bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reporting guidelines for clinical trial reports for interventions involving artificial intelligence: the CONSORT-AI extension
Authors: Liu Xiaoxuan , Cruz Rivera Samantha , Moher David , Calvert Melanie J. , Denniston Alastair K. ,   The SPIRIT-AI and CONSORT-AI Working Group,   SPIRIT-AI and CONSORT-AI Steering Group, Chan An-Wen , Darzi Ara , Holmes Christopher , Yau Christopher , Ashrafian Hutan , Deeks Jonathan J. , Ferrante di Ruffano Lavinia , Faes Livia , Keane Pearse A. , Vollmer Sebastian J. ,   SPIRIT-AI and CONSORT-AI Consensus Group, Lee Aaron Y. , Jonas Adrian , Esteva Andre , Beam Andrew L. , Chan An-Wen , Panico Maria Beatrice , Lee Cecilia S. , Haug Charlotte , Kelly Christopher J. , Yau Christopher , Mulrow Cynthia , Espinoza Cyrus , Fletcher John , Paltoo Dina , Manna Elaine , Price Gary , Collins Gary S. , Harvey Hugh , Matcham James , Monteiro Joao , ElZarrad M. Khair , Ferrante di Ruffano Lavinia , Oakden-Rayner Luke , McCradden Melissa , Keane Pearse A. , Savage Richard , Golub Robert , Sarkar Rupa , Rowley Samuel 
Published: September 2020

AbstractThe CONSORT 2010 statement provides minimum guidelines for reporting randomized trials. Its widespread use has been instrumental in ensuring transparency in the evaluation of new interventions. More recently, there has been a growing recognition that interventions involving artificial intelligence (AI) need to undergo rigorous, prospective evaluation to demonstrate impact on health outcomes. The CONSORT-AI (Consolidated Standards of Reporting Trials–Artificial Intelligence) extension is a new reporting guideline for clinical trials evaluating interventions with an AI component. It was developed in parallel with its companion statement for clinical trial protocols: SPIRIT-AI (Standard Protocol Items: Recommendations for Interventional Trials–Artificial Intelligence). Both guidelines were developed through a staged consensus process involving literature review and expert consultation to generate 29 candidate items, which were assessed by an international multi-stakeholder group in a two-stage Delphi survey (103 stakeholders), agreed upon in a two-day consensus meeting (31 stakeholders) and refined through a checklist pilot (34 participants). The CONSORT-AI extension includes 14 new items that were considered sufficiently important for AI interventions that they should be routinely reported in addition to the core CONSORT 2010 items. CONSORT-AI recommends that investigators provide clear descriptions of the AI intervention, including instructions and skills required for use, the setting in which the AI intervention is integrated, the handling of inputs and outputs of the AI intervention, the human–AI interaction and provision of an analysis of error cases. CONSORT-AI will help promote transparency and completeness in reporting clinical trials for AI interventions. It will assist editors and peer reviewers, as well as the general readership, to understand, interpret and critically appraise the quality of clinical trial design and risk of bias in the reported outcomes.
Regulatory effects of the Uty/Ddx3y locus on neighboring chromosome Y genes and autosomal mRNA transcripts in adult mouse non-reproductive cells
Authors: Deschepper Christian F. 
Published: September 2020

AbstractIn addition to sperm-related genes, the male-specific chromosome Y (chrY) contains a class of ubiquitously expressed and evolutionary conserved dosage-sensitive regulator genes that include the neighboring Uty, Ddx3y and (in mice) Eif2s3y genes. However, no study to date has investigated the functional impact of targeted mutations of any of these genes within adult non-reproductive somatic cells. We thus compared adult male mice carrying a gene trap within their Uty gene (UtyGT) to their wild-type (WT) isogenic controls, and performed deep sequencing of RNA and genome-wide profiling of chromatin features in extracts from either cardiac tissue, cardiomyocyte-specific nuclei or purified cardiomyocytes. The apparent impact of UtyGT on gene transcription concentrated mostly on chrY genes surrounding the locus of insertion, i.e. Uty, Ddx3y, long non-coding RNAs (lncRNAs) contained within their introns and Eif2s3y, in addition to possible effects on the autosomal Malat1 lncRNA. Notwithstanding, UtyGT also caused coordinate changes in the abundance of hundreds of mRNA transcripts related to coherent cell functions, including RNA processing and translation. The results altogether indicated that tightly co-regulated chrY genes had nonetheless more widespread effects on the autosomal transcriptome in adult somatic cells, most likely due to mechanisms other than just transcriptional regulation of corresponding protein-coding genes.
A pan-cancer assessment of alterations of the kinase domain of ULK1, an upstream regulator of autophagy
Authors: Kumar Mukesh , Papaleo Elena 
Published: September 2020

