bluuebunny/crossref_metadata_2025_split huggingface dataset:
Seeing What is Representative
Authors: Esponda Ignacio , Oprea Ryan , Yuksel Sevgi 
Published: May 2023

AbstractWe provide evidence for a bias that we call “representative signal distortion” (RSD), which is particularly relevant to settings of statistical discrimination. Experimental subjects distort their evaluation of new evidence on individual group members and interpret such information to be more representative of the group to which the individual belongs (relative to a reference group) than it really is. This produces a discriminatory gap in the evaluation of members of the two groups. Because it is driven by representativeness, the bias (and the discriminatory gap) disappears when subjects are prevented from contrasting different groups; because it is a bias in the interpretation of information, it disappears when subjects receive information before learning of the individual’s group. We show that this bias can be easily estimated from appropriately constructed data sets and can be distinguished from previously documented inferential biases in the literature. Importantly, we document how removing the bias produces a kind of free lunch in reducing discrimination, making it possible to significantly reduce discrimination without lowering accuracy of inferences.
Investigation of liver-targeted peripheral focused ultrasound stimulation (pFUS) and its effect on glucose homeostasis and insulin resistance in type 2 diabetes mellitus: a proof of concept, phase 1 trial
Authors: Ashe J , Graf J , Madhavan R , Wallace K , Cotero V , Abate S , Pandey R K , Herzog R , Porindla S N , Shoudy D , Fan Y , Kao T -J , Puleo C 
Published: May 2023

Summary

Background
Mechanical waves produced by ultrasound pulses have been shown to activate mechanosensitive ion channels and modulate peripheral nerves. However, while peripheral ultrasound neuromodulation has been demonstrated in vitro and in pre-clinical models, there have been few reports of clinical tests.

Aim
We modified a diagnostic imaging system for ultrasound neuromodulation in human subjects. We report the first safety and feasibility outcomes in subjects with type 2 diabetes (T2D) mellitus and discuss these outcomes in relation to previous pre-clinical results.

Design
The study was performed as an open label feasibility study to assess the effects of hepatic ultrasound (targeted to the porta hepatis) on glucometabolic parameters in subjects with T2D. Stimulation (peripheral focused ultrasound stimulation treatment) was performed for 3 days (i.e. 15 min per day), preceded by a baseline examination and followed by a 2-week observation period.

Methods
Multiple metabolic assays were employed including measures of fasting glucose and insulin, insulin resistance and glucose metabolism. The safety and tolerability were also assessed by monitoring adverse events, changes in vital signs, electrocardiogram parameters and clinical laboratory measures.

Results and conclusion
We report post-pFUS trends in several outcomes that were consistent with previous pre-clinical findings. Fasting insulin was lowered, resulting in a reduction of HOMA-IR scores (P-value 0.01; corrected Wilcoxon signed-rank test). Additional safety and exploratory markers demonstrated no device-related adverse impact of pFUS. Our findings demonstrate that pFUS represents a promising new treatment modality that could be used as a non-pharmaceutical adjunct or even alternative to current drug treatments in diabetes.
Morphological classification of radio galaxies with Wasserstein generative adversarial network-supported augmentation
Authors: Rustige Lennart , Kummer Janis , Griese Florian , Borras Kerstin , Brüggen Marcus , Connor Patrick L S , Gaede Frank , Kasieczka Gregor , Knopp Tobias , Schleper Peter 
Published: May 2023

ABSTRACT
Machine learning techniques that perform morphological classification of astronomical sources often suffer from a scarcity of labelled training data. Here, we focus on the case of supervised deep learning models for the morphological classification of radio galaxies, which is particularly topical for the forthcoming large radio surveys. We demonstrate the use of generative models, specifically Wasserstein generative adversarial networks (wGANs), to generate data for different classes of radio galaxies. Further, we study the impact of augmenting the training data with images from our wGAN on three different classification architectures. We find that this technique makes it possible to improve models for the morphological classification of radio galaxies. A simple fully connected neural network benefits most from including generated images into the training set, with a considerable improvement of its classification accuracy. In addition, we find it is more difficult to improve complex classifiers. The classification performance of a convolutional neural network can be improved slightly. However, this is not the case for a vision transformer.
Does international R&D cooperation under institutional agreements have a greater impact than those without agreements?
Authors: Feitosa Paulo Henrique Assis , Salles-Filho Sergio , Bin Adriana , Juk Yohanna , Colugnati Fernando Antonio Basile 
Published: May 2023

