bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Bayesian Multi-Task Approach for Detecting Global Microbiome Associations
Authors: Hatami Farhad , Beamish Emma , Rigby Rachael , Dondelinger Frank 
Published: January 2020

AbstractMotivationThe human gut microbiome has been shown to be associated with a variety of human diseases, including cancer, metabolic conditions and inflammatory bowel disease. Current statistical techniques for microbiome association studies are limited by relying on measures of ecological distance, or only allowing for the detection of associations with individual bacterial species, rather than the whole microbiome.ResultsIn this work, we develop a novel Bayesian multi-task approach for detecting global microbiome associations. Our method is not dependent on a choice of distance measure, and is able to incorporate phylogenetic information about microbial species. We apply our method to simulated data and show that it allows for consistent estimation of global microbiome effects. Additionally, we investigate the performance of the model on two real-world microbiome studies: a study of microbiome-metabolome associations in inflammatory bowel disease (Beamish, 2017), and a study of associations between diet and the gut microbiome in mice (Turnbaughet al., 2009). We show that we can use the method to reliably detect associations in real-world datasets with varying numbers of samples and covariates.AvailabilityOur method is implemented using the R interface to the Stan Hamiltonian Monte Carlo sampler. Software for running our methods is available athttps://github.com/FrankD/MicrobiomeGlobalAssociations.Contactf.dondelinger@lancaster.ac.uk
Proteomics Dissection of Cardiac Protein Profiles of Humans and Model Organisms
Authors: Linscheid Nora , Santos Alberto , Poulsen Pi Camilla , Mills Robert W. , Stolte Christian , Leurs Ulrike , Ye Johan Z. , Calloe Kirstine , Thomsen Morten B. , Bentzen Bo H. , Lundegaard Pia R. , Olesen Morten S. , Jensen Lars J. , Olsen Jesper V. , Lundby Alicia 
Published: January 2020

AbstractThe study of human cardiac pathologies often relies on research conducted in model organisms to gain molecular insight into disease and to develop novel treatment strategies; however, translating findings from model organisms back to human can present a significant challenge, in part due to a lack of knowledge about the differences across species in cardiac protein abundances and their interactions. Here we set out to bridge this knowledge gap by presenting a global analysis of cardiac protein expression profiles in humans and commonly used model organisms. Using quantitative mass spectrometry-based proteomics, we measured the abundance of ~7,000 proteins in samples from the separate chambers of human, pig, horse, rat, mouse and zebrafish hearts. This knowledgebase of cardiac protein signatures is accessible through an online database at: atlas.cardiacproteomics.com. Quantitative comparison of the protein profiles support the pig as model organism of choice for arrhythmogenic right ventricular cardiomyopathy whereas comparison of profiles from the two-chambered zebrafish heart suggests a better resemblance to the right side of mammalian hearts. This proteomics resource facilitates translational prospect of cardiac studies from model organisms to humans by enabling direct comparison of disease-linked protein networks across species.
Sound context modulates perceived vocal emotion
Authors: Liuni Marco , Ponsot Emmanuel , Bryant Gregory A. , Aucouturier JJ 
Published: January 2020

AbstractMany animal vocalizations contain nonlinear acoustic phenomena as a consequence of physiological arousal. In humans, nonlinear features are processed early in the auditory system, and are used to efficiently detect alarm calls and other urgent signals. Yet, high-level emotional and semantic contextual factors likely guide the perception and evaluation of roughness features in vocal sounds. Here we examined the relationship between perceived vocal arousal and auditory context. We presented listeners with nonverbal vocalizations (yells of a single vowel) at varying levels of portrayed vocal arousal, in two musical contexts (clean guitar, distorted guitar) and one non-musical context (modulated noise). As predicted, vocalizations with higher levels of portrayed vocal arousal were judged as more negative and more emotionally aroused than the same voices produced with low vocal arousal. Moreover, both the perceived valence and emotional arousal of vocalizations were significantly affected by both musical and non-musical contexts. These results show the importance of auditory context in judging emotional arousal and valence in voices and music, and suggest that nonlinear features in music are processed similarly to communicative vocal signals.
Individual differences among deep neural network models
Authors: Mehrer Johannes , Spoerer Courtney J. , Kriegeskorte Nikolaus , Kietzmann Tim C. 
Published: January 2020

