bluuebunny/crossref_metadata_2025_split huggingface dataset:
Technical Outcomes in Pediatric Endoscopic Retrograde Cholangiopancreatography: Data from an International Collaborative
Authors: Troendle David M. , Ruan Wenly , Fishman Douglas S. , Barth Bradley A. , Liu Quin Y. , Giefer Matthew , Kim Kyung Mo , Martinez Mercedes , Dall’oglio Luigi , Torroni Filippo , De Angelis Paola , Faraci Simona , Bitton Sam , Wilsey Michael , Khalaf Racha , Werlin Steven , Dua Kulwinder , Gugig Roberto , Huang Clifton , Mamula Petar , Quiros J. Antonio , Zheng Yuhua , Grover Amit , Fox Victor L. 
Published: September 2022

Objectives:
Endoscopic retrograde cholangiopancreatography (ERCP) in adults has been extensively studied through multicenter prospective studies. Similar pediatric studies are lacking. The Pediatric ERCP Database Initiative (PEDI) is a multicenter collaborative aiming to evaluate the indications and technical outcomes in pediatric ERCPs.

Methods:
In this prospective cohort study, data were recorded for pediatric ERCPs performed across 15 centers. A pre-procedure, procedure, 2-week post-procedure follow-up, and adverse event form were completed for each ERCP performed. Univariate and stepwise linear regression was performed to identify factors associated with technically successful procedures and adverse events.

Results:
A total of 1124 ERCPs were performed on 857 patients from May 1, 2014 to May 1, 2018. The median age was 13.5 years [interquartile range (IQR) 9.0–15.7]. Procedures were technically successful in the majority of cases (90.5%) with success more commonly encountered for procedures with biliary indications [odds ratio (OR) 4.2] and less commonly encountered for native papilla anatomy (OR 0.4) and in children <3 years (OR 0.3). Cannulation was more often successful with biliary cannulation (95.9%) compared to pancreatic cannulation via the major papilla (89.6%, P < 0.0001) or minor papilla (71.2%, P < 0.0005). The most commonly identified adverse events included post-ERCP pancreatitis (5%), pain not related to post-ERCP pancreatitis (1.8%), and bleeding (1.2%). Risk factors for the development of each were identified.

Conclusions:
This large prospective study demonstrates that ERCP is reliable and safe in the pediatric population. It highlights the utility of PEDI in evaluating the technical outcomes of pediatric ERCPs and demonstrates the potential of PEDI for future studies in pediatric ERCPs.
Application of Prospect Theory in Obstetrics by Evaluating Mode of Delivery and Outcomes in Neonates Born Small or Appropriate for Gestational Age
Authors: Michaeli Jennia , Michaeli Ofir , Rozitzky Ariel , Grisaru-Granovsky Sorina , Feldman Naomi , Srebnik Naama 
Published: September 2022

(Abstracted from JAMA Network Open 2022;5(3):e222177)
The antenatal diagnosis of fetal weight is a challenge that relies on sonographic estimations and the clinical assessment of fetal and maternal status. Meanwhile, the rate of detection of fetal growth restriction (FGR) is <40%.
Risk of Pregnancy Complications in Living Kidney Donors: A Systematic Review and Meta-analysis
Authors: Bellos Ioannis , Pergialiotis Vasilios 
Published: September 2022

(Abstracted from Eur J Obstet Gynecol Reprod Biol 2022;270:35–41)
The criterion standard for management of end-stage kidney disease is kidney donation. However, kidney donation remains a complicated medical issue for the donor, as mid- and long-range complications are possible as a result of the procedure.
Neurofibromin 1 mediates sleep depth in Drosophila
Authors: Brown Elizabeth B. , Zhang Jiwei , Lloyd Evan , Lanzon Elizabeth , Botero Valentina , Tomchik Seth , Keene Alex C. 
Published: September 2022

