bluuebunny/crossref_metadata_2025_split huggingface dataset:
Autoimmune neuromyotonia
Authors: Comperat Louis , Pegat Antoine , Honnorat Jérôme , Joubert Bastien 
Published: August 2022

Purpose of review
Autoimmune neuromyotonia encompasses a group of rare immune-mediated neurological disorders frequently associated with anti-contactin-associated protein-like 2 (CASPR2) antibodies and featuring clinical and electrical signs of peripheral nerve hyperexcitability (PNH). We aim to summarize the current knowledge on immune-mediated neuromyotonia, focusing on clinical presentations, pathophysiology, and management.

Recent findings
Neuromyotonia is a major feature of several autoimmune neurological syndromes characterized by PNH with or without central neurological system involvement. Experimental and clinical evidence suggest that anti-CASPR2 antibodies are directly pathogenic in autoimmune neuromyotonia patients.

Summary
Neuromyotonia, a form of PNH, is a major feature in several syndromes associated with anti-CASPR2 antibodies, including cramp-fasciculation syndrome, Isaacs syndrome, Morvan syndrome, and autoimmune limbic encephalitis. Diagnosis relies on the identification of motor, sensory, and autonomic signs of PNH along with other neurological symptoms, anti-CASPR2 antibody-positivity, and of characteristic electroneuromyographic abnormalities. Paraneoplastic associations with thymoma are possible, especially in Morvan syndrome. Patients usually respond to immune-active treatments, including steroids, intravenous immunoglobulins, plasma exchanges, and rituximab.
Autoimmune nodopathies, an emerging diagnostic category
Authors: Martín-Aguilar Lorena , Lleixà Cinta , Pascual-Goñi Elba 
Published: August 2022

Purpose of review
In the last decade, antibodies targeting cell adhesion molecules of the node of Ranvier were described in patients with autoimmune neuropathies. These nodal/paranodal antibodies associate with specific clinicopathological features that are different from classical chronic inflammatory demyelinating polyneuropathy (CIDP). In this review, we will summarize recent findings establishing autoimmune nodopathies (AN) as a new category of autoimmune neuropathies.

Recent findings
AN include anti-contactin 1, anti-contactin-associated protein 1, anti-neurofascin 155 and anti-pan-neurofascin antibody-mediated neuropathies. Their clinical spectrum includes acute, subacute or chronic onset sensory-motor neuropathies mimicking Guillain-Barré syndrome (GBS) and CIDP, although they differ in their response to standard therapy with intravenous immunoglobulin (IVIG). Neurophysiologically they overlap with acquired demyelinating neuropathies, but ultrastructural studies and animal models demonstrated antibody-mediated pathology restricted to the node of Ranvier. Anti-contactin1 and anti-pan-neurofascin also associate with nephrotic syndrome. Nodal/paranodal antibodies are predominantly of the immunoglobulin (IgG)4 subclass during the chronic phase of the disease, but complement-fixing IgG3 antibodies are detected during the early phase and associate with aggressive onset and IVIG response. Nodal/paranodal antibodies testing is key in the diagnosis of AN.

Summary
AN have emerged as a new diagnostic category pathologically different from acquired demyelinating neuropathies. Clinically they overlap with GBS and CIDP although they associate with specific clinical features that should lead to clinical suspicion. Nodal/paranodal antibodies are key effector mechanisms of disease and good diagnostic and disease-monitoring biomarkers in AN.
Selfish, promiscuous and sometimes useful: how mobile genetic elements drive horizontal gene transfer in microbial populations
Authors: Haudiquet Matthieu , de Sousa Jorge Moura , Touchon Marie , Rocha Eduardo P. C. 
Published: August 2022

