bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Guide to Establishing a Pediatric Neurogastroenterology and Motility Program
Authors: Patel Dhiren , Sood Vibha , Ambartsumyan Lusine , Wheeler Justin , Kaul Ajay , Khlevner Julie , Darbari Anil , Rodriguez Leonel 
Published: January 2022

ABSTRACTThe purpose of this document is to provide guidance for establishing a pediatric neurogastroenterology and motility (PNGM) program, including considerations for personnel, equipment, and physical space requirements, and business planning, from members of the neurogastroenterology and motility (NGM) Committee of the North American Society for Pediatric Gastroenterology, Hepatology and Nutrition (NASPGHAN) who have developed PNGM programs at various institutions. A business plan defining the needs for required personnel, dedicated physical space, procedures, clinical care, and equipment storage is a prerequisite. Thoughtful logistical planning should address provider schedules, clinical visits, procedure coordination, and prior authorization processes. A business‐plan outlining equipment purchase with projected costs, revenue generation, and goals for future growth is desirable for obtaining institutional support, which is imperative to building a successful PNGM program.
Emerging Trends in Smartphone Photo Documentation of Child Physical Abuse
Authors: Schulte Ansley G. , Ricci Lawrence R. , Melville John D. , Brown Jocelyn 
Published: January 2022

Abstract
Photo documentation of injuries on children is universally recommended in cases of suspected child physical abuse. As technology improves, the ability to document physical examination findings through smartphone photography is increasingly accessible and practical. The quality of images captured on smartphones now rivals traditional photography and the integration of photo capture within the electronic medical record has led to a variety of fields adopting smartphone photo documentation for diagnosis, consult, and follow-up. However, in cases of child physical abuse, practitioners have been hesitant to adopt smartphones as a primary means of photo documentation because of concerns around image quality, privacy, and security. In this article, we discuss the technology of available smartphone cameras and current evidence regarding their use for photo documentation, use existing guidelines to propose a workflow to improve the yield of smartphone photo documentation in child physical abuse, and discuss common medicolegal concerns.
Regulators of proteostasis are translationally repressed in fibroblasts from sporadic and LRRK2-G2019S Parkinson’s patients
Authors: Flinkman Dani , Hong Ye , Deshpande Prasannakumar , Peltonen Sirkku , Kaasinen Valtteri , James Peter , Coffey Eleanor T. 
Published: January 2022

ABSTRACTParkinson’s disease (PD) is characterized by heterogeneous motor and non-motor symptoms. The majority of PD cases are sporadic, whereas the leucine-rich repeat kinase 2 (LRRK2) G2019S mutation is the most common monogenic cause of familial PD and symptomatically indistinguishable from the sporadic form. Deficits in protein synthesis have been reported in PD. However, it is not known which proteins are affected or if there are synthesis differences between patients with sporadic and LRRK2 G2019S PD. Here we used non-canonical amino acid labeling and mass-spectrometry based proteomics to perform a quantitative comparison of nascent proteins in fibroblasts from sporadic and G2019S mutation PD patients compared to healthy individuals. We found that several proteins were under-represented among nascent proteins in cells from PD patients. Among these were regulators endo-lysosomal sorting, mRNA processing and translation itself. We further validated which of these proteins were dysregulated at the static proteome level using targeted proteomics. Key downregulated proteins included the autophagy regulator ATG9A and translational stability regulator YTHDF3. Notably, 68% of the identified proteins were downregulated in both sporadic and LRRK2-G2019S forms of PD. We identify translational repression of key regulators of proteostasis in patient fibroblasts that are common to both sporadic and LRRK2-G2019S PD.
Higher aboveground carbon stocks in mixed-species planted forests than monocultures – a meta-analysis
Authors: Warner Emily , Cook-Patton Susan C. , Lewis Owen T. , Brown Nick , Koricheva Julia , Eisenhauer Nico , Ferlian Olga , Gravel Dominique , Hall Jefferson S. , Jactel Hervé , Mayoral Carolina , Meredieu Céline , Messier Christian , Paquette Alain , Parker William C. , Potvin Catherine , Reich Peter B. , Hector Andy 
Published: January 2022

