bluuebunny/crossref_metadata_2025_split huggingface dataset:
BundleWarp, streamline-based nonlinear registration of white matter tracts
Authors: Chandio Bramsh Qamar , Olivetti Emanuele , Romero-Bascones David , Harezlak Jaroslaw , Garyfallidis Eleftherios 
Published: January 2023

AbstractNonlinear registration plays a central role in most neuroimage analysis methods and pipelines, such as in tractography-based individual and group-level analysis methods. However, nonlinear registration is a non-trivial task, especially when dealing with tractography data that digitally represent the underlying anatomy of the brain’s white matter. Furthermore, such process often changes the structure of the data, causing artifacts that can suppress the underlying anatomical and structural details. In this paper, we introduce BundleWarp, a novel and robust streamline-based nonlinear registration method for the registration of white matter tracts. BundleWarp intelligently warps two bundles while preserving the bundles’ crucial topological features. BundleWarp has two main steps. The first step involves the solution of an assignment problem that matches corresponding streamlines from the two bundles (iterLAP step). The second step introduces streamline-specific point-based deformations while keeping the topology of the bundle intact (mlCPD step).We provide comparisons against streamline-based linear registration and image-based nonlinear registration methods. BundleWarp quantitatively and qualitatively outperforms both, and we show that Bundle-Warp can deform and, at the same time, preserve important characteristics of the original anatomical shape of the bundles. Results are shown on 1,728 pairs of bundle registrations across 27 different bundle types. In addition, we present an application of BundleWarp for quantifying bundle shape differences using the generated deformation fields.
The metacognitive control of decisions predicts whether and how mice override their default policy
Authors: Schreiweis C. , Euvrard M. , Burguière E. , Daunizeau J. 
Published: January 2023

AbstractDecisions permeate every aspect of our lives - what to eat, where to live, etc. - but the amount of effort that we put into different decisions varies tremendously. Rather than processing all decision-relevant information, we often rely on fast habitual and/or intuitive decision policies, which can lead to irrational biases and errors. Yet, we don’t always follow the fast and negligent lead of habits or intuitions. So what determines how much time and effort we invest when making decisions? A possibility is that the amount of cognitive resources the brain allocates to a given task (in particular, a decision task) optimizes a cost-benefit tradeoff. Our working hypothesis is that decision confidence serves as the benefit term of this resource allocation problem, hence the “metacognitive” nature of decision control. Here, we provide behavioural evidence that mice regulate their allocation of cognitive resources according to a confidence/effort a tradeoff. The importance of this work is twofold. On the computational side of things, we show whether and how this eventually enables them to override their default/automatic policy. On the behavioural side of things, we validate all the ensuing model predictions, in the context of an experimental setup with high ecological validity.
Home-field advantage affects the local adaptive interaction betweenAndropogon gerardiiecotypes and rhizobiome
Authors: Kazarina Anna , Sarkar Soumyadev , Thapa Shiva , Heeren Leah , Kamke Abigail , Ward Kaitlyn , Hartung Eli , Ran Qinghong , Galliart Matthew , Jumpponen Ari , Johnson Loretta , Lee Sonny T.M. 
Published: January 2023

