bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative Features From CHO PET Distinguish the WHO Grades of Primary Diffuse Glioma
Authors: Kong Ziren , Jiang Chendan , Liu Delin , Chen Wenlin , Ma Wenbin , Cheng Xin , Wang Yu 
Published: November 2020

Purpose
The aim of this study was to investigate the quantitative 18F-fluoroethylcholine (CHO) PET characteristics for differentiating lower-grade glioma (LGG) from glioblastoma (GBM).

Patients and Methods
Thirty-nine patients who underwent CHO PET with histopathologically confirmed primary diffuse glioma were prospectively enrolled. The 3-dimensional region of interest was semiautomatically defined based on the SUV threshold, and a total of 74 quantitative features, including 13 shape features, 31 SUV-based features, and 30 normalized SUV-based features, were calculated. Wilcoxon rank sum test, receiver operating characteristic curve, and correlation coefficient analyses were applied to select independent representative features, and patient prognosis was stratified by the World Health Organization (WHO) grade and CHO features.

Results
A total of 89.2% of the quantitative features were significantly different between LGG and GBM, and the SUV-based features displayed higher area under the receiver operating characteristic curve (AUC) values than the other feature groups. Among the 5 traditional features, the SUVmax and the total lesion CHO uptake were the most distinguishing, with AUCs of 0.880 and 0.860 (0.938 and 0.927 after reclassification of 2 outliers), respectively, both of which could also stratify patient prognosis better than WHO grade. Five alternative features, including 2 shape features and 3 SUV-based features, were considered representative, with AUCs ranging from 0.754 to 0.854.

Conclusions
Quantitative features from CHO PET are reliable in determining the WHO grade of primary diffuse gliomas. Our findings suggest that GBM has a larger volume, a more spherical shape, higher choline activity in most interval segments, and a more symmetrical distribution than LGG.
Liver Transplantation for Intrahepatic Cholangiocarcinoma: A Meta-analysis and Meta-regression of Survival Rates
Authors: Ziogas Ioannis A. , Giannis Dimitrios , Economopoulos Konstantinos P. , Hayat Muhammad H. , Montenovo Martin I. , Matsuoka Lea K. , Alexopoulos Sophoclis P. 
Published: November 2020

Background.
Intrahepatic cholangiocarcinoma (iCCA) is a contraindication to liver transplantation in most centers worldwide. Therefore, only a few such cases have been performed in each individual center, and the need for a systematic review and meta-analysis to cumulatively pool these results is apparent.

Methods.
A systematic literature review was conducted using the MEDLINE and Cochrane Library databases according to the Preferred Reporting Items for Systematic Reviews and Meta-analyses statement (end-of-search date: May 29, 2020). Meta-analyses of proportions were conducted to pool the overall survival (OS), recurrence-free survival (RFS), and overall recurrence rates using the random-effects model. Meta-regression was used to examine cirrhosis and incidental diagnosis as confounders on OS and RFS.

Results.
Eighteen studies comprising 355 patients and a registry study of 385 patients were included. The pooled 1-, 3-, and 5-y OS rates were 75% (95% CI, 64%-84%), 56% (95% CI, 46%-67%), and 42% (95% CI, 29%-55%), respectively. The pooled 1-, 3-, and 5-y RFS rates were 70% (95% CI, 63%-75%), 49% (95% CI, 41%-57%), and 38% (95% CI, 27%-50%), respectively. Cirrhosis was positively associated with RFS, while incidental diagnosis was not. Neither cirrhosis nor incidental diagnosis was associated with OS. The pooled overall recurrence rate was 43% (95% CI, 33%-53%) over a mean follow-up of 40.6 ± 37.7 mo. Patients with very early (single ≤2 cm) iCCA exhibited superior pooled 5-y RFS (67%; 95% CI, 47%-86%) versus advanced iCCA (34%; 95% CI, 23%-46%).

Conclusions.
Cirrhotics with very early iCCA or carefully selected patients with advanced iCCA after neoadjuvant therapy may benefit from liver transplantation under research protocols.
Characteristics, Trends, and Outcomes of Liver Transplantation for Primary Sclerosing Cholangitis in Female Versus Male Patients: An Analysis From the European Liver Transplant Registry
Authors: Berenguer Marina , Di Maira Tommaso , Baumann Ulrich , Mirza Darius F. , Heneghan Michael A. , Klempnauer Jurgen L. , Bennet William , Ericzon Bo-Goran , Line Pål-Dag , Lodge Peter A. , Zieniewicz Krzysztof , Watson Christopher J. E. , Metselaar Herold J. , Adam René , Karam Vincent , Aguilera Victoria 
Published: November 2020

Background.
The influence of sex on primary sclerosing cholangitis (PSC), pre- and postliver transplantation (LT) is unclear. Aims are to assess whether there have been changes in incidence, profile, and outcome in LT-PSC patients in Europe with specific emphasis on sex.

