bluuebunny/crossref_metadata_2025_split huggingface dataset:
The evolution of color naming reflects pressure for efficiency: Evidence from the recent past
Authors: Zaslavsky Noga , Garvin Karee , Kemp Charles , Tishby Naftali , Regier Terry 
Published: November 2021

AbstractIt has been proposed that semantic systems evolve under pressure for efficiency. This hypothesis has so far been supported largely indirectly, by synchronic cross-language comparison, rather than directly by diachronic data. Here, we directly test this hypothesis in the domain of color naming, by analyzing recent diachronic data from Nafaanra, a language of Ghana and Côte d’Ivoire, and comparing it with quantitative predictions derived from the mathematical theory of efficient data compression. We show that color naming in Nafaanra has changed over the past four decades while remaining near-optimally efficient, and that this outcome would be unlikely under a random drift process that maintains structured color categories without pressure for efficiency. To our knowledge, this finding provides the first direct evidence that color naming evolves under pressure for efficiency, supporting the hypothesis that efficiency shapes the evolution of the lexicon.
BamToCov: an efficient toolkit for sequence coverage calculations
Authors: Birolo Giovanni , Telatin Andrea 
Published: November 2021

AbstractMany genomics applications requires the calculation of nucleotide coverage of a reference or counting how many reads maps in a reference region.Here we present BamToCov, a suite of tools for rapid and flexible coverage calculations relying on a memory efficient algorithm and designed for flexible integration in bespoke pipelines. The tools of the suite will process sorted BAM or CRAM files, allowing to extract coverage information using different filtering approaches.BamToCov tools, unlike existing tools already available, have been developed to require a minimum amount of memory, to be easily integrated in workflows, and to allow for strand-specific coverage analyses. The unique coverage calculation algorithm makes it the ideal choice for the analysis of long reads alignments. The programs and their documentation are freely available at https://github.com/telatin/bamtocov.
Not Quite All in Our Head: Intervention is a Better Predictor of tDCS Mind-Wandering Effects than Subjective Beliefs About Experimental Results
Authors: Gordon Matilda S. , Dux Paul E. , Filmer Hannah L. 
Published: November 2021

AbstractBackgroundEstablishing adequate blinding for non-invasive brain stimulation research is a topic of extensive debate, especially regarding the efficacy of sham control methods for transcranial direct current stimulation (tDCS) studies. Fassi and Cohen Kadosh [1] assessed the influence of subjective participant belief regarding stimulation type (active or sham) and dosage on behaviour using data from Filmer et al. [2] who applied five stimulation protocols (anodal 1.0mA, cathodal 1.0mA, cathodal 1.5mA, cathodal 2.0mA and sham) to assess the neural substrates of mind wandering. Fassi and Cohen Kadosh [1] concluded that subjective belief drove the pattern of results observed by Filmer et al. [2].ObjectiveFassi and Cohen Kadosh [1] did not assess the key contrast between conditions in Filmer et al. (2019) – 2mA vs sham – rather they examined all stimulation conditions. Here, we consider the relationship between objective and subjective intervention in this key contrast.MethodsWe replicated the analysis and findings of both Filmer et al. [2] and Fassi and Cohen Kadosh [1] before assessing 2mA vs. sham via Bayesian ANOVA on subjective belief regarding stimulation type and dosage.ResultsOur results support objective intervention as the strongest predictor of stimulation effects on mind-wandering when 2mA vs sham was examined, over and above that of subjective intervention.ConclusionsThe conclusions made by Filmer et al. [2] are confirmed. However, it is important to control for and understand the possible effects of subjective beliefs in sham-controlled studies. Best practice to prevent these issues remains the inclusion of active control conditions.
A Novel Ex Vivo Peritoneal Model to Investigate Mechanisms of Peritoneal Metastasis in Gastric Adenocarcinoma
Authors: Ng Deanna , Ali Aiman , Lee Kiera , Eymael Denise , Abe Kento , Luu Shelly , Kazazian Karineh , Brar Savtaj , Conner James , Magalhaes Marco , Swallow Carol J 
Published: November 2021

