bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inertial Focusing of Particles and Cells in the Microfluidic Labyrinth Device: Role of Sharp Turns
Authors: Gangadhar Anirudh , Vanapalli Siva A. 
Published: June 2022

AbstractInertial, size-based focusing was investigated in the microfluidic labyrinth device consisting of several U-shaped turns along with circular loops. Turns are associated with tight curvature, and therefore induce strong Dean forces for separating particles, however, systematic studies exploring this possibility do not exist. We characterized the focusing dynamics of different-sized rigid particles, cancer cells and white blood cells over a range of fluid Reynolds numbers Ref. Streak widths of the focused particle streams at all the turns showed intermittent fluctuations which were substantial for smaller particles and at higher Ref. In contrast, cell streaks were less prone to fluctuations. Computational fluid dynamics simulations revealed the existence of strong turn-induced Dean vortices which help explain the intermittent fluctuations seen in particle focusing. Next, we developed a measure of pairwise separability to evaluate the quality of separation between focused streams of two different particle sizes. Using this, we assessed the impact of a single sharp turn on separation. In general, the separability was found to vary significantly as particles traversed the tight-curvature U-turn. Comparing the separability at the entry and exit sections, we found that turns either improved or reduced separation between different-sized particles depending on Ref. Finally, we evaluated the separability at the downstream expansion section to quantify the performance of the labyrinth device in terms of achieving size-based enrichment of particles and cells. Overall, our results show that turns are better for cell focusing and separation given that they are more immune to curvature-driven fluctuations in comparison to rigid particles.
Gene expression patterns associated with fin shape differ between two lamprologine cichlids
Authors: Ahi Ehsan Pashay , Richter Florian , Sefc Kristina M. 
Published: June 2022

AbstractComparing gene regulatory patterns between seemingly similar phenotypic traits can provide important insights on the molecular mechanisms underlying the evolution of those traits. In this study, we investigate the molecular basis of the formation of a spade-shaped caudal fin, which is a rare phenotype among teleost fish characterized by an elongated medial region of the fin. We examined the expression patterns of candidate fin-shape genes in the spade-shaped caudal fin of the related speciesLamprologus tigripictilis, an East African cichlid in the tribe Lamprologini. The candidate gene set consisted of a previously identified gene regulatory network (GRN) associated with the elongation of fin regions in another Lamprologini cichlid species and further genes selected on the basis of co-expression data and transcription factor prediction. Unexpectedly, the anatomical features of elongated fin rays differed and gene expression patterns associated with fin elongation were only weakly conserved between the two related species. We report 20 genes and transcription factors (includingangptl5, cd63, csrp1a, cx43, esco2, gbf1andrbpj), whose expression levels differed between the elongated and the short caudal fin regions ofL. tigripictilis, and which are therefore candidates for the regulation of the spade-like fin shape.
Understanding spatiotemporal effects of food supplementation on host-parasite interactions using community-based science
Authors: Knutie Sarah A. , Bahouth Rachel , Bertone Matthew A. , Webb Caroline , Mehta Mahima , Nahom Mia , Barta Rachael M. , Ghai Sharan , Love Ashley C. , Horan Sydney , Soldo Alexandria , Cochrane Elizabeth , Bartholomew Jenna , Cowan Emily , Bjerke Heather , Balenger Susan L. , Butler Michael W. , Cornell Allison , Kennedy Ashley C. , Rolland Virginie , Schultz Elizabeth M. , Stanback Mark , Taff Conor C. , Albery Gregory F. 
Published: June 2022

