bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predation increases prey fitness via transgenerational priming
Authors: Kost Silvia , Muhsal Linea Katharina , Kost Christian 
Published: March 2022

ABSTRACTPreparing your offspring for future challenges via priming can directly enhance its fitness. However, evidence for transgenerational priming has been limited to eukaryotic organisms. Here we test the hypothesis that predation primes bacteria such that their future generations respond with a more effective defence induction. In an evolution experiment, Escherichia coli was cultivated either in monoculture or in coculture with the predatory ciliate Tetrahymena thermophila. After 18 days, fitness and defensive clustering capabilities of derived bacterial populations were determined. Our results reveal that (i) predation can prime E.coli to induce their defensive cluster formation across generations and that (ii) three days of predation are sufficient to increase the fitness of predator-exposed over that of predator-free populations. Thus, our study shows that predation can have priming effects in bacterial populations that operate across generations, which concurs with the emerging perception that bacteria feature mechanisms to actively shape their evolutionary fate.
Unsupervised clustering reveals phenotypes of AKI in ICU Covid19 patients
Authors: Sangla Frederic , Marchi Elisa , Assouline Benjamin , Leterrier Christophe , Sgardello Sebastian , Pugin Jérôme , Criton Gilles , Legouis David 
Published: March 2022

AbstractBackgroundAcute Kidney Injury (AKI) is a very frequent condition, occurring in about one in three patients admitted to an intensive care unit (ICU). AKI is a syndrome defined as a sudden decrease in glomerular filtration rate. However, this unified definition does not reflect the various mechanisms involved in AKI pathophysiology, each with its own characteristics and sensitivity to therapy. In this study, we aimed at developing an innovative machine learning based method able to subphenotype AKI according to its pattern of risk factors.MethodsWe adopted a three-step pipeline of analyses. Firstly, we looked for factors associated with AKI using a generalized additive model. Secondly, we calculated the importance of each identified AKI related factor in the estimated AKI risk to find the main risk factor for AKI, at the single patient level. Lastly, we clusterized AKI patients according to their profile of risk factors and compared the clinical characteristics and outcome of every cluster. We applied this method to a cohort of severe Covid19 patients hospitalized in the ICU of Geneva University Hospitals.ResultsAmong the 250 patients analyzed, we found ten factors associated with AKI development. Using the individual expression of these factors, we identified three groups of AKI patients, based on the use of Lopinavir/Ritonavir, a prior history of diabetes mellitus and baseline eGFR and ventilation. The three clusters expressed distinct characteristic in terms of AKI severity and recovery, metabolic patterns and ICU mortality.ConclusionWe propose here a new method to phenotype AKI patients according to their most important individual risk factors for AKI development. When applied to an ICU cohort of Covid19 patients, we were able to differentiate three groups of patients. Each expressed specific AKI characteristics and outcomes, which probably reflects a distinct pathophysiology.
Portable, Low-Field Magnetic Resonance Imaging Sensitively Detects and Accurately Quantifies Multiple Sclerosis Lesions
Authors: Arnold T. Campbell , Tu Danni , Okar Serhat V. , Nair Govind , By Samantha , Kawatra Karan , Robert-Fitzgerald Timothy E. , Desiderio Lisa M. , Schindler Matthew K. , Shinohara Russell T. , Reich Daniel S. , Stein Joel M. 
Published: March 2022