ABSTRACTPeritoneal metastases (PM) portend limited survival in patients with Gastric Adenocarcinoma (GCa), and strategies to prevent and/or more effectively treat PM are needed. Existing models are limited in recapitulating key elements of the peritoneal metastatic cascade. To explore the underlying cellular and molecular mechanisms of PM, we have developed an ex vivo human peritoneal explant model. Fresh peritoneal tissue samples were obtained from patients undergoing abdominal surgery and suspended, mesothelial layer down but without direct contact, above a monolayer of red-fluorescent stained AGS human GCa cells for 24hrs, then washed and cultured for a further 3 days. Implantation and invasion of GCa cells within the explant were examined using real-time confocal fluorescence microscopy. Superficial implantation of AGS GCa cells within the mesothelial surface was readily detected, and colonies expanded over 3 days. To investigate the sensitivity of the model to altered GCa cellular implantation, we stably transfected AGS cells with E-Cadherin, restoring the E-Cadherin that they otherwise lack. This markedly suppressed implantation and invasion of AGS cells into the submesothelial mesenchymal layer. Here we show that this ex vivo human peritoneal explant model is responsive to manipulation of genetic factors that regulate peritoneal implantation and invasion by GCa cells, with reproducible results.
A Post-hurricane Quantitative Assessment of the Red-bellied Racer (Alsophis rufiventris) on Saba and Comparison with St. Eustatius
Authors: Madden Hannah , Mielke Lara 
Published: November 2021

ABSTRACTWe estimated occupancy, abundance (lambda), detection probability, density/ha and abundance of a regionally endemic snake in the Colubrid family on the Dutch Caribbean island of Saba in 2021, four years after hurricanes Irma and Maria impacted the island. Line transect surveys were conducted at 74 sites covering 6.7 ha. The proportion of sites occupied was estimated at 0.74 (min 0.48, max 0.90), with occupancy varying between vegetation types and across elevational gradients. Similarly, lambda was estimated at 1.61 (min 0.7, max 3.7) but varied between vegetation types and elevational gradients. Detection probability was estimated at 0.15 (min 0.10, max 0.21). Using Distance sampling, we estimated 10.9 (min 7.3, max 16.2) racers/ha, with a total population estimate of 4,917 (min 2,577, max 6,362) across the entire study region (438.6 ha.) Based on anecdotal observations from Saban residents and prior literature describing the pre-hurricane population as “abundant” (at least 2.0 racers/hour), we posit that the population experienced a hurricane-induced decline but may have since recovered, though not to previous levels (1.28 racers/hour). Nevertheless, our results suggest that racer densities on Saba are currently higher than those on St. Eustatius. Despite this, given the species’ extremely limited extant range and the presence of invasive species on both islands, prevention of local extirpation should be a high conservation priority.
Collective chemotaxis in a Voronoi model for confluent clusters
Authors: Lawson-Keister E. , Manning M. L 
Published: November 2021

AbstractCollective chemotaxis, where single cells cannot climb a biochemical signaling gradient but clusters of cells can, has been observed in different biological contexts, including confluent tissues where there are no gaps or overlaps between cells. Although particle-based models have been developed that predict important features of collective chemotaxis, the mechanisms in those models depend on particle overlaps, and so it remains unclear if they can explain behavior in confluent systems. Here, we develop an open-source code that couples a 2D Voronoi simulation for confluent cell mechanics to a dynamic chemical signal that can diffuse, advect, and/or degrade, and use the code to study potential mechanisms for collective chemotaxis in cellular monolayers. We first study the impact of advection on collective chemotaxis, and delineate a regime where advective terms are important. Next, we investigate two possible chemotactic mechanisms, contact inhibition of locomotion and heterotypic interfacial tension, and demonstrate that both can drive collective chemotaxis in certain parameter regimes. We further demonstrate that the scaling behavior of cluster motion is well-captured by simple analytic theories.1Statement of SignificanceThe ability of cell collectives to respond to biochemical signals, called collective chemotaxis, is crucial for many important processes including embryonic development and wound healing. We developed an open-source computational model that couples biochemical signaling gradients to confluent cell layers, where there are no gaps between cells. Our model demonstrates that two experimentally observed local cell behaviors – neighbor-induced changes to interfacial tension or a tendency of cells to repel one another after they come into contact – can drive collective chemotaxis. We also highlight a regime in which the motion of migrating cells can alter the gradient.
RNA-guidedAsCas12a- andSpCas9-catalyzed knockout and homology directed repair of theomega-1locus of the human blood fluke,Schistosoma mansoni
Authors: Ittiprasert Wannaporn , Chatupheeraphat Chawalit , Mann Victoria H. , Li Wenhui , Miller André , Ogunbayo Taiwo , Tran Kenny , Alrefaei Yousef , Mentink-Kane Margaret , Brindley Paul J. 
Published: November 2021