AbstractSupplemental feeding can increase the overall health of animals but also can have variable effects on how animals defend themselves against parasites. However, the spatiotemporal effects of food supplementation on host-parasite interactions remain poorly understood, likely because large-scale, coordinated efforts are difficult.Here, we introduce the Nest Parasite Community Science Project, which is a community-based science project that coordinates studies with bird nest box “stewards” from the public and scientific community. This project was established to understand broad ecological patterns between hosts and their parasites.The goal of this study was to determine the effect of food supplementation on eastern bluebirds (Sialia sialis) and their nest parasite community across the geographic range of the bluebirds from 2018–2021. We received 646 nests from 68 stewards in 26 states in the eastern United States. Nest box stewards reported whether or not they fed their bluebirds mealworms or suet, then followed the nesting success of the birds (number of eggs laid and hatched, percent hatched, number and percent fledged). We then identified and quantified parasites in the nests.We found that food supplementation increased fledgling numbers and proportional fledging success. The main nest parasite taxa were parasitic blow flies (Protocalliphora sialia), but a few nests contained fleas (Ceratophyllus idius, C. gallinae, Orchopeas leucopus) and mites (Dermanyssusspp. andOrnithonyssusspp.). Blow flies were primarily found at northern latitudes, where food supplementation affected blow fly abundance. However, the direction of this effect varied substantially in direction and magnitude across years. More stewards fed bluebirds at southern latitudes than at northern latitudes, which contradicted the findings of other community-based science projects.Overall, food supplementation of birds was associated with increased host fitness but did not appear to play a consistent role in defense against these parasites across all years. Our study demonstrates the importance of coordinated studies across years and locations to understand the effects of environmental heterogeneity, including human-based food supplementation, on host-parasite dynamics. Studies during a single year or considering only a single population might not provide the necessary data to develop management strategies for species.
Feasibility of 3T layer-dependent fMRI with GE-BOLD using NORDIC and phase regression
Authors: Knudsen Lasse , Bailey Christopher J. , Blicher Jakob U. , Yang Yan , Zhang Peng , Lund Torben E. 
Published: June 2022

AbstractIntroductionFunctional MRI with spatial resolution in the submillimeter domain enables measurements of activation across cortical layers in humans. This is valuable as different types of cortical computations, e.g., feedforward versus feedback related activity, take place in different cortical layers. Layer-dependent fMRI (L-fMRI) studies have almost exclusively employed 7T scanners to overcome the reduced signal stability associated with small voxels. However, such systems are relatively rare and only a subset of those are clinically approved. In the present study, we examined the feasibility of L-fMRI at 3T using NORDIC denoising.Methods5 healthy subjects were scanned on a Siemens MAGNETOM Prisma 3T scanner. To assess across-session reliability, each subject was scanned in 3-8 sessions on 3-4 consecutive days. A 3D gradient echo EPI (GE-EPI) sequence was used for BOLD acquisitions (voxel size 0.82 mm isotopic, TR = 2.2 s) using a block designed finger tapping paradigm. NORDIC denoising was applied to the magnitude and phase time series to overcome limitations in tSNR and the denoised phase time series were subsequently used to correct for large vein contamination through phase regression.Results and conclusionNORDIC denoising resulted in temporal signal-to-noise ratio (tSNR) values comparable to or higher than commonly observed at 7T. Layer-dependent activation profiles could thus be extracted robustly, within and across sessions, from regions of interest located in the hand knob of the primary motor cortex (M1). Phase regression led to substantially reduced superficial bias in obtained layer profiles, although residual macrovascular contribution remained. We believe the present results support the feasibility of L-fMRI at 3T, which might help make L-fMRI available to a much wider community.
Mutations in OsRZF1, encoding a zinc-finger protein, causes reduced magnesium uptake in roots and translocation to shoots in rice
Authors: Kobayashi Natsuko I. , Takagi Hiroki , Yang Xiaoyu , Nishizawa-Yokoi Ayako , Hoshina Tatsuaki , Oonishi Takayuki , Suzuki Hisashi , Iwata Ren , Toki Seiichi , Nakanishi Tomoko M. , Tanoi Keitaro 
Published: June 2022

