bluuebunny/crossref_metadata_2025_split huggingface dataset:
Visual stimuli modulate local field potentials but drive no high-frequency activity in human auditory cortex
Authors: Ahveninen Jyrki , Lee Hsin-Ju , Yu Hsiang-Yu , Lee Cheng-Chia , Chou Chien-Chen , Ahlfors Seppo P. , Kuo Wen-Jui , Jääskeläinen Iiro P. , Lin Fa-Hsuan , Statement Significance 
Published: July 2022

AbstractNeuroimaging studies suggest cross-sensory visual influences in human auditory cortices. Whether these influences reflect active visual processing in human auditory cortices (ACs), which drives neuronal firing and concurrent broadband high-frequency activity (BHFA; >70 Hz), or whether they merely modulate sound processing is still debatable. Here, we presented auditory, visual, and audiovisual stimuli to 16 participants (7 women, 9 men) with stereo-EEG depth electrodes implanted near ACs for presurgical monitoring. Anatomically normalized group analyses were facilitated by inverse modeling of intracranial source currents. Analyses of intracranial event-related potentials (iERP) suggested cross-sensory responses to visual stimuli in ACs, which lagged the earliest auditory responses by several tens of milliseconds. Visual stimuli also modulated the phase of intrinsic low-frequency oscillations and triggered 15–30-Hz event-related desynchronization in ACs. However, BHFA, a putative correlate of neuronal firing, was not significantly increased in ACs after visual stimuli, not even when they coincided with auditory stimuli. Intracranial recordings demonstrate cross-sensory modulations, but no indication of active visual processing in human ACs.Significance StatementVisual information has a profound influence on auditory processing, particularly in noisy conditions. These “cross-sensory” influences start already in auditory cortices, the brain area that processes sound signals. It has, however, been unclear whether auditory cortex actively processes visual information or whether visual signals only change the way sounds are processed. We studied this question by neurophysiological recordings from 16 participants with epilepsy who had electrodes implanted in their brains due to medical reasons. Using these intracranial recordings, we show that cross-sensory visual information modulates sound processing but triggers no high-frequency activity -- a correlate of local neuronal firing -- in auditory cortex. This result provides important information on the role of sensory areas in multisensory processing in the human brain.
Conservation networks do not match the ecological requirements of amphibians
Authors: Florence Matutini , Baudry Jacques , Fortin Marie-Josée , Pain Guillaume , Pithon Joséphine 
Published: July 2022

AbstractAmphibians are among the most threatened taxa as they are highly sensitive to habitat degradation and fragmentation. They are considered as model species to evaluate habitats quality in agricultural landscapes. In France, all amphibian species have a protected status requiring recovery plans for their conservation. Conservation networks combining protected areas and green infrastructure can help the maintenance of their habitats while favouring their movement in fragmented landscapes such as farmlands. Yet, assessing the effectiveness of conservation networks is challenging.Here, we compared the ecological requirements of amphibian species with existing conservation network coverage in a human-dominated region of western France. First, we mapped suitable habitat distributions for nine species of amphibian with varying ecological requirements and mobility. Second, we used stacking species distribution modelling (SSDM) to produce multi-species habitat suitability maps. Then, to identify spatial continuity in suitable habitats at the regional scale, we defined species and multi-species core habitats to perform a connectivity analysis using Circuitscape theory. Finally, we compared different suitability maps with existing conservation networks to assess conservation coverage and efficiency.We highlighted a mismatch between the most suitable amphibian habitats at the regional scale and the conservation network, both for common species and for species of high conservation concern. We also found two bottlenecks between areas of suitable habitat which might be crucial for population movements induced by global change, especially for species associated with hedgerow mosaic landscapes. These bottlenecks were not covered by any form of protection and are located in an intensive farmland context.Synthesis and applications- We advocate the need to better integrate agricultural landscape mosaics into species conservation planning as well as to protect and promote agroecological practices suitable for biodiversity, including mixed and extensive livestock farming. We also emphasize the importance of interacting landscape elements of green infrastructure for amphibian conservation and the need for these to be effectively considered in land-use planning policies.Abstract FigurePCI recommendation :https://ecology.peercommunityin.org/articles/rec?id=504
Distributional coding of associative learning within projection-defined populations of midbrain dopamine neurons
Authors: Avvisati Riccardo , Kaufmann Anna-Kristin , Young Callum J. , Portlock Gabriella E. , Cancemi Sophie , Costa Rui Ponte , Magill Peter J. , Dodson Paul D. 
Published: July 2022