Methods.
Analysis of the European Liver Transplant Registry database (PSC patients registered before 2018), including baseline demographics, donor, biochemical, and clinical data at LT, immunosuppression, and outcome.

Results.
European Liver Transplant Registry analysis (n = 6463, 32% female individuals) demonstrated an increasing number by cohort (1980–1989, n = 159; 1990–1999, n = 1282; 2000–2009, n = 2316; 2010–2017, n = 2549) representing on average 4% of all transplant indications. This increase was more pronounced in women (from 1.8% in the first cohort to 4.3% in the last cohort). Graft survival rate at 1, 5, 10, 15, 20, and 30 y was 83.6%, 70.8%, 57.7%, 44.9%, 30.8%, and 11.6%, respectively. Variables independently associated with worse survival were male sex, donor and recipient age, cholangiocarcinoma at LT, nondonation after brain death donor, and reduced size of the graft. These findings were confirmed using a more recent LT population closer to the current standard of care (LT after the y 2000).

Conclusions.
An increasing number of PSC patients, particularly women, are being transplanted in European countries with better graft outcomes in female recipients. Other variables impacting outcome include donor and recipient age, cholangiocarcinoma, nondonation after brain death donor, and reduced graft size.
Early chains of transmission of COVID-19 in France
Authors: Paireau Juliette , Mailles Alexandra , Eisenauher Catherine , de Laval Franck , Delon François , Bosetti Paolo , Salje Henrik , Pontiès Valérie , Cauchemez Simon 
Published: November 2020

AbstractIntroductionSARS-CoV-2, which causes COVID-19, has spread rapidly across the world. A dedicated surveillance system was implemented in France in January 2020 to improve early detection of cases and their contacts and limit secondary transmission. Our objective was to use contact-tracing data collected during this initial phase of the epidemic to better characterize SARS-CoV-2 transmission.MethodsWe analysed data collected during contact tracing and retrospective epidemiological investigations in France from 24 January to 30 March 2020. We assessed the secondary clinical attack rate and characterized the risk of a contact becoming a case. We described chains of transmission and estimated key parameters of spread.ResultsOver the study period, 6,082 contacts of 735 confirmed cases were traced. The overall secondary clinical attack rate was 4.1% (95%CI 3.6-4.6) and increased with age of the index case and of the contact. Family contacts were at higher risk of becoming cases (adjusted odds ratio 2.1 (95%CI 1.4-3.0)) while nosocomial contacts were at lower risk (adjusted odds ratio 0.3 (95%CI 0.1-0.7)), compared to coworkers/friends. We identified 328 infector/infectee pairs, 49% of which were family members. The distribution of secondary cases was highly over-dispersed with 80% of secondary cases being caused by 10% of cases. The mean serial interval was 5.1 days (interquartile range 2-8 days) in contact-tracing pairs where late transmission events may be censored, and 6.8 (3-8) days in pairs investigated retrospectively.ConclusionThis study contributes to improving our knowledge of SARS-CoV-2 transmission, such as the importance of superspreading events. Contact-tracing data are challenging to collect but are key to better understand emerging pathogens.Funding statementThis work was supported by the LabEx “Integrative Biology of Emerging Infectious Diseases (IBEID)” (Grant Number ANR-10-LABX-62-IBEID), Santé Publique France, the INCEPTION project (PIA/ANR-16-CONV-0005), and the European Union’s Horizon 2020 research and innovation program under grants 101003589 (RECOVER) and 874735 (VEO).
Risk of evolutionary escape from neutralizing antibodies targeting SARS-CoV-2 spike protein
Authors: Van Egeren Debra , Novokhodko Alexander , Stoddard Madison , Tran Uyen , Zetter Bruce , Rogers Michael , Pentelute Bradley L. , Carlson Jonathan M. , Hixon Mark , Joseph-McCarthy Diane , Chakravarty Arijit 
Published: November 2020