AbstractMagnesium (Mg) homeostasis is critical for maintaining many biological processes, but little information is available to comprehend the molecular mechanisms regulating Mg concentration in rice (Oryza sativa). To make up for the lack of information, we aimed to identify mutants defective in Mg homeostasis through a forward genetic approach. As a result of the screening of about 3,000 M2 seedlings mutated by ion-beam irradiation, we found a rice mutant that showed reduced Mg content in leaves and slightly increased Mg content in roots. Radiotracer 28Mg experiments showed that this mutant, named low magnesium content 1 (LMGC1), has decreased Mg2+ influx in the root and Mg2+ translocation from root to shoot. The MutMap method identified 7.4 kbp deletion in the LMGC1 genome leading to a loss of two genes. Genome editing using CRISPR-Cas9 further revealed that one of the two lost genes, a gene belonging to RanBP2-type zinc finger family, was the causal gene of the low-Mg phenotype. Considering this gene, named OsRZF1, has never been reported to be involved in ion transport, the phenotype of LMGC1 would be associated with a novel mechanism of Mg homeostasis in plants.
Data-driven machine learning for pattern recognition supports environmental quality prediction for irrigated rice in Brazil
Authors: Costa-Neto Germano , da Matta David Henriques , Kuivjogi Fernandes Igor , Stone Luís Fernando , Heinemann Alexandre Bryan 
Published: June 2022

ABSTRACTThe sustainability of irrigated rice (Oryza sativa L.) production systems in Brazilian tropical region highly depends on the success of developing stable cultivars. To achieve this goal, many steps in product development must address the environmental variability and genotype by environment interactions (GE), which makes difficult the design and development of local-specific adapted cultivars. Thus, the adoption of new strategies for characterizing environmental-phenotype relations are the key for optimizing this process. In addition, it could also benefit post-breeding stages of seed production. To overcome this situation, we implemented a data-driven approach to link environmental characterization to yield clustering using historical data (1982-2017, 31 locations, 471 genotypes), 42 envirotyping covariables and machine learning (ML), combining two unsupervised (K-means and decision tree models, DTC) algorithms. Additionally, linear mixed models (LMM) were applied to explore the relations between the outcomes of our approach and GE analysis for irrigated rice yield in Brazilian tropical region. Four environments were identified: Very Low Yield (1.7 Mg.ha-1), Low Yield (5.1 Mg.ha-1), High Yield (7.2 Mg.ha-1), and Very High Yield (9.0 Mg.ha-1), considering all genotypes and regions. Our approach allows the prediction of environments (yield clusters) for a diverse set of growing conditions and revealed geographic and climatic causes of environmental quality, which differ according to each region and genotype group. From the LMM analysis, we found that the current relation between genetics (G), environmental variation (E), and GE for rainfed rice in Brazil is 1:6:2, but when we introduced our data-driven clusters (ME), the ratio decreased to 1:5:1. Consequently, the selection reliability for local adaptability across an extensive region increases. Our approach helps to identify mega-environments in Brazil that could be used as a target population of environments (TPE) of breeding programs. Additionally, it helps to identify more productive and stable seed production fields.HighlightsA nationwide environmental characterization and its relation to the genotype by environment interaction (GE) for grain yield of rainfed rice growing regions in Brazil.A data-driven approach capable to identifying clusters of yield levels and a machine learning approach to relate those clusters with environmental typologies.Unrevealed geographic and climatic causes of environmental quality for a group of genotypes or cultivar-specific predictions.The strategy benefits diverse stages of breeding (multiple environmental trial analysis) and post-breeding (selection of fields for seed production) as an alternative approach to reduce costs and support decisions on cultivar planting locations.
600+ insect genomes reveal repetitive element dynamics and highlight biodiversity-scale repeat annotation challenges
Authors: Sproul John S. , Hotaling Scott , Heckenhauer Jacqueline , Powell Ashlyn , Marshall Dez , Larracuente Amanda M. , Kelley Joanna L. , Pauls Steffen U. , Frandsen Paul B. 
Published: June 2022

