bluuebunny/crossref_metadata_2025_split huggingface dataset:
Behavioral signatures of Y-like neuronal responses in human vision
Authors: Ramirez Ana L. , Thompson Lowell W. , Rosenberg Ari , Baker Curtis L. 
Published: February 2022

AbstractRetinal ganglion cells initiating the magnocellular/Y-cell visual pathways respond nonlinearly to high spatial frequencies (SFs) and temporal frequencies (TFs). This nonlinearity is implicated in the processing of contrast modulation (CM) stimuli in cats and monkeys, but its contribution to human visual perception is not well understood. Here, we evaluate human psychophysical performance for CM stimuli, consisting of a high SF grating carrier whose contrast is modulated by a low SF sinewave envelope. Subjects reported the direction of motion of CM envelopes or luminance modulation (LM) gratings at different eccentricities. The performance on SF (for LMs) or carrier SF (for CMs) was measured for different TFs (LMs) or carrier TFs (CMs). The best performance for LMs was at lower TFs and SFs, decreasing systematically with eccentricity. However, performance with CMs was bandpass with carrier SF, largely independent of carrier TF, and at the highest carrier TF (20 Hz) decreased minimally with eccentricity. Since the nonlinear subunits of Y-cells respond better at higher TFs compared to the linear response components and respond best at higher SFs that are relatively independent of eccentricity, these results suggest that behavioral tasks employing CM stimuli might reveal nonlinear contributions of retinal Y-like cells to human perception.
The impacts of anesthetic regimens on the middle cerebral artery occlusion outcomes in male rats
Authors: Mousavi Seyedeh Maryam , Karimi-Haghighi Saeideh , Chavoshinezhad Sara , Pandamooz Sareh , Belém-Filho Ivaldo Jesus Almeida , Keshavarz Somaye , Bayat Mahnaz , Hooshmandi Etrat , Jaberi Abbas Rahimi , Salehi Mohammad Saied , Borhani-Haghighi Afshin 
Published: February 2022

AbstractObjectivesThe middle cerebral artery occlusion (MCAO) model was introduced more than three decades ago to simulate human stroke. Till now, it is the most common platform to investigate stroke-induced pathological changes as well as discover new drugs and treatments. Induction of general anesthesia is mandatory to induce this model, and different laboratories are using various anesthetic drugs, which might affect MCAO results. Therefore, the present study was designed to compare the impacts of several widely used anesthetic regimens on the MCAO outcomes.Materials and MethodsHere, adult male rats were anesthetized by isoflurane inhalation, intraperitoneal injection of chloral hydrate, intraperitoneal injection of ketamine-xylazine, or subcutaneous administration of ketamine-xylazine, then subjected to 30 min MCAO. Mortality rate, body weight change, infarct size, as well as cognitive and neurological performance were evaluated up to three days after the surgery.ResultsOur findings revealed chloral hydrate caused the highest, while subcutaneous ketamine-xylazine led to the lowest mortality rate. Meanwhile, there were no significant differences in the body weight loss, infarct size, cognitive impairments, and neurological deficits among the experimental groups.ConclusionsBased on the current results, we proposed that subcutaneous injection of ketamine-xylazine could be an effective anesthetic regimen in the rat model of MCAO with several advantages such as low mortality, cost-effectiveness, safety, ease of administration, and not requiring specialized equipment.
Unbiased pangenome graphs
Authors: Garrison Erik , Guarracino Andrea 
Published: February 2022

