bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel risk factors for Coronavirus disease-associated mucormycosis (CAM): a case control study during the outbreak in India
Authors: Arora Umang , Priyadarshi Megha , Katiyar Varidh , Soneja Manish , Garg Prerna , Gupta Ishan , Bharadiya Vishwesh , Berry Parul , Ghosh Tamoghna , Patel Lajjaben , Sarda Radhika , Garg Shreya , Agarwal Shubham , Arora Veronica , Ramprasad Aishwarya , Kumar Amit , Garg Rohit Kumar , Kodan Parul , Nischal Neeraj , Singh Gagandeep , Jorwal Pankaj , Kumar Arvind , Baitha Upendra , Meena Ved Prakash , Ray Animesh , Sethi Prayas , Xess Immaculata , Vikram Naval , Sinha Sanjeev , Biswas Ashutosh , Thakar Alok , Bhatnagar Sushma , Trikha Anjan , Wig Naveet 
Published: July 2021

AbstractBackgroundThe epidemiology of the Coronavirus-disease associated mucormycosis (CAM) syndemic is poorly elucidated. We aimed to identify risk factors that may explain the burden of cases and help develop preventive strategies.MethodsWe performed a case-control study comparing cases diagnosed with CAM and those who had recovered from COVID-19 without developing mucormycosis (controls). Information on comorbidities, glycemic control, and practices related to COVID-19 prevention and treatment was recorded.Results352 patients (152 cases and 200 controls) diagnosed with COVID-19 during April-May 2021 were included. In the CAM group, symptoms of mucormycosis began a mean 18.9 (SD 9.1) days after onset of COVID-19, and predominantly rhino-sinus and orbital involvement was present. All, but one, CAM cases carried conventional risk factors of diabetes and steroid use. On multivariable regression, increased odds of CAM were associated with the presence of diabetes (adjusted OR 3.5, 95%CI 1.1-11), use of systemic steroids (aOR 7.7,95% CI 2.4-24.7), prolonged use of cloth and surgical masks (vs no mask, aOR 6.9, 95%CI 1.5-33.1), and repeated nasopharyngeal swab testing during the COVID-19 illness (aOR 1.6,95% CI 1.2-2.2). Zinc therapy, probably due to its utility in immune function, was found to be protective (aOR 0.05, 95%CI 0.01-0.19). Notably, the requirement of oxygen supplementation or hospitalization did not affect the risk of CAM.ConclusionJudicious use of steroids and stringent glycemic control are vital to preventing mucormycosis. Use of clean masks, preference for N95 masks if available, and minimizing swab testing after the diagnosis of COVID-19 may further reduce the incidence of CAM.
A yeast lysosomal biogenesis map uncovers the cargo spectrum of lysosomal protein targeting pathways
Authors: Eising Sebastian , Esch Bianca M. , Wälte Mike , Duarte Prado Vargas , Walter Stefan , Ungermann Christian , Bohnert Maria , Fröhlich Florian 
Published: July 2021

AbstractThe lysosome is the major catabolic organelle and a key metabolic signaling center of the cell. Mutations in lysosomal proteins can have catastrophic effects, causing neurodegeneration, cancer, and age-related diseases. The vacuole is the lysosomal analog of Saccharomyces cerevisiae that harbors many conserved proteins. Vacuolar proteins reach their destination via the endosomal vacuolar protein sorting (VPS) pathway, via the alkaline phosphatase (ALP or AP-3) pathway, and via the cytosol-to-vacuole transport (CVT) pathway. While these pathways have been extensively studied, a systematic understanding of the cargo spectrum of each pathway is completely lacking. Here we combine quantitative proteomics of purified vacuoles with mutant analyses to generate the lysosomal biogenesis map. This dataset harbors information on the cargo-receptor relationship of virtually all vacuolar proteins. We map binding motifs of Vps10 and the AP-3 complex and identify a novel cargo of the CVT pathway under nutrient-rich conditions. Our data uncover how organelle purification and quantitative proteomics can uncover fundamental insights into organelle biogenesis.
A dopamine-gated learning circuit underpins reproductive state-dependent odor preference in Drosophila females
Authors: Boehm Ariane C. , Friedrich Anja B. , Hunt Sydney , Bandow Paul , Siju K.P. , De Backer Jean-Francois , Claussen Julia , Link Marie-Helen , Hofmann Thomas F. , Dawid Corinna , Grunwald Kadow Ilona C. 
Published: July 2021