Abstract
Funding agencies (FAs) have increasingly engaged in international cooperation agreements (ICAs) to encourage world-class research and achieve more promising outcomes in the context of increasing competition for research resources. While the benefits of International Research Collaboration are largely supported by literature, less attention was paid to the influence of ICA on scientific and technological outputs. We employed a quasi-experimental evaluation with a comparison between funding for international collaboration carried under ICA (treatment) and funding for international collaboration not carried under ICA (control). The sample was collected from the database of the São Paulo Research Foundation (FAPESP) between 1990 and 2018. We have found that ICA has a positive and significant impact on the quality of scientific production measured by the number of citations, h-index, and the number of national and international papers co-authorship. However, no significant difference was found in terms of scholarly and technological outputs.
Biosynthesis of cannabigerol and cannabigerolic acid: the gateways to further cannabinoid production
Authors: Kearsey Lewis J , Yan Cunyu , Prandi Nicole , Toogood Helen S , Takano Eriko , Scrutton Nigel S 
Published: May 2023

Abstract
Cannabinoids are a therapeutically valuable class of secondary metabolites with a vast number of substituents. The native cannabinoid biosynthetic pathway of Cannabis sativa generates cannabigerolic acid (CBGA), the common substrate to multiple cannabinoid synthases. The bioactive decarboxylated analog of this compound, cannabigerol (CBG), represents an alternate gateway into the cannabinoid space as a substrate either to non-canonical cannabinoid synthase homologs or to synthetic chemical reactions. Herein, we describe the identification and repurposing of aromatic prenyltransferase (AtaPT), which when coupled with native enzymes of C. sativa can form an Escherichia coli production system for CBGA in cell lysates and CBG in whole cells. Engineering of AtaPT, guided by structural analysis, was performed to enhance its kinetics toward CBGA production for subsequent use in a proof-of-concept lysate system. For the first time, we show a synthetic biology platform for CBG biosynthesis in E. coli cells by employing AtaPT under an optimized microbial system. Our results have therefore set the foundation for sustainable production of well-researched and rarer cannabinoids in an E. coli chassis.
Graphical Abstract
Evolution of anelloviruses from a circovirus-like ancestor through gradual augmentation of the jelly-roll capsid protein
Authors: Butkovic Anamarija , Kraberger Simona , Smeele Zoe , Martin Darren P , Schmidlin Kara , Fontenele Rafaela S , Shero Michelle R , Beltran Roxanne S , Kirkham Amy L , Aleamotu’a Maketalena , Burns Jennifer M , Koonin Eugene V , Varsani Arvind , Krupovic Mart 
Published: May 2023

Abstract
Anelloviruses are highly prevalent in diverse mammals, including humans, but so far have not been linked to any disease and are considered to be part of the ‘healthy virome’. These viruses have small circular single-stranded DNA (ssDNA) genomes and encode several proteins with no detectable sequence similarity to proteins of other known viruses. Thus, anelloviruses are the only family of eukaryotic ssDNA viruses currently not included in the realm Monodnaviria. To gain insights into the provenance of these enigmatic viruses, we sequenced more than 250 complete genomes of anelloviruses from nasal and vaginal swab samples of Weddell seal (Leptonychotes weddellii) from Antarctica and a fecal sample of grizzly bear (Ursus arctos horribilis) from the USA and performed a comprehensive family-wide analysis of the signature anellovirus protein ORF1. Using state-of-the-art remote sequence similarity detection approaches and structural modeling with AlphaFold2, we show that ORF1 orthologs from all Anelloviridae genera adopt a jelly-roll fold typical of viral capsid proteins (CPs), establishing an evolutionary link to other eukaryotic ssDNA viruses, specifically, circoviruses. However, unlike CPs of other ssDNA viruses, ORF1 encoded by anelloviruses from different genera display remarkable variation in size, due to insertions into the jelly-roll domain. In particular, the insertion between β-strands H and I forms a projection domain predicted to face away from the capsid surface and function at the interface of virus–host interactions. Consistent with this prediction and supported by recent experimental evidence, the outermost region of the projection domain is a mutational hotspot, where rapid evolution was likely precipitated by the host immune system. Collectively, our findings further expand the known diversity of anelloviruses and explain how anellovirus ORF1 proteins likely diverged from canonical jelly-roll CPs through gradual augmentation of the projection domain. We suggest assigning Anelloviridae to a new phylum, ‘Commensaviricota’, and including it into the kingdom Shotokuvirae (realm Monodnaviria), alongside Cressdnaviricota and Cossaviricota.
Control of Mandibular Width With 3D Printed Occlusal Splint in Children With Multiple Mandibular Fractures
Authors: Wu Benxing , Lv Kun 
Published: May 2023