AbstractDeep neural networks (DNNs) excel at visual recognition tasks and are increasingly used as a modelling framework for neural computations in the primate brain. However, each DNN instance, just like each individual brain, has a unique connectivity and representational profile. Here, we investigate individual differences among DNN instances that arise from varying only the random initialization of the network weights. Using representational similarity analysis, we demonstrate that this minimal change in initial conditions prior to training leads to substantial differences in intermediate and higher-level network representations, despite achieving indistinguishable network-level classification performance. We locate the origins of the effects in an under-constrained alignment of category exemplars, rather than a misalignment of category centroids. Furthermore, while network regularization can increase the consistency of learned representations, considerable differences remain. These results suggest that computational neuroscientists working with DNNs should base their inferences on multiple networks instances instead of single off-the-shelf networks.
A strategy for complete telomere-to-telomere assembly of ciliate macronuclear genome using ultra-high coverage Nanopore data
Authors: Wang Guangying , Chai Xiaocui , Zhang Jing , Yang Wentao , Jiang Chuanqi , Chen Kai , Miao Wei , Xiong Jie 
Published: January 2020

ABSTRACTCiliates contain two kinds of nuclei: the germline micronucleus (MIC) and the somatic macronucleus (MAC) in a single cell. The MAC usually have fragmented chromosomes. These fragmented chromosomes, capped with telomeres at both ends, could be gene size to several megabases in length among different ciliate species. So far, no telomere-to-telomere assembly of entire MAC genome in ciliate species is finished. Development of the third generation sequencing technologies allows to generate sequencing reads up to megabases in length that could possibly span an entire MAC chromosome. Taking advantage of ultra-long Nanopore reads, we established a simple strategy for the complete assembly of ciliate MAC genomes. Using this strategy, we assembled the complete MAC genomes of two ciliate speciesTetrahymena thermophilaandTetrahymena shanghaiensis, composed of 181 and 214 chromosomes telomere-to-telomere respectively. The established strategy as well as the high-quality genome data will provide a useful approach for ciliate genome assembly, and a valuable community resource for further biological, evolutionary and population genomic studies.
Acute Stress Reduces Reward-Related Neural Activity: Evidence from the Reward Positivity
Authors: Burani Kreshnik , Gallyer Austin , Ryan Jon , Jordan Carson , Joiner Thomas , Hajcak Greg 
Published: January 2020

ABSTRACTStress and blunted reward processing are risk factors for mood disorders, including Major Depressive Disorder (MDD). The experience of acute stress reduces fMRI correlates of reward-related neural activity; however, few studies have examined how acute stress impacts measures of reward derived from event-related potentials (ERPs). The current study examined the impact of an acute stressor on the Reward Positivity (RewP), an ERP that indexes reward sensitivity, in twenty-seven college students. Participants completed a monetary reward task while they placed their left hand in cold water set at 13 degrees Celsius (i.e., acute stress condition) and again while their hand was placed in room temperature water (i.e., control condition). These conditions were separated by one week and performed in a counter-balanced order across participants. The results revealed that the RewP amplitude was blunted in the acute stress condition compared to the control condition. Moreover, there was a trend toward this effect interacting with self-reported depressive symptoms: the RewP was only reduced among individuals who reported low depressive symptoms. The current study suggests that an acute stressor reduces the RewP, and that this effect might be moderated by current depressive symptoms. Future studies might examine the temporal association between reward processing and stress —and how they interact to predict depressive symptoms.
Cell autonomous versus systemic Akt isoform deletions uncovered new roles for Akt1 and Akt2 in breast cancer
Authors: Chen Xinyu , Ariss Majd M. , Ramakrishnan Gopalkrishnan , Nogueira Veronique , Blaha Catherine , Putzbach William , Islam Abul B. M. M. K. , Frolov Maxim V. , Hay Nissim 
Published: January 2020