AbstractDue to climate change, drought frequencies and severities are predicted to increase across the United States. Plant responses and adaptation to stresses depend on plant genetic and environmental factors. Understanding the effect of those factors on plant performance is required to predict the species responses to environmental change. We used reciprocal gardens planted with distinct regionalAndropogon gerardiiecotypes adapted to dry, mesic, and wet environments to characterize their rhizosphere communities using 16S rRNA metabarcode sequencing. Even though the local microbial pool was the main driver of these rhizosphere communities, the significant plant ecotype effect highlighted active microbial recruitment in the rhizosphere driven by ecotype or plant genetic background. Our data also suggest that ecotypes were more successful in recruiting rhizosphere community members unique to their local homesites, supporting the “home field advantage” hypothesis. These unique homesite microbes may represent microbial specialists that are linked to plant stress responses. Further, our data support ecotypic variation in the recruitment of congeneric but distinct bacterial variants, highlighting the nuanced effects of plant ecotypes on the rhizosphere microbiome recruitment. Our results should facilitate expanded studies on understanding the complexity of plant host interactions with local soil microbes and identification of functional potential of recruited microbes. Our study has the potential to aid in predicting ecosystem responses to climate change and the impact of management on restoration practices.ImportanceIn this study, we used reciprocal gardens located across a sharp precipitation gradient to characterize rhizosphere communities of distinct dry, mesic, and wet regionalAndropogon gerardiiecotypes. We used16S rRNA amplicon sequencing and focused oligotyping analysis and showed that even though the location was the main driver of the microbial communities, ecotypes could potentially recruit distinct bacterial populations. We showed that differentA. gerardiiecotypes were more successful in overall community recruitment and recruitment of microbes unique to the “home” environment, when growing at their “home site”. We found evidence for “home field advantage” interactions between the host and associated rhizobiomes, and the capability of ecotypes to recruit specialized microbes that were potentially linked to plant stress responses. Our study provides insights into the understanding of factors effecting the plant adaptation, improving management strategies, and predicting of the future landscape under the changing climate.
Neural mechanisms to incorporate visual counterevidence in self motion estimation
Authors: Tanaka Ryosuke , Zhou Baohua , Agrochao Margarida , Badwan Bara A. , Au Braedyn , Matos Natalia C. B. , Clark Damon A. 
Published: January 2023

SummaryIn selecting appropriate behaviors, animals should weigh sensory evidence both for and against specific beliefs about the world. For instance, animals measure optic flow to estimate and control their own rotation. However, existing models of flow detection can confuse the movement of external objects with genuine self motion. Here, we show that stationary patterns on the retina, which constitute negative evidence against self rotation, are used by the fruit flyDrosophilato suppress inappropriate stabilizing rotational behavior.In silicoexperiments show that artificial neural networks optimized to distinguish self and world motion similarly detect stationarity and incorporate negative evidence. Employing neural measurements and genetic manipulations, we identified components of the circuitry for stationary pattern detection, which runs parallel to the fly’s motion- and optic flow-detectors. Our results exemplify how the compact brain of the fly incorporates negative evidence to improve heading stability, exploiting geometrical constraints of the visual world.
Corynebacterium of thediphtheriaecomplex in companion animals: clinical and microbiological characterization of 64 cases from France
Authors: Museux Kristina , Arcari Gabriele , Rodrigo Guido , Hennart Melanie , Badell Edgar , Toubiana Julie , Brisse Sylvain 
Published: January 2023

AbstractObjectivesCorynebacteria of thediphtheriaecomplex (Cdc) can cause diphtheria in humans and have been reported from companion animals. We aimed to describe animal infection cases caused byCdcisolates.Methods18 308 animals (dogs, cats, horses and small mammals) with rhinitis, dermatitis, non-healing wounds and otitis were sampled in metropolitan France (August 2019 to August 2021). Data on symptoms, age, breed, and the administrative region of origin were collected. Cultured bacteria were analyzed fortoxgene presence, for production of the diphtheria toxin, for antimicrobial susceptibility, and genotyped by multilocus sequence typing.ResultsC. ulceranswas identified in 51 cases, 24 of which were toxigenic. Rhinitis was the most frequent presentation (18/51). Eleven cases (6 cats, 4 dogs, 1 rat) were mono-infections. Large breed dogs, especially German Shepherds (9 of 28 dogs; p < 0.00001) were overrepresented.C. ulceransisolates were susceptible to all tested antibiotics.tox-positiveC. diphtheriaewas identified in 2 horses. Last, 11 infections cases (9 dogs, 2 cats; mostly chronic otitis, and 2 sores) hadtox-negativeC. rouxii, a recently defined species.C. rouxiiandC. diphtheriaeisolates were susceptible to most antibiotics tested, and almost all of these infections were polymicrobial.ConclusionsMonoinfections withC. ulceranspoint towards a primary pathogenic potential to animals.C. ulceransrepresents an important zoonotic risk, andC. rouxiimay represent a novel zoonotic agent. This case series provides novel clinical and microbiological data onCdcinfections, and underlines the need for management of animals and their human contacts.ImportanceWe report on the occurrence, clinical and microbiological characteristics of infections caused by members of the Corynebacteria of thediphtheriaecomplex (Cdc) in companion animals. This is the first study based on the systematic analysis of a very large animal cohort (18 308 samples), which provides data on the frequency of Cdc isolates in various types of clinical samples from animals. Awareness of this zoonotic bacterial group remains low among veterinarians and veterinary laboratories, among which it is often considered a commensal bacteria of animals. We suggest that in case of Cdc detection in animals, the veterinary laboratories should be encouraged to send the samples to a reference laboratory for analysis of the presence of thetoxgene. This work is relevant to the development of guidelines in case of Cdc infections in animals, and underlines their public health relevance given the zoonotic transmission risk.
Monitoring the battleground: Antimicrobial resistance, antibiofilm patterns, and virulence factors of wound bacterial isolates from patients in hospital system
Authors: Awuor Silas O. , Mariita Richard , Omwenga Eric O. , Musila Jonathan , Musyoki Stanslaus 
Published: January 2023