AbstractWe compared the efficiency of gene knockout (KO) and precision of insertion (knock-in, KI) of the RNA-guidedAsCas12a nuclease ofAcidaminococcussp. with that ofSpCas9 fromStreptococcus pyogenes, aiming to enhance the functional genomics toolkit forSchistosoma mansoni. Programmed DNA cleavages catalyzed by Cas12a and Cas9 result in staggered and blunt ended strand breaks, respectively. TTTV, the optimal protospacer adjacent motif forAsCas12a would occur frequently within the AT-rich genome of this platyhelminth. We deployed optimized conditions for the ratio of guide RNAs to the nuclease, donor templates, and electroporation parameters, to target a key enzyme termed omega-1 that is secreted by the schistosome egg.AsCas12a was more efficient thanSpCas9 for gene knockout ofomega-1as determined by tracking of indels by decomposition (P< 0.001). Resulting from CRISPREsso2 analysis, most mutations were deletions;SpCas9 induced short deletions of 3 nt in length whereasAsCas12a induced deletions of 2 to 26 nt. Knockout efficiency of both nucleases markedly increased in the presence of short, single stranded oligodeoxynucleotide (ssODN) donor templates. WithAsCas12a, ssODNs representative of both the non-CRISPR target (NT) and target (T) strands of the targeted gene were tested, resulting in KO efficiencies of 15.67, 28.71 and 21.43% in theSpCas9 plus donor ssODN,AsCas12a plus NT-ssODN, andAsCas12a plus T-ssODN groups, respectively.Transcleavage activity against the ssODNs by activatedAsCas12a was not apparentin vitro. ProgrammedSpCas9 editing led to more precise transgene insertion thanAsCas12a, with KI efficiencies of 17.07% for the KI_SpCas9 group, 14.58% for KI_AsCas12a-NT-ssODN and 12.37% for KI_AsCas12a-T-ssODN. AlthoughAsCas12a induced fewer mutations per genome thanSpCas9, the phenotypic impact on transcription and expression of omega-1 was similar for both nucleases. These findings revealed thatAsCas12a andSpCas9 both provide tractable routes for RNA-guided programmed mutation of the genome of the schistosome egg.
Effects of Chronic Intermittent Hypoxia and Chronic Sleep Fragmentation on Gut Microbiome, Serum Metabolome, Liver and Adipose Tissue Morphology
Authors: Wang Fan , Zou Juanjuan , Xu Huajun , Huang Weijun , Zhang Xiaoman , Wei Zhicheng , Li Xinyi , Liu Yupu , Zou Jianyin , Liu Feng , Zhu Huaming , Yi Hongliang , Guan Jian , Yin Shankai 
Published: November 2021

AbstractChronic intermittent hypoxia (CIH) and chronic sleep fragmentation (CSF) are two cardinal pathological features of obstructive sleep apnea (OSA). Dietary obesity is a crucial risk intermediator for OSA and metabolic disorders. Gut microbiota affect hepatic and adipose tissue morphology under conditions of CIH or CSF through downstream metabolites. However, the exact relationship is unclear. Herein, chow and high-fat diet (HFD)-fed mice were subjected to CIH or CSF for 10 weeks each and compared to normoxia (NM) or normal sleep (NS) controls. 16S rRNA amplicon sequencing, untargeted liquid chromatography-tandem mass spectrometry, and histological assessment of liver and adipose tissues were used to investigate the correlations between the microbiome, metabolome, and lipid metabolism under CIH or CSF condition. Our results demonstrated that CIH and CSF regulate the abundance of intestinal microbes (such as Akkermansia mucinphila, Clostridium spp., Lactococcus spp., and Bifidobacterium spp.) and functional metabolites, such as tryptophan, free fatty acids, branched amino acids, and bile acids, which influence adipose tissue and hepatic lipid metabolism, and the level of lipid deposition in tissues and peripheral blood. In conclusion, CIH and CSF adversely affect fecal microbiota composition and function, and host metabolism; these findings provide new insight into the independent and synergistic effects of CIH, CSF, and HFD on lipid disorders.
Bacterial LomR Induces the Vibriophage VP882 VqmA-Directed Quorum-Sensing Lysogeny-Lysis Transition
Authors: Sun Jennifer S. , Mashruwala Ameya A. , Fei Chenyi , Bassler Bonnie L. 
Published: November 2021