ABSTRACTMidbrain dopamine neurons are thought to play key roles in learning by conveying the difference between expected and actual outcomes. While this teaching signal is often considered to be uniform, recent evidence instead supports diversity in dopamine signaling. However, it remains poorly understood how heterogeneous signals might be organized to facilitate the role of downstream circuits mediating distinct aspects of behavior. Here we investigated the organizational logic of dopaminergic signaling by recording and labeling individual midbrain dopamine neurons during associative behavior. We defined combinations of protein expression and cellular localization to sort recorded neurons according to the striatal regions they innervate. Our findings show that reward information and task variables are not only heterogeneously encoded, with multiplexing, but also differentially distributed across populations of dopamine neurons projecting to different regions of striatum. These data, supported by computational modelling, indicate that such distributional coding can maximize dynamic range and tailor dopamine signals to facilitate the specialized roles of different striatal regions.
MCT1-dependent energetic failure and neuroinflammation underlie optic nerve degeneration in Wolfram syndrome mice
Authors: Rossi Greta , Ordazzo Gabriele , Vanni Niccolò N. , Castoldi Valerio , Iannielli Angelo , Di Silvestre Dario , Bellini Edoardo , Bernardo Letizia , Giannelli Serena G. , Muggeo Sharon , Letizia Leocani , Mauri PierLuigi , Broccoli Vania 
Published: July 2022

SummaryWolfram syndrome 1 (WS1) is a rare genetic disorder caused by mutations in the WFS1 gene leading to a wide spectrum of clinical dysfunctions, among which blindness, diabetes and neurological deficits are the most prominent. WFS1 encodes for the endoplasmic reticulum (ER) resident transmembrane protein Wolframin with multiple functions in ER processes. However, the WFS1-dependent etiopathology in retinal cells is unknown. Herein, we showed that Wfs1 mutant mice developed early retinal electrophysiological impairments followed by marked visual loss. Interestingly, axons and myelin disruption in the optic nerve preceded the degeneration of the retinal ganglion cell bodies in the retina. Transcriptomics at pre-degenerative stage revealed the STAT3-dependent activation of proinflammatory glial markers with reduction of the homeostatic and pro-survival factors Glutamine synthetase and BDNF. Furthermore, label-free comparative proteomics identified a significant reduction of the monocarboxylate transport isoform 1 (MCT1) and its partner Basigin that are highly enriched on retinal astrocytes and myelin-forming oligodendrocytes in optic nerve together with Wolframin. Loss of MCT1 caused a failure in lactate transfer from glial to neuronal cell bodies and axons leading to a chronic hypometabolic state. Thus, this bioenergetic impairment is occurring concurrently both in the axonal regions and cell bodies of the retinal ganglion cells, selectively endangering their survival while impacting less on other retinal cells. This metabolic dysfunction occurs months before the frank RGC degeneration suggesting an extended time window for intervening with new therapeutic strategies focused on boosting retinal and optic nerve bioenergetics in WS1.
An integrase clade that repeatedly targets prophage late genes, yielding helper-embedded satellites
Authors: Tommasini Dario , Mageeney Catherine M. , Williams Kelly P. 
Published: July 2022

ABSTRACTSatellites are mobile genetic elements that rely on helper phages for their mobilization. The many known satellite-helper interactions are trans-regulatory, with gene products from one partner modulating the nucleic acid or protein activities of the other. We discovered a satellite type with a more intimate cis-regulatory configuration: integrated within, and co-oriented with, a late gene of its lambdoid helper prophage. This helper-embedded satellite (HES) configuration would delay expression of the interrupted helper late gene until the satellite excises; it also offers potential passive components to both HES replication and late transcription, driven by the helper. Induction of a helper-satellite composite was monitored; precise excision of the entire composite was observed, followed by its replication, and the excision of the satellite from it. We mapped 491 HESs to one of 14 sites in cognates of phage lambda late genes A, B, C, E, V, T, H, L and J. The associated integrases form a single phylogenetic clade with subclades respecting the 14 site groups, while the attP attachment site regions contained a new doubled DNA sequence motif. This clade thus exhibits a repeated tropism for prophage late genes as it develops new integration sites. HESs bear close genomic similarities to gram-negative phage-induced chromosomal islands (PICIs, of which we found many more integrated into fis and hpt genes). We describe four ordered zones in a general HES/PICI genome organization: an integration zone encoding integrase and AlpA, a Bro zone encoding members of the Bro-N network of domain-swapping DNA-interactive proteins and immunity repressor RNAs, a replication zone, and a late zone in which clusters as large as 18 consecutive helper late genes have been captured. Like the late zone, the Bro zone is dynamic, perhaps due to activity of the Bro proteins themselves.
One-to-one mapping between deep network units and real neurons uncovers a visual population code for social behavior
Authors: Cowley Benjamin R. , Calhoun Adam J. , Rangarajan Nivedita , Turner Maxwell H. , Pillow Jonathan W. , Murthy Mala 
Published: July 2022