AbstractAs many prophylactics targeting SARS-CoV-2 are aimed at the spike protein receptor-binding domain (RBD), we examined the risk of immune evasion from previously published RBD-targeting neutralizing antibodies (nAbs). Epitopes for RBD-targeting nAbs overlap one another substantially and can give rise to escape mutants with ACE2 affinities comparable to wild type that still infect cells in vitro. We used evolutionary modeling to predict the frequency of immune escape before and after the widespread presence of nAbs due to vaccines, passive immunization or natural immunity. Our modeling suggests that SARS-CoV-2 mutants with one or two mildly deleterious mutations are expected to exist in high numbers due to neutral genetic variation, and consequently resistance to single or double antibody combinations can develop quickly under positive selection.One Sentence SummarySARS-CoV-2 will evolve quickly to evade widely deployed spike RBD-targeting monoclonal antibodies, requiring combinations that rely on at least three antibodies targeting distinct epitopes to suppress viral immune evasion.
Magnaporthe oryzaepopulations in Sub-Saharan Africa are diverse and show signs of local adaptation
Authors: Onaga Geoffrey , Suktrakul Worrawit , Wanjiku Margaret , Quibod Ian Lorenzo , Entfellner Jean-Baka Domelevo , Bigirimana Joseph , Habarugira George , Murori Rosemary , Asea Godfrey , Ismail Abdelbagi M. , Jantasuriyarat Chatchawan , Oliva Ricardo 
Published: November 2020

AbstractRice blast caused byMagnaporthe oryzaeis one of the most economically damaging diseases of rice worldwide. The disease originated in Asia but was detected for the first time in Sub-Saharan Africa (SSA) around 100 years ago. Despite its importance, the evolutionary processes involved in shaping the population structure ofM. oryzaein SSA remain unclear. In this study, we investigate the population history ofM. oryzaeusing a combined dataset of 180 genomes. Our results show that SSA populations are more diverse than earlier perceived, and harbor all genetic groups previously reported in Asia. WhileM. oryzaepopulations in SSA and Asia draw from the same genetic pools, both are experiencing different evolutionary trajectories resulting from unknown selection pressures or demographic processes. The distribution of rare alleles, measured as Tajima’sDvalues, show significant differences at the substructure level. Genome-wide analysis indicates potential events of population contraction strongly affectingM. oryzaein SSA. In addition, the distribution and haplotype diversity of effectors might suggest a process of local adaptation to SSA conditions. These findings provide additional clues about the evolutionary history ofM. oryzaeoutside the center of origin and help to build customized disease management strategies.
More than the sum of its parts: Merging network psychometrics and network neuroscience with application in autism
Authors: Bathelt Joe , Geurts Hilde M. , Borsboom Denny 
Published: November 2020

ABSTRACTNetwork approaches that investigate the interaction between symptoms and behaviours have opened new ways of understanding psychological phenomena in health and disorder in recent years. In parallel, network approaches that characterise the interaction between brain regions have become the dominant approach to understanding brain function in neuroimaging research. Combining these parallel approaches would enable new insights into the interaction between behaviours and their brain-level correlates. In this paper, we introduce a methodology for combining network psychometrics and network neuro-science. This approach utilises the information from the psychometric network to obtain neural correlates that are associated with each node in the psychometric network (network-based regression). Moreover, we combine the behavioural variables and their neural correlates in a joint network to characterise their interactions. We illustrate the approach by highlighting the interaction between the triad of autistic traits and their resting-state functional connectivity associations. To this end, we utilise data from 172 male autistic participants (10-21 years) from the autism brain data exchange (ABIDE, ABIDE-II) that completed resting-state fMRI and were assessed using the autism diagnostic interview (ADI-R). Our results indicate that the network-based regression approach can uncover both unique and shared neural correlates of behavioural measures. In addition, because the shared variance between behavioural measures is controlled for in the approach, the methodology enables us to isolate mechanisms at the brain-level that are unique to particular behavioural variables. For instance, our example analysis indicates that the overlap between communication and social difficulties is not reflected in the overlap between their functional brain correlates.
Temporal dynamics of implicit memory underlying serial dependence
Authors: Bilacchi Cristiano Moraes , Sirius Esaú Ventura Pupo , Cravo André Mascioli , de Azevedo Neto Raymundo Machado 
Published: November 2020

AbstractSerial dependence is the effect in which the immediately preceding trial influences participants' responses to the current stimulus. But for how long does this bias last in the absence of interference from other stimuli? Here, we had 20 healthy young adult participants (12 women) perform a coincident timing task using different inter-trial intervals to characterize the serial dependence effect as the time between trials increases. Our results show that serial dependence abruptly decreases from 0.1 s to 1 s inter-trial interval, but it remains pronounced after that for up to 8 s. In addition, participants' response variability slightly decreases over longer intervals. We discuss these results in light of recent models suggesting that serial dependence might rely on a short-term memory trace kept through changes in synaptic weights, which might explain its long duration and apparent stability over time.
Fast neutron mutagenesis in soybean creates frameshift mutations
Authors: Wyant Skylar R. , Rodriguez M. Fernanda , Carter Corey K. , Parrott Wayne A. , Jackson Scott A. , Stupar Robert M. , Morrell Peter L. 
Published: November 2020