AbstractAutophagy is a key clearance process to recycle damaged cellular components. One important upstream regulator of autophagy is ULK1 kinase. Several three-dimensional structures of the ULK1 catalytic domain are available, but a comprehensive study, including molecular dynamics, is missing. Also, an exhaustive description of ULK1 alterations found in cancer samples is presently lacking. We here applied a framework which links -omics data to structural protein ensembles to study ULK1 alterations from genomics data available for more than 30 cancer types. We predicted the effects of mutations on ULK1 function and structural stability, accounting for protein dynamics, and the different layers of changes that a mutation can induce in a protein at the functional and structural level. ULK1 is down-regulated in gynecological tumors. In other cancer types, ULK2 could compensate for ULK1 downregulation and, in the majority of the cases, no marked changes in expression have been found. 36 missense mutations of ULK1, not limited to the catalytic domain, are co-occurring with mutations in a large number of ULK1 interactors or substrates, suggesting a pronounced effect of the upstream steps of autophagy in many cancer types. Moreover, our results pinpoint that more than 50% of the mutations in the kinase domain of ULK1, here investigated, are predicted to affect protein stability. Three mutations (S184F, D102N, and A28V) are predicted with only impact on kinase activity, either modifying the functional dynamics or the capability to exert effects from distal sites to the functional and catalytic regions. The framework here applied could be extended to other protein targets to aid the classification of missense mutations from cancer genomics studies, as well as to prioritize variants for experimental validation, or to select the appropriate biological readouts for experiments.
Administration of cardiac mesenchymal cells modulates innate immunity in the acute phase of myocardial infarction in mice
Authors: Kang Yi , Nasr Marjan , Guo Yiru , Uchida Shizuka , Weirick Tyler , Li Hong , Kim Jae , Moore Joseph B. , Muthusamy Senthilkumar , Bolli Roberto , Wysoczynski Marcin 
Published: September 2020

AbstractAlthough cardiac mesenchymal cell (CMC) therapy mitigates post-infarct cardiac dysfunction, the underlying mechanisms remain unidentified. It is acknowledged that donor cells are neither appreciably retained nor meaningfully contribute to tissue regeneration—suggesting a paracrine-mediated mechanism of action. As the immune system is inextricably linked to wound healing/remodeling in the ischemically injured heart, the reparative actions of CMCs may be attributed to their immunoregulatory properties. The current study evaluated the consequences of CMC administration on post myocardial infarction (MI) immune responses in vivo and paracrine-mediated immune cell function in vitro. CMC administration preferentially elicited the recruitment of cell types associated with innate immunity (e.g., monocytes/macrophages and neutrophils). CMC paracrine signaling assays revealed enhancement in innate immune cell chemoattraction, survival, and phagocytosis, and diminished pro-inflammatory immune cell activation; data that identifies and catalogues fundamental immunomodulatory properties of CMCs, which have broad implications regarding the mechanism of action of CMCs in cardiac repair.
Pre-symptomatic modified phytohormone profile is associated with lower phytoplasma titres in an Arabidopsis seor1ko line
Authors: Bernardini Chiara , Pagliari Laura , De Rosa Valeria , Almeida-Trapp Marilia , Santi Simonetta , Martini Marta , Buoso Sara , Loschi Alberto , Loi Nazia , Chiesa Fiorella , Mithöfer Axel , van Bel Aart J. E. , Musetti Rita 
Published: September 2020