AbstractNatural forest is declining globally as the area of planted forest increases. Planted forests are often monocultures, despite results suggesting that higher species richness improves ecosystem functioning and stability. To test if this is generally the case, we performed a meta-analysis of available results. We assessed aboveground carbon stocks in mixed-species planted forests vs (a) the average of constituent species monocultures, (b) the best constituent species monoculture, and (c) commercial species monocultures. We investigated whether any advantage of mixtures over monocultures was positively related to species richness, as well as potential mechanisms driving differences in carbon stocks between mixtures and monocultures. The meta-analysis dataset included 79 comparisons from 21 sites. Carbon stocks in mixed planted forests were higher than the average of stocks in monocultures of their constituent species, containing on average 70% more carbon. Mixed planted forests also out-performed commercial monocultures, containing on average 77% more carbon. There was c.25% more carbon in mixed planted forests relative to the best performing monocultures, although this difference was not statistically significant. Overyielding was highest in four-species mixtures (richness range 2-6 species). More data providing better coverage of richness and age gradients (study sites aged 3.5-28 years) is needed to increase confidence in these results. None of the potential mechanisms we examined (nitrogen-fixer present vs absent; native vs non-native/mixed origin; tree diversity experiment vs forestry plantation) consistently explained variation in the diversity effects. This suggests that our findings are driven by a combination of small (statistically insignificant) effects from these sources or further unidentified mechanisms or some combination of the two. We conclude that increasing tree species richness in planted forests can increase carbon stocks while bringing other potential benefits associated with diversification. However, implementation will depend on the balance of these benefits relative to the operational challenges and costs of diversification.
ccnWheat: A Database for Comparing Co-expression Networks Analysis of Allohexaploid Wheat and Its Progenitors
Authors: Li Zhongqiu , Hu Yiheng , Ma Xuelian , Da Lingling , She Jiajie , Liu Yue , Yi Xin , Cao Yaxin , Xu Wenying , Jiao Yuannian , Su Zhen 
Published: January 2022

AbstractGenetic and epigenetic changes after polyploidization events could result in variable gene expression and modified regulatory networks. Here, using large-scale transcriptome data, we constructed co-expression networks for diploid, tetraploid, and hexaploid wheat species, and built a platform for comparing co-expression networks of allohexaploid wheat and its progenitors, named ccnWheat. ccnWheat is a platform for searching and comparing specific functional co-expression networks, as well as identifying the related functions of the genes clustered therein. Functional annotations like pathway, gene family, protein-protein interactions, microRNA (miRNA), and several lines of epigenome data are integrated in this platform, and Gene Ontology (GO) annotation, gene set enrichment analysis (GSEA), motif identification, and other useful tools are also included. Using ccnWheat, we found that the network of WHEAT ABERRANT PANICLE ORGANIZATION 1 (WAPO1) has more co-expressed genes related to spike development in hexaploid wheat than its progenitors. We also found a novel motif of CArG specifically in the promoter region of WAPO-A1, suggesting that neofunctionalization of the WAPO-A1 gene affects spikelet development in hexaploid wheat. ccnWheat is useful for investigating co-expression networks and conducting other associated analyses, and thus facilitates comparative and functional genomic studies in wheat. ccnWheat is freely available at http://bioinformatics.cau.edu.cn/ccnWheat.
Isolating perceptual biases caused by trial history during auditory categorization
Authors: Duque Daniel , de la Rocha Jaime 
Published: January 2022