AbstractThe rich variety of behaviors observed in animals arises through the complex interplay between sensory processing and motor control. To understand these sensorimotor transformations, it is useful to build models that predict not only neural responses to sensory input [1, 2, 3, 4, 5] but also how each neuron causally contributes to behavior [6, 7]. Here we demonstrate a novel modeling approach to identify a one-to-one mapping between internal units in a deep neural network and real neurons by predicting the behavioral changes arising from systematic perturbations of more than a dozen neuron types. A key ingredient we introduce is “knockout training”, which involves perturb-ing the network during training to match the perturbations of the real neurons during behavioral experiments. We apply this approach to model the sensorimotor transformation ofDrosophila melanogastermales during a com-plex, visually-guided social behavior [8, 9, 10]. The visual projection neurons at the interface between the eye and brain form a set of discrete channels, suggesting each channel encodes a single visual feature [11, 12, 13]. Our model reaches a different conclusion: The visual projection neurons form a highly distributed population code that collectively sculpts social behavior. Overall, our framework consolidates behavioral effects elicited from various neural perturbations into a single, unified model, providing a detailed map from stimulus to neuron to behavior.
Building bridges from genome to physiology using machine learning and Drosophila experimental evolution
Authors: Kezos James N. , Barter Thomas T. , Phillips Mark. A. , Cabral Larry G. , Azatian Grigor , Buenrostro José , Bhangoo Punjot Singh , Khong Annie , Reyes Gabriel T. , Rahman Adil , Humphrey Laura A. , Bradley Timothy J. , Mueller Laurence D. , Rose Michael R. 
Published: July 2022

AbstractDrosophila experimental evolution, with its well-defined selection protocols, has long supplied useful genetic material for the analysis of functional physiology. While there is a long tradition of interpreting the effects of large-effect mutants physiologically, in the genomic era identifying and interpreting gene-to-phenotype relationships has been challenging, with many labs not resolving how physiological traits are affected by multiple genes throughout the genome. Drosophila experimental evolution has demonstrated that multiple phenotypes change due to the evolution of many loci across the genome, creating the scientific challenge of sifting out differentiated but noncausal loci for individual characters. The fused lasso additive model method (FLAM) allows us to infer some of the differentiated loci that have relatively greater causal effects on the differentiation of specific phenotypes.The experimental material used in the present study comes from 50 populations that have been selected for different life-histories and levels of stress resistance. Differentiation of cardiac robustness, starvation resistance, desiccation resistance, lipid content, glycogen content, water content, and body masses was assayed among 40 to 50 of these experimentally-evolved populations. Through FLAM, we combined physiological analysis from eight parameters with whole-body pooled-seq genomic data to identify potentially causally linked genomic regions. We have identified approximately 1,900 significantly differentiated 50 kb genomic windows among our 50 populations, with 161 of those identified genomic regions highly likely to have a causal effect connecting specific genome sites to specific physiological characters.
Community evenness and sample size affect estimates of predation intensity and prey selection: A model-based validation
Authors: Bhattacherjee Madhura , Chattopadhyay Devapriya 
Published: July 2022

AbstractPredation estimates inferred from the preserved records of predation traces are essential in evaluating the evolutionary effect of ecological interactions. It is, however, crucial to establish how sampling intensity and community composition of an assemblage influence the reliability of these measures.Using a resampling technique, we evaluated the effect of sampling intensity and a community’s evenness on the inferred predation estimates. We theoretically simulated model communities representing different levels of evenness, predation intensity, and predatory behavior (selective, non-selective). We calculated the total predation intensity and the number of prey species for each community. We then resampled each community without replacement and noted variations in the inferred measure from the accurate estimate as the sampling intensity increased. Our results demonstrate that the evenness of a community does not influence the inferred predation intensity for non-selective predation. However, communities with highly selective predation are sensitive to evenness and sampling intensity; inferred predation intensity of these assemblages can substantially differ from the actual value. The inferred number of prey species is also influenced by the community’s original evenness, predation selectivity, and predation intensity. When predation is selective, sampling intensity heavily influences communities with low evenness and low predation intensity; inferred predation intensity is underrepresented in smaller sample sizes. For communities of low evenness and predation intensity where rare species are attacked preferentially, the inferred prey richness differs significantly at a small sample size.We proposed a post-facto standardization method for comparing predation estimates of discrete communities that differ in the sample size. We validated its utility using the published predation data of the Plio-Pleistocene molluscan fossil assemblage. The present approach attempts to provide critical insight into the reliability of predation estimates and may help in comparing predation patterns across time and space. Several factors, including preservation bias, might impact the final predation signature of an assemblage. It warrants a future research direction to develop a comprehensive framework of post-hoc standardization of assemblages with differing predation styles and preservation history.
Is there a placental microbiota? A critical review and re-analysis of published placental microbiota datasets
Authors: Panzer Jonathan , Romero Roberto , Greenberg Jonathan M. , Winters Andrew D. , Galaz Jose , Gomez-Lopez Nardhy , Theis Kevin R. 
Published: July 2022