AbstractRepetitive elements (REs) are integral to the composition, structure, and function of eukaryotic genomes, yet remain understudied in most taxonomic groups. We investigated REs across 601 insect species and report wide variation in REs dynamics across groups. Analysis of associations between REs and protein-coding genes revealed dynamic evolution at the interface between REs and coding regions across insects, including notably elevated RE-gene associations in lineages with abundant long interspersed nuclear elements (LINEs). We leveraged this large, empirical data set to quantify impacts of long-read technology on RE detection and investigate fundamental challenges to RE annotation in diverse groups. In long-read assemblies we detected ∼36% more REs than short-read assemblies, with long terminal repeats (LTRs) showing 162% increased detection, while DNA transposons and LINEs showed less respective technology-related bias. In most insect lineages, 25–85% of repetitive sequences were “unclassified” following automated annotation, compared to only ∼13% inDrosophilaspecies. Although the diversity of available insect genomes has rapidly expanded, we show the rate of community contributions to RE databases has not kept pace, preventing efficient annotation and high-resolution study of REs in most groups. We highlight the tremendous opportunity and need for the biodiversity genomics field to embrace REs and suggest collective steps for making progress towards this goal.
Ploidy variation and spontaneous haploid-diploid switching of Candida glabrata clinical isolates
Authors: Zheng Qiushi , Liu Jing , Qin Juanxiu , Wang Bingjie , Bing Jian , Du Han , Li Min , Yu Fangyou , Huang Guanghua 
Published: June 2022

AbstractThe human fungal pathogen Candida glabrata is phylogenetically closely related to Saccharomyces cerevisiae, a model eukaryotic organism. Unlike S. cerevisiae with both haploid and diploid forms and a complete sexual cycle, C. glabrata has long been considered a haploid and asexual species. In this study, we analyzed the ploidy states of 500 clinical isolates of C. glabrata from four Chinese hospitals and found that approximately 4% of the isolates were in or able to spontaneously switch to an aneuploidy (genomic DNA: 1N-2N), diploidy (2N), or hyperdiploid (>2N) form under in vivo or in vitro conditions. Stable diploid-form cells were identified in 3% of the isolates (15/500). Of particular interest, one clinical strain only existed in the diploid form. Multilocus sequence typing (MLST) assays revealed two major genetic clusters (A and B) of C. glabrata isolates. Most of the isolates (70%) from China belonged to the A cluster, whereas most of the isolates from other countries (such as Iran, Japan, USA, and European countries) belonged to the B cluster. Further investigation indicated that C. glabrata cells of different ploidy forms differed in a number of aspects, including morphologies, antifungal susceptibility, virulence, and global gene expression profiles. Additionally, C. glabrata could undergo spontaneous switching between the diploid and haploid form under both in vitro and in vivo conditions. Given the absence of an apparent sexual phase, one would expect that the ploidy shifts could function as an alternative strategy that promotes genetic diversity and benefits the ability of the fungus to rapidly adapt to the changing environment.ImportanceThe human fungal pathogen Candida glabrata has long been thought to be a haploid organism. Here we report the population structure and ploidy states of 500 clinical isolates of C. glabrata from China. To our surprise, we found that the ploidy of a subset of clinical isolates varied dramatically. Some isolates were in or able to switch to an aneuploid, diploid, or hyperdiploid form. C. glabrata cells with different ploidy differed in a number of biological aspects, including morphologies, antifungal susceptibility, virulence, and global gene expression profiles. Given the absence of an apparent sexual phase in this fungus, we propose that ploidy switching could be a rapid adaption strategy to environmental changes and could function as an alternative strategy of sexual reproduction.
Pseudomonas aeruginosa strains from both clinical and environmental origins readily adopt a stable small colony variant (SCV) phenotype resulting from single mutations in c-di-GMP pathways
Authors: Besse Alison , Groleau Marie-Christine , Trottier Mylène , Vincent Antony T. , Déziel Eric 
Published: June 2022

