bluuebunny/crossref_metadata_2025_split huggingface dataset:
Entropy, free energy, symmetry and dynamics in the brain
Authors: Jirsa Viktor , Sheheitli Hiba 
Published: January 2022

Abstract
Neuroscience is home to concepts and theories with roots in a variety of domains including information theory, dynamical systems theory, and cognitive psychology. Not all of those can be coherently linked, some concepts are incommensurable, and domain-specific language poses an obstacle to integration. Still, conceptual integration is a form of understanding that provides intuition and consolidation, without which progress remains unguided. This paper is concerned with the integration of deterministic and stochastic processes within an information theoretic framework, linking information entropy and free energy to mechanisms of emergent dynamics and self-organization in brain networks. We identify basic properties of neuronal populations leading to an equivariant matrix in a network, in which complex behaviors can naturally be represented through structured flows on manifolds establishing the internal model relevant to theories of brain function. We propose a neural mechanism for the generation of internal models from symmetry breaking in the connectivity of brain networks. The emergent perspective illustrates how free energy can be linked to internal models and how they arise from the neural substrate.
Predicting future links with new nodes in temporal academic networks
Authors: Ran Yijun , Liu Si-Yuan , Yu Xiaoyao , Shang Ke-Ke , Jia Tao 
Published: January 2022

Abstract
Most real-world systems evolve over time in which entities and the interactions between entities are added and removed—new entities or relationships appear and old entities or relationships vanish. While most network evolutionary models can provide an iterative process for constructing global properties, they cannot capture the evolutionary mechanisms of real systems. Link prediction is hence proposed to predict future links which also can help us understand the evolution law of real systems. The aim of link prediction is to uncover missing links from known parts of the network or quantify the likelihood of the emergence of future links from current structures of the network. However, almost all existing studies ignored that old nodes tend to disappear and new nodes appear over time in real networks, especially in social networks. It is more challenging for link prediction since the new nodes do not have pre-existing structure information. To solve the temporal link prediction problems with new nodes, here we take into account nodal attribute similarity and the shortest path length, namely, ASSPL, to predict future links with new nodes. The results tested on scholar social network and academic funding networks show that it is highly effective and applicable for ASSPL in funding networks with time-evolving. Meanwhile, we make full use of an efficient parameter to exploit how network structure or nodal attribute has an impact on the performance of temporal link prediction. Finally, we find that nodal attributes and network structure complement each other well for predicting future links with new nodes in funding networks.
Measuring optical loss in yttrium orthosilicate using a whispering gallery mode resonator
Authors: Norman Daniel S , Azeem Farhan , Longdell Jevon J , Schwefel Harald G L 
Published: January 2022

Abstract
The fabrication of a yttrium orthosilicate (YSO) whispering gallery mode (WGM) resonator is described, displaying quality (Q)-factors as high as 1.1 × 109. An overview of the experimental setup is presented including the procedure for spatial and spectral characterisation of the WGMs. We consider the optical losses present in such a resonator and what steps were taken in order to minimise these losses. The surface scattering in such a resonator is considered and we show that in the wavelength range of 1.5 μm, the Q-factor is not limited by scattering losses for the case in which surface inhomogeneities are weakly correlated. The high Q-factors we demonstrate have implications for rare earth ion dopant based quantum technologies because YSO is an important host material for these applications.
A practice game changer: Impact of tenecteplase for acute ischemic stroke in a multicenter quality improvement project
Authors: Noh Lydia , Pham Felix , Haddad Lara , Burkhard Theresa , Paletz Laurie , Pech Marco , Lewis Maya , Manoukian Vicki , Schlick Konrad H , Song Shlee 
Published: January 2022

Abstract

Purpose
Tenecteplase is a thrombolytic that is more fibrin specific, has a longer half-life, and is easier to administer than alteplase for acute ischemic stroke (AIS). This article outlines the pharmacy experience and perspective on implementation of tenecteplase as the treatment of choice for AIS.

