bluuebunny/crossref_metadata_2025_split huggingface dataset:
Atlantic Cod as an indicator of rapid climate change
Authors: Choi Jae S. 
Published: May 2022

AbstractAtlantic cod (Gadus morhua) in the northwest Atlantic has become the textbook example of overfishing. However, this narrative has blinded us from the larger environmental context of this decline. Cod prefer cold and shallow habitats, environments that are also the most susceptible to rapid climate change. Cod habitat deterioration was evident well before their numerical decline, and as such, cod was a harbinger of rapid climate change. Recovery requires their habitat quality to first improve and stabilize. Calls for a cull of seals, the consensus actor causing the lack of recovery of cod, may therefore be unwise. Recovery will only occur once the variability associated with rapid climate change subsides and habitat quality improves. The timeline for this is of course unknown.One-Sentence SummaryWas the decline of cod a harbinger of rapid climate change in the northwest Atlantic?
The arthropod associates of 155 North American cynipid oak galls
Authors: Ward Anna K.G. , Busbee Robert W. , Chen Rachel A. , Davis Charles K. , Driscoe Amanda L. , Egan Scott P. , Goldberg Bailey A.R. , Hood Glen Ray , Jones Dylan G. , Kranz Adam J. , Meadely Dunphy Shannon A. , Milks Alyson K. , Ott James R. , Prior Kirsten M. , Sheikh Sofia I. , Shzu Shihan , Weinersmith Kelly L. , Zhang Linyi , Zhang Y. Miles , Forbes Andrew A. 
Published: May 2022

AbstractThe identities of most arthropod associates of cynipid-induced oak galls in the western Palearctic are generally known. However, a comprehensive accounting of associates has been performed for only a small number of the galls induced by the estimated 700 species of cynipid gall wasp in the Nearctic. This gap in knowledge stymies many potential studies of diversity, coevolution, and community ecology, for which oak gall systems are otherwise ideal models. We report rearing records of insects and other arthropods from more than 527,306 individual galls representing 201 different oak gall types collected from 32 oak tree species in North America. Of the 201 gall types collected, 155 produced one or more animals. A total of 151,075 animals were found in association with these 155 gall types, and of these 61,044 (40.4%) were gall wasps while 90,031 (59.6%) were other arthropods. We identified all animals to superfamily, family, or, where possible, to genus. We provide raw numbers and summaries of collections, alongside notes on natural history, ecology, and previously published associations for each taxon. For eight common gall-associated genera (Synergus,Ceroptres,Euceroptres,Ormyrus,Torymus,Eurytoma,Sycophila, andEuderus), we also connect rearing records to gall wasp phylogeny, geography, and ecology - including host tree and gall location (host organ), and their co-occurrence with other insect genera. Though the diversity of gall wasps and the large size of these communities is such that many Nearctic oak gall-associated insects still remain undescribed, this large collection and identification effort should facilitate the testing of new and varied ecological and evolutionary hypotheses in Nearctic oak galls.
Clinical Features and Outcomes of COVID-19 at a Teaching Hospital in Kingston, Jamaica
Authors: Thompson Tamara , Dawkins Yvonne , Rowe-Gardener Swane , Chin-Harty Lisa , Hoe Kyaw Kyaw , Ferguson Trevor S. , Ehikhametalor Kelvin , Gordon-Johnson Kelly Ann , Deyde Varough 
Published: May 2022