ABSTRACTA subpopulation of Small Colony Variants (SCVs) is a frequently observed feature of Pseudomonas aeruginosa isolated from colonized cystic fibrosis lungs. Since most SCVs have until now been isolated from clinical samples, it remains unclear how widespread is the ability of P. aeruginosa to develop this phenotype and the genetic mechanism(s) behind SCVs emergence according to the origin of the isolate. In the present work, we investigated the ability of 22 P. aeruginosa isolates from various environmental origins to, under laboratory culture conditions, spontaneously adopt a SCV-like smaller alternative morphotype distinguishable from the ancestral parent strain. We found that all the P. aeruginosa strains tested could adopt a SCV phenotype, regardless of their origin. Whole genome sequencing of SCVs obtained from clinical and environmental sources revealed single mutations exclusively in two distinct c-di-GMP signaling pathways, Wsp and YfiBNR. We conclude that the ability to switch to a SCV phenotype is a conserved feature of P. aeruginosa and results from the acquisition of a stable genetic mutation, regardless of the origin of the strain.IMPORTANCEP. aeruginosa is an opportunistic pathogen that thrives in many environments. It poses a significant health concern, notably because this bacterium is the most prevalent pathogen found in the lungs of people with cystic fibrosis. In infected hosts, its persistence is considered related to the emergence of an alternative small colony variant (SCV) phenotype. By reporting the distribution of P. aeruginosa SCVs in various non-clinical environments and the involvement of c-di-GMP in SCV emergence from both clinical and environmental strains, this work contributes to understanding a conserved adaptation mechanism used by P. aeruginosa to adapt readily in all environments. Hindering this adaptation strategy could help control P. aeruginosa persistent infection.
Gargle sample is an effective option in a novel fully automated molecular point-of-care test for influenza: a multicenter study
Authors: Kaku Norihito , Urabe Tomohito , Iida Tetsuya , Yun Chyuns , Nishida Yoshiyuki , Onitsuka Yasunori , Hashiguchi Kohji , Hirose Kiyoto , Tomonaga Akimitsu , Izumikawa Koichi , Mukae Hiroshi , Yanagihara Katsunori 
Published: June 2022

AbstractBackgroundWe conducted a multicenter study to evaluate the performance of a novel fully automated molecular point-of-care test using transcription-reverse transcription concerted reaction that can detect influenza A and B within 15 minutes in nasopharyngeal swabs and gargle samples (TRCsatFLU).MethodsPatients who visited or were hospitalized at eight clinics and hospitals with influenza-like illnesses between December 2019 and March 2020 participated in this study. We collected nasopharyngeal swabs from all patients and gargle samples from patients whom the physician judged fit to perform gargling. The result of TRCsatFLU was compared to a conventional reverse transcription-polymerase chain reaction (RT-PCR). If the results of TRCsatFLU and conventional RT-PCR were different, the samples were analyzed by sequencing.ResultsWe evaluated 233 nasopharyngeal swabs and 213 gargle samples from 244 patients.. The average age of the patients was 39.3 ± 21.2. Of the patients, 68.9% visited a hospital within 24 h of symptom onset. The most common symptoms were fever (93.0%), fatigue (79.5%), and nasal discharge (64.8%). All patients in whom the gargle sample was not collected were children. Influenza A or B was detected in 98 and 99 patients in nasopharyngeal swabs and gargle samples using TRCsatFLU, respectively. Four and five patients in nasopharyngeal swabs and gargle samples, respectively, with different TRCsatFLU and conventional RT-PCR results. Influenza A or B was detected using sequencing in all samples with different results. Based on the combined conventional RT-PCR and sequencing results, the sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of TRCsatFLU for influenza detection in nasopharyngeal swabs were 0.990, 1.000, 1.000, and 0.993, respectively. In the gargle samples, the sensitivity, specificity, PPV, and NPV of the TRCsatFLU for detecting influenza were 0.971, 1.000, 1.000, and 0.974, respectively.ConclusionsThe TRCsatFLU showed great sensitivity and specificity for the detection of influenza in nasopharyngeal swabs and gargle samples.Trial registrationThis study was registered in the UMIN Clinical Trials Registry (reference number: UMIN000038276) on October 11, 2019. Before sample collection, written informed consent for the participation and publication of this study was obtained from all participants.