Background:
The fracture of mandibular symphysis combined with bilateral condylar fractures often leads to changes in the width of the mandible, which significantly widens the face of the child. Therefore, it is necessary to reposition the mandible through accurate adduction.

Methods:
To ensure that the mandible can be accurately repositioned, a 3D printed occlusal splint was used. Bilateral maxillomandibular fixation screws were implanted. The 3D printed occlusal splint was located on the maxillary dentition and fixed to the maxillomandibular fixation screws with wire loops. The reference basis for adduction is to make the mandibular dentition located in the occlusal splint. The absorbable plate was contoured according to the restored model and fixed at the fracture site. The 3D printed occlusal splint was retained in the maxillary dentition for two months.

Results and Discussion:
Postoperative computed tomography showed that the mandible had been adducted according to the preoperative design. Two months of follow-up showed that the child's facial development, mouth opening type, occlusion, and range of motion were good. It is especially suitable for children with mandibular symphyseal fractures accompanied by bilateral condylar fractures.
The Effectiveness of Releasing the Lower Lateral Cartilage Through Intranasal Z-plasty Incision on the Vestibular Web During Secondary Correction of Nasal Deformities in Complete Unilateral Cleft Lip and Palate
Authors: Jeon Sungmi , Kim Yung Hoon , Kim Byung Jun , Kim Sukwha , Chung Jee Hyeok 
Published: May 2023

The primary goal in the secondary correction of unilateral cleft lip nose deformity is to achieve symmetry of the nose and nostril. This study aimed to investigate the efficacy of freeing the lower lateral cartilage from the pyriform ligament through an intranasal Z-plasty incision on the vestibular web in adult patients with complete unilateral cleft lip and palate. Thirty-six patients with complete unilateral cleft lip and palate, who underwent open rhinoplasty between August 2014 and December 2021, were identified retrospectively. Five parameters for nose form and nostril symmetry were measured on basal views through 2-dimensional photographic analysis. The patients were divided into subgroups with or without septoplasty. Cleft-to-non-cleft ratios between the Z (13 patients) and non-Z groups (23 patients) were compared using the Mann-Whitney U test. The mean follow-up was 12.9 months (6–31 mo). In the Z group, there were significant differences between the preoperative and postoperative values for nostril angulation, regardless of septoplasty (all P<0.05). Despite septoplasty, significant differences in the postoperative changes in nostril angulation were found between the Z and non-Z groups (all P<0.05). Intranasal Z-plasty on the plica vestibularis is an effective technique for releasing the lower lateral cartilage, improving the nostril asymmetry in cleft lip nose deformity.
Untangling an insect virome from its endogenous viral elements
Authors: Rozo-Lopez Paula , Brewer William , Käfer Simon , Martin McKayla M. , Parker Benjamin J. 
Published: May 2023