Horizontal gene transfer (HGT) drives microbial adaptation but is often under the control of mobile genetic elements (MGEs) whose interests are not necessarily aligned with those of their hosts. In general, transfer is costly to the donor cell while potentially beneficial to the recipients. The diversity and plasticity of cell–MGEs interactions, and those among MGEs, result in complex evolutionary processes where the source, or even the existence of selection for maintaining a function in the genome, is often unclear. For example, MGE-driven HGT depends on cell envelope structures and defense systems, but many of these are transferred by MGEs themselves. MGEs can spur periods of intense gene transfer by increasing their own rates of horizontal transmission upon communicating, eavesdropping, or sensing the environment and the host physiology. This may result in high-frequency transfer of host genes unrelated to the MGE. Here, we review how MGEs drive HGT and how their transfer mechanisms, selective pressures and genomic traits affect gene flow, and therefore adaptation, in microbial populations. The encoding of many adaptive niche-defining microbial traits in MGEs means that intragenomic conflicts and alliances between cells and their MGEs are key to microbial functional diversification.
This article is part of a discussion meeting issue ‘Genomic population structures of microbial pathogens’.
The effect of sequencing and assembly on the inference of horizontal gene transfer on chromosomal and plasmid phylogenies
Authors: Huisman Jana S. , Vaughan Timothy G. , Egli Adrian , Tschudin-Sutter Sarah , Stadler Tanja , Bonhoeffer Sebastian 
Published: August 2022

The spread of antibiotic resistance genes on plasmids is a threat to human and animal health. Phylogenies of bacteria and their plasmids contain clues regarding the frequency of plasmid transfer events, as well as the co-evolution of plasmids and their hosts. However, whole genome sequencing data from diverse ecological or clinical bacterial samples are rarely used to study plasmid phylogenies and resistance gene transfer. This is partially due to the difficulty of extracting plasmids from short-read sequencing data. Here, we use both short- and long-read sequencing data of 24 clinical extended-spectrumβ-lactamase (ESBL)-producingEscherichia colito estimate chromosomal and plasmid phylogenies. We compare the impact of different sequencing and assembly methodologies on these phylogenies and on the inference of horizontal gene transfer. We find that chromosomal phylogenies can be estimated robustly with all methods, whereas plasmid phylogenies have more variable topology and branch lengths across the methods used. Specifically, hybrid methods that use long reads to resolve short-read assemblies (HybridSPAdes and Unicycler) perform better than those that started from long reads during assembly graph generation (Canu). By contrast, the inference of plasmid and antibiotic resistance gene transfer using a parsimony-based criterion is mostly robust to the choice of sequencing and assembly method.This article is part of a discussion meeting issue ‘Genomic population structures of microbial pathogens’.
A scalable analytical approach from bacterial genomes to epidemiology
Authors: Didelot Xavier , Parkhill Julian 
Published: August 2022

Recent years have seen a remarkable increase in the practicality of sequencing whole genomes from large numbers of bacterial isolates. The availability of this data has huge potential to deliver new insights into the evolution and epidemiology of bacterial pathogens, but the scalability of the analytical methodology has been lagging behind that of the sequencing technology. Here we present a step-by-step approach for such large-scale genomic epidemiology analyses, from bacterial genomes to epidemiological interpretations. A central component of this approach is the dated phylogeny, which is a phylogenetic tree with branch lengths measured in units of time. The construction of dated phylogenies from bacterial genomic data needs to account for the disruptive effect of recombination on phylogenetic relationships, and we describe how this can be achieved. Dated phylogenies can then be used to perform fine-scale or large-scale epidemiological analyses, depending on the proportion of cases for which genomes are available. A key feature of this approach is computational scalability and in particular the ability to process hundreds or thousands of genomes within a matter of hours. This is a clear advantage of the step-by-step approach described here. We discuss other advantages and disadvantages of the approach, as well as potential improvements and avenues for future research.This article is part of a discussion meeting issue ‘Genomic population structures of microbial pathogens’.
Fetoscopic Endoluminal Tracheal Occlusion with Smart-TO balloon: efficacy of removal and safety
Authors: Sananès Nicolas , Basurto David , Cordier Anne-Gaël , Elie Caroline , Russo Francesca , Benachi Alexandra , Deprest Jan 
Published: August 2022