AbstractMagnetic resonance imaging is a fundamental tool in the diagnosis and management of neurological diseases such as multiple sclerosis (MS). New portable, low-field MRI scanners could potentially lower financial and technical barriers to neuroimaging and reach underserved or disabled populations. However, the sensitivity of low-field MRI for MS lesions is unknown. We sought to determine if white matter lesions can be detected on a 64mT low-field MRI, compare automated lesion segmentations and total lesion burden between paired 3T and 64mT scans, and identify features that contribute to lesion detection accuracy. In this prospective, cross-sectional study, same-day brain MRI (FLAIR, T1, and T2) scans were collected from 36 adults (32 women; mean age, 50 ± 14 years) with known or suspected MS using 3T (Siemens) and 64mT (Hyperfine) scanners at two centers. Images were reviewed by neuroradiologists. MS lesions were measured manually and segmented using an automated algorithm. Statistical analyses assessed accuracy and variability of segmentations across scanners and systematic scanner biases in automated volumetric measurements. Lesions were identified on 64mT scans in 94% (31/33) of patients with confirmed MS. The smallest lesions manually detected were 5.7 ± 1.3 mm in maximum diameter at 64mT vs 2.1 ± 0.6 mm at 3T. Automated lesion burden estimates were highly correlated between 3T and 64mT scans (r = 0.89, p < 0.001). Bland-Altman analysis identified bias in 64mT segmentations (mean = 1.6 ml, standard error = 5.2 ml, limits of agreement = -19.0–15.9 ml), which over-estimated low lesion burden and under-estimated high burden (r = 0.74, p < 0.001). Visual inspection revealed over-segmentation was driven by flow-related hyperintensities in veins on 64mT FLAIR. Lesion size drove segmentation accuracy, with 93% of lesions >1.0 ml and all lesions >1.5 ml being detected. These results demonstrate that in established MS, a portable 64mT MRI scanner can identify white matter lesions, and disease burden estimates are consistent with 3T scans.HighlightsPaired, same-day 3T and 64mT MRI studies were collected in 36 patients64mT MRI showed 94% sensitivity for detecting any lesions in established MS casesThe diameter of the smallest detected lesion was larger at 64mT compared to 3TDisease burden estimates were strongly correlated between 3T and 64mT scansLow-field MRI can detect white matter lesions, though smaller lesions may be missed
Optimal dosing of cefotaxime and desacetylcefotaxime for critically ill paediatric patients. Can we use microsampling?
Authors: Guerra Valero Yarmarly C. , Dorofaeff Tavey , Coulthard Mark G , Sparkes Louise , Lipman Jeffrey , Wallis Steven C. , Roberts Jason A. , Parker Suzanne L. 
Published: March 2022

SynopsisObjectivesThis study aimed to describe the population pharmacokinetics of cefotaxime and desacetylcefotaxime in critically ill paediatric patients and provide dosing recommendations. We also sought to evaluate the use of capillary microsampling to facilitate data-rich blood sampling.MethodsPatients were recruited into a pharmacokinetic study, with cefotaxime and desacetylcefotaxime concentrations from plasma samples collected at 0, 0.5, 2, 4 and 6 h used to develop a population pharmacokinetic model using Pmetrics. Monte Carlo dosing simulations were tested using a range of estimated glomerular filtration rates (60, 100, 170 and 200 mL/min/1.73 m2) and body weights (4, 10, 15, 20 and 40 kg) to achieve PK/PD targets, including 100% ƒT>MIC with an MIC breakpoint of 1 mg/L.Results36 patients (0.2 – 12 y) provided 160 conventional samples for inclusion in the model. The pharmacokinetics of cefotaxime and desacetylcefotaxime were best described using one-compartmental model with first-order elimination. The clearance and volume of distribution for cefotaxime were 12.8 L and 39.4 L/h, respectively. The clearance for desacetylcefotaxime was 10.5 L/h. Standard dosing of 50 mg/kg Q6h was only able to achieve the PK/PD target of 100% ƒT>MIC in patients > 10 kg and with impaired renal function or patients of 40 kg with normal renal function.ConclusionsDosing recommendations support the use of extended or continuous infusion to achieve cefotaxime exposure suitable for bacterial killing in critically ill paediatric patients, including those with severe or deep-seated infection. An external validation of capillary microsampling demonstrated skin-prick sampling can facilitate data-rich pharmacokinetic studies.
Dimensionality reduction of calcium-imaged neuronal population activity
Authors: Koh Tze Hui , Bishop William E. , Kawashima Takashi , Jeon Brian B. , Srinivasan Ranjani , Kuhlman Sandra J. , Ahrens Misha B. , Chase Steven M. , Yu Byron M. 
Published: March 2022