ABSTRACTMotherhood induces a drastic, sometimes long-lasting, change in internal state and behavior in most female animals. How a change in reproductive state or the discrete event of mating modulates specific female behaviors is still incompletely understood. Using calcium imaging of the whole brain of Drosophila females, we find that mating does not induce a global change in brain activity. Instead, mating modulates the pheromone response of dopaminergic neurons innervating the fly’s learning and memory center, the mushroom body (MB). Using the mating-induced increased attraction to the odor of important nutrients, polyamines, we show that disruption of the female fly’s ability to smell, for instance the pheromone cVA, during mating leads to a reduction in polyamine preference for days later indicating that the odor environment at mating lastingly influences female perception and choice behavior. Moreover, dopaminergic neurons including innervation of the β’1 compartment are sufficient to replace mating experience in virgin females inducing the lasting behavioral increase in polyamine preference. We further show that MB output neurons (MBON) of the β’1 compartment are activated by pheromone odor and their activity during mating bidirectionally modulates preference behavior in mated and virgin females. Their activity is not required, however, for the expression of polyamine attraction. Instead, inhibition of another type of MBON innervating the β’2 compartment enables expression of high polyamine attraction. In addition, the response of a lateral horn (LH) neuron, AD1b2, which output is required for the expression of polyamine attraction, shows a modulated polyamine response after mating. Taken together, our data in the fly suggests that mating-related sensory experience regulates female odor perception and expression of choice behavior through a dopamine-gated learning circuit.
A distinct CD115-erythro-myeloid precursor present at the maternal-embryonic interface and in the bone marrow of adult mice
Authors: Tikoo Shweta , Jain Rohit , Martinez Brendon , Song Renhua , Wielscher Matthias , Rizzetto Simone , Shaw Lisa E , Mitchell Andrew J , Torres-Pacheco Maria Elizabeth , Luciani Fabio , Farlik Matthias , Wong Justin JL , Jung Steffen , Fraser Stuart T , Weninger Wolfgang 
Published: July 2021

AbstractDuring ontogeny, macrophages develop from CD115+precursors, including erythro-myeloid progenitors (EMP). EMP arise in the embryonic yolk sac, the primary site of early haematopoiesis. In adults, CD115+bone marrow-derived monocytes represent essential macrophage precursors. Herein, we identify a CD115-macrophage precursor within the adult bone marrow that is unrelated to the classical monocyte lineage but rather shares transcriptomic and functional characteristics of embryonic EMP. These EMPROR (forErythroMyeloidPrecursor) cells are capable of efficiently generating macrophages in disease settings. During early development, EMPROR cells were largely absent from the yolk sac but were instead found at the embryonic-maternal interface in the uterine wall. Unexpectedly, the latter site contains robust haematopoietic activity and harbours defined embryonic haematopoietic progenitor cells, including classical CD115+EMP. Our data suggest the existence of an alternative pathway of macrophage generation in the adult. Further, we uncover a hitherto unknown site of earliest blood cell development.
Epigenetic reprogramming ameliorates type 1 diabetes by decreasing the generation of Th1 and Th17 subsets and restoring self-tolerance in CD4+ T cells
Authors: Patel Vasu , Jayaraman Arathi , Jayaraman Sundararajan 
Published: July 2021

SUMMARYThe histone modifier Trichostatin A (TSA) ameliorated diabetes and repressed IFN-γ and IL-17A expression in prediabetic female NOD mice. Purified CD4+ cells could be polarized ex vivo into Th1 and Th17 subsets, which comparably transferred diabetes into NOD.scid mice. Polarized Th1 cells were devoid of IL-17A-producing cells and did not transdifferentiate into Th17 cells in an immunodeficient environment. However, Th17 cells had contaminant Th1 cells, which expressed IFN-γ upon adoptive transfer into lymphopenic recipients. Notably, TSA treatment abrogated the transfer of diabetes by CD4+ T-cells cultured under Th1 or Th17 polarizing conditions accompanied by the absence of Ifng and Il17a expression in NOD.scid recipients. Significantly, the histone modifier restored the ability of CD4+ but not CD8+ T-cells to undergo CD3-mediated apoptosis ex vivo in a caspase-dependent manner. Thus, the histone modifier afforded protection against autoimmune diabetes by negative regulation of signature lymphokines and restitution of self-tolerance in CD4+ T cells.
Protection afforded by the BNT162b2 and mRNA-1273 COVID-19 vaccines in fully vaccinated cohorts with and without prior infection
Authors: Abu-Raddad Laith J. , Chemaitelly Hiam , Ayoub Houssein H. , Yassine Hadi M. , Benslimane Fatiha M. , Al Khatib Hebah A. , Tang Patrick , Hasan Mohammad R. , Coyle Peter , Kanaani Zaina Al , Kuwari Einas Al , Jeremijenko Andrew , Kaleeckal Anvar Hassan , Latif Ali Nizar , Shaik Riyazuddin Mohammad , Abdul Rahim Hanan F. , Nasrallah Gheyath K. , Al Kuwari Mohamed Ghaith , Butt Adeel A. , Al Romaihi Hamad Eid , Al-Thani Mohamed H. , Khal Abdullatif Al , Bertollini Roberto 
Published: July 2021