AbstractThe proteins AtSEOR1 and AtSEOR2 occur as conjugates in the form of filaments in sieve elements ofArabidopsis thaliana. A reduced phytoplasma titre found in infected defective-mutantAtseor1koplants in previous work raised the speculation that non-conjugated SEOR2 is involved in the phytohormone-mediated suppression of Chrysanthemum Yellows (CY)-phytoplasma infection transmitted byEuscelidius variegatus(Ev). This early and long-lasting SEOR2 impact was revealed inAtseor1koplants by the lack of detectable phytoplasmas at an early stage of infection (symptomless plants) and a lower phytoplasma titre at a later stage (fully symptomatic plants). The high insect survival rate onAtseor1koline and the proof of phytoplasma infection at the end of the acquisition access period confirmed the high transmission efficiency of CY-phytoplasma by the vectors. Transmission electron microscopy analysis ruled out a direct role of SE filament proteins in physical phytoplasma containment. Time-correlated HPLC–MS/MS-based phytohormone analyses revealed increased jasmonate levels in midribs ofAtseor1koplants at an early stage of infection and appreciably enhanced levels of indole acetic acid and abscisic acid at the early and late stages. Effects of Ev-probing on phytohormone levels was not found. The results suggest that SEOR2 interferes with phytohormonal pathways in Arabidopsis midrib tissues in order to establish early defensive responses to phytoplasma infection.
Spatial variance-mass allometry of population density in felids from camera-trapping studies worldwide
Authors: Anile Stefano , Devillard Sébastien 
Published: September 2020

AbstractPower laws are cornerstone relationships in ecology and evolutionary biology. The density-mass allometry (DMA), which predicts an allometric scaling of population abundance, and Taylor’s law (TL), which predicts a decrease in the population abundance variation along with a decrease in population density, have enhanced our knowledge of inter- and intra-specific variation in population abundance. When combined, these two power laws led to the variance-mass allometry (VMA), which states that larger species have lower spatial variation in population density than smaller species. The VMA has been predicted through theoretical models, however few studies have investigated if this law is also supported by empirical data. Here, to formally test the VMA, we have used the population density estimates obtained through worldwide camera trapping studies for an emblematic and ecologically important carnivorous taxa, the Felidae family. Our results showed that the VMA law hold in felids, as well as the TL and the DMA laws; bigger cat species showed less variation for the population density than smaller species. These results have important implications for the conservation of wildlife population and confirm the validity of important ecological concepts, like the allometric scaling of population growth rate and the slow-fast continuum of life history strategies.
An early gall-inducing parasitic wasp adversely affects the fitness of its host Ficus tree but not the pollinator
Authors: Zhang Xiao-Wei , Li Liang-Heng 
Published: September 2020

AbstractThe fig tree-fig pollinator mutualism is one of the most tightly knit symbiotic systems. The research on the ecology of non-pollinators which exploit the mutualism without providing services to the host is very limited and conclusions about the role they play in the maintenance of this mutualism are full of contradictions. The non-pollinating fig wasps species are highly diverse in their feeding habit and ecological function, which may result in different consequences on the mutualism. Sycophaga testacea is an early-ovipositing galler hosted by Ficus racemosa, which is a potencial competitor to the pollinators as they use the same female flowers in the fig as their ovipositing sites. In this study, we investigate the effect of S. testacea on the production of both pollinator and fig tree with a field control experiment. Seed production is decreased significantly when the figs were parasitized, while the offspring production of the pollinator is not significantly affected, which indicates that this galler species has a harmful effect on the fitness of its host fig tree but not the pollinator. The overall development ratio of the galls is decreased significantly when the figs were parasitized, and we found that the intrinsic low development ratio of S. testacea is responsible for the decrease in the overall development ratio.
Study on the effect of heat treatment on amethyst color and the cause of coloration
Authors: Cheng Renping , Guo Ying 
Published: September 2020