AbstractMotivationPangenome variation graphs model the mutual alignment of collections of DNA sequences. A set of pairwise alignments implies a variation graph, but there are no scalable methods to generate such a graph from these alignments. Existing related approaches depend on a single reference, a specific ordering of genomes, or ade Bruijnmodel based on a fixedk-mer length. A scalable, self-contained method to build pangenome graphs without such limitations would be a key step in pangenome construction and manipulation pipelines.ResultsWe design theseqwishalgorithm, which builds a variation graph from a set of sequences and alignments between them. We first transform the alignment set into an implicit interval tree. To build up the variation graph, we query this tree-based representation of the alignments to reduce transitive matches into single DNA segments in a sequence graph. By recording the mapping from input sequence to output graph, we can trace the original paths through this graph, yielding a pangenome variation graph. We present an implementation that operates in external memory, using disk-backed data structures and lock-free parallel methods to drive the core graph induction step. We demonstrate that our method scales to very large graph induction problems by applying it to build pangenome graphs for several species.Availabilityseqwishis published as free software under the MIT open source license. Source code and documentation are available athttps://github.com/ekg/seqwish.seqwishcan be installed via Biocondahttps://bioconda.github.io/recipes/seqwish/README.htmlor GNU Guixhttps://github.com/ekg/guix-genomics/blob/master/seqwish.scm.Contactegarris5@uthsc.edu
The invasive land flatworm Obama nungara in La Réunion, a French island in the Indian Ocean, the first report of the species for Africa
Authors: Justine Jean-Lou , Marie Amandine Delphine , Gastineau Romain , Fourcade Yoan , Winsor Leigh 
Published: February 2022

AbstractThe land flatworm Obama nungara, a species originating from South America and already invasive in many European countries, is recorded from La Réunion, a French island in the Indian Ocean. This is the first record of O. nungara from this locality and also the first record of the species for Africa. Two specimens were collected, one from Petite France (commune of Saint Paul) and one from La Plaine des Grègues (commune of Saint Joseph); the two localities are widely separated, one in the Western part and one in the South-eastern part of the island. This suggests that the species is already present in several locations in La Réunion. The sightings were communicated to us in 2021, but it is likely that the species is already present since 2020. A molecular analysis of the specimen from Petite France showed that it had the same cox1 haplotype as specimens previously recorded from several countries of Europe; it is hypothesized that the species was imported from Europe, probably from France. We mapped climatic suitability of the species in La Réunion and found that O. nungara could potentially invade a large part of the island. One record was apparently associated with the transport of plates of travertine, a construction material which has numerous cavities, suitable for the transport and survival of adult or cocoons of land flatworms.
Therapeutic resistance in acute myeloid leukemia cells is mediated by a novel ATM/mTOR pathway regulating oxidative phosphorylation
Authors: Park Hae J. , Gregory Mark A. , Zaberezhnyy Vadym , Goodspeed Andrew , Jordan Craig T. , Kieft Jeffrey S. , DeGregori James 
Published: February 2022

ABSTRACTWhile leukemic cells are susceptible to various therapeutic insults, residence in the bone marrow microenvironment typically confers protection from a wide range of drugs. Thus, understanding the unique molecular changes elicited by the marrow is of critical importance towards improving therapeutic outcomes. In the present study, we demonstrate that aberrant activation of oxidative phosphorylation serves to induce therapeutic resistance in FLT3 mutant human AML cells challenged with FLT3 inhibitor drugs. Importantly, our findings show that AML cells are protected from apoptosis following FLT3 inhibition due to marrow-mediated activation of ATM, which in turn up-regulates oxidative phosphorylation via mTOR signaling. mTOR is required for the bone marrow stroma-dependent maintenance of protein translation, with selective polysome enrichment of oxidative phosphorylation transcripts, despite FLT3 inhibition. To investigate the therapeutic significance of this finding, we tested the mTOR inhibitor everolimus in combination with the FLT3 inhibitor quizartinib in primary human AML xenograft models. While marrow resident AML cells were highly resistant to quizartinib alone, the addition of everolimus induced profound reduction in tumor burden and prevented relapse. Taken together, these data provide a novel mechanistic understanding of marrow-based therapeutic resistance, and a promising strategy for improved treatment of FLT3 mutant AML patients.
Gut Microbiome Contributes to Cold-climate Adaptation in Lizards
Authors: Chen Jun-Qiong , Zhang Lu-Wen , Zhao Ru-Meng , Wu Hai-Xia , Lin Long-Hui , Li Peng , Li Hong , Qu Yan-Fu , Ji Xiang 
Published: February 2022