ABSTRACTThe existence of a placental microbiota is under debate. The human placenta has historically been considered sterile and microbial colonization has been associated with adverse pregnancy outcomes. Yet, recent investigations using DNA sequencing reported a microbiota in human placentas from typical term pregnancies. However, this detected microbiota could represent background DNA contamination. Using fifteen publicly available 16S rRNA gene datasets, existing data were uniformly re-analyzed. 16S rRNA gene Amplicon Sequence Variants (ASVs) identified as Lactobacillus were highly abundant in eight of fifteen studies. However, the prevalence of Lactobacillus, a typical vaginal bacterium, was clearly driven by bacterial contamination from vaginal delivery and background DNA. After removal of likely DNA contaminants, Lactobacillus ASVs were highly abundant in only one of five studies for which data analysis could be restricted to placentas from term cesarean deliveries. A six study sub-analysis targeting the 16S rRNA gene V4 hypervariable region demonstrated that bacterial profiles of placental samples and technical controls share principal bacterial ASVs and that placental samples clustered primarily by study origin and mode of delivery. Across studies, placentas from typical term pregnancies did not share a consistent bacterial taxonomic signal. Contemporary DNA- based evidence does not support the existence of a placental microbiota.IMPORTANCEEarly-gestational microbial influences on human development are unclear. By applying DNA sequencing technologies to placental tissue, bacterial DNA signals were observed, leading some to conclude that a live bacterial placental microbiome exists in typical term pregnancy. However, the low-biomass nature of the proposed microbiome and high sensitivity of current DNA sequencing technologies indicate that the signal may alternatively derive from environmental or delivery-associated bacterial DNA contamination. Here we address these alternatives with a re- analysis of 16S rRNA gene sequencing data from 15 publicly available placental datasets. After identical DADA2 pipeline processing of the raw data, subanalyses were performed to control for mode of delivery and environmental DNA contamination. Both environment and mode of delivery profoundly influenced the bacterial DNA signal from term-delivered placentas. Aside from these contamination-associated signals, consistency was lacking across studies. Thus, placentas delivered at term are unlikely to be the original source of observed bacterial DNA signals.
Walking the line between assessment, improvement, and learning: an exploratory study on opportunities and risks of peer discussion of audit and feedback
Authors: van der Winden Dorien , van Dijk Nynke , Visser Mechteld , Bont Jettie 
Published: July 2022

AbstractIntroductionThere is a broad call for change in existing quality systems within health care. One of the anticipated reforms, is transferring ownership back to care deliverers. A promising way to establish this in general practice care, is to combine audit and feedback with peer group discussion. However, it is unknown what different stakeholder groups think of giving prominence to this type of quality improvement. In this study we explore ideas and opinions of different stakeholder groups in general practice on the opportunities and risks that could arise.MethodsWe conducted an exploratory qualitative study, combining interviews with focus discussion groups. Included stakeholder groups were general practitioners, patients, professional organizations and insurance companies. Within a constructivist paradigm, two researchers coded the data in three rounds, using thematic analysis. After continuously comparing and discussing codes with a third researcher, a final code tree emerged, presenting us with the main themes.ResultsIn eight interviews and two focus discussion groups, 22 participants reflected upon opportunities and risks. We identified three main opportunities: deeper levels of reflection upon data, adding context to numbers and more ownership, and three main risks: handling of unwilling colleagues, lacking a safe group and the necessity of patient involvement. An additional theme concerned disagreement on the amount of transparency that should be offered: insurance companies and patients advocated for complete transparency on data and improvement of outcomes, while GPs and professional organizations urged to restrict transparency to giving insight into the process.ConclusionPeer discussion of audit and feedback could be part of a change movement, towards a quality system based on learning and trust, that is powered from within the profession. Creating a safe learning environment is key herein. Caution is needed when complete transparency is asked, since it can jeopardize practitioners’ reflection and learning in safety.Strengths and limitations of this studyExploratory study of a gap in the knowledge towards implementation of a promising intervention.Participants included the four main stakeholder groups that are involved in implementation, in order to study agreement and disagreement between different stakeholders.Additional stakeholders, such as governmental agencies, were not included. They may have offered other perspectives.This exploratory qualitative study offers insight into opportunities and risks. In order to get a broad overview of how these findings are supported by GPs in general, additional quantitative research is necessary.