Summary
Tenecteplase has been of increasing interest for AIS and is currently being studied in several clinical trials. Although it is not indicated by the Food and Drug Administration for AIS, several published studies and an update to stroke guidelines from the American Heart Association and American Stroke Association support its use in this setting. In January 2021, Cedars-Sinai Health System made the decision to add tenecteplase to the formulary for AIS in addition to keeping alteplase for patients who met the criterion of being outside the 4.5-hour window following stroke onset. Along with the added benefits of having tenecteplase on formulary come challenges of managing multiple thrombolytics for the same indication. Identifying key stakeholders and creating an interdisciplinary team are critical to ensure safe transitions.

Conclusion
Institutions can safely transition from alteplase to tenecteplase as a thrombolytic of choice for AIS.
Plasma Angiopoietin-Like Protein 2 Levels and Mortality Risk Among Younger-Old Japanese People: A Population-Based Case–Cohort Study
Authors: Zhao Wenjing , Morinaga Jun , Ukawa Shigekazu , Endo Motoyoshi , Yamada Hiroya , Kawamura Takashi , Wakai Kenji , Tsushita Kazuyo , Ando Masahiko , Suzuki Koji , Oike Yuichi , Tamakoshi Akiko 
Published: January 2022

Abstract
Aging is an important medical and social problem. Excessive angiopoietin-like protein (ANGPTL)-2 signaling causes chronic tissue inflammation, promoting development and progression of aging-related diseases. Moreover, circulating ANGPTL2 levels reportedly predict the risk of some aging-related diseases and subsequent death. However, there are, as yet, no reports of whether circulating ANGPTL2 levels predict vital prognosis in younger-old, community-dwelling populations. This study investigated associations between plasma ANGPTL2 levels and all-cause and specific-cause mortality in this population. The case–cohort study was abstracted from an ongoing, age-specific prospective cohort study: the New Integrated Suburban Seniority Investigation Project. This project enrolled 3 073 participants aged 64 years at the beginning of the investigation from 1996 through 2005. A subcohort of 714 randomly sampled participants plus 387 cases representing deceased participants followed through 2015 underwent survival analysis. Plasma ANGPTL2 concentrations were positively associated with &gt;80% and 100% higher risk of all-cause mortality and cancer mortality, respectively, after adjustment for gender, smoking, alcohol consumption, walking time, sleep duration, caloric intake, medical status, disease history, BMI, and triglyceride, creatinine, uric acid, and high sensitivity C-reactive protein levels. A more robust association between ANGPTL2 levels and all-cause and cancer mortality was seen in participants with either frailties or with lifestyles of heavier drinking or current smoking. Elevated plasma ANGPTL2 levels are associated with high all-cause and cancer mortality in a community-dwelling sample of younger-old adults. These findings expand our knowledge of human aging and associated diseases.
Future-Proofing Organizational Knowledge Management and Human Resourcing: Identifying Early Retirement Predictors in a Modern Police Force
Authors: AlKaabi Faisal Ahmed Mohamed , Davies Amanda 
Published: January 2022

Abstract
An acknowledged challenge for human resource management is building resilience against loss of organizational knowledge through employee early retirement. In the highly competitive business world of the 21st century in which human capital is emerging as a commercial and competitive asset, developing an understanding of the non-work factors which predicate early retirement has the capacity to inform on strategies for mitigating the organizational, professional, and personal impact of employee early retirement. A study conducted within a Middle East policing organization identified the imbalance between work and family, limited support for workplace stress from social and organization avenues increases early retirement intentions. The study evaluated demographic factors, level of satisfaction with work, and social circumstances correlated with odds of early retirement intentions. The findings offer a contribution to the developing body of research and resultant policy formulation focused on identifying the influence on early retirement through (a) the replicable design and analysis approach applied in the study and (b) the non-work social factors evaluated.
ATAC-Seq Reveals the Landscape of Open Chromatin and cis-Regulatory Elements in thePhytophthora sojaeGenome
Authors: Zhang Zhichao , Lin Long , Chen Han , Ye Wenwu , Dong Suomeng , Zheng Xiaobo , Wang Yuanchao 
Published: January 2022