ABSTRACTThe metabolic cold-climate adaption hypothesis predicts that animals from cold environments have relatively high metabolic rates compared with their warm-climate counterparts. However, studies testing this hypothesis are sparse. Here, we compared gut microbes between two cold-climate lizard species of the genusPhrynocephalusto test the hypothesis that gut microbiota can help lizards adapt to cold environments by promoting metabolism and absorption efficiency. We kept lizards at 24°C and 30°C for 25 d, and then collected their fecal samples to analyze and compare the microbiota based on 16S rRNA gene sequencing technology. The gut microbiota was mainly composed of Proteobacteria, Firmicutes, Bacteroidetes, and Verrucomicrobia at the phylum level in both species (Proteobacteria > Firmicutes > Verrucomicrobiota inP. erythrurus, and Bacteroidota > Proteobacteria > Firmicutes inP. przewalskii). Further analysis revealed that the gut microbiota contributed to the host’s cold adaptation, but with differences in the relative abundance of these contributory bacteria between the two species. KEGG analysis revealed that the gut microbiota primarily played roles in metabolism, genetic information processing, cellular processes, and environmental information processing in both species. Furthermore, genes related to metabolism were more abundant inP. erythrurusat 24 °C than in other species × temperature combinations, indicating the role of gut microbiota in long-term cold-climate adaptation. Our finding that gut microbiome contributes to cold-climate adaptation in both species but more evidently inP. erythrurususing colder habitats thanP. przewalskiithroughout a year confirms the gut microbiota’s role in the cold-climate adaptation in lizards.IMPORTANCEThis study proves that temperature affects the composition and relative abundance of the gut microbiota in twoPhrynocephaluslizards in a species-specific manner. Both species harbor specific gut microbiota with significant roles in cold-climate adaptation. Specifically,P. erythrurushas a higher Proteobacteria ratio and relative abundance of metabolism-related microbial genes in the gut thanP. przewalskii. Given thatP. erythrurususes colder habitats thanP. przewalskiithroughout a year, these results suggest that gut microbiota contributes to cold-climate adaptation in both species lizards but more evidently inP. erythrurus. This study provides evidence linking gut microbiome with cold adaptation. The co-evolution mechanism between gut microbiota and their hosts in extreme environments will provide new insights into animal adaptation.
Hand Hygiene Products and Adverse Skin Reactions: A Comparison between Health Care and Non-Health Care Workers
Authors: Roy Simanta , Saha Aishik Dipta , Iktidar Mohammad Azmain , Chowdhury Sreshtha , Tanvir Syed Md. Sayeem , Hawlader Mohammad Delwer Hossain 
Published: February 2022

AbstractBackgroundSince December 2019, a deadly coronavirus epidemic has swept the globe. Due to the significant risk of infection, frontline health workers had to use Personal Protective Equipment, including hand hygiene products, to keep their hands hygienic. The present study aims to compare adverse skin responses between Health Care Worker (HCW) and Non-Health Care Worker (NHCW).Materials and MethodsA descriptive, cross-sectional study of HCW and NHCW throughout the country was executed. A self-structured questionnaire was utilized to gather data from 404 HCWs and 826 NHCWs during a two-month period using multistage sampling. STATA (v16) was used to analyse the data.Results41.87% of the study participants experienced adverse skin reactions, which were more prevalent among HCW (65.10%) than NHCW (30.51%). The most often reported skin condition was skin dryness (34.39%), followed by skin peeling (11.71%). Users of alcohol-based hand sanitizers (ABHS) were more likely to get itch (8.13%), whereas soap water users were more likely to suffer skin peeling (35.74%) and rash (7.46%). There was a significant (p<0.001) association between occupation and adverse skin responses, with HCW being 3.5 times more likely to have adverse skin manifestations than NHCW.ConclusionThe research showed that health care workers had a greater prevalence of skin conditions than the overall population. Hand hygiene guidelines for frontline employees should be equipped with instructions on how to protect oneself from these adverse skin manifestations, since frequent use constitutes a significant risk factor. Above all, health care professionals and the general population should be educated on good hand hygiene practices.
The C. elegans ASPP homolog APE-1 is a junctional protein phosphatase 1 modulator
Authors: Beacham Gwendolyn M. , Wei Derek T. , Beyrent Erika , Zhang Ying , Zheng Jian , Camacho Mari M. K. , Florens Laurence , Hollopeter Gunther 
Published: February 2022