AbstractInsects are an important reservoir of viral biodiversity, but the vast majority of viruses associated with insects have not been discovered. Recent studies have therefore employed high-throughput sequencing of RNA, which has led to rapid advances in our understanding of insect viral diversity. However, insect genomes frequently contain transcribed endogenous viral elements with significant homology to exogenous viruses, complicating the use of RNAseq for viral discovery. In this study, we use a multi-pronged sequencing approach to study the virome of an important agricultural pest and prolific vector of plant pathogens, the potato aphidMacrosiphum euphorbiae. We first used rRNA-reduced RNAseq to characterize the bacteria and viruses found in individual insects. We then characterized the frequency of a heritable Flavivirus and an Ambidensovirus in our population. We next generated a quality draft genome assembly forM. euphorbiaeusing Illumina-corrected Nanopore sequencing. This analysis showed that the Ambidensovirus, previously described from an RNAseq viral screen, is not a exogenous virus and instead is a transcribed endogenous viral element in theM. euphorbiaegenome. Our study generates key insight into an important agricultural pest and highlights a widespread challenge for the study of viral diversity using RNAseq.
Tumor-specific neutrophils originating from meninges promote glioblastoma
Authors: Zhao Jiarui , Wu Di , Liu Jiaqi , Zhang Yang , Cao Penghui , Li Chunzhao , Wu Shixuan , Li Mengyuan , Cui Yiwen , Sun Yiwen , Yang Ence , Ji Nan , Yang Jing , Chen Jian 
Published: May 2023

AbstractGlioma is one of the most aggressive human cancers with limited therapeutic options. Though research has extensively examined immune components in those malignant tumors, the pathophysiological mechanism establishing their immunosuppressive microenvironment remains incompletely characterized. In this study, we report for the first time the unique presence of tumor-specific neutrophils (TSNs) in human glioblastoma (GBM) tumors. This newly defined neutrophil subtype exhibits the high expression of several immunosuppressive genes (e.g., CD274 and IDO1) and is strongly correlated with glioma grades and poor prognosis of patients. TSNs with comparable gene signatures are similarly present in the tumors but not bone marrow or spleen of mouse glioma models. Blockage of TSN recruitment by eitherCxcl1-knockout in glioma cells orCxcr2-deletion in host mice significantly enhances antitumor immunity and inhibits tumor progression. Surprisingly, we further identify the meninges as the key extratumoral source of generating TSNs in both human GBM patients and mouse glioma models. These results have elucidated a novel mechanism of neutrophils designating the tumor immune microenvironment and the essential link of meningeal immunity to glioma.
An evolutionary mechanism to assimilate new nutrient sensors into the mTORC1 pathway
Authors: Liu Grace Y. , Jouandin Patrick , Bahng Raymond E. , Perrimon Norbert , Sabatini David M. 
Published: May 2023

AbstractAnimals must sense and respond to nutrient availability in their local niche. This task is coordinated in part by the mTOR complex 1 (mTORC1) pathway, which regulates growth and metabolism in response to nutrients1-5. In mammals, mTORC1 senses specific amino acids through specialized sensors that act through the upstream GATOR1/2 signaling hub6-8. To reconcile the conserved architecture of the mTORC1 pathway with the diversity of environments that animals can occupy, we hypothesized that the pathway might maintain plasticity by evolving distinct nutrient sensors in different metazoan phyla1,9,10. Whether such customization occurs— and how the mTORC1 pathway might capture new nutrient inputs—is not known. Here, we identify theDrosophila melanogasterprotein Unmet expectations (Unmet, formerly CG11596) as a species-restricted nutrient sensor and trace its incorporation into the mTORC1 pathway. Upon methionine starvation, Unmet binds to the fly GATOR2 complex to inhibit dTORC1.S-adenosylmethionine (SAM), a proxy for methionine availability, directly relieves this inhibition. Unmet expression is elevated in the ovary, a methionine-sensitive niche11, and flies lacking Unmet fail to maintain the integrity of the female germline under methionine restriction. By monitoring the evolutionary history of the Unmet-GATOR2 interaction, we show that the GATOR2 complex evolved rapidly in Dipterans to recruit and repurpose an independent methyltransferase as a SAM sensor. Thus, the modular architecture of the mTORC1 pathway allows it to co-opt preexisting enzymes and expand its nutrient sensing capabilities, revealing a mechanism for conferring evolvability on an otherwise highly conserved system.
splicekit: a comprehensive toolkit for splicing analysis from short-read RNA-seq
Authors: Rot Gregor , Wehling Arne , Schmucki Roland , Berntenis Nikolaos , Zhang Jitao David , Ebeling Martin 
Published: May 2023