Nucleosome-free open chromatin often harbors transcription factor (TF)-binding sites that are associated with active cis-regulatory elements. However, analysis of open chromatin regions has rarely been applied to oomycete or fungal plant pathogens. In this study, we performed the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) to identify open chromatin and cis-regulatory elements in Phytophthora sojae at the mycelial stage. We identified 10,389 peaks representing nucleosome-free regions (NFRs). The peaks were enriched in gene-promoter regions and associated with 40% of P. sojae genes; transcription levels were higher for genes with multiple peaks than genes with a single peak and were higher for genes with a single peak than genes without peak. Chromatin accessibility was positively correlated with gene transcription level. Through motif discovery based on NFR peaks in core promoter regions, 25 candidate cis-regulatory motifs with evidence of TF-binding footprints were identified. These motifs exhibited various preferences for location in the promoter region and associations with the transcription level of their target genes, which included some putative pathogenicity-related genes. As the first study revealing the landscape of open chromatin and the correlation between chromatin accessibility and gene transcription level in oomycetes, the results provide a technical reference and data resources for future studies on the regulatory mechanisms of gene transcription.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Emerging scale invariance in a model of turbulence of vortices and waves
Authors: Shavit M. , Vladimirova N. , Falkovich G. 
Published: January 2022

This note is devoted to broken and emerging scale invariance of turbulence. Pumping breaks the symmetry: the statistics of every mode explicitly depend on the distance from the pumping. And yet the ratios of mode amplitudes, called Kolmogorov multipliers, are known to approach scale-invariant statistics away from the pumping. This emergent scale invariance deserves an explanation and a detailed study. We put forward the hypothesis that the invariance of multipliers is due to an extreme non-locality of their interactions (similar to the appearance of mean-field properties in the thermodynamic limit for systems with long-range interaction). We analyse this phenomenon in a family of models that connects two very different classes of systems: resonantly interacting waves and wave-free incompressible flows. The connection is algebraic and turns into an identity for properly discretized models. We show that this family provides a unique opportunity for an analytic (perturbative) study of emerging scale invariance in a system with strong interactions.
This article is part of the theme issue ‘Scaling the turbulence edifice (part 1)’.
Remarks on anomalous dissipation for passive scalars
Authors: Mazzucato A. L. 
Published: January 2022

We consider the problem of anomalous dissipation for passive scalars advected by an incompressible flow. We review known results on anomalous dissipation from the point of view of the analysis of partial differential equations, and present simple rigorous examples of scalars that admit a Batchelor-type energy spectrum and exhibit anomalous dissipation in the limit of zero scalar diffusivity.
This article is part of the theme issue ‘Scaling the turbulence edifice (part 1)’.
Memory effects and static disorder reduce information in single-molecule signals
Authors: Song Kevin , Makarov Dmitrii E. , Vouga Etienne 
Published: January 2022

AbstractA key theoretical challenge posed by single-molecule studies is the inverse problem of deducing the underlying molecular dynamics from the time evolution of low-dimensional experimental observables. Toward this goal, a variety of low-dimensional models have been proposed as descriptions of single-molecule signals, including random walks with or without conformational memory and/or with static or dynamics disorder. Differentiating among different models presents a challenge, as many distinct physical scenarios lead to similar experimentally observable behaviors such as anomalous diffusion and nonexponential relaxation. Here we show that information-theory-based analysis of single-molecule time series, inspired by Shannon’s work studying the information content of printed English, can differentiate between Markov (memoryless) and non-Markov single-molecule signals and between static and dynamic disorder. In particular, non-Markov time series are more predictable and thus can be compressed and transmitted within shorter messages (i.e. have a lower entropy rate) than appropriately constructed Markov approximations, and we demonstrate that in practice the LZMA compression algorithm reliably differentiates between these entropy rates across several simulated dynamical models.
Functional variability in adhesion and flocculation of yeast megasatellite genes
Authors: Saguez Cyril , Viterbo David , Descorps-Declère Stéphane , Cormack Brendan , Dujon Bernard , Richard Guy-Franck 
Published: January 2022