AbstractEffect of prior SARS-CoV-2 infection on vaccine protection remains poorly understood. Here, we investigated whether persons vaccinated after a prior infection have better protection against future infection than those vaccinated without prior infection. Effect of prior infection was assessed in Qatar’s population, where the Alpha (B.1.1.7) and Beta (B.1.351) variants dominate incidence, using two national retrospective, matched-cohort studies, one for the BNT162b2 (Pfizer-BioNTech) vaccine, and one for the mRNA-1273 (Moderna) vaccine. Incidence rates of infection among BNT162b2-vaccinated persons, with and without prior infection, were estimated, respectively, at 1.66 (95% CI: 1.26-2.18) and 11.02 (95% CI: 9.90-12.26) per 10,000 person-weeks. The incidence rate ratio was 0.15 (95% CI: 0.11-0.20). Analogous incidence rates among mRNA-1273-vaccinated persons were estimated at 1.55 (95% CI: 0.86-2.80) and 1.83 (95% CI: 1.07-3.16) per 10,000 person-weeks. The incidence rate ratio was 0.85 (95% CI: 0.34-2.05). Prior infection enhanced protection of those BNT162b2-vaccinated, but not those mRNA-1273-vaccinated. These findings may have implications for dosing, interval between doses, and potential need for booster vaccination.
The first crested duck genome reveals clues to genetic compensation and crest cushion formation
Authors: Chang Guobin , Yuan Xiaoya , Guo Qixin , Bai Hao , Cao Xiaofang , Liu Meng , Wang Zhixiu , Li Bichun , Wang Shasha , Jiang Yong , Wang Zhiquan , Zhang Yang , Xu Qi , Song Qianqian , Pan Rui , Zheng Shenghan , Qiu Lingling , Gu Tiantian , Wu Xinsheng , Bi Yulin , Cao Zhengfeng , Zhang Yu , Chen Yang , Li Hong , Liu Jianfeng , Dai Wangcheng , Chen Guohong 
Published: July 2021

AbstractThe Chinese crested (CC) duck is a unique indigenous waterfowl breed with a phenotypic crest trait that affects its high survival rate. Therefore, the CC duck is an ideal model to investigate the genetic compensation response to maintain genetic stability. In the present study, we first generated a chromosome-level genome of CC ducks. Comparative genomics revealed genes related to tissue repair, immune function, and tumors were under strong positive selection, which suggested that these adaptive changes might enhance cancer resistance and immune response to maintain the genetic stability of CC ducks. We sub-assembled a Chinese spot-billed duck genome and detected genome-assembled structure variants among three ducks. Functional analysis revealed that a large number of structural variants were related to the immune system, which strongly suggests the occurrence of genetic compensation in the anti-tumor and immune systems to further support the survival of CC ducks. Moreover, we confirmed that the CC duck originated from the mallard ducks. Finally, we revealed the physiological and genetic basis of crest traits and identified a causative mutation in TAS2R40 that leads to crest formation. Overall, the findings of this study provide new insights into the role of genetic compensation in adaptive evolution.
The high-throughput gene prediction of more than 1,700 eukaryote genomes using the software package EukMetaSanity
Authors: Neely Christopher J. , Hu Sarah K. , Alexander Harriet , Tully Benjamin J. 
Published: July 2021