AbstractNeural regulation of sleep and metabolic homeostasis are critical in many aspects of human health. Despite extensive epidemiological evidence linking sleep dysregulation with obesity, diabetes, and metabolic syndrome, little is known about the neural and molecular basis for the integration of sleep and metabolic function. The RAS GTPase-activating gene Neurofibromin (Nf1) has been implicated in the regulation of sleep and metabolic rate, raising the possibility that it serves to integrate these processes, but the effects on sleep consolidation and physiology remain poorly understood. A key hallmark of sleep depth in mammals and flies is a reduction in metabolic rate during sleep. Here, we use indirect calorimetry to define the role of Nf1 on sleep-dependent changes in metabolic rate. Flies lacking Nf1 fail to suppress metabolic rate during sleep, raising the possibility that loss of Nf1 prevents flies from integrating sleep and metabolic state. Sleep of Nf1 mutant flies is fragmented with a reduced arousal threshold in Nf1 mutants, suggesting Nf1 flies fail to enter deep sleep. The effects of Nf1 on sleep can be localized to a subset of neurons expressing the GABA receptor Rdl. Selective knockdown of Nf1 in Rdl-expressing neurons increases gut permeability and reactive oxygen species (ROS) in the gut, suggesting a critical role for deep sleep in gut homeostasis. Together, these findings suggest Nf1 acts in GABA-sensitive neurons to modulate sleep depth in Drosophila.
Electrochemical disruption of extracellular electron transfer inhibits Pseudomonas aeruginosa cell survival within biofilms and is synergistic with antibiotic treatment
Authors: Otero Fernanda Jiménez , Newman Dianne K. , Tender Leonard M. 
Published: September 2022

AbstractSurvival of cells within oxygen-limited regions in Pseudomonas aeruginosa biofilms is enabled by using small redox active molecules as electron shuttles to access distal oxidants. This respiratory versatility makes P. aeruginosa biofilms common in chronic wound infections and recalcitrant to treatment. Here, we show that electrochemically controlling the redox state of these electron shuttles, specifically pyocyanin, can impact cell survival within anaerobic P. aeruginosa biofilms and can act synergistically with antibiotic treatment. We inhibited pyocyanin redox cycling under anoxic conditions by blocking its ability to be re-oxidized and thus serve as an electron shuttle via poising an electrode at a reductive potential that cannot regenerate oxidized pyocyanin (i.e. −400mV vs Ag/AgCl). This resulted in a decrease in CFUs within the biofilm of 100x compared to samples exposed to an electrode poised at an oxidizing potential that permits pyocyanin re-oxidation (i.e. +100mV vs Ag/AgCl). Phenazine-deficient Δphz* biofilms were not affected by the redox potential of the electrode, but were re-sensitized by adding pyocyanin. The effect of EET disruption was exacerbated when biofilms were treated with sub-MICs of a range of antibiotics. Most notably, 4 μg/ml of the aminoglycoside gentamicin in a reductive environment almost completely eradicated wild type biofilms but had no effect on the survival of Δphz* biofilms, suggesting reduced phenazines are toxic, and combined with antibiotic treatment can lead to extensive killing.ImportanceBiofilms provide a protective environment but they also present challenges to the cells living within them, such as overcoming diffusion limitation of nutrients and oxygen. Pseudomonas aeruginosa overcomes oxygen limitation by secreting soluble redox active molecules as electron shuttles to access distal oxygen. Here, we show that electrochemically blocking the redox cycling of one of these electron shuttles, pyocyanin, decreases cell survival within biofilms and acts synergistically with gentamicin to kill cells. Our results highlight the importance of the role that the redox cycling of electron shuttles fulfills within P. aeruginosa biofilms.
The Psychosis Human Connectome Project: Design and rationale for studies of visual neurophysiology
Authors: Schallmo Michael-Paul , Weldon Kimberly B. , Kamath Rohit S. , Moser Hannah R. , Montoya Samantha A. , Killebrew Kyle W. , Demro Caroline , Grant Andrea N. , Marjańska Małgorzata , Sponheim Scott R. , Olman Cheryl A. 
Published: September 2022