SUMMARYThe bacterial cell-cell communication process called quorum sensing enables groups of bacteria to synchronously alter behavior in response to changes in cell population density. Quorum sensing relies on the production, release, accumulation, and detection of extracellular signal molecules called autoinducers. Here, we investigate a mechanism employed by a vibriophage to surveil host quorum sensing and tune its lysogeny-lysis decision to host cell density. The phage possesses a gene called vqmAPhage encoding a quorum-sensing receptor homologous to vibrio VqmA. Both VqmA receptors can detect the host bacteria-produced autoinducer called DPO. DPO-bound VqmAPhage launches the phage lysis process. We discover that the bacterial host produces an inducer of the VqmAPhage-directed quorum-sensing lysogeny-lysis transition. Production of the inducer appears to be widespread among bacteria. A screen of the Escherichia coli Keio collection for mutants impaired for inducer production revealed lomR, located in a prophage, and encoding a poorly understood protein. In the E. coli screening strain, lomR is interrupted by DNA encoding an insertion element. The 3’ domain of this LomR protein is sufficient to induce VqmAPhage-directed lysis. Alanine-scanning mutagenesis showed that substitution at either of two key residues abrogates inducer activity. Full-length LomR is similar to the outer membrane porin OmpX in E. coli and Vibrio parahaemolyticus O3:K6, and OmpT in Vibrio cholerae C6706, and indeed, OmpX and OmpT can induce VqmAPhage-directed activity. Possibly, development of the LomR, OmpX, or OmpT proteins as tools to direct phage lysis of host cells could be used to control bacteria in medical or industrial settings.ABSTRACT IMPORTANCEBacteria communicate with chemical signal molecules using a process called quorum sensing. Quorum sensing allows bacteria to track their cell numbers and orchestrate collective behaviors. Recently, we discovered that a virus that infects and kills bacteria “eavesdrops” on its host’s quorum-sensing process. Specifically, the virus monitors host cell growth by detecting the accumulation of host quorum-sensing signal molecules. In response to the garnered quorum-sensing information, the virus kills the host bacterial cells when the bacterial population has reached a high cell density. This strategy presumably enhances transmission of viruses to new host cells. Here, we discover and characterize three closely-related bacterial host-produced proteins called LomR, OmpX, and OmpT that are capable of inducing the viral quorum-sensing-mediated killing program. Development of this class of inducer proteins as tools to drive “on demand” virus-mediated lysis of pathogenic host bacterial cells could be used to control bacteria in medical or industrial settings.
Disruption of vacuolin microdomains in the host Dictyostelium discoideum increases resistance to Mycobacterium marinum-induced membrane damage and infection
Authors: Bosmani Cristina , Perret Angélique , Leuba Florence , Guého Aurélie , Hanna Nabil , Soldati Thierry 
Published: November 2021

ABSTRACTMycobacterium tuberculosis (Mtb), the causative agent of tuberculosis, manipulates the host phagosome maturation pathway to replicate intracellularly. Mycobacterium marinum, a closely-related species, and Dictyostelium discoideum, a social amoeba and alternative phagocytic host, have been used as models to study host-pathogen interactions occurring during mycobacterial infections. Vacuolins, functional homologues of the mammalian flotillins, organize membrane microdomains and play a role in vesicular trafficking. Various pathogens have been reported to manipulate their membrane association and function. During infection of D. discoideum with M. marinum, Vacuolin C was specifically and highly induced and all three vacuolin isoforms were enriched at the mycobacteria-containing-vacuole (MCV). In addition, absence of vacuolins reduced escape from the MCV and conferred resistance to M. marinum infection. Moreover, ESAT-6, the membrane-disrupting virulence factor of M. marinum, was less associated with membranes when vacuolins were absent. Together, these results suggest that vacuolins are important host factors that are manipulated by mycobacteria to inflict membrane damage and escape from their compartment.
Looking for lipases and lipolytic organisms in low-temperature anaerobic reactors treating domestic wastewater
Authors: Bashiri Reihaneh , Allen Ben , Shamurad Burhan , Pabst Martin , Curtis Thomas P. , Ofiţeru Irina D. 
Published: November 2021