AbstractGene prediction and annotation for eukaryotic genomes is challenging with large data demands and complex computational requirements. For most eukaryotes, genomes are recovered from specific target taxa. However, it is now feasible to reconstruct or sequence hundreds of metagenome-assembled genomes (MAGs) or single-amplified genomes directly from the environment. To meet this forth-coming wave of eukaryotic genome generation, we introduce EukMetaSanity, which combines state-of-the-art tools into three pipelines that have been specifically designed for extensive parallelization on high-performance computing infrastructure. EukMetaSanity performs an automated taxonomy search against a protein database of 1,482 species to identify phylogenetically compatible proteins to be used in downstream gene prediction. We present the results for intron, exon, and gene locus prediction for 112 genomes collected from NCBI, including fungi, plants, and animals, along with 1,669 MAGs and demonstrate that EukMetaSanity can provide reliable preliminary gene predictions for a single target taxon or at scale for hundreds of MAGs. EukMetaSanity is freely available at https://github.com/cjneely10/EukMetaSanity.
Software for Non-Parametric Image Registration of 2-Photon Imaging Data
Authors: Flotho Philipp , Nomura Shinobu , Kuhn Bernd , Strauss Daniel J. 
Published: July 2021

AbstractFunctional 2-photon microscopy is a key technology for imaging neuronal activity. The recorded image sequences, however, can contain non-rigid movement artifacts which requires high-accuracy movement correction. Variational optical flow (OF) estimation is a group of methods for motion analysis with established performance in many computer vision areas. However, it has yet to be adapted to the statistics of 2-photon neuroimaging data. In this work, we present the motion compensation method Flow-Registration that outperforms previous alignment tools and allows to align and reconstruct even low signal-to-noise ratio 2-photon imaging data and is able to compensate high-divergence displacements during local drug injections. The method is based on statistics of such data and integrates previous advances in variational OF estimation. Our method is available as an easy-to-use ImageJ / FIJI plugin as well as a MATLAB toolbox with modular, object oriented file IO, native multi-channel support and compatibility with existing 2-photon imaging suites.
Monitoring Spore Dispersal and Early Infections of Diplocarpon coronariae Causing Apple Blotch Using Spore Traps and a New qPCR Method
Authors: Boutry Clémence , Bohr Anne , Buchleither Sascha , Ludwig Mathias , Oberhänsli Thomas , Tamm Lucius , Schärer Hans-Jakob , Flury Pascale 
Published: July 2021

AbstractApple blotch (AB) is a major disease of apple in Asia and recently emerged in Europe and the USA. It is caused by the fungus Diplocarpon coronariae (Dc) (formerly: Marssonina coronaria; teleomorph: Diplocarpon mali) and leads to severe defoliation of apple trees in late summer resulting in reduced yield and fruit quality. To develop effective disease management strategies, a sound knowledge of the pathogen’s biology is crucial. Data on the early phase of disease development is scarce: no data on spore dispersal in Europe is available. We developed a highly sensitive TaqMan qPCR method to quantify Dc conidia in spore trap samples. We monitored temporal and spatial dispersal of conidia of Dc, and progress of AB in spring and early summer in an extensively managed apple orchard in Switzerland in 2019 and 2020. Our results show that Dc overwinters in leaf litter and spore dispersal and primary infections occur in late April and early May. We provide the first results describing early-season dispersal of conidia of Dc, which, combined with the observed disease progress, helps to understand the disease dynamics and will be a basis for improved disease forecast models. Using the new qPCR method, we detected Dc in buds, on bark and fruit mummies, suggesting that several apple tissues may serve as overwintering habitats for the fungus, in addition to fallen leaves.
Phylogenetic distribution and expression pattern analyses identified a divergent basal body assembly protein involved in land plant spermatogenesis
Authors: Koshimizu Shizuka , Minamino Naoki , Nishiyama Tomoaki , Yoro Emiko , Ebine Kazuo , Sakakibara Keiko , Ueda Takashi , Yano Kentaro 
Published: July 2021