AbstractMotivationAnalysis of alternative splicing using short-read RNA-seq data is a complex process that involves several steps: alignment of reads to the reference genome, identification of alternatively spliced features, motif discovery, analysis of RNA-protein binding near donor and acceptor splice sites, and exploratory data visualization.ResultsWe introducesplicekit, a python package that provides a comprehensive set of tools for conducting splicing analysis.Availability and implementationhttps://github.com/bedapub/splicekitand over PyPI.
Ongoing convergent evolution of a selfing syndrome threatens plant-pollinator interactions
Authors: Acoca-Pidolle Samson , Gauthier Perrine , Devresse Louis , Deverge Merdrignac Antoine , Pons Virginie , Cheptou Pierre-Olivier 
Published: May 2023

SummaryPlant-pollinator interactions evolved early in the angiosperm radiation. Ongoing environmental changes are however leading to pollinator declines that may cause pollen limitation to plants and change the evolutionary pressures shaping plant mating systems.We used resurrection ecology methodology to contrast ancestors and contemporary descendants in four natural populations of the field pansy (Viola arvensis) in the Paris region (France), a depauperate pollinator environment. We combine population genetics analysis, phenotypic measurements and behavioural tests on a common garden experiment.Population genetics analysis reveals 27% increase in realized selfing rates in the field during this period. We documented trait evolution towards smaller and less conspicuous corollas, reduced nectar production and reduced attractiveness to bumblebees, with these trait shifts convergent across the four studied populations.We demonstrate the rapid evolution of a selfing syndrome in the four studied plant populations, associated with a weakening of the interactions with pollinators over the last three decades. This study demonstrates that plant mating systems can evolve rapidly in natural populations in the face of ongoing environmental changes. The rapid evolution towards a selfing syndrome may in turn further accelerate pollinator declines, in an eco-evolutionary feedback loop with broader implications to natural ecosystems.
Multi-omic Profiling Reveals Early Immunological Indicators for Identifying COVID-19 Progressors
Authors: Drake Katherine A. , Talantov Dimitri , Tong Gary J. , Lin Jack T. , Verheijden Simon , Katz Samuel , Leung Jacqueline M. , Yuen Benjamin , Krishna Vinod , Wu Michelle J. , Sutherland Alex , Short Sarah A. , Kheradpour Pouya , Mumbach Maxwell , Franz Kate , Trifonov Vladimir , Lucas Molly V. , Merson James , Kim Charles C. ,   PRESCO Study Group
Published: May 2023

AbstractThe pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to a rapid response by the scientific community to further understand and combat its associated pathologic etiology. A focal point has been on the immune responses mounted during the acute and post-acute phases of infection, but the immediate post-diagnosis phase remains relatively understudied. We sought to better understand the immediate post-diagnosis phase by collecting blood from study participants soon after a positive test and identifying molecular associations with longitudinal disease outcomes. Multi-omic analyses identified differences in immune cell composition, cytokine levels, and cell subset-specific transcriptomic and epigenomic signatures between individuals on a more serious disease trajectory (Progressors) as compared to those on a milder course (Non-progressors). Higher levels of multiple cytokines were observed in Progressors, with IL-6 showing the largest difference. Blood monocyte cell subsets were also skewed, showing a comparative decrease in non-classical CD14−CD16+and intermediate CD14+CD16+monocytes. Additionally, in the lymphocyte compartment, CD8+T effector memory cells displayed a gene expression signature consistent with stronger T cell activation in Progressors. Importantly, the identification of these cellular and molecular immune changes occurred at the early stages of COVID-19 disease. These observations could serve as the basis for the development of prognostic biomarkers of disease risk and interventional strategies to improve the management of severe COVID-19.One Sentence SummaryImmunological changes associated with COVID-19 progression can be detected during the early stages of infection.