AbstractStudies in three mouse models of breast cancer identified profound discrepancies between cell autonomous and systemic Akt1 or Akt2 deletion on breast cancer tumorigenesis and metastasis. First, unlike systemic Akt1 deletion, which inhibits metastasis, cell autonomous Akt1 deletion does not. Second, systemic Akt2 deletion does not inhibit mammary tumorigenesis and metastasis, but cell autonomous Akt2 deletion eliminates ErbB2 expressing cells in the mammary gland and prevents tumorigenesis. However, the elevation in insulin by Akt2 systemic deletion hyperactivates tumor Akt, enabling ErbB2 expression, and exacerbates mammary tumorigenesis. Decreasing insulin level inhibits accelerated tumorigenesis by systemic Akt2 deletion. Single cell mRNA sequencing revealed that systemic Akt1 deletion maintains the pro-metastatic cluster within primary tumors but ablates pro-metastatic neutrophils. Systemic Akt1 deletion inhibits metastasis by impairing the survival and mobilization of tumor-associated neutrophils. Importantly, neutrophil-specific deletion of Akt1 is sufficient to exert resistance to metastasis. The results underscore the importance of determining systemic effects rather than cell autonomous effects as a proof of concept for cancer therapy.
Bright and tunable far-red chemigenetic indicators
Authors: Deo Claire , Abdelfattah Ahmed S. , Bhargava Hersh K. , Berro Adam J. , Falco Natalie , Moeyaert Benjamien , Chupanova Mariam , Lavis Luke D. , Schreiter Eric R. 
Published: January 2020

AbstractFunctional imaging using fluorescent indicators has revolutionized biology but additional sensor scaffolds are needed to access properties such as bright, far-red emission. We introduce a new platform for ‘chemigenetic’ fluorescent indicators, utilizing the self-labeling HaloTag protein conjugated to environmentally sensitive synthetic fluorophores. This approach affords bright, far-red calcium and voltage sensors with highly tunable photophysical and chemical properties, which can reliably detect single action potentials in neurons.
Genomic structure, evolutionary origins, and reproductive function of a large amplified intrinsically disordered protein gene on the X chromosome (Laidx) in mice
Authors: Arlt Martin F. , Brogley Michele A. , Stark-Dykema Evan R. , Hu Yueh-Chiang , Mueller Jacob L. 
Published: January 2020

AbstractMouse sex chromosomes are enriched for co-amplified gene families, present in tens to hundreds of copies. Co-amplification ofSlx/Slxl1on the X chromosome andSlyon the Y chromosome are involved in dose-dependent genetic conflict, however the role of other co-amplified genes remains poorly understood. Here we demonstrate that the co-amplified gene familySrsx, along with two additional partial gene annotations, is actually part of a larger transcription unit, which we nameLaidx.Laidxis harbored in a 229 kb amplicon that represents the ancestral state as compared to a 525 kb Y-amplicon containing the rearrangedLaidy.Laidxcontains a 25,011 nucleotide open reading frame, predominantly expressed in round spermatids, predicted to encode an 871 kDa protein.Laidxhas orthologous copies with the rat and also the 825-MY diverged parasitic Chinese liver fluke,Clonorchis sinensis, the likely result of a horizontal gene transfer of rodentLaidxto an ancestor of the liver fluke. To assess the male reproductive functions ofLaidx, we generated mice carrying a multi-megabase deletion of theLaidx-ampliconic region.Laidx-deficient male mice do not show detectable reproductive defects in fertility, fecundity, testis histology, and offspring sex ratio. We speculate thatLaidxandLaidyrepresent a now inactive X versus Y chromosome conflict that occurred in an ancestor of present day mice.
A novel transcriptional signalling pathway mediated by the trafficking protein Ambra1 via scaffolding Atf2 complexes
Authors: Schoenherr Christina , Byron Adam , Frame Margaret C 
Published: January 2020

ABSTRACTPreviously, we reported that Ambra1 is a core component of a cytoplasmic trafficking network, acting as a spatial rheostat to control active Src and FAK levels in addition to its critical roles in autophagy during neurogenesis. Here we identify a novel nuclear scaffolding function for Ambra1 that controls gene expression. Ambra1 binds to nuclear pore proteins, to other adaptor proteins like FAK and Akap8 in the nucleus, as well as to chromatin modifiers and transcriptional regulators such as Brg1, Cdk9 and the cAMP-regulated transcription factor Atf2. Ambra1 contributes to their association with chromatin and we identified genes whose transcription is regulated by Ambra1 complexes, likely via histone modifications and phospho-Atf2-dependent transcription. Therefore, Ambra1 scaffolds protein complexes at chromatin, regulating transcriptional signalling in the nucleus; in particular, it recruits chromatin modifiers and transcriptional regulators to control expression of genes such asangpt1, tgfb2, tgfb3, itga8anditgb7that likely contribute to the role of Ambra1 in cancer cell invasion.
Regulating AMPKα and insulin level by Vinegar, Swimming and Refeeding on High-Fat Diet Rats to Rebuild Lipid Homeostasis
Authors: Yang Yuan , Zhang Feng , Xiao Xiao , Ma Chunlian , Liu Hua , Yang Yi 
Published: January 2020