AbstractOogamy is a form of sexual reproduction and evolved independently in animals, fungi, and plants. In streptophyte plants, Charophyceae, Coleochaetophyceae, bryophytes, lycophytes, ferns (monilophytes), and some gymnosperms (Cycads and Ginkgo) utilize spermatozoids as the male gamete. Plant spermatozoids commonly possess characteristic structures such as the spline, which consists of a microtubule array, the multilayered structure (MLS) in which the uppermost layer is continuum of the spline, and multiple flagella. However, the molecular mechanisms underpinning plant spermatogenesis remain to be elucidated. To identify the genes involved in plant spermatogenesis, we performed computational analyses and successfully found deeply divergent BLD10s by combining multiple methods and omics-data. We then validated the functions of candidate genes in the liverwort Marchantia polymorpha and the moss Physcomitrium patens and found that MpBLD10 and PpBLD10 are required for normal basal body and flagella formation. Mpbld10 mutants exhibited defects in remodeling of the cytoplasm and nucleus during spermatozoid formation, thus MpBLD10 should be involved in chromatin reorganization and elimination of the cytoplasm during spermiogenesis. Streptophyte BLD10s are orthologous to BLD10/CEP135 family proteins, which function in basal body assembly, but we found that BLD10s evolved especially fast in land plants and MpBLD10 might obtain additional functions in spermatozoid formation through the fast molecular evolution. This study provides a successful example of combinatorial study from evolutionary and molecular genetic perspectives that elucidated a function of the key protein of the basal body formation that fast evolved in land plants.
Reward-dependent selection of feedback gains impacts rapid motor decisions
Authors: De Comite Antoine , Crevecoeur Frédéric , Lefèvre Philippe 
Published: July 2021

AbstractTarget reward influences motor planning strategies through modulation of movement vigor. Considering current theories of sensorimotor control suggesting that movement planning consists in selecting a goal-directed control strategy, we sought to investigate the influence of reward on feedback control. Here we explored this question in three human reaching experiments. First, we altered the explicit reward associated with the goal target and found an overall increase in feedback gains for higher target rewards, highlighted by larger velocities, feedback responses to external loads, and background muscle activity. Then, we investigated whether the differences in target rewards across multiple goals impacted rapid motor decisions during movement. We observed idiosyncratic switching strategies dependent on both target rewards and, surprisingly, the feedback gains at perturbation onset: the more vigorous movements were less likely to switch to a new goal following perturbations. To gain further insight into a causal influence of the feedback gains on rapid motor decisions, we demonstrated that biasing the baseline activity and reflex gains by means of a background load evoked a larger proportion of target switches in the direction opposite to the background load associated with lower muscle activity. Together, our results demonstrate an impact of target reward on feedback control and highlight the competition between movement vigor and flexibility.Significance statementHumans can modulate their movement vigor based on the expected reward. However, a potential influence of reward on feedback control has not been documented. Here we investigated reaching control strategies in different contexts associated with explicit rewards for one or multiple goals, while exposed to external perturbations. We report two strategies: reward could either increase feedback gains, or promote flexible switches between goals. The engagement of peripheral circuits in the modulation of feedback gains was confirmed by the application of a background load that biased feedback vigor directionally, evoking differences in switching behavior in the opposite direction. We conclude that feedback vigor and flexible changes in goal are two competing mechanisms to be selected when interacting with a dynamic environment.
Overexpression of the gene encoding neurosecretory protein GL precursor prevents excessive fat accumulation in the adipose tissue of mice fed a long-term high-fat diet
Authors: Fukumura Keisuke , Narimatsu Yuki , Moriwaki Shogo , Iwakoshi-Ukena Eiko , Furumitsu Megumi , Ukena Kazuyoshi 
Published: July 2021

AbstractWe previously identified a novel small hypothalamic protein, neurosecretory protein GL (NPGL), which induces feeding behavior and fat accumulation in rodents depending on their diet. In the present study, we explored the effects of NPGL on feeding behavior and energy metabolism in mice placed on a long-term high-fat diet with 60% calories from fat (HFD 60). Overexpression of the NPGL precursor gene (Npgl) over 18 weeks increased food intake and body mass. The weekly body mass gain of Npgl-overexpressing mice was higher than that of controls until 7 weeks from induction of overexpression, after which it ceased to be so. Oral glucose tolerance tests showed that Npgl overexpression maintained glucose tolerance and increased blood insulin levels, and intraperitoneal insulin tolerance tests showed that it maintained insulin sensitivity. At the experimental endpoint, Npgl overexpression was associated with increased mass of the perirenal white adipose tissue (WAT) and decreased mass of the epididymal WAT (eWAT), resulting in little effect on the total WAT mass. These results suggest that under long-term HFD 60 feeding, Npgl overexpression may play a role in avoiding metabolic disturbance both by accelerating energy storage and by suppressing excess fat accumulation in certain tissues, such as the eWAT.