ABSTRACTIntroductionOne of the drawbacks of fetoscopic endoluminal tracheal occlusion (FETO) for congenital diaphragmatic hernia is the need for a second invasive intervention to reestablish airway patency. The “Smart-TO” (Strasbourg University-BSMTI, France) is a new balloon for FETO, which spontaneously deflates when positioned near a strong magnetic field, e.g., generated by a magnetic resonance image (MRI) scanner. Translational experiments have demonstrated its efficacy and safety. We will now use the Smart-TO balloon for the first time in humans. Our main objective is the efficacy of prenatal deflation of the balloon by the magnetic field generated by an MRI scanner.Material and methodsThis is a phase-I study conducted in the fetal medicine units of Antoine–Béclère Hospital, France, and UZ Leuven, Belgium. Conceived in parallel, protocols were amended by the local Ethics Committees, resulting in some minor differences. This trial is a single-arm interventional feasibility study. Twenty (France) and 25 (Belgium) participants will have FETO with the Smart-TO balloon. Balloon deflation will be scheduled at 34 weeks or earlier if clinically required. The primary endpoint is the successful deflation of the Smart-TO balloon after exposure to the magnetic field of an MRI, assessed through ultrasound immediately after MRI-exposure. The secondary objective is to report on the safety of the balloon. The percentage of fetuses in whom the balloon is deflated after exposure will be calculated with its 95% confidence interval. Safety will be evaluated by reporting the nature, number, and percentage of serious unexpected or adverse reactions.ConclusionThis phase-I study may provide the first evidence of the potential to reverse the occlusion by Smart-TO and free the airways non-invasively, as well a safety data.
Combining cash transfers and cognitive behavioral therapy to reduce antisocial behavior in young men: A mediation analysis of a randomized controlled trial in Liberia
Authors: Carpena Marina Xavier , Paula Cristiane Silvestre , Loret de Mola Christian , Hessel Philipp , Avendano Mauricio , Evans-Lacko Sara , Matijasevich Alicia 
Published: August 2022

AbstractBackgroundInterventions that combine cognitive behavioral therapy (CBT) with unconditional cash transfers (UCT) reduce the risk of antisocial behavior (ASB), but the underlying mechanisms are unclear. In this paper, we test the role of psychological and cognitive mechanisms in explaining this effect. We assessed the mediating role of executive function, self-control, and time preferences.MethodsWe used data from the Sustainable Transformation of Youth in Liberia, a community-based randomized controlled trial of criminally engaged men. The men were randomized into: Group-1: control (n=237); and Group-2: CBT+UCT (n=207). ASB was measured 12-13 months after the interventions were completed, and the following mediators were assessed 2-5 weeks later: (i) self-control, (ii) time preferences and (iii) executive functions. We estimated the natural direct effect (NDE) and the natural indirect effect (NIE) of the intervention over ASB.ResultsSelf-control, time preferences and a weighted index of all three mediators were associated with ASB scores, but the intervention had an effect on time preferences only [B= 0.09 95%CI (0.03; 0.15)]. There was no evidence that the effect of the intervention on ASB was mediated by self-control [BNIE= 0.007 95%CI (-0.01; 0.02)], time preferences [BNIE= -0.02 95%CI (-0.05; 0.01)], executive functions [BNIE= 0.002 95%CI (-0.002; 0.006)] or the weighted index of the mediators [BNIE= -0.0005 95%CI (-0.03; 0.02)].ConclusionsUCT and CBT lead to improvements in ASB, even in the absence of mediation via psychological and cognitive functions. Findings suggest that the causal mechanisms may involve non-psychological pathways.
Subjective Cognitive Decline is a Better Marker for Future Cognitive Decline in Females than in Males
Authors: Oliver Michael D. , Morrison Cassandra , Kamal Farooq , Graham Jillian , Dadar Mahsa 
Published: August 2022