AbstractThe effect of heat treatment on amethyst color was studied from a new perspective of chromaticity of gemstones and the cause of amethyst coloration was discussed based on the results of X-ray diffraction, ultraviolet–visible spectroscopy. The results show that the amethyst color has no significant relationship with cell parameters but the crystallinity index decreases as temperature rises. The absorption band at 545 nm in the UV–visible spectrum can be related to a charge-transfer transition of Fe3+ and O2−, which has a significant relationship with amethyst lightness and chroma. The color at different temperatures can be divided into three stages: The amethyst stage with temperature below 420 °C, the prasiolite stage with temperature between 420 and 440 °C where the color center is the most unstable, the citrine stage with temperature above 440 °C. The color change degree of heated amethyst is related to its initial color. When the initial color is darker, the color difference of heated amethyst is larger, and the easier it is to change the color after heat treatment. A more appropriate heating temperature to obtain citrine by heating amethyst is about 560 °C.
Inhibition of purinergic P2X receptor 7 (P2X7R) decreases granulocyte-macrophage colony-stimulating factor (GM-CSF) expression in U251 glioblastoma cells
Authors: Drill Matthew , Powell Kim L. , Kan Liyen Katrina , Jones Nigel C. , O’Brien Terence J. , Hamilton John A. , Monif Mastura 
Published: September 2020

AbstractGlioblastoma is the most aggressive form of primary brain cancer, with a median survival of 12–15 months. The P2X receptor 7 (P2X7R) is upregulated in glioblastoma and is associated with increased tumor cell proliferation. The cytokine granulocyte-macrophage colony-stimulating factor (GM-CSF) is also upregulated in glioblastoma and has been shown to have both pro- and anti-tumor functions. This study investigates the potential mechanism linking P2X7R and GM-CSF in the U251 glioblastoma cell line and the therapeutic potential of P2X7R antagonism in this setting. P2X7R protein and mRNA was demonstrated to be expressed in the U251 cell line as assessed by immunocytochemistry and qPCR. Its channel function was intact as demonstrated by live cell confocal imaging using a calcium indicator Fluo-4 AM. Inhibition of P2X7R using antagonist AZ10606120, decreased both GM-CSF mRNA (P < 0.05) and protein (P < 0.01) measured by qPCR and ELISA respectively. Neutralization of GM-CSF with an anti-GM-CSF antibody did not alter U251 cell proliferation, however, P2X7R antagonism with AZ10606120 significantly reduced U251 glioblastoma cell numbers (P < 0.01). This study describes a novel link between P2X7R activity and GM-CSF expression in a human glioblastoma cell line and highlights the potential therapeutic benefit of P2X7R inhibition with AZ10606120 in glioblastoma.
Complement protein levels and MBL2 polymorphisms are associated with dengue and disease severity
Authors: Giang Ngo Truong , van Tong Hoang , Quyet Do , Hoan Nghiem Xuan , Nghia Trinh Huu , Nam Nguyen Minh , Hung Hoang Vu , Anh Do Tuan , Van Mao Can , Son Ho Anh , Meyer Christian G. , Velavan Thirumalaisamy P. , Toan Nguyen Linh 
Published: September 2020

AbstractThe complement system may be crucial during dengue virus infection and progression to severe dengue. This study investigates the role of MBL2 genetic variants and levels of MBL in serum and complement proteins in Vietnamese dengue patients. MBL2 genotypes (− 550L/H, MBL2 codon 54), MBL2 diplotypes (XA/XO, YA/XO) and MBL2 haplotypes (LXPB, HXPA, XO) were associated with dengue in the study population. The levels of complement factors C2, C5, and C5a were higher in dengue and dengue with warning signs (DWS) patients compared to those in healthy controls, while factor D levels were decreased in dengue and DWS patients compared to the levels determined in healthy controls. C2 and C5a levels were associated with the levels of AST and ALT and with WBC counts. C9 levels were negatively correlated with ALT levels and WBC counts, and factor D levels were associated with AST and ALT levels and with platelet counts. In conclusions, MBL2 polymorphisms are associated with dengue in the Vietnamese study population. The levels of the complement proteins C2, C4b, C5, C5a, C9, factor D and factor I are modulated in dengue patients during the clinical course of dengue.
Fibrovascular pigment epithelial detachment in eyes with subretinal hemorrhage secondary to neovascular AMD or PCV: a morphologic predictor associated with poor treatment outcomes
Authors: Kim Jae Hui , Kim Joo Yeon , Lee Dong Won , Kim Chul Gu , Kim Jong Woo 
Published: September 2020