AbstractVisual perception is abnormal in psychotic disorders such as schizophrenia. In addition to hallucinations, laboratory tests show differences in fundamental visual processes including contrast sensitivity, center-surround interactions, and perceptual organization. A number of hypotheses have been proposed to explain visual dysfunction in psychotic disorders, including an imbalance between excitation and inhibition. However, the precise neural basis of abnormal visual perception in people with psychotic psychopathology (PwPP) remains unknown. Here, we describe the behavioral and 7 tesla MRI methods we used to interrogate visual neurophysiology in PwPP as part of the Psychosis Human Connectome Project (HCP). In addition to PwPP (n = 66) and healthy controls (n = 43), we also recruited first-degree biological relatives (n = 44) in order to examine the role of genetic liability for psychosis in visual perception. Our visual tasks were designed to assess fundamental visual processes in PwPP, whereas MR spectroscopy enabled us to examine neurochemistry, including excitatory and inhibitory markers. We show that it is feasible to collect high-quality data across multiple psychophysical, functional MRI, and MR spectroscopy experiments with a sizable number of participants at a single research site. These data, in addition to those from our previously described 3 tesla experiments, will be made publicly available in order to facilitate further investigations by other research groups. By combining visual neuroscience techniques and HCP brain imaging methods, our experiments offer new opportunities to investigate the neural basis of abnormal visual perception in PwPP.
Ancient multiplicity in cyclic nucleotide-gated (CNG) cation channel repertoire was reduced in the ancestor of Olfactores before re-expansion by whole genome duplications in vertebrates
Authors: Lagman David , Haines Helen J. , Abalo Xesús M. , Larhammar Dan 
Published: September 2022

AbstractCyclic nucleotide-gated (CNG) cation channels are important heterotetrameric proteins in the retina, with different subunit composition in cone and rod photoreceptor cells: three CNGA3 and one CNGB3 in cones and three CNGA1 and one CNGB1 in rods. CNGA and CNGB subunits form separate subfamilies. We have analyzed the evolution of the CNG gene family in metazoans, with special focus on vertebrates by using sequence-based phylogeny and conservation of chromosomal synteny to deduce paralogons resulting from the early vertebrate whole genome duplications (WGDs). Our analyses show, unexpectedly, that the CNGA subfamily had four sister subfamilies in the ancestor of bilaterians and cnidarians that we named CNGC, CNGD, CNGE and CNGF. Of these, CNGC, CNGE and CNGF were lost in the ancestor of Olfactores while CNGD was lost in the vertebrate ancestor. The remaining CNGA and CNGB genes were expanded by a local duplication of CNGA and the subsequent chromosome duplications in the basal vertebrate WGD events. Upon some losses, this resulted in the gnathostome ancestor having three members in the visual CNGA subfamily (CNGA1-3), a single CNGA4 gene, and two members in the CNGB subfamily (CNGB1 and CNGB3). The nature of chromosomal rearrangements in the vertebrate CNGA paralogon was resolved by including the genomes of a non-teleost actinopterygian and an elasmobranch. After the teleost-specific WGD, additional duplicates were generated and retained for CNGA1, CNGA2, CNGA3 and CNGB1. Furthermore, teleosts retain a local duplicate of CNGB3. The retention of duplicated CNG genes is explained by their subfunctionalisation and photoreceptor-specific expression. In conclusion, this study provides evidence for four previously unknown CNG subfamilies in invertebrates and further evidence that the early vertebrate WGD events were instrumental in the evolution of the vertebrate visual and central nervous systems.
Mental fatigue impairs physical performance but not the neural drive to the muscle
Authors: Alix-Fages Carlos , Jiménez-Martínez Pablo , de Oliveira Daniela Souza , Möck Sebastian , Balsalobre-Fernández Carlos , Del Vecchio Alessandro 
Published: September 2022

ABSTRACTMental fatigue (MF) does not only affect cognitive but also physical performance. This study aimed to explore the effects of MF on muscle endurance, rate of perceived exertion (RPE), and motor units’ activity. Ten healthy males participated in a randomised crossover study. The subjects attended two identical experimental sessions separated by three days with the only difference of a cognitive task (incongruent Stroop task [ST]) and a control condition (watching a documentary). Perceived MF and motivation were measured for each session at baseline and after each cognitive task. Four contractions at 20% of maximal voluntary contraction (MVIC) were performed at baseline, after each cognitive and after muscle endurance task while measuring motor units by high-density surface electromyography. Muscle endurance until failure at 50% of MVIC was measured after each cognitive task and the RPE was measured right after failure. ST significantly increased MF (p = 0.001) reduced the motivation (p = 0.008) for the subsequent physical task and also impaired physical performance (p = 0.044). However, estimates of common synaptic inputs and motor unit discharge rates as well as RPE were not affected by MF (p> 0.11). In conclusion, MF impairs muscle endurance and motivation for the physical task but not the neural drive to the muscle at any frequency bands. Although it is physiologically possible for mentally fatigued subjects to generate an optimal neuromuscular function, the altered perception and motivation seems to limit physical performance. Our results suggest that the corticospinal pathways are not affected by MF.
How do age, available support, gender and attitudes affect the quality of data collected by young citizen scientists in an ecological research project?
Authors: Aivelo Tuomas 
Published: September 2022