AbstractBackgroundThe identification of biomarkers and other mechanisms for early detection of Alzheimer’s disease is critical to the development and further advancement of therapies and interventions targeted at managing symptoms and tracking the pathophysiology of disease. The endorsement of subjective cognitive decline (SCD) has emerged as a potential indicator of early change in cognitive status that may be predictive of future impairment at a time when measurable declines in neuropsychological performance cannot be detected. While there are numerous findings revealing sex differences in the prevalence of Alzheimer’s disease, there is a paucity of research examining sex differences in SCD. Therefore, the goal of this project is to determine if the relationship between the endorsement of SCD and future cognitive changes differ as a function of biological sex.MethodsA sample of 3019 male and female healthy older adults (2188 without SCD, 831 with SCD), with a mean follow-up time of 5.7 years, were included from the Rush Alzheimer’s Disease Center Research Sharing Hub. Linear regressions were performed to determine group differences in baseline cognitive scores, while linear mixed effects models were computed to determine group differences in the rate of cognitive change over time.ResultsIndividuals endorsing SCD had significantly lower baseline cognitive scores and increased rates of decline in all cognitive domains compared to those without SCD. Males exhibited significantly lower scores in baseline performance in global cognition, episodic memory, semantic memory, and perceptual speed regardless of SCD classification. Females with SCD were found to decline at significantly faster rates than both males with SCD and males and females without SCD in all cognitive domains over 15-year follow-up.ConclusionsSCD is related to lower baseline cognitive performance and faster cognitive decline compared to those who do not endorse SCD. Females with SCD have the fastest rate of decline suggesting that SCD may be more predictive of future decline in females than in males. Therapeutic interventions targeting SCD in females may aid in the mitigation of sex disparities in AD prevalence.
Pre-symptomatic reduction of individuality in the AppNL-F knock-in model of Alzheimer’s disease
Authors: Ehret Fanny , Pelz Meike S. , Senko Anna N. , Soto Karla E. G. , Liu Hang , Kempermann Gerd 
Published: August 2022

AbstractWhile one third of the risk for Alzheimer’s disease (AD) is explained by environment and lifestyle, AD pathology also affects individual lifestyle, possibly long before clinical manifestation of dementia. To study this hidden disease effect with its potentially large impact on coping with AD, we examined in mice how the AppNL-F/NL-F (NL-F) knock-in mutation affects the pre-symptomatic response to environmental enrichment (ENR). We assessed the emergence of inter-individual phenotypic variation while both genetic background and the shared environment were held constant, thereby isolating the contribution of individual behavior (‘non-shared environment’). After 4 months of ENR, in NL-F both mean and variability of plasma ApoE were increased, suggesting a pre-symptomatic variation in pathogenic processes. Roaming entropy (RE) as a measure of behavioral activity was continuously assessed with radiofrequency identification (RFID) technology and revealed reduced habituation and variance in NL-F compared to controls. Intra-individual variation decreased but behavioral predictability and stability were reduced in NL-F. Seven months after discontinuation of ENR we found no difference in plaque size and number, but ENR increased variance in hippocampal plaque counts in NL-F. A reactive increase in adult hippocampal neurogenesis in NL-F, known from other models, was normalized by ENR. Our data suggest that, while NL-F has early effects on individual behavioral patterns in response to ENR, there are lasting effects at the level of cellular plasticity even after discontinuation of ENR. Hence, early behavior matters for maintaining individual behavioral trajectories and brain plasticity even under maximally constraint conditions.
How to optimally sample a sequence for rapid analysis
Authors: Frith Martin C. , Shaw Jim , Spouge John L. 
Published: August 2022

AbstractWe face an increasing flood of genetic sequence data, from diverse sources, requiring rapid computational analysis. Rapid analysis can be achieved by sampling a subset of positions in each sequence. Previous sequence-sampling methods, such as minimizers, syncmers, and minimally-overlapping words, were developed by heuristic intuition, and are not optimal.We present a sequence-sampling approach that provably optimizes sensitivity for a whole class of sequence comparison methods, for randomly-evolving sequences. It it likely near-optimal for a wide range of alignmentbased and alignment-free analyses. For real biological DNA, it increases specificity by avoiding simple repeats. Our approach generalizes universal hitting sets (which guarantee to sample a sequence at least once), and polar sets (which guarantee to sample a sequence at most once). This helps us understand how to do rapid sequence analysis as accurately as possible.
Estimating bone marrow adiposity from head MRI and identifying its genetic architecture
Authors: Kaufmann Tobias , Bjørnstad Pål Marius , Falck Martin , Nerland Stener , O’Connell Kevin , Frei Oleksandr , Andreassen Ole A. , Westlye Lars T. , Djurovic Srdjan , Hughes Timothy 
Published: August 2022