AbstractThe mutagenic effects of ionizing radiation have been used for decades to create novel variants in experimental populations. Fast neutron (FN) bombardment as a mutagen has been especially widespread in plants, with extensive reports describing the induction of large structural variants, i.e., deletions, insertions, inversions, and translocations. However, the full spectrum of FN-induced mutations is poorly understood. We contrast small insertions and deletions (indels) observed in 27 soybean lines subject to FN irradiation with the standing indels identified in 107 diverse soybean lines. We use the same populations to contrast the nature and context (bases flanking a nucleotide change) of single nucleotide variants. The accumulation of new single nucleotide changes in FN lines is marginally higher than expected based on spontaneous mutation. In FN treated lines and in standing variation, C→T transitions and the corresponding reverse complement G→A transitions are the most abundant and occur most frequently in a CpG local context. These data indicate that most SNPs identified in FN lines are likely derived from spontaneous de novo processes in generations following mutagenesis, rather than from the FN irradiation mutagen. However, small indels in FN lines differ from standing variants. Short insertions, from 1 – 6 base pairs, are less abundant than in standing variation. Short deletions are more abundant and prone to induce frameshift mutations that should disrupt the structure and function of encoded proteins. These findings indicate that FN irradiation generates numerous small indels, increasing the abundance of loss of function mutations that will impact single genes.Significance StatementIrradiation mutagenesis is commonly viewed as a method to induce large structural variants in genomes. We also find enrichment in small insertion and deletion (indel) variants. The radiation-mutagenized lines averaged 32 indels per line, far exceeding the number estimated to occur by spontaneous processes, indicating that these arose from the irradiation treatment. Nevertheless, naturally-occurring standing variation among soybean accessions is still four orders of magnitude higher than the level of diversity introduced by mutagenesis. Induced mutations from any source are likely to constitute a relatively small portion of the genetic variation present in crop species. However, irradiation mutagenesis is useful for altering genomes by introducing small indels into single genes or disrupting gene clusters by creating structural variants.
Genomic analyses of high-grade neuroendocrine gynecological malignancies reveal a unique mutational landscape and therapeutic vulnerabilities
Authors: Mahdi Haider , Joehlin-Price Amy , Dowlati Afshin , Abbas Ata 
Published: November 2020

AbstractThe high-grade neuroendocrine carcinoma of gynecologic origin (NEC-GYN) is a highly aggressive cancer affecting young women. The clinical management of NEC-GYN is often extrapolated from their counterpart, small cell carcinoma of the lung (SCLC), but, unfortunately, they have limited effect. In our NEC-GYN cohort, median progression-free survival (PFS) and overall survival (OS) were 1 and 12 months, respectively, indicating their highly lethal nature. Our comprehensive genomic analyses unveiled that NEC-GYN harbors a higher mutational burden with distinct mutational landscapes from SCLC. We identified 14 cancer driver genes (FDR <0.01) including the most frequently alteredKMT2C(100%),KNL1(100%),NCOR2(100%), andCCDC6(93%) genes. Transcriptomic analyses identified several novel gene fusions in NEC-GYN. Furthermore, NEC-GYN exhibited a highly immunosuppressive state and uniquely belonged to theYAP1high molecular subtype that promotes multidrug resistance. Our study suggests an urgent need to reevaluate the therapeutic options and targets for NEC-GYN.
AbaM Regulates Quorum Sensing, Biofilm Formation and Virulence inAcinetobacter baumannii
Authors: López-Martín Mario , Dubern Jean-Frédéric , Alexander Morgan R. , Williams Paul 
Published: November 2020

ABSTRACTAcinetobacter baumanniipossesses a single divergentluxR/luxI-type quorum sensing (QS) locus namedabaR/abaI. This locus also contains a third gene located betweenabaRandabaIwhich we termabaMthat codes for an uncharacterized member of the RsaM protein family known to regulateN-acylhomoserine lactone (AHL) dependent QS in other β- and γ-proteobacteria. Here we show that disruption ofabaMvia a T26 insertion inA. baumanniistrain AB5075 resulted in increased production of N-(3-hydroxydodecanoyl)-L-homoserine lactone (OHC12) and enhanced surface motility and biofilm formation. In contrast to the wild type andabaI::T26 mutant, the virulence of theabaM::T26 mutant was completely attenuated in a Galleria mellonella infection model. Transcriptomic analysis of theabaM::T26 mutant revealed thatabaMdifferentially regulates at least 76 genes including thecsupilus operon and the acinetin 505 lipopeptide biosynthetic operon, that are involved in surface adherence, biofilm formation and virulence. A comparison of the wild type,abaM::T26 andabaI::T26 transcriptomes, indicates thatabaMregulates ~21% of the QS regulon including the csu