ABSTRACTMegasatellites are large tandem repeats found in all fungal genomes but especially abundant in the opportunistic pathogenCandida glabrata. They are encoded in genes involved in cell-cell interactions, either between yeasts or between yeast and human cells. In the present work, we have been using an iterative genetic system to delete severalC. glabratamegasatellite-containing genes and found that two of them were positively involved in adhesion to epithelial cells, whereas three genes controlled negatively adhesion. Two of the latter,CAGL0B05061gorCAGL0A04851g,are also negative regulators of yeast-to-yeast adhesion, making them central players in controllingC. glabrataadherence properties. Using a series of syntheticSaccharomyces cerevisiaestrains in which theFLO1megasatellite was replaced by other tandem repeats of similar length but different sequences, we showed that the capacity of a strain to flocculate in liquid culture was unrelated to its capacity to adhere to epithelial cells or to invade agar. Finally, in order to understand how megasatellites were initially created and subsequently expanded, an experimental evolution system was set up, in which modified yeast strains containing different megasatellite seeds were grown in bioreactors for more than 200 generations and selected for their ability to sediment at the bottom of the culture tube. Several flocculation-positive mutants were isolated. Functionally relevant mutations included general transcription factors as well as a 230 kb segmental duplication.
Comprehensive assessment of functional effects of commonly used sweeteners on ex vivo human gut microbiome
Authors: Sun Zhongzhi , Wang Wenju , Li Leyuan , Zhang Xu , Ning Zhibin , Mayne Janice , Walker Krystal , Stintzi Alain , Figeys Daniel 
Published: January 2022

AbstractThe gut microbiome composition and function are associated with health and diseases. Sweeteners are widely used food additives, although many studies using animal models have linked sweetener consumption to gut microbial changes and health issues. Whether sweeteners directly change the human gut microbiome functionality remains largely unknown. In this study, we systematically investigated the responses of five human gut microbiomes to 21 common sweeteners, using an approach combining high-throughput ex vivo microbiome culturing and metaproteomics to quantify functional changes in different taxa. Hierarchical clustering based on metaproteomic responses of individual microbiomes resulted in two clusters. The first cluster was composed of non-caloric artificial sweeteners (NAS) and two sugar alcohols with shorter carbon backbones (4-5 carbon atoms), and the second cluster was composed of sugar alcohols with longer carbon backbones. The metaproteomic functional responses of the second cluster were similar to the prebiotic fructooligosaccharides and kestose, indicating that these sugar alcohol-type sweeteners have potential prebiotic functions. This study provides a comprehensive evaluation of the direct effects of commonly used sweeteners on the functions of the human gut microbiome using a functional metaproteomics approach, improving our understanding of the roles of sweeteners on microbiome-associated human health and disease issues.
Genome assembly, structural variants, and genetic differentiation between Lake Whitefish young species pairs (Coregonus sp.) with long and short reads
Authors: Mérot Claire , Stenløkk Kristina S R , Venney Clare , Laporte Martin , Moser Michel , Normandeau Eric , Árnyasi Mariann , Kent Matthew , Rougeux Clément , Flynn Jullien M. , Lien Sigbjørn , Bernatchez Louis 
Published: January 2022