ABSTRACTExtensive use of antibiotics in the treatment of bacterial infections has led to a challenge of antibiotic resistance, contributing to morbidity and mortality. Herein, evaluation of bacterial isolates from patients with wound discharge was performed and drug susceptibility patterns examined, with a goal of deciphering antibacterial resistance. A cross-sectional study was conducted between March to June 2022, in which samples were collected from patients with chronic wounds and were inoculated into appropriate media for identification and characterization. The bacterial pathogens were identified using standard microbiological methods. Shockingly, the majority of wound isolates showed positive growth in microbial analysis with high prevalence in male candidates. Further,Staphylococcus aureus28 (20.7%) was identified as the most predominant pathogen followed byKlebsiella spp. 20 (14.8%),P. aeruginosa spp. 10 (14.8%) and lastlyE. coli6 (4.4%) bacteria in the wound isolates while cotrimoxazole 13 (48.1%) followed by clindamycin 7 (25.9%) and erythromycin 7 (25.9%) were the most antibacterial resistant drugs to both Gram positive and Gram-negative bacteria. Out of the four isolates, 3 (75%) isolates were able to produce the haemolysin and protease and 2 (50%) isolates were able to produce the lipase and phospholipase. The findings herein form a clinical basis for identification of antimicrobial resistance in chronic wounds that can be applied in responsible use of antibacterial in chronic wound management and as an illumination in development of more potent antibiotics for chronic wound treatment
Genomic characterization of multidrug-resistant extended spectrum β-lactamase-producingKlebsiella pneumoniaefrom clinical samples of a tertiary hospital in South Kivu Province, eastern Democratic Republic of Congo
Authors: Irenge Leonid M. , Ambroise Jérôme , Bearzatto Bertrand , Durant Jean-François , Bonjean Maxime , Gala Jean-Luc 
Published: January 2023

AbstractMultidrug-resistant (MDR) and Extended Spectrum β-Lactamase (ESBL)-producing extraintestinalK. pneumoniaeare associated with increased morbidity and mortality. This study aimed to characterize the resistance and virulence profiles of extra-intestinal MDR ESBL-producingK. pneumoniaeassociated with infections at a tertiary hospital in South-Kivu province, DRC. Whole-genome sequencing (WGS) was carried out on 37 K.pneumoniaeisolates displaying MDR, and ESBL-producing phenotype. The assembled genomes were analysed for phylogeny, virulence factors and antimicrobial resistance genes (ARG) determinants. These isolates were compared to sub-Saharan counterparts.K. pneumoniaeisolates displayed a high genetic variability with up to 16 sequence types (ST). AMR was widespread against β-lactamases (including third and fourth-generation cephalosporins, but not carbapenems), aminoglycosides, ciprofloxacin, tetracycline, erythromycin, nitrofurantoin, and cotrimoxazole. TheblaCTXM-15gene was the most common β-lactamase gene amongK. pneumoniaeisolates. No carbapenemase gene was found. ARG for aminoglycosides, quinolones, phenicols, tetracyclines, sulfonamides, nitrofurantoin were widely distributed among the isolates. Nine isolates had the colistin-resistant R256G substitution in thepmrBefflux pump gene without displaying reduced susceptibility to colistin. Despite carrying virulence genes, none had hypervirulence genes. Our results highlight the genetic diversity of MDR ESBL-producingK. pneumoniaeisolates, and underscore the importance of monitoring simultaneously the evolution of phenotypic and genotypic AMR in Bukavu and DRC, while calling for caution in administering colistin and carbapenem to patients.
Deep learning-driven fragment ion series classification enables highly precise and sensitive de novo peptide sequencing
Authors: Klaproth-Andrade Daniela , Hingerl Johannes , Smith Nicholas H. , Träuble Jakob , Wilhelm Mathias , Gagneur Julien 
Published: January 2023