Abstract1: Citizen science is increasingly used to collect ecological data. Specifically, participation of school students in authentic research has been suggested as having a multitude of benefits from data collection to science education. Nevertheless, the overall quality and quantity of data concerns ecologists who are using data for further analysis.2: I coordinate a citizen science project, the Helsinki Urban Rat Project where lower and upper secondary school students collect data on urban rat occurrence through the use of track plates that record rat footprints. Within the project, both the success and accuracy of participating young citizen scientists can be assessed by comparing their results by professional researchers’ results and due to the use of an additional questionnaire relate this to the background variables (i.e., age, gender, available support, attitudes and sensitivity to disgust).3: I found out that, in contrast to results from previous studies, age was not a significant variable, but rather available support and voluntary participation with rewards increased data quality. Additionally, higher liking of biology as a school subject was associated with the lower accuracy, whereas a higher interest in environment with higher accuracy.4: The young citizen scientists provided reliable data with the exception of overrepresented false positive observations. My results suggest that the quality and quantity of citizen-generated data are not straightforwardly dependent on the selected target groups. Citizen science activities should be planned by careful consideration of the context, for example the school strongly shapes the participatory activities.
PICKLES v3: the updated database of pooled in vitro CRISPR knockout library essentiality screens
Authors: Novak Lance C , Chou Juihsuan , Colic Medina , Bristow Christopher A. , Hart Traver 
Published: September 2022

AbstractPICKLES (https://pickles.hart-lab.org) is an updated web interface to a freely available database of genome-scale CRISPR knockout fitness screens in human cell lines. Using a completely rewritten interface, researchers can explore gene knockout fitness phenotypes across cell lines and tissue types and compare fitness profiles with fitness, expression, or mutation profiles of other genes. The database has been updated to include data from three CRISPR libraries (Avana, Score, and TKOv3), and includes information from 1,162 whole-genome screens probing the knockout fitness phenotype of 18,959 genes. Source code for the interface and the integrated database are available for download.
FrameRate: learning the coding potential of unassembled metagenomic reads
Authors: Liu-Wei Wang , Aubrey Wayne , Clare Amanda , Hoehndorf Robert , Creevey Christopher J. , Dimonaco Nicholas J. 
Published: September 2022

AbstractMotivationMetagenomic assembly is a slow and computationally intensive process and despite needing iterative rounds for improvement and completeness the resulting assembly often fails to incorporate many of the input sequencing reads. This is further complicated when there is reduced read-depth and/or artefacts which result in chimeric assemblies both of which are especially prominent in the assembly of metagenomic datasets. Many of these limitations could potentially be overcome by exploiting the information content stored in the reads directly and thus eliminating the need for assembly in a number of situations.ResultsWe explored the prediction of coding potential of DNA reads by training a machine learning model on existing protein sequences. Named ‘FrameRate’, this model can predict the coding frame(s) from unassembled DNA sequencing reads directly, thus greatly reducing the computational resources required for genome assembly and similarity-based inference to pre-computed databases. Using the eggNOG-mapper function annotation tool, the predicted coding frames from FrameRate were functionally verified by comparing to the results from full-length protein sequences reconstructed with an established metagenome assembly and gene prediction pipeline from the same metagenomic sample. FrameRate captured equivalent functional profiles from the coding frames while reducing the required storage and time resources significantly. FrameRate was also able to annotate reads that were not represented in the assembly, capturing this ‘missing’ information. As an ultra-fast read-level assembly-free coding profiler, FrameRate enables rapid characterisation of almost every sequencing read directly, whether it can be assembled or not, and thus circumvent many of the problems caused by contemporary assembly workflows.Availabilityhttps://github.com/NickJD/FrameRateContactliuwei.wang@fu-berlin.deandnicholas@dimonaco.co.uk
Robust eIF4B levels undermine invasive growth and immune evasion mechanisms in murine triple negative breast cancer models
Authors: Smith Randall , Diba Leila Zabihi , Srinivasan Aravind , Zollo Robert , Ossevoort Thomas , He Qian , Colligan Sean H. , Dolan Melissa , Vedire Yeshwanth , Sultana Tomina , Venkatesh Meera , Arora Aayush P. , Gawlak Sarah , Washington Deschana , Brackett Craig M. , Yao Song , Ebos John M.L. , Abrams Scott I. , Barbi Joseph , Walker Sarah E. 
Published: September 2022