AbstractNascent pairs of ecologically differentiated species offer an opportunity to get a better glimpse at the genetic architecture of speciation. Of particular interest is our recent ability to consider a wider range of genomic variants, not only single-nucleotide polymorphisms (SNPs), thanks to long-read sequencing technology. We can now identify structural variants (SVs) like insertions, deletions, and other rearrangements, allowing further insights into the genetic architecture of speciation and how different types of variants are involved in species differentiation. Here, we investigated genomic patterns of differentiation between sympatric species pairs (Dwarf and Normal) belonging to the Lake Whitefish (Coregonus clupeaformis) species complex. We assembled the first reference genomes for both C. clupeaformis sp. Normal and C. clupeaformis sp. Dwarf, annotated the transposable elements, and analysed the genomes in the light of related coregonid species. Next, we used a combination of long-read and short-read sequencing to characterize SVs and genotype them at population-scale using genome-graph approaches, showing that SVs cover five times more of the genome than SNPs. We then integrated both SNPs and SVs to investigate the genetic architecture of species differentiation in two different lakes and highlighted an excess of shared outliers of differentiation. In particular, a large fraction of SVs differentiating the two species correspond to insertions or deletions of transposable elements (TEs), suggesting that TE accumulation may represent a key component of genetic divergence between the Dwarf and Normal species. Altogether, our results suggest that SVs may play an important role in speciation and that, by combining second and third generation sequencing, we now have the ability to integrate SVs into speciation genomics.
Multiple parameters shape the 3D chromatin structure of single nuclei
Authors: Götz Markus , Messina Olivier , Espinola Sergio , Fiche Jean-Bernard , Nollmann Marcelo 
Published: January 2022

AbstractThe spatial organization of chromatin at the scale of topologically associating domains (TADs) and below displays large cell-to-cell variations. Up until now, how this heterogeneity in chromatin conformation is shaped by chromatin condensation, TAD insulation, and transcription has remained mostly elusive. Here, we used Hi-M, a multiplexed DNA-FISH imaging technique providing developmental timing and transcriptional status, to show that the emergence of TADs at the ensemble level partially segregates the conformational space explored by single nuclei during the early development of Drosophila embryos. Surprisingly, a substantial fraction of nuclei displayed strong insulation even before TADs emerged. Moreover, active transcription within a TAD led to minor changes to the local inter- and intra-TAD chromatin conformation in single nuclei and only weakly affected insulation to the neighboring TAD. Overall, our results indicate that multiple parameters contribute to shaping the chromatin architecture of single nuclei at the TAD scale.
Escherichia coli response to subinhibitory concentration of Colistin: Insights from study of membrane dynamics and morphology
Authors: Ponmalar Ilanila Ilangumaran , Swain Jitendriya , Basu Jaydeep K. 
Published: January 2022

AbstractPrevalence of wide spread bacterial infections bring forth a critical need in understanding the molecular mechanisms of the antibiotics as well as the bacterial response to those antibiotics. Improper usage of antibiotics, which can be in sub-lethal concentrations is one among the multiple reasons for acquiring antibiotic resistance which makes it vital to understand the bacterial response towards sub-lethal concentrations of antibiotics. In this work, we have used colistin, a well-known membrane active antibiotic used to treat severe bacterial infections and explored the impact of its sub-minimum inhibitory concentration (MIC) on the lipid membrane dynamics and morphological changes of E. coli. Upon investigation of live cell membrane properties such as lipid dynamics using fluorescence correlation spectroscopy, we observed that colistin disrupts the lipid membrane at sub-MIC by altering the lipid diffusivity. Interestingly, filamentation-like cell elongation was observed upon colistin treatment which led to further exploration of surface morphology with the help of atomic force spectroscopy. The changes in the surface roughness upon colistin treatment provides additional insight on the colistin-membrane interaction corroborating with the altered lipid diffusion. Although altered lipid dynamics could be attributed to an outcome of lipid rearrangement due to direct disruption by antibiotic molecules on the membrane or an indirect consequence of disruptions in lipid biosynthetic pathways, we were able to ascertain that altered bacterial membrane dynamics is due to direct disruptions. Our results provide a broad overview on the consequence of the cyclic polypeptide, colistin on membrane specific lipid dynamics and morphology of a live Gram-negative bacterial cell.