AbstractObjectiveWe examined the demographic, clinical characteristics and indicators of poor outcomes among hospitalized adults with COVID-19 at the University Hospital of the West Indies, Jamaica.MethodsA retrospective medical record review between March 10 and December 31, 2020 analyzed data for 362 participants.ResultsThere were 218 males (mean age 59.5 years) and 144 females (mean age 55.7 years). Hypertension, diabetes mellitus, cardiovascular disease, obesity and chronic kidney disease were the most common comorbidities. Cough, shortness of breath, fever and malaise were the most common presenting complaints. Fifty-one percent of patients were moderately to severely ill on admission; 11% were critically ill; 18% were admitted to the Intensive Care Unit (ICU). Death occurred in 62 (17%) patients (95% CI 13.6-21.4%). Among obese participants, there were increased odds of developing respiratory failure (OR 5.2, p < 0.001), acute kidney injury (OR 4.7, p < 0.001), sepsis (OR 2.9, p =0.013) and the need for ICU care (OR 3.7, p < 0.001). Factors independently associated with increased odds of death were age (OR 1.03 per year, p = 0.013) and obesity (OR 2.26, p = 0.017). Mortality also correlated significantly with D-dimer > 1000 ng/ml (OR 2.78; p = 0.03), serum albumin < 40 g/L (OR 3.54; p = 0.03) and serum LDH > 485 U/L OR 1.92, p = 0.11).ConclusionsTargeted interventions among these high-risk patient subgroups may reduce in-patient morbidity and mortality.
Cognitive improvement after dual-task training in Parkinson’s disease: a follow-up study
Authors: Szögedi Dalma , Stone Trevor W. , Dinya Elek , Málly Judit 
Published: May 2022

AbstractThe reaction times of patients with Parkinson’s disease (PD) in tests of simultaneous dual-task accuracy are dependent on the subjects’ cognitive ability. We now report that one week training on dual-task tests improved cognitive function. Forty-six PD patients were compared with 47 age matched healthy controls and 26 patients were followed for one year. Five dual-task tests consisting of a primary cognitive task to be performed simultaneously with a secondary motor task were repeated for five consecutive days. Testing was repeated after 6 and 12 months. Participants’ reaction times, including Hits and Misses, were quantified. Initial tests indicated slower reaction times in patients compared to controls, with fewer Hits and more Misses, especially in PD patients over 65 years of age. Training by daily repeated dual-task tests improved performance within 3 days (p < 0. 01 or p < 0.001), with no deterioration after 6 months. We conclude that dual-tasks are objective and sensitive tests for detecting early cognitive difficulties in PD, with improvements in both by repeated exposure to testing. A few days of testing produced cognitive improvement lasting many months. It is recommended that the use of simultaneous, dual-task testing is used to produce long-lasting improvement of cognitive function in PD patients.
Quantitative environmental DNA metabarcoding shows high potential as a novel approach to quantitatively assess fish community
Authors: Tsuji Satsuki , Inui Ryutei , Nakao Ryohei , Miyazono Seiji , Saito Minoru , Kono Takanori , Akamatsu Yoshihisa 
Published: May 2022

AbstractThe simultaneous conservation of species richness and evenness is important to effectively reduce biodiversity loss and keep ecosystem health. Environmental DNA (eDNA) metabarcoding has been used as a powerful tool for identifying community composition, but it does not necessarily provide quantitative information due to several methodological limitations. Thus, the quantification of eDNA through metabarcoding is an important frontier of eDNA-based biomonitoring. Particularly, the qMiSeq approach has recently been developed as a quantitative metabarcoding method and has attracted much attention due to its usefulness. The aim here was to evaluate the performance of the qMiSeq approach as a quantitative monitoring tool for fish communities by comparing the quantified eDNA concentrations with the results of fish capture surveys. The eDNA water sampling and the capture surveys using the electrical shocker were conducted at a total of 21 sites in four rivers in Japan. As a result, we found significant positive relationships between eDNA concentrations of each species quantified by qMiSeq and both the abundance and biomass of each captured taxon at each site. Furthermore, for seven out of eleven taxa, a significant positive relationship was observed between quantified DNA concentrations by sample and the abundance and/or biomass. In total, our results demonstrated that eDNA metabarcoding with the qMiSeq approach is a suitable and useful tool for quantitative monitoring of fish communities. Due to the simplicity of the eDNA analysis, the eDNA metabarcoding with qMiSeq approach would promote further growth of quantitative monitoring of biodiversity.HighlightseDNA analysis and capture surveys of fishes were conducted at a total of 21 sites.Quantitative eDNA metabarcoding (qMiSeq) successfully quantified the eDNA of fishes.For each site, the estimated eDNA conc. reflected the abundance and biomass of fishes.For each taxon, the estimated eDNA conc. were comparable among sites.qMiSeq is a suitable and useful tool for quantitative monitoring of fish community.
CLARITY increases sensitivity and specificity of fluorescence immunostaining in long-term archived human brain tissue
Authors: Woelfle Sarah , Deshpande Dhruva , Feldengut Simone , Roselli Francesco , Deisseroth Karl , Michaelis Jens , Boeckers Tobias M. , Schön Michael 
Published: May 2022