AbstractDysregulated protein synthesis is seen in many aggressive cancers, including metastatic breast cancer. However, the specific contributions of certain translation initiation factors to in vivo disease remain undefined. This is particularly true of eIF4B, an RNA-binding protein and cofactor of the RNA helicase eIF4A and associated eIF4F cap-binding complex. While eIF4A, eIF4G, and eIF4E are well-known to contribute to the progression of many cancer types including metastatic breast cancers, the role played by eIF4B in breast cancer remains relatively unclear. We therefore explored how naturally divergent and experimentally modulated eIF4B levels impact tumor growth and progression in well-characterized murine triple negative breast cancer (TNBC) models. Surprisingly, we found that higher eIF4B levels in mouse and human breast cancers were associated with less aggressive phenotypes. shRNA-mediated eIF4B knockdown in TNBC lines failed to markedly alter proliferation and global translation in the cells in vitro and only modestly hindered their growth as primary mammary tumors growth in mice. However, eIF4B knockdown significantly enhanced invasive growth in vitro and exacerbated both tumor burden and mortality relative to nontargeting shRNA controls in a model of metastatic disease. Analysis of eIF4B levels and breast cancer patient survival reinforced a link to better outcomes. Interestingly, low eIF4B expression was also associated with more formidable immune evasion in vitro and in vivo, implicating a novel immunomodulatory role for this factor in the malignant setting that suggests a mode of action beyond its historical role as a co-activator of eIF4A/F.Significance StatementMetastasis is the leading cause of cancer-related mortality. Despite many advances in our understanding of this complex process and the molecular and cellular events involved, mechanisms that allow secondary tumors to arise and persist remain incompletely understood. Uncharacterized metastatic determinants active at the level of translational control may be exploitable as novel therapy targets or biomarkers predicting a tumor’s potential for spread and recurrence. Here we describe previously unrecognized consequences of dysregulated eIF4B levels in murine breast cancer that shed light on how this translation initiation factor contributes to disease outcomes. Our findings suggest that eIF4B levels direct metastatic risk and immune evasion, and further study should establish its value in personalized treatment decisions and development of future therapies.
Prefrontal neuronal dynamics in the absence of task execution
Authors: Pu Shusen , Dang Wenhao , Qi Xue-Lian , Constantinidis Christos 
Published: September 2022

SUMMARYPrefrontal cortical activity represents stimuli in working memory tasks in a low-dimensional manifold that transforms over the course of a trial. Such transformations reflect specific cognitive operations, so that, for example, the rotation of stimulus representations is thought to reduce interference by distractor stimuli. Here we show that rotations occur in the low-dimensional activity space of prefrontal neurons in naïve monkeys, while passively viewing familiar stimuli. Moreover, some aspects of these rotations remain remarkably unchanged after training to perform working memory tasks. Significant training effects are still present in population dynamics, which further distinguish correct and error trials during task execution. Our results reveal automatic functions of prefrontal neural circuits, allow transformations that may aid cognitive flexibility.
Single-cell Pairwise Relationships Untangled by Composite Embedding model
Authors: Subedi Sishir , Park Yongjin P. 
Published: September 2022

SummaryIn multi-cellular organisms, cell identity and functions are primed and refined through interactions with other surrounding cells. Here, we propose a scalable machine learning method, termed SPRUCE, which is designed to systematically ascertain common cell-cell communication patterns embedded in single-cell RNA-seq data. We applied our approach to investigate tumour microenvironments consolidating multiple breast cancer data sets and found seven frequently-observed interaction signatures and underlying gene-gene interaction networks. Our results implicate that a part of tumour heterogeneity, especially within the same subtype, is better understood by differential interaction patterns rather than the static expression of known marker genes.