AbstractTo evaluate the influence of fibrovascular pigment epithelial detachment (FVPED) on treatment outcomes in eyes with subretinal hemorrhage secondary to neovascular age-related macular degeneration (AMD) and polypoidal choroidal vasculopathy (PCV). This retrospective study included 83 eyes diagnosed with fovea-involving submacular hemorrhage secondary to neovascular AMD or PCV. All the patients were treated with intravitreal anti-vascular endothelial growth factor. Eyes showing definite FVPED, which involves the subfoveal region, were included in the FVPED group. Eyes without subfoveal PED, shallow irregular PEDs, or serous/hemorrhagic PED were stratified to the non-FVPED group. The best-corrected visual acuity (BCVA) at diagnosis, at 3 months, at 12 months, and lesion re-activation after initial treatment were compared between the two groups. The mean size of hemorrhage was 8.6 ± 7.6 disc diameter areas. In the FVPED group, the mean logarithm of minimal angle of resolution BCVA was 1.11 ± 0.49 at diagnosis, 0.89 ± 0.58 at 3 months, and 1.05 ± 0.63 at 12 months. In the non-FVPED group, the values were 0.97 ± 0.56, 0.56 ± 0.55, and 0.45 ± 0.50, respectively. The BCVA at 3 months (P = 0.036) and at 12 months (P < 0.001) was significantly worse in the FVPED group than in the non-FVPED group. In addition, the incidence of lesion reactivation was greater in the FVPED group (83.3%) than in the non-FVPED group (38.5%) (P < 0.001). The presence of subfoveal FVPED was associated with a high incidence of lesion re-activation and poor treatment outcomes in eyes with subretinal hemorrhage. This result suggests that different treatment strategies are needed between eyes with and without FVPED.
Towards a minimal EEG channel array for a biometric system using resting-state and a genetic algorithm for channel selection
Authors: Moctezuma Luis Alfredo , Molinas Marta 
Published: September 2020

AbstractWe present a new approach for a biometric system based on electroencephalographic (EEG) signals of resting-state, that can identify a subject and reject intruders with a minimal subset of EEG channels. To select features, we first use the discrete wavelet transform (DWT) or empirical mode decomposition (EMD) to decompose the EEG signals into a set of sub-bands, for which we compute the instantaneous and Teager energy and the Higuchi and Petrosian fractal dimensions for each sub-band. The obtained features are used as input for the local outlier factor (LOF) algorithm to create a model for each subject, with the aim of learning from it and rejecting instances not related to the subject in the model. In search of a minimal subset of EEG channels, we used a channel-selection method based on the non-dominated sorting genetic algorithm (NSGA)-III, designed with the objectives of minimizing the required number EEG channels and increasing the true acceptance rate (TAR) and true rejection rate (TRR). This method was tested on EEG signals from 109 subjects of the public motor movement/imagery dataset (EEGMMIDB) using the resting-state with the eyes-open and the resting-state with the eyes-closed. We were able to obtain a TAR of $$1.000 \pm 0.000$$

1.000
±
0.000

and TRR of $$0.998 \pm 0.001$$

0.998
±
0.001

using 64 EEG channels. More importantly, with only three channels, we were able to obtain a TAR of up to $$0.993 \pm 0.01$$

0.993
±
0.01

and a TRR of up to $$0.941 \pm 0.002$$

0.941
±
0.002

for the Pareto-front, using NSGA-III and DWT-based features in the resting-state with the eyes-open. In the resting-state with the eyes-closed, the TAR was $$0.997 \pm 0.02$$

0.997
±
0.02

and the TRR $$0.950 \pm 0.05,$$

0.950
±
0.05
,

also using DWT-based features from three channels. These results show that our approach makes it possible to create a model for each subject using EEG signals from a reduced number of channels and reject most instances of the other 108 subjects, who are intruders in the model of the subject under evaluation. Furthermore, the candidates obtained throughout the optimization process of NSGA-III showed that it is possible to obtain TARs and TRRs above 0.900 using LOF and DWT- or EMD-based features with only one to three EEG channels, opening the way to testing this approach on bigger datasets to develop a more realistic and usable EEG-based biometric system.