ABSTRACTCalcium imaging has been widely adopted for its ability to record from large neuronal populations. To summarize the time course of neural activity, dimensionality reduction methods, which have been applied extensively to population spiking activity, may be particularly useful. However, it is unclear if the dimensionality reduction methods applied to spiking activity are appropriate for calcium imaging. We thus carried out a systematic study of design choices based on standard dimensionality reduction methods. We also developed a novel method to perform deconvolution and dimensionality reduction simultaneously (termed CILDS). CILDS most accurately recovered the single-trial, low-dimensional time courses from calcium imaging that would have been recovered from spiking activity. CILDS also outperformed the other methods on calcium imaging recordings from larval zebrafish and mice. More broadly, this study represents a foundation for summarizing calcium imaging recordings of large neuronal populations using dimensionality reduction in diverse experimental settings.
Dynamics of brain-fluid circulation are altered in the mature-onset Tet-off APP mouse model of amyloidosis
Authors: Ben-Nejma Inès R.H. , Keliris Aneta J. , Vanreusel Verdi , Ponsaerts Peter , Van der Linden Annemie , Keliris Georgios A. 
Published: March 2022

ABSTRACTAlzheimer’s disease (AD), the most common type of dementia, is an incurable brain disorder characterised by the progressive build-up of toxic amyloid-beta (Aβ) and tau protein aggregates. AD gradually inflicts cognitive functions of an individual such as memory, thinking, reasoning, and language by degrading synaptic function and the integrity of neuronal networks. It has been recently suggested that the efficacy of different brain-clearance systems like the glymphatic system (GS), involved in the removal of toxic waste and homeostatic balance, plays a key role in the pathology of AD. Moreover, the observed coupling between brain fluid movement and global brain activity implies that an alteration of the neuronal network integrity can impact brain fluid circulation throughout the brain and thereby the efficacy of the GS. Here, we investigated the dynamics of brain fluid circulation in Tet-Off APP (AD) mice, a mature-onset model of amyloidosis in which we have recently shown a deterioration of neuronal network integrity by resting-state fMRI. By utilizing dynamic contrast enhanced-MRI and gadoteric acid (Gd-DOTA) T1 contrast agent injected into the cisterna magna, we demonstrated that brain fluid exchange was significantly altered in 14-month-old AD mice compared to control littermates. More specifically, AD mice showed higher Gd-DOTA accumulation in areas proximal to the injection cite and computational modeling of time courses demonstrated significantly lower inflow time constants relative to the controls. Immunohistochemistry demonstrated abundant amyloid plaque burden in the forebrain of the AD group coinciding with extensive astrogliosis and microgliosis. The neuroinflammatory responses were also found in plaque-devoid regions, potentially impacting brain fluid circulation.
E-cigarette vapour from base components propylene glycol and vegetable glycerine inhibits the inflammatory response in macrophages and epithelial cells
Authors: Bell Rachael L. , McAuley Danny F. , Shyamsundar Murali , O’Kane Cecila M. , Dombrowski Yvonne 
Published: March 2022

AbstractE-cigarettes are a highly popular nicotine replacement therapy in the process of smoking cessation. Despite this, research on the effects of E-vapours to human health remains limited. The popularity of vaping and mass production of cheap E-liquids has led to compromised safety regulations, with contaminants such as heavy metals and alkaloids detected in multiple liquids. Vaporised E-liquids increase cellular ROS generation and inflammatory cytokine release from pulmonary macrophages. This suggests that E-cigarette usage might activate inflammasomes. Common food additives vegetable glycerine (VG) and propylene glycol (PG) form the base of all E-liquids, but little is known about their inflammatory potential once inhaled. Here, the effect of base components PG and VG on inflammasome activation and cytokine release was investigated in macrophages and epithelial cells exposed to E-liquids and vaporised E-liquid extract (E-vapour). Base E-liquid and E-vapour did not induce cellular cytotoxicity and non-vapourised E-liquid had no effect on IL-8 release. However, basic PG/VG E-vapour inhibited both IL-8 release and conventional inflammasome activation by known inflammatory activators in macrophages and epithelial cells. These results propose a novel inhibitory effect of basic E-vapour components to inflammatory challenges.
Ecology and evolution of chlamydial symbionts of arthropods
Authors: Halter Tamara , Köstlbacher Stephan , Collingro Astrid , Sixt Barbara S. , Tönshoff Elena R. , Hendrickx Frederik , Kostanjšek Rok , Horn Matthias 
Published: March 2022