AbstractPoor lipid degradation limits low-temperature anaerobic treatment of domestic wastewater even when psychrophiles are used. We combined metagenomics and metaproteomics to find lipolytic bacteria and their potential, and actual, cold-adapted extracellular lipases in anaerobic membrane bioreactors treating domestic wastewater at 4°C and 15°C. Of the 40 recovered putative lipolytic metagenome-assembled genomes (MAGs), only three (Chlorobium, Desulfobacter, and Mycolicibacterium) were common and abundant (relative abundance ≥ 1%) in all reactors. Notably, some MAGs that represented aerobic autotrophs contained lipases. Therefore, we hypothesised that the lipases we found are not always associated with exogenous lipid degradation and can have other roles such as polyhydroxyalkanoates (PHA) accumulation/degradation and interference with the outer membranes of other bacteria. Metaproteomics did not provide sufficient proteome coverage for relatively lower abundant proteins such as lipases though the expression of fadL genes, long-chain fatty acid transporters, was confirmed for four genera (Dechloromonas, Azoarcus, Aeromonas and Sulfurimonas), none of which were recovered as putative lipolytic MAGs. Metaproteomics also confirmed the presence of 15 relatively abundant (≥1%) genera in all reactors, of which at least 6 can potentially accumulate lipid/polyhydroxyalkanoates. For most putative lipolytic MAGs, there was no statistically significant correlation between the read abundance and reactor conditions such as temperature, phase (biofilm and bulk liquid), and feed type (treated by ultraviolet light or not). Results obtained by metagenomics and metaproteomics did not confirm each other and further work is required to identify the true lipid degraders in these systems.
Host casein kinase 1-mediated phosphorylation modulates phase separation of a rhabdovirus phosphoprotein and virus infection
Authors: Fang Xiao-Dong , Gao Qiang , Zang Ying , Qiao Ji-Hui , Gao Dong-Min , Xu Wen-Ya , Wang Ying , Li Dawei , Wang Xian-Bing 
Published: November 2021

AbstractLiquid–liquid phase separation (LLPS) plays important roles in forming cellular membraneless organelles. However, how host factors regulate LLPS of viral proteins during negative-sense RNA (NSR) virus infections is largely unknown. Here, we used Barley yellow striate mosaic virus (BYSMV) as a model to demonstrate regulation of host casein kinase 1 in phase separation and infection of NSR viruses. We first found that the BYSMV phosphoprotein (P) formed spherical granules with liquid properties and recruited viral nucleotide (N) and polymerase (L) proteins in vivo. Moreover, the P-formed granules were tethered to the ER/actin network for trafficking and fusion. BYSMV P alone formed droplets and incorporated the N protein and genomic RNA in vitro. Interestingly, phase separation of BYSMV P was inhibited by host casein kinase 1 (CK1)-dependent phosphorylation of an intrinsically disordered P protein region. Genetic assays demonstrated that the unphosphorylated mutant of BYSMV P exhibited condensed phase, which promoted virus replication through concentrating the N, L proteins, and genome RNA into viroplasms. Whereas, the phosphorylation-mimic mutant existed in diffuse phase state leading to enhanced virus transcription. Collectively, our results demonstrate that host CK1 modulates phase separation of viral P protein and virus infection.
Generic Approach For Mathematical Model of Multi-Strain Pandemics
Authors: Lazebnik Teddy , Bunimovich-Mendrazitsky Svetlana ,   with the Lorem Ipsum Consortium
Published: November 2021

AbstractPandemics with multi-strain have become a major concern. We introduce a new model for assessing the connection between multi-strain pandemic and the mortality rate, basic reproduction number, and the maximum of infected individuals. The proposed model provides a general mathematical approach for representing multi-strain pandemics, generalizing for an arbitrary number of strains. We show the proposed model fits well with epidemiological historical data world health over a long period. From a theoretical point of view, we show that the increasing number of strains increases logarithmically the maximum number of infected individuals and the mean mortality rate. Moreover, the mean basic reproduction number is statistically identical to the single, most aggressive strain pandemic for multi-strain pandemics.