AbstractHow serine/threonine phosphatases are spatially and temporally tuned by regulatory subunits is a fundamental question in cell biology. Ankyrin repeat, SH3 domain, proline-rich-region-containing proteins (ASPPs) are protein phosphatase 1 (PP1) binding partners associated with cardiocutaneous diseases. ASPPs localize PP1 to cell-cell junctions, but how ASPPs localize and whether they regulate PP1 activity in vivo is unclear. Through a C. elegans genetic screen, we find that loss of the ASPP homolog, APE-1, suppresses a pathology called ‘jowls,’ providing us with an in vivo assay for APE-1 activity. Using structure-function analysis, we discover that APE-1’s N-terminal half directs the APE-1–PP1 complex to intercellular junctions. Additionally, we isolated mutations in highly conserved residues of APE-1’s ankyrin repeats that suppress jowls yet do not preclude PP1 binding, implying ASPPs do more than simply localize PP1. Indeed, in vivo reconstitution of APE-1 suggests the ankyrin repeats modulate phosphatase output, a function we find to be conserved among vertebrate homologs.
An electrophysiological and kinematic model ofParamecium, the “swimming neuron”
Authors: Elices Irene , Kulkarni Anirudh , Escoubet Nicolas , Pontani Léa-Laetitia , Prevost Alexis Michel , Brette Romain 
Published: February 2022

AbstractParameciumis a large unicellular organism that swims in fresh water using cilia. When stimulated by various means (mechanically, chemically, optically, thermally), it often swims backward then turns and swims forward again in a new direction: this is called the avoiding reaction. This reaction is triggered by a calcium-based action potential. For this reason, several authors have calledParameciumthe “swimming neuron”. Here we present an empirically constrained model of its action potential based on electrophysiology experiments on live immobilized paramecia, together with simultaneous measurement of ciliary beating using particle image velocimetry. Using these measurements and additional behavioral measurements of free swimming, we extend the electrophysiological model by coupling calcium concentration to kinematic parameters, turning it into a swimming model. In this way, we obtain a model of autonomously behavingParamecium. Finally, we demonstrate how the modeled organism interacts with an environment, can follow gradients and display collective behavior. This work provides a modeling basis for investigating the physiological basis of autonomous behavior ofParameciumin ecological environments.Author SummaryBehavior depends on a complex interaction between a variety of physiological processes, the body and the environment. We propose to examine this complex interaction in an organism consisting of a single excitable and motile cell,Paramecium. The behavior ofParameciumis based on trial and error: when it encounters an undesirable situation, it backs up and changes direction. This avoiding reaction is triggered by an action potential. Here we developed an empirically constrained biophysical model ofParamecium’s action potential, which we then coupled to its kinematics. We then demonstrate the potential of this model in investigating various types of autonomous behavior, such as obstacle avoidance, gradient-following and collective behavior.
Finding coarse and fine scale population structure in a coastal species: population demographics meets genomics
Authors: Catarino Diana , Jorde Per Erik , Rogers Lauren , Albretsen Jon , Jahnke Marlene , Sodeland Marte , Mellerud Ida , Andre Carl , Knutsen Halvor 
Published: February 2022

AbstractPopulation genetic studies often focus on patterns at a regional scale and use spatially aggregated samples to draw inferences about population structure and drivers, potentially masking ecologically relevant population sub-structure and dynamics. In this study we use a multidisciplinary approach combining genomic, demographic, and habitat data with an oceanographic particle drift model, to unravel the patterns of genetic structure at different scales in the black goby (Gobius niger) along the Norwegian coast. Using a high-density sampling protocol, we observed restricted gene flow both at a surprisingly fine (kms) and large (100s km) scale. Our results showed a pattern of isolation by distance related to the level of exposure along the Skagerrak coast, where sheltered sampling stations had an overall level of genetic divergence about three times higher (FST =0.0046) than levels observed among exposed samples (FST =0.0015). These results were corroborated by demographic analyses which showed that population-fluctuations decrease in synchrony with distance at much smaller scales for sheltered samples (20 km) than for exposed sites (80 km), suggesting higher population connectivity among exposed sites. We also found a pronounced genetic discontinuity between populations along the Norwegian west and east coasts, with a sharp “break” around the southern tip of Norway, likely driven both by lack of habitat and by oceanographic features.
An efficient early-pooling protocol for environmental DNA metabarcoding
Authors: Ushio Masayuki , Furukawa Saori , Murakami Hiroaki , Masuda Reiji , Nagano Atsushi J. 
Published: February 2022