AbstractThe phylum Chlamydiae consists of obligate intracellular bacteria including major human pathogens and diverse environmental representatives. Here we investigated the Rhabdochlamydiaceae, which is predicted to be the largest and most diverse chlamydial family, with the few described members known to infect arthropod hosts. Using published 16S rRNA gene sequence data we identified at least 388 genus-level lineages containing about 14 051 putative species within this family. We show that rhabdochlamydiae are mainly found in freshwater and soil environments, suggesting the existence of diverse, yet unknown hosts. Next, we used a comprehensive genome dataset including metagenome assembled genomes classified as members of the family Rhabdochlamydiaceae, and we added novel complete genome sequences of Rhabdochlamydia porcellionis infecting the woodlouse Porcellio scaber, and of ‘Candidatus R. oedothoracis’ associated with the linyphiid dwarf spider Oedothorax gibbosus. Comparative analysis of basic genome features and gene content with reference genomes of well-studied chlamydial families with known host ranges, namely Parachlamydiaceae (protist hosts) and Chlamydiaceae (human and other vertebrate hosts) suggested distinct niches for members of the Rhabdochlamydiaceae. We propose that members of the family represent intermediate stages of adaptation of chlamydiae from protists to vertebrate hosts. Within the genus Rhabdochlamydia, pronounced genome size reduction could be observed (1.49-1.93 Mb). The abundance and genomic distribution of transposases suggests transposable element expansion and subsequent gene inactivation as a mechanism of genome streamlining during adaptation to new hosts. This type of genome reduction has never been described before for any member of the phylum Chlamydiae. This study provides new insights into the molecular ecology, genomic diversity, and evolution of representatives of one of the most divergent chlamydial families.
Urbanization and green corridors influence reproductive success and pollinators of common milkweed
Authors: Breitbart Sophie , Tomchyshyn Albert , Wagner Helene , Johnson Marc 
Published: March 2022

AbstractUrbanization exerts many pressures on species, yet little is known about how these pressures impact species interactions. Studies of urban plant-pollinator systems provide mounting evidence that urbanization impairs pollinator movement in fragmented urban landscapes, yet the consequences for pollinator-mediated plant reproduction remains unclear. In non-urban areas, habitat corridors can facilitate the movement of organisms including pollinators, but whether these corridors facilitate plant-pollinator interactions in urban areas remains understudied. To examine how urban environments and green corridors influence plant-pollinator interactions, we measured reproductive success in the native plant common milkweed (Asclepias syriaca), and the community structure of its pollinators, for two years along two urban-rural transects in the Greater Toronto Area, Canada, one of which followed a green corridor. We found that urbanization decreased male fitness (i.e., pollen removal), increased fruit set (i.e., mean no. of follicles per inflorescence), and inconsistently affected female fitness (i.e., no. of follicles) in A. syriaca. Urbanization simultaneously decreased pollinator abundance but increased pollinator richness. Proximity to a green corridor inconsistently affected male fitness but increased reproductive effort (i.e., no. of inflorescences) in A. syriaca, while pollinator diversity and richness was lower in corridors. Notably, there were no consistent relationships between pollinator community structure and reproductive success in A. syriaca in both the presence, and absence, of a green corridor. These results demonstrate the complexity with which urbanization, green corridors, and pollinator communities can shape the reproductive investment and fitness of native plant populations.
GRAPE: Genomic Relatedness Detection Pipeline
Authors: Medvedev Aleksandr , Lebedev Mikhail , Ponomarev Andrew , Kosaretskiy Mikhail , Osipenko Dmitriy , Tischenko Alexander , Kosaretskiy Egor , Wang Hui , Kolobkov Dmitry , Chamberlain-Evans Vitalina , Vakhitov Ruslan , Nikonorov Pavel 
Published: March 2022