AbstractBone marrow adiposity changes radically through the lifespan, but this phenomenon is poorly characterised and understood in humans. Large datasets of magnetic resonance imaging (MRI) scans of the head have been collected to study the human brain, but also contain unexploited information about other organs. We developed an artificial neural network that localises calvarial bone marrow in T1-weighted MRI head scans, enabling us to study its composition in several large MRI datasets, and to model sex-dimorphic age trajectories, including the effect of menopause. We revealed high heritability in single-nucleotide polymorphism and twin data, and identified 41 genetic loci significantly associated with the trait, including six sex-specific loci. Integrating mapped genes with existing bone marrow single-cell RNA-sequencing data revealed patterns of adipogenic lineage differentiation and lipid loading. Finally, we identified significant genetic correlations with several human traits, including cognitive ability and Parkinson’s disease, which is intriguing in light of the recently discovered channels that link calvarial bone marrow to the meninges.
Upper-room germicidal ultraviolet light reduced respiratory-related absenteeism among pre-school students: an analysis of newly discovered historical data
Authors: Ryan Christopher W. 
Published: August 2022

AbstractObjectivesTo assess the effect of upper-room germicidal ultraviolet light systems (GUV) on child absenteeism from a preschool.MethodsI fit a generalized linear model for interventional time series to a newly-discovered historical dataset of attendance records from a preschool from 1941 to 1949, where GUV was installed in December 1945.ResultsIn all but peak summer months, the presence of GUV was associated with a sizable reduction in child absenteeism due to respiratory illnesses of any cause. Odds ratios for the effect ranged from 0.49 to 0.77, depending on season. In all but high summer, model-predicted absenteeism rates with GUV were a third to a half what they were without it.ConclusionsInstallation of upper-room germicidal light in a preschool in December 1945 was associated with a signficant and operationally meaningful reduction in absenteeism due to respiratory illness of any cause. While today’s overall epidemiological environment may be different from that of the 1940s, COVID-19 has shown us that the human species remains vulnerable to pandemics of novel respiratory pathogens, to say nothing of annual influenza outbreaks. Thus air disinfection in congregate indoor settings remains a critical issue. Wider use of upper-room germicidal UV systems in schools and preschools may be worthwhile to reduce absenteeism due to illness, and the educational, social, and economic consequences that ensue.
Enhancing global preparedness during an ongoing pandemic from partial and noisy data
Authors: Klamser Pascal , d’Andrea Valeria , Di Lauro Francesco , Zachariae Adrian , Bontorin Sebastiano , di Nardo Antonello , Hall Matthew , Maier Benjamin F. , Ferretti Luca , Brockmann Dirk , De Domenico Manlio 
Published: August 2022

AbstractAs the coronavirus disease 2019 (COVID-19) spread globally, emerging variants such as B.1.1.529 quickly became dominant worldwide. Sustained community transmission favors the proliferation of mutated sub-lineages with pandemic potential, due to cross-national mobility flows, which are responsible for consecutive cases surge worldwide. We show that, in the early stages of an emerging variant, integrating data from national genomic surveillance and global human mobility with large-scale epidemic modeling allows to quantify its pandemic potential, providing quantifiable indicators for pro-active policy interventions. We validate our framework on worldwide spreading variants and gain insights about the pandemic potential of BA.5, BA.2.75 and other sub- and lineages. We combine the different sources of information in a simple estimate of the pandemic delay and show that only in combination, the pandemic potentials of the lineages are correctly assessed relative to each other. Country-level epidemic intelligence is not enough to contrast the pandemic of respiratory pathogens such as SARS-CoV-2 and a scalable integrated approach, i.e. pandemic intelligence, is required to enhance global preparedness.