AbstractEnvironmental DNA (eDNA) metabarcoding, a method that applies high-throughput sequencing and universal primer sets to eDNA analysis, has been a promising approach for efficient, comprehensive biodiversity monitoring. However, significant money-, labor-, and time-costs are still required for performing eDNA metabarcoding. In the present study, we assessed the performance of an “early-pooling” protocol (a protocol based on the 1st PCR indexing) to reduce the experimental costs of the library preparation for eDNA metabarcoding. Specifically, we performed three experiments to test the effects of 1st PCR and 2nd PCR indexing protocols on the community composition revealed by eDNA metabarcoding, of post-1st-PCR exonuclease purification on index-hopping, and of the number of PCR replicates and eDNA template volume on the number of detected OTUs. By analyzing 204 eDNA libraries from 3 natural aquatic ecosystems and 1 mock eDNA sample, we show that (i) the 1st PCR indexing does not cause clear biases in the outcomes of eDNA metabarcoding, (ii) post-1st-PCR exonuclease purification reduces the risk of index-hopping, and (iii) increasing the eDNA template volume can increase the number of detected OTUs and reduce the variations in detected community compositions, as can increasing the number of the 1st PCR replicates. Our results show that an early-pooling protocol with post-1st-PCR exonuclease purification and an increased amount of DNA template will reduce the risk of index-hopping, the costs for consumables and reagents, and the handling time in the library preparation, and that it produces comparable results to a 2nd-PCR-indexing protocol. Therefore, once a target metabarcoding region is determined and a set of indexed-1st-PCR primers is prepared, the early-pooling protocol provides a cost-, labor-, and time-efficient way to process a large number of samples.
Task-specific effects of biological sex and sex hormones on object recognition memories in a 6-hydroxydopamine-lesion model of Parkinson’s disease in adult male and female rats
Authors: Pinizzotto Claudia C. , Patwardhan Aishwarya , Aldarondo Daniel , Kritzer Mary F. 
Published: February 2022

ABSTRACTMany patients with Parkinson’s disease (PD) experience impairments in cognition and memory with few therapeutic options currently available to mitigate them. This has fueled interest in determining how factors including biological sex and sex hormones might modulate higher order function in PD. Previous studies have investigated this in female rats and in gonadally intact and gonadectomized males, with and without hormone replacement, that received bilateral neostriatal 6-hydroxydopamine (6-OHDA) lesions to model PD. Barnes maze and What Where When Episodic-like memory testing showed that 6-OHDA lesions disrupted spatial working and episodic memory functions in both sexes, and that in males, androgen-sensitive behaviors could be rescued in subjects where circulating androgen levels were diminished. Here we tested similar animal groups using the Novel Object Preference (NOP) and Object-in-Place (OiP) tasks. This revealed two entirely different patterns of sex and sex hormone influence. First, for both tasks, 6-ODHA lesions impaired object discrimination in males but not females. Further, for the NOP task, 6-OHDA lesions disrupted discrimination in males rats independently of hormone status. And finally, 6-OHDA lesions impaired OiP performance in males regardless of whether androgen levels were high or low but had no effect on discrimination in gonadectomized rats given 17β-estradiol. Together with previous findings, these data identify the impacts of sex and sex hormones on cognition and memory in PD as behavioral task/behavioral domain specific. This specificity could explain why a cohesive clinical picture of endocrine impacts on higher order function in PD has remained elusive.HIGHLIGHTS6-OHDA lesions impair Novel Object performance in male but not female rats.6-OHDA lesions impair Object-in-Place performance in male but not female rats.Gonadectomy has no effect on 6-OHDA-induced deficits in Novel Object Preference.Estrogen replacement prevents 6-OHDA-induced Object-in-Place deficits in males.