AbstractImmunohistochemistry on archival human brains is often limited because several conditions arise that complicate the use for high-resolution fluorescence microscopy. In this study, we developed a novel clearing approach for immunofluorescence-based analysis of perfusion- and immersion-fixed post mortem human brain tissue, termed hCLARITY. hCLARITY is optimized for specificity by reducing off-target labeling and yields very sensitive stainings in human brain sections allowing for super-resolution microscopy with unprecedented imaging of pre- and postsynaptic compartments. Moreover, hallmarks of the Alzheimer’s disease were preserved with hCLARITY, and importantly classical DAB or Nissl stainings are compatible with this protocol. hCLARITY is extremely versatile as demonstrated by the use of more than 30 well performing antibodies and allows for de- and subsequent re-staining of the same tissue section, which is important for multi-labelling approaches, e.g., in super-resolution microscopy. Taken together, hCLARITY enables research of the human brain with highest sensitivity and down to sub-diffraction resolution and therefore has enormous potential for the investigation of local morphological changes, e.g., in neurodegenerative diseases.Striking Image / Graphical abstractSummary of the main advantages of hCLARITY. CLARITY was applied on human post mortem brain tissue in direct comparison to untreated sections (minus CLARITY). Owing to removal of lipids during the clearing with SDS and the resulting reduction in light scattering, cleared sections were less opaque. The denaturing effect of the detergent SDS most likely results in better accessibility of certain epitopes. The major benefits of hCLARITY were found in an increased sensitivity and specificity of antibodies for neuronal cells. The adapted hCLARITY protocol is compatible with staining techniques for confocal microscopy, super-resolution microscopy, and light microscopy.
Stem cell heterogeneity and reiteration of developmental signaling underlie melanocyte regeneration in zebrafish
Authors: Frantz William Tyler , Iyengar Sharanya , Neiswender James , Cousineau Alyssa , Maehr Rene , Ceol Craig J. 
Published: May 2022

AbstractTissue-resident stem cells are present in many adult organs, where they are important for organ homeostasis and repair in response to injury. However, the signals that activate these cells and the mechanisms governing how these cells self-renew or differentiate are highly context-dependent and incompletely understood, particularly in non-hematopoietic tissues. In the skin, melanocyte stem cells (McSCs) are responsible for replenishing mature pigmented melanocytes. In mammals, these cells reside in the hair follicle bulge and bulb niches where they are activated during homeostatic hair follicle turnover and following melanocyte destruction, as occurs in vitiligo and other skin hypopigmentation disorders. Recently, we identified adult McSCs in the zebrafish. To elucidate mechanisms governing McSC self-renewal and differentiation we analyzed individual transcriptomes from thousands of melanocyte lineage cells during the regeneration process. We identified transcriptional signatures for McSCs, deciphered transcriptional changes and intermediate cell states during regeneration, and analyzed cell-cell signaling changes to discover mechanisms governing melanocyte regeneration. We identified KIT signaling via the RAS/MAPK pathway as a regulator of McSC direct differentiation. Analysis of the scRNAseq dataset also revealed a population of mitfa/aox5 co-expressing cells that divides following melanocyte destruction, likely corresponding to cells that undergo self-renewal. Our findings show how activation of different subpopulations of mitfa-positive cells underlies self-renewal and differentiation to properly reconstitute the melanocyte pigmentary system following injury.
Powdery mildew effectors AVRA1and BEC1016 target the ER J-domain proteinHvERdj3B required for immunity in barley
Authors: Li Zizhang , Velásquez-Zapata Valeria , Elmore J. Mitch , Li Xuan , Xie Wenjun , Deb Sohini , Tian Xiao , Banerjee Sagnik , Jørgensen Hans J. L. , Pedersen Carsten , Wise Roger P. , Thordal-Christensen Hans 
Published: May 2022