ABSTRACTJust as most experiences have their origin in our perceptions, our perceptions can also be fundamentally shaped by our experiences. However, isolating which events in the recent past can impact perceptual judgments remains a difficult question, partly because post-perceptual processes can also introduce strong history dependencies. Two mechanisms have been hypothesized to specifically modulate perception: 1) the repulsive influence caused by previous stimuli and generally labeled as aftereffects, and 2) the modulation caused by stimulus predictions based on learned temporal regularities of the sensory environment, a key assumption in the predictive coding framework. Here, we ask whether these two mechanisms do indeed bias perception by training rats in an auditory task featuring serial correlations along the sequence of stimuli. We develop a detailed behavioral model that isolates the repulsive aftereffect generated by previous stimuli and shows that this repulsion cannot be explained from an interaction between past and current stimuli, and that it is still present in catch trials lacking the current stimulus. Moreover, the model describes that the bias caused by the animals’ expectation, as they leverage the predictability of the stimulus sequence, is present in a foraging task without the sensory component but with the same serial correlations in the sequence of rewards. These results indicate that the aftereffect and the prediction biases observed during an auditory task can all be revealed in the absence of a sensory stimulus, putting into question their perceptual nature.
Metastability, fractal scaling, and synergistic information processing: what phase relationships reveal about intrinsic brain activity
Authors: Hancock Fran , Cabral Joana , Luppi Andrea I. , Rosas Fernando E. , Mediano Pedro A.M. , Dipasquale Ottavia , Turkheimer Federico E. 
Published: January 2022

AbstractDynamic functional connectivity (dFC) in resting-state fMRI holds promise to deliver candidate biomarkers for clinical applications. However, the reliability and interpretability of dFC metrics remain contested. Despite a myriad of methodologies and resulting measures, few studies have combined metrics derived from different conceptualizations of brain functioning within the same analysis - perhaps missing an opportunity for improved interpretability. Using a complexity-science approach, we assessed the reliability and interrelationships of a battery of phase-based dFC metrics including tools originated from dynamical systems, stochastic processes, and information dynamics approaches. Our analysis revealed novel relationships between these metrics, which allowed us to build a predictive model for integrated information using metrics from dynamical systems and information theory. Furthermore, global metastability - a metric reflecting simultaneous tendencies for coupling and decoupling - was found to be the most representative and stable metric in brain parcellations that included cerebellar regions. Additionally, spatiotemporal patterns of phase-locking were found to change in a slow, non-random, continuous manner over time. Taken together, our findings show that the majority of characteristics of resting-state fMRI dynamics reflect an interrelated dynamical- and informational-complexity profile, which is unique to each acquisition. This finding challenges the interpretation of results from cross-sectional designs for brain neuromarker discovery, suggesting that individual life-trajectories may be more informative than sample means.HighlightsSpatiotemporal patterns of phase-locking tend to be time-invariantGlobal metastability is representative and stable in a cohort of heathy young adultsdFC characteristics are in general unique to any fMRI acquisitionDynamical- and informational-complexity are interrelatedComplexity science contributes to a coherent description of brain dynamics
Balancing sensitivity and specificity in preclinical research
Authors: Danziger Meggie , Collazo Anja , Dirnagl Ulrich , Toelch Ulf 
Published: January 2022

AbstractThe success of scientific discovery in preclinical research is based on the different roles of exploration and confirmation. Exploration involves identifying potential effects (high sensitivity), which are then tested more rigorously during confirmation (high specificity). Here, we examine different experimental strategies and their ability to balance sensitivity and specificity to identify relevant effects. In simulations based on empirical data, we specifically compare a conventional p-value based approach with a method based on an a priori determined smallest effect size of interest (SESOI). Using a SESOI increases transition rates from exploration to confirmation and leads to higher detection rates across the trajectory. In particular, specificity in the SESOI trajectory increases if number of true effects are low. We conclude that employing a SESOI is superior to a p-value based approach in many contexts. Based on our findings, we propose a reconsideration of planning and conducting preclinical experiments, especially when the prior probability of true hypotheses is low.
Contractility-induced self-organization of smooth muscle cells: from multilayer cell sheets to dynamic three-dimensional clusters
Authors: Wang Xiuyu , Gonzalez-Rodriguez David , Vourc’h Thomas , Silberzan Pascal , Barakat Abdul I. 
Published: January 2022