AbstractClassifying the degree of relatedness between pairs of individuals has both scientific and commercial applications. As an example, GWAS may suffer from high rates of false positive results due to unrecognized population structure. This problem becomes especially relevant with recent increases in large-cohort studies. Accurate relationship classification is also required for genetic linkage analysis to identify disease-associated loci. Additionally, DNA relatives matching service is one of the leading drivers for the direct-to-consumer genetic testing market. Despite the availability of scientific and research information on the methods for determining kinship and the accessibility of relevant tools, the assembly of the pipeline, that stably operates on a real-world genotypic data, requires significant research and development resources. Currently, there is no open-source end-to-end solution for relatedness detection in genomic data, that is fast, reliable and accurate for both close and distant degrees of kinship, combines all the necessary processing steps to work on real data, and is ready for production integration. To address this, we developed GRAPE: Genomic RelAtedness detection PipelinE. It combines data preprocessing, identity-by-descent (IBD) segments detection, and accurate relationship estimation. The project uses software development best practices, as well as GA4GH standards and tools. Pipeline efficiency is demonstrated on both simulated and real-world datasets.
Deletion of can1/cat1 genes and expression of a dominant any1 mutation establish an effective canavanine selection in fission yeast
Authors: Saada Anissia Ait , Costa Alex B. , Lobachev Kirill S. 
Published: March 2022

AbstractPositive and counter-selectable markers have been successfully integrated as a part of numerous genetic assays in many model organisms. In this study, we investigate the mechanism of resistance to arginine analog canavanine and its applicability for genetic selection inSchizosaccharomyces pombe. Deletion of both arginine permease genescat1andcan1provides strong drug resistance, while the singlecan1deletion does not have impact on canavanine resistance. Surprisingly, the widely usedcan1-1allele does not match to thecan1gene but rather corresponds to theany1-523C>Tallele. The strong canavanine-resistance conferred by this allele arises from an inability to deposit basic amino acid transporters on the cellular membrane.any1-523C>Tleads to reduced post-translational modifications of Any1 regulated by the Tor2 kinase. We also demonstrate thatany1-523C>Tis a dominate allele. Our results uncover the mechanisms of canavanine-resistance in fission yeast and open the opportunity of usingcat1, can1andany1mutant alleles in genetic assays.
MUC5B mobilizes and MUC5AC spatially aligns mucociliary transport on human airway epithelium
Authors: Song Daniel , Iverson Ethan , Kaler Logan , Scull Margaret A. , Duncan Gregg A. 
Published: March 2022

AbstractAirway mucus acts as a protective barrier and vehicle for clearance of pathogens, providing the lungs with a defense mechanism called mucociliary clearance (MCC). Airway mucus is composed of two mucins, mucin 5B (MUC5B) and 5AC (MUC5AC) that form a hydrogel that enables functional clearance in health. However, abnormalities in mucin expression, specifically increases in MUC5AC is observed in chronic respiratory diseases and leading to defective MCC. Our current understanding of MCC impairment focuses on mucin concentration, while the impact of mucin composition remains unclear. Here, we use MUC5AC/B-knock out (KO) human airway epithelial (HAE) tissue cultures to understand the role and contribution of individual secreted mucins on MCC mechanisms. We find that KO cultures result in impaired or discoordinated mucociliary transport demonstrating the importance of each of these mucins to effective MCC and shedding light on a new mechanism of mucin composition-dependent airway clearance.
Strength-mass scaling law governs mass distribution inside honey bee swarms
Authors: Shishkov Olga , Chen Claudia , Madonna Claire Allison , Jayaram Kaushik , Peleg Orit 
Published: March 2022

AbstractTo survive during colony reproduction, bees create dense clusters of thousands of suspended individuals. How can this swarm, which is orders of magnitude larger than the size of an individual, maintain mechanical stability? We hypothesize that the internal structure in the bulk of the swarm, about which there is little prior information, plays a key role in mechanical stability and thermoregulation. Here, we provide the first-ever 3D reconstructions of the positions of the bees in the bulk of the swarm using x-ray computed tomography. We find that the mass of bees in a layer decreases with distance from the attachment surface. By quantifying the distribution of bees within swarms varying in size (made up of 4000-10000 bees), we find that the same power law governs the smallest and largest swarms, with the weight supported by each layer scaling with the mass of each layer to the ≈ 1.5 power. This arrangement ensures that each layer exerts the same fraction of its total strength, and on average a bee supports a lower weight than its maximum grip strength. This illustrates the extension of the scaling law relating weight to strength of single organisms to the weight distribution within a superorganism made up of thousands of individuals.