AbstractOur aims were to explore the effects of dietary and behavior interventions on lipometabolism caused by unhealthy high-fat diet and the best method to rebuild lipid homeostasis of this lifestyle. Apart from normal diet rats, 34 rats were fed with high-fat emulsion for 4 weeks before being divided into 4 groups and intervened for another 4 weeks. 8 of them were classified into high-fat control group and 9 were sorted into high-fat diet with rice vinegar group. Meanwhile, 10 were put into high-fat diet with swimming group and 7 were just for refeeding normal diet group. Then the data of body weight was recorded and analyzed. Serum, pancreas, liver, cardiac tissues and epididymis adipose were sampled as required. Indexes of serum were tested by kits. AMPKα, HNF1α, CTRP6 from tissues were detected by western blot. According to our experiments, Swimming and refeeding groups reflected a better regulation on lipid homeostasis mainly by up-regulating the expression of pancreas AMPKα. To be more specific, the refeeding rats showed lower T-CHO (P<0.001) and LDL-C (P<0.05), but higher weight gain (P<0.001),insulin level (P<0.01)and pancreas AMPKα (P<0.01)than high-fat control rats. Compared with rats experimented by swimming or rice vinegar, they showed higher weight gain (P<0.001),insulin level (P<0.01)and HNF1α, but lower of CTRP6. In summary, refeeding diet functioned better in regulating the lipometabolic level after high-fat diet. Whatever approach mentioned above we adopted to intervene, the best policy to keep the balance of lipid homeostasis is to maintain a healthy diet.
Ubiquitous overexpression of CXCL12 confers radiation protection and enhances mobilization of hematopoietic stem and progenitor cells
Authors: Rajendiran Smrithi , Smith-Berdan Stephanie , Kunz Leo , Risolino Maurizio , Selleri Licia , Schroeder Timm , Forsberg E Camilla 
Published: January 2020

ABSTRACTC-X-C Motif Chemokine Ligand 12 (CXCL12; aka SDF1α) is a major regulator of a number of cellular systems, including hematopoiesis where it influences hematopoietic cell trafficking, proliferation, and survival during homeostasis and upon stress and disease. A variety of constitutive, temporal, ubiquitous and cell-specific loss-of-function models have documented the functional consequences on hematopoiesis upon deletion ofCxcl12. Here, in contrast to loss-of-function experiments, we implemented a gain-of-function approach by generating a dox-inducible transgenic mouse model that enables spatial and temporal overexpression ofCxcl12. We demonstrated that ubiquitous CXCL12 overexpression led to an increase in multipotent progenitors in the bone marrow and spleen. The CXCL12+ mice displayed reduced reconstitution potential as either donors or recipients in transplantation experiments. Additionally, we discovered thatCxcl12overexpression improved hematopoietic stem and progenitor cell mobilization into the blood, and conferred radioprotection by promoting quiescence. Thus, this new CXCL12+ mouse model provided new insights on major facets of hematopoiesis and serves as a versatile resource for studying CXCL12 function in a variety of contexts.
Three dimensional parallelized RESOLFT nanoscopy for volumetric live cell imaging
Authors: Bodén Andreas , Pennacchietti Francesca , Testa Ilaria 
Published: January 2020

AbstractThe volumetric architecture of organelles and molecules inside cells can only be investigated with microscopes featuring sufficiently high resolving power in all three spatial dimensions. Current methods suffer from severe limitations when applied to live cell imaging such as long recording times and/or photobleaching. By introducing a novel optical scheme to switch reversibly switchable fluorescent molecules, we demonstrate volumetric nanoscopy of living cells with resolution below 100 nm in 3D, large field of view and minimal illumination intensities (W-kW/cm2).
The effectiveness of using colors in L1 and L2 vocabulary development of autistic children
Authors: Altakhaineh Abdel Rahman Mitib , Mahmoud Hodan , Abukhater Alaa Y. 
Published: January 2020

Purpose
The purpose of this paper is to examine the effectiveness of using colors and learner’s intelligence quotient (IQ) in teaching new vocabulary in Arabic (L1) and English (L2) to children with autism spectrum disorder (henceforth, ASD).