ABSTRACTUnlike for DNA and RNA, accurate and high-throughput sequencing methods for proteins are lacking, hindering the utility of proteomics in applications where the sequences are unknown including variant calling, neoepitope identification, and metaproteomics. We introduce Spectralis, a new de novo peptide sequencing method for tandem mass spectrometry. Spectralis leverages several innovations including a new convolutional neural network layer connecting peaks in spectra spaced by amino acid masses, proposing fragment ion series classification as a pivotal task for de novo peptide sequencing, and a new peptide-spectrum confidence score. On spectra for which database search provided a ground truth, Spectralis surpassed 40% sensitivity at 90% precision, nearly doubling state-of-the-art sensitivity. Application to unidentified spectra confirmed its superiority and showcased its applicability to variant calling. Altogether, these algorithmic innovations and the substantial sensitivity increase in the high-precision range constitute an important step toward broadly applicable peptide sequencing.
A glia cell dependent mechanism at a peripheral nerve plexus critical for target-selective axon regeneration
Authors: Walker Lauren J , Guevara Camilo , Kawakami Koichi , Granato Michael 
Published: January 2023

ABSTRACTA critical step for functional recovery from peripheral nerve injury is for regenerating axons to connect with their pre-injury targets. Reestablishing pre-injury target specificity is particularly challenging for limb-innervating axons as they encounter a plexus, a network where peripheral nerves converge, axons from different nerves intermingle, and then re-sort into target-specific bundles. Here, we examine this process at a plexus located at the base of the zebrafish pectoral fin, equivalent to tetrapod forelimbs. Using live cell imaging and sparse axon labeling, we find that regenerating motor axons from three nerves coalesce into the plexus. There, they intermingle and sort into distinct branches, and then navigate to their original muscle domains with high fidelity that restores functionality. We demonstrate that this regeneration process includes selective retraction of mistargeted axons, suggesting active correction mechanisms. Moreover, we find that Schwann cells are enriched and associate with axons at the plexus, and that Schwann cell ablation during regeneration causes profound axonal mistargeting. Our data provide the first real time account of regenerating vertebrate motor axons navigating a nerve plexus and reveal a previously unappreciated role for Schwann cells to promote axon sorting at a plexus during regeneration.
The complex inhibitory mechanism of glycomimetics with human heparanase
Authors: Whitefield Cassidy , Vo Yen , Schwartz Brett D , Hepburn Caryn , Ahmed F. Hafna , Onagi Hideki , Banwell Martin G. , Nelms Keats , Malins Lara R. , Jackson Colin J 
Published: January 2023

AbstractHeparanase (HPSE) is the only mammalian endo-β-glucuronidase known to catalyse the degradation of heparan sulfate. Dysfunction of HPSE activity has been linked to several disease states, resulting in HPSE becoming the target of numerous therapeutic programs, yet no drug has passed clinical trials to date. Pentosan polysulfate sodium (PPS) is a heterogeneous FDA-approved drug for the treatment of interstitial cystitis and a known HPSE inhibitor. However, due to its heterogeneity, characterisation of its mechanism of HPSE inhibition is challenging. Here we show that inhibition of HPSE by PPS is complex, involving multiple overlapping binding events, each influenced by factors such as oligosaccharide length and inhibitor-induced changes in protein secondary structure. The present work advances our molecular understanding of the inhibition of HPSE, which will aid the development of therapeutics for the treatment of a broad range of pathologies associated with enzyme dysfunction including cancer, inflammatory disease and viral infections.
Bouts of rest and physical activity in C57BL/6J mice
Authors: Pernold K. , Rullman E. , Ulfhake B. 
Published: January 2023

