggregates, such a dramatic change was not detected using methods such as size-exclusion chromatography, polyacrylamide gel electrophoresis, and dynamic light scattering at 173°. A more complete understanding of the heterogeneous protein sample was achieved only through a combination of 173° and 13° backward and forward scattering, a combination of derived count rate measurements, and micro-flow imaging (MFI). Finally, compared to the low-shear dripping used in the TFFD process, lactoferrin underwent a relatively fast conformational change upon exposure to the high air-water interface of the two-fluid atomization nozzle used in the SFD process as compared to the low shear dripping used in the TFFD process. The interfacial induced denaturation that occurred during spraying was governed primarily by the size of the atomized droplets, regardless of the duration of exposure to air.
Summary statistics knockoff inference empowers identification of putative causal variants in genome-wide association studies
Authors: He Zihuai , Liu Linxi , Belloy Michael E. , Le Guen Yann , Sossin Aaron , Liu Xiaoxia , Qi Xinran , Ma Shiyang , Wyss-Coray Tony , Tang Hua , Sabatti Chiara , Candès Emmanuel , Greicius Michael D. , Ionita-Laza Iuliana 
Published: December 2021

AbstractRecent advances in genome sequencing and imputation technologies provide an exciting opportunity to comprehensively study the contribution of genetic variants to complex phenotypes. However, our ability to translate genetic discoveries into mechanistic insights remains limited at this point. In this paper, we propose an efficient knockoff-based method, GhostKnockoff, for genome-wide association studies (GWAS) that leads to improved power and ability to prioritize putative causal variants relative to conventional GWAS approaches. The method requires only Z-scores from conventional GWAS and hence can be easily applied to enhance existing and future studies. The method can also be applied to meta-analysis of multiple GWAS allowing for arbitrary sample overlap. We demonstrate its performance using empirical simulations and two applications: (1) analysis of 1,403 binary phenotypes from the UK Biobank data in 408,961 samples of European ancestry, and (2) a meta-analysis for Alzheimer’s disease (AD) comprising nine overlapping large-scale GWAS, whole-exome and whole-genome sequencing studies. The UK Biobank analysis demonstrates superior performance of the proposed method compared to conventional GWAS in both statistical power (2.05-fold more discoveries) and localization of putative causal variants at each locus (46% less proxy variants due to linkage disequilibrium). The AD meta-analysis identified 55 risk loci (including 31 new loci) with ~70% of the proximal genes at these loci showing suggestive signal in downstream single-cell transcriptomic analyses. Our results demonstrate that GhostKnockoff can identify putatively functional variants with weaker statistical effects that are missed by conventional association tests.