Design/methodology/approach
To this end, 12 autistic children whose ages ranged between 7 and 12 were observed while they were being taught ten new words. The children were divided into two groups based on their IQ: Low (70–74) and High (76–79). The children were also divided into two groups: Group 1 studied the words written in a black font, whereas Group 2 studied the same words, but written in colors (each letter in the word in a different color), and an illustrative picture was provided with each word for both groups. The pictures were also different in color in the former group, while the picture was in black and white in the latter. The children involved in the study have a relatively slight ability to read letters based on an annual language assessment conducted by the center, and they learn a new word by learning its shape and by repetition. The experiment took place over a two-week period that involved teaching, revising and testing.

Findings
The results of the study showed that the children’s IQ played a crucial role in learning L1 and L2 vocabulary. The results also demonstrated that using colors had no significant impact on the children’s performance in the test. Finally, the results showed that teaching new words to children with ASD through repetition and drilling could be regarded as a useful technique. The study concludes with some recommendations for further studies.

Originality/value
The study shows that using pictures is a very useful tool in teaching L1 and L2 vocabulary to children with ASD.
Emotional intelligence strategies to achieve subjective career success: implications for learning and development in knowledge industry
Authors: Singh Nishant , Warrier Uma , Bharti Teena 
Published: January 2020

Purpose
This paper exemplifies the role of emotional intelligence (EI) achieving subjective career success in the global knowledge industry.

Design/methodology/approach
Discussion based on the literature, report, and industry experts.

Findings
EI can be used as an effective tool to influence the attributes of subjective career success such as job satisfaction, new skill acquisition, work-life balance, healthy relationship with peers and pride in work. Employees feel empowered and successful in their careers if their social ability, emotionality, self-control, well-being and, expressed behavior are properly taken care of by their organizations.

Originality/value
This paper introduces a new factor expressed behavior in EI model and suggests various strategies to enhance EI and achieve subjective career success in the knowledge industry.
Magneto hydrodynamic convection in a nanofluid saturated enclosure with porous fins
Authors: Wang Lei , Cai Yang , Wang Wei-Wei , Liu Run-Zhe , Liu Di , Zhao Fu-Yun , Wang Hanqing 
Published: January 2020

Purpose
This paper aims to numerically investigate the magnetohydrodynamic (MHD) convection heat transfer of nanofluid inside a differentially heated enclosure with various fin morphologies.

Design/methodology/approach
The fluid flow within the cavity was governed by N-S equations while it within porous medium was solved by the non-Darcy model, called the Darcy–Forchheimer model based on representative element-averaging method. Empirical correlations from experimental data are used to evaluate the effective thermal conductivity and dynamic viscosity. Relevant governing parameters, including thermal Rayleigh number (105-107), Hartmann number (0-50), Darcy number (10−6-10−1), thermal conductivity ratio of porous matrix (1-103), nanoparticles volume fraction (0-0.04) and topology designs of porous fins, are sensitively varied to identify their effects and roles on the fluid flow and heat transfer. Particularly, heatlines are used to investigate the mechanism of heat transport.

Findings
Numerical results demonstrate that the predictions of average Nusselt number are augmented by using more porous fins with high permeability, and this effect becomes opposite in tiny Darcy numbers. Particularly, for high Darcy and Rayleigh numbers, the shortest fins could achieve the best performance of heat transfer. In addition, the prediction of average Nusselt number reduces with an increase in Hartmann numbers. An optimal nanoparticles concentration also exists to maximize heat transfer enhancement. Finally, numerical correlations for the average Nusselt number were proposed as functions of these governing parameters.

Practical implications
Present work could benefit the thermal design of electronic cooling and thermal carriers in nanofluid engineering.

Social implications
Present work could benefit the thermal design of electronic cooling and thermal carriers in nanofluid engineering. In addition, optimum thermal removals could enhance the lifetime of electronics, therefore reducing the cost of energy and materials.

Originality/value
To the best knowledge of authors, there are not any studies considering the synergetic effects of porous fins on MHD convection of nanofluids. Present work could benefit the thermal design of electronic cooling and thermal carriers in nanofluid engineering.