AbstractSmooth muscle cells (SMCs) are mural cells that play a vital contractile function in many tissues. Abnormalities in SMC organization are associated with many diseases including atherosclerosis, asthma, and uterine fibroids. Various studies have reported that SMCs cultured on flat surfaces can spontaneously form three-dimensional clusters whose organization resembles that encountered in some of these pathological settings. Remarkably, how these structures form remains unknown. Here we combine in vitro experiments and physical modeling to show that three-dimensional clusters initiate when cellular contractile forces induce a hole in a flat SMC sheet, a process that can be modeled as the brittle fracture of a viscoelastic material. The subsequent evolution of the nascent cluster can be modeled as an active dewetting process with cluster shape evolution driven by a balance between cluster surface tension, arising from both cell contractility and adhesion, and cluster viscous dissipation. The description of the physical mechanisms governing the spontaneous emergence of these intriguing three-dimensional clusters offers insight into SMC-related disorders.
Sequencing of individual barcoded cDNAs on Pacific Biosciences and Oxford Nanopore reveals platform-specific error patterns
Authors: Mikheenko Alla , Prjibelski Andrey D , Joglekar Anoushka , Tilgner Hagen U 
Published: January 2022

AbstractLong-read transcriptomics requires understanding error sources inherent to technologies. Current approaches cannot compare methods for an individual RNA molecule. Here, we present a novel platform comparison method that combined barcoding strategies and long-read sequencing to sequence cDNA copies representing an individual RNA molecule on both Pacific Biosciences and Oxford Nanopore. We compared these long reads pairs in terms of sequence content and splicing structure. Although individual read pairs show high similarity, we found differences in (i) aligned length, (ii) TSS and (iii) polyA-site assignment, and (iv) exon-intron structures. Overall 25% of read pairs disagreed on either TSS, polyA-site, or a splice site. Intron-chain disagreement typically arises from alignment errors of microexons and complicated splice sites. Our single-molecule technology comparison revealed that inconsistencies are often caused by sequencing-error induced inaccurate ONT alignments, especially to downstream GTNNGT donor motifs. However, annotation-disagreeing upstream shifts in NAGNAG acceptors in ONT are often confirmed by PacBio and thus likely real. In both barcoded and non-barcoded ONT reads, we found that intron number and proximity of other GT/AGs better predict inconsistency with the annotation than read quality alone. We summarized these findings in an annotation-based algorithm for spliced alignment correction that improves subsequent transcript construction with ONT reads.
Exploiting color space geometry for visual stimulus design across animals
Authors: Christenson Matthias P. , Mousavi S. Navid , Heath Sarah L. , Behnia Rudy 
Published: January 2022

AbstractColor vision represents a vital aspect of perception that ultimately enables a wide variety of species to thrive in the natural world. However, unified methods for constructing chromatic visual stimuli in a laboratory setting are lacking. Here, we present stimulus design methods and an accompanying programming package to efficiently probe the color space of any species in which the photoreceptor spectral sensitivities are known. Our hardware-agnostic approach incorporates photoreceptor models within the framework of the principle of univariance. This enables experimenters to identify the most effective way to combine multiple light sources to create desired distributions of light, and thus easily construct relevant stimuli for mapping the color space of an organism. We include methodology to handle uncertainty of photoreceptor spectral sensitivity as well as to optimally reconstruct hyperspectral images given recent hardware advances. Our methods support broad applications in color vision science and provide a framework for uniform stimulus designs across experimental systems.
Nirmatrelvir, Molnupiravir, and Remdesivir maintain potent in vitro activity against the SARS-CoV-2 Omicron variant
Authors: Rosales Romel , McGovern Briana L. , Rodriguez M. Luis , Rai Devendra K. , Cardin Rhonda D. , Anderson Annaliesa S. ,   PSP study group, Sordillo Emilia Mia , van Bakel Harm , Simon Viviana , García-Sastre Adolfo , White Kris M. 
Published: January 2022