ABSTRACTThe barley powdery mildew fungus,Blumeria hordei(Bh), secretes hundreds of candidate secreted effector proteins (CSEPs) to facilitate pathogen infection and colonization. One of these, CSEP0008, is directly recognized by the barley nucleotide-binding leucine-rich-repeat (NLR) receptor, MLA1, and therefore designated AVRA1. Here we show that AVRA1and the sequence-unrelatedBheffector BEC1016 (CSEP0491) suppress immunity in barley. We used yeast two-hybrid next-generation interaction screens (Y2H-NGIS), followed by binary Y2H andin plantaprotein-protein interactions studies, and identified a common barley target of AVRA1and BEC1016, the endoplasmic reticulum (ER)-localized J-domain protein,HvERdj3B. Silencing of this ER quality control (ERQC) protein increased theBhpenetration.HvERdj3B is ER luminal, and we showed using split GFP that AVRA1and BEC1016 translocate into the ER - signal peptide-independently. Silencing ofHvERdj3B and expression the two effectors hampered trafficking of a vacuolar marker through the ER as a shared cellular phenotype, agreeing with the effectors targeting this ERQC component. Together, these results suggest that the barley innate immunity, preventingBhentry into epidermal cells, is dependent on ERQC, which in turn requires the J-domain protein,HvERdj3B, regulated by AVRA1and BEC1016. Plant disease resistance often occurs upon direct or indirect recognition of pathogen effectors by host NLR receptors. Previous work has shown that AVRA1is directly recognized in the cytosol by the immune receptor, MLA1. We speculate that the AVRA1J-domain target being inside the ER, where it is inapproachable by NLRs, has forced the plant to evolve this challenging direct recognition.SIGNIFICANCEThe complex plant immune system is highly dependent on fundamental cellular machineries, such as the endomembrane system and the ER quality control (ERQC), essential for delivery of immunity-associated membrane-bound and endomembrane soluble proteins to their destinations. We now find that pathogen effectors can interact with an ERQC component and suppress immunity, thereby adding to the molecular insight in plant-pathogen interactions.
FASTAptameR 2.0: A Web Tool for Combinatorial Sequence Selections
Authors: Kramer Skyler T. , Gruenke Paige R. , Alam Khalid K. , Xu Dong , Burke Donald H. 
Published: May 2022

AbstractCombinatorial selections are powerful strategies for identifying biopolymers with specific biological, biomedical, or chemical characteristics. Unfortunately, most available software tools for high-throughput sequencing analysis have high entrance barriers for many users because they require extensive programming expertise. FASTAptameR 2.0 is an R-based reimplementation of FASTAptamer designed to minimize this barrier while maintaining the ability to answer complex sequence-level and population-level questions. This opensource toolkit features a user-friendly web tool, interactive graphics, up to 100x faster clustering, an expanded module set, and an extensive user guide. FASTAptameR 2.0 accepts diverse input polymer types and can be applied to any sequence-encoded selection.
Floral humidity as a signal – not a cue – in a nocturnal pollination system
Authors: Dahake Ajinkya , Jain Piyush , Vogt Caleb , Kandalaft William , Stroock Abraham , Raguso Robert A. 
Published: May 2022