AbstractThe objective was to exploit the raw data output from a scalable home cage (type IIL IVC) monitoring (HCM) system (DVC®), to characterize pattern of undisrupted rest and physical activity (PA) of C57BL/6J mice. The system’s tracking algorithm show that mice in isolation spend 67% of the time in bouts of long rest (≥40s) and 59 % of the time was interpreted as sleep. Twenty percent is physical activity (PA), split equally between local movements and locomotion. Decomposition revealed that a day contains ∼6500 discrete bouts of short and long rest, local and locomotor movements. Mice travel ∼330m per day, mainly during the dark hours, while travelling speed is similar through the light-dark cycle. Locomotor bouts are usually <0.2m and <1% are >1m. Tracking revealed also fits of abnormal behaviour. The starting positions of the bouts showed no preference for the rear over the front of the cage floor, while there was a strong bias for the peripheral (75%) over the central floor area. The composition of bouts has a characteristic circadian pattern, however, intrusive husbandry routines increased bout fragmentation by ∼40%.Extracting electrode activations density (EAD) from the raw data yielded results close to those obtained with the tracking algorithm, with 59% of time in long rest (<1 EAD s-1) and 20% in PA. We confirm that EAD correlates closely with movement distance (rs>0.95) and the data agreed in ∼96% of the file time. Thus, albeit EAD being less informative it may serve as a proxy for PA and rest, enabling monitoring group housed mice. The data show that a change in housing density from one to two, and up to three mice had the same effect size on EAD (∼2) with no difference between sexes. The EAD deviated significantly from this stepwise increase with 4 mice per cage, suggesting a crowdedness stress inducing sex specific adaptations.We conclude that informative metrics on rest and PA can be automatically extracted from the raw data flow in near-real time (< 1 hrs). These metrics relay useful longitudinal information to those that use or care for the animals.
Efficient, robust, and versatile fluctuation data analysis using MLE MUtation Rate calculator (mlemur)
Authors: Łazowski Krystian 
Published: January 2023

AbstractAlmost 80 years since the publication of the seminal work by Salvador Luria and Max Delbrück, the fluctuation assay has remained an important tool for analysing the levels of mutagenesis in microbial populations. The mutant counts originating from some average number of mutations are usually assumed to obey the Luria–Delbrück distribution. While several tools for estimating mutation rates are available, they sometimes lack accuracy or versatility under non-standard conditions. In this work we developed extensions to the Luria– Delbrück protocol to account for phenotypic lag and cellular death with either perfect or partial plating. Hence, our novel MLE MUtation Rate calculator, or mlemur, is the first tool that provides a user-friendly graphical interface allowing the researchers to model their data with consideration for partial plating, differential growth of mutants and non-mutants, phenotypic lag, cellular death, variability of the final number of cells, post-exponential-phase mutations, and the size of inoculum. Additionally, mlemur allows the users to incorporate most of these special conditions at the same time to obtain highly accurate estimates of mutation rates andpvalues, confidence intervals for an arbitrary function of data (such as fold) and perform power analysis and sample size determination for the likelihood ratio test. We assess the accuracy of point and interval estimates produced by mlemur against historical and simulated fluctuation experiments. We believe both mlemur and the analyses in this work might be of great help when evaluating fluctuation experiments and increase the awareness of the limitations of the widely-used Lea–Coulson formulation of the Luria-Delbrück distribution in the more realistic biological contexts.Author SummaryDespite many recent developments in the department of fluctuation data analysis, geneticists are often limited to either a very strict classical Luria–Delbrück protocol, or possibly a modified one with relaxation of just one assumption (e.g., differential fitness of mutants and wild-type cells). In some cases, such as partial plating, researchers use historical methods whose accuracy strictly depends on the conditions of the experiment and thus are not optimal in a wide range of parameters. A novel tool for fluctuation data analysis, mlemur (MLE MUtation Rate calculator), alleviates these problems and provides new extensions that allow to account for phenotypic lag and cellular death. Additionally, we find that the failure to properly account for these additional parameters might lead to inaccurate point and interval estimates of the mutation rate. Our results underline the importance of careful examination of the fluctuation assay to ensure that the chosen statistical model reflects the biological and technical conditions of the experiment.