AbstractVariants of SARS-CoV-2 have become a major public health concern due to increased transmissibility, and escape from natural immunity, vaccine protection, and monoclonal antibody therapeutics. The highly transmissible Omicron variant has up to 32 mutations within the spike protein, many more than previous variants, heightening these concerns of immune escape. There are now multiple antiviral therapeutics that have received approval for emergency use by the FDA and target both the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) and the main protease (Mpro), which have accumulated fewer mutations in known SARS-CoV-2 variants. Here we test nirmatrelvir (PF-07321332), and other clinically relevant SARS-CoV-2 antivirals, against a panel of SARS-CoV-2 variants, including the novel Omicron variant, in live-virus antiviral assays. We confirm that nirmatrelvir and other clinically relevant antivirals all maintain activity against all variants tested, including Omicron.
Assessing the impact of roadkill on the persistence of wildlife populations: a case study on the giant anteater
Authors: Ascensão Fernando , Desbiez Arnaud L.J. 
Published: January 2022

AbstractHuman activity is depleting biodiversity, and road networks are directly contributing to this trend due to roadkill. Nevertheless, few studies empirically estimated the impact of roadkill on wildlife populations. We integrated information on roadkill rates, population abundance, and animal movement to estimate the survival rates and the proportion of the population likely to be extirpated due to roadkill, using giant anteater (Myrmecophaga tridactyla) as model species. We then assessed the consequent implications of roadkill on population persistence using population viability analysis (PVA). The yearly survival rate of resident anteaters inhabiting road vicinity areas (0.78; CI:0.62-0.97) was considerably lower than for those living far from roads (0.95; CI:0.86-1.00). The real number of anteaters being road-killed is considerably higher than the one recorded in previous studies (by a factor of 2.4), with ca. 20% of the population inhabiting road vicinity areas being road-killed every year. According to PVA results, roadkill can greatly affect the persistence of the giant anteater populations by reducing the growth rate down to null or negative values. This study confirms that roads have significant impacts on local population persistence. Such impacts are likely to be common to other large mammals, calling for effective mitigation to reduce roadkill rates.
Modified viral-genetic mapping reveals local and global connectivity relationships of ventral tegmental area dopamine cells
Authors: Beier Kevin T. 
Published: January 2022

ABSTRACTDopamine cells in the ventral tegmental area (VTADA) are critical for a variety of motivated behaviors. These cells receive synaptic inputs from over 100 anatomically-defined brain regions, which enables control from a distributed set of inputs across the brain. Extensive efforts have been made to map inputs to VTA cells based on neurochemical phenotype and output site. However, all of these studies have the same fundamental limitation that inputs local to the VTA cannot be properly assessed due to non-Cre-dependent uptake of EnvA-pseudotyped virus. Therefore, the quantitative contribution of local inputs to the VTA, including GABAergic, DAergic, and serotonergic, is not known. Here, we used a modified viral-genetic strategy that enables examination of both local as well as long-range inputs to VTADAcells. We found that nearly half of the total inputs to VTADAcells are located locally, revealing a substantial portion of inputs that have been missed by previous analyses. The majority of inhibition to VTADAcells arises from the substantia nigra pars reticulata, with large contributions from the VTA and the substantia nigra pars compacta. In addition to receiving inputs from VTAGABAneurons, DA neurons are connected with other DA neurons within the VTA as well as the nearby retrorubal field. Lastly, we show that VTADAneurons receive inputs from distributed serotonergic neurons throughout the midbrain and hindbrain, with the majority arising from the dorsal raphe. Our study highlights the importance of using the appropriate combination of viral-genetic reagents to unmask the complexity of connectivity relationships to defined cells in the brain.