AbstractAlthough visual and olfactory floral signals attract pollinators from a distance, at the flower’s threshold, pollinators can use floral humidity as an index cue for nectar presence. We evaluate the role of floral humidity in theDatura wrightii-Manduca sextanocturnal pollination system. In addition to our finding thatM. sextashows strong innate attraction toward humid flowers, we identify the hygrosensing sensillum on their antennae, demonstrate its extreme sensitivity to minute changes in RH, and observe the elimination of moths’ behavioral preference towards humid flowers following experimental occlusion of the sensilla. Despite Manduca’s attraction toward humid flowers, we find that floral humidity is not a reliable cue for nectar presence in this system. While Datura floral headspace sustains an enormous humidity gradient, it is not a consequence of nectar evaporation, but an outcome of gas exchange through floral stomata and is decoupled from nectar presence. Using interdisciplinary tools, we demonstrate the function of floral humidity as an attractive signal, not a cue, in this pollination system, thus showcasing an underappreciated modality by which flowers may manipulate their visitors.
UniTVelo: temporally unified RNA velocity reinforces single-cell trajectory inference
Authors: Gao Mingze , Qiao Chen , Huang Yuanhua 
Published: May 2022

AbstractThe recent breakthrough of single-cell RNA velocity methods brings attractive promises to reveal directed trajectory on cell differentiation, states transition and response to perturbations. However, the existing RNA velocity methods are often found to return erroneous results, partly due to model violation or lack of temporal regularization. Here, we present UniTVelo, a statistical framework of RNA velocity that models the dynamics of spliced and unspliced RNAs via flexible transcription activities. Uniquely, it also supports the inference of a unified latent time across the transcriptome. With ten datasets, we demonstrate that UniTVelo returns the expected trajectory in different biological systems, including hematopoietic differentiation and those even with weak kinetics or complex branches.
The lateral habenula mediates the association of a conditioned stimulus with the absence of an appetitive unconditioned stimulus
Authors: Kim Dong-Hee , Jin In-Beom , Kim Nam-Heon , Jeon Yong-Jae , Choi Bo-Ryoung , Gallagher Michela , Han Jung-Soo 
Published: May 2022

AbstractThe lateral habenula (LHb) has been implicated in conditioned inhibition. Here, the modulating effects of LHb activity on the association of a conditioned stimulus (CS) with the nonoccurrence of an unconditioned stimulus (US) were assessed in vivo using chemogenetic methods. Animals initially received explicitly unpaired CS light and US food presentations. Animals subjected to a retardation-of-acquisition task subsequently underwent light and food pairings, whereas those subjected to a summation task underwent compound light-tone and food pairings. The inhibitory light strength was assessed based on retardation of the acquisition of food-cup conditioned responses (CRs) in light-food pairings and comparisons of food-cup CRs to each stimulus in a CS-alone test following compound training. Neurotoxic LHb lesions and chemogenetic LHb inhibition throughout unpaired training attenuated the inhibitory light strength. Furthermore, chemogenetic LHb activation accelerated the decline in CR induced by repeated light-alone presentations following light-food pairings. Therefore, the LHb critically contributes to conditioned inhibition.
scTopoGAN: unsupervised manifold alignment of single-cell data
Authors: Singh Akash , Reinders Marcel J.T. , Mahfouz Ahmed , Abdelaal Tamim 
Published: May 2022

AbstractMotivationSingle-cell technologies allow deep characterization of different molecular aspects of cells. Integrating these modalities provides a comprehensive view of cellular identity. Current integration methods rely on overlapping features or cells to link datasets measuring different modalities, limiting their application to experiments where different molecular layers are profiled in different subsets of cells.ResultsWe present scTopoGAN, a method for unsupervised manifold alignment of single-cell datasets with non-overlapping cells or features. We use topological autoencoders to obtain latent representations of each modality separately. A topology-guided Generative Adversarial Network then aligns these latent representations into a common space. We show that scTopoGAN outperforms state-of-the-art manifold alignment methods in complete unsupervised settings. Interestingly, the topological autoencoder for individual modalities also showed better performance in preserving the original structure of the data in the low-dimensional representations when compared to other manifold projection methods. Taken together, we show that the concept of topology preservation might be a powerful tool to align multiple single modality datasets, unleashing the potential of multi-omic interpretations of cells.Availability and implementationImplementation available on GitHub (https://github.com/AkashCiel/scTopoGAN). All datasets used in this study are publicly available.Contactt.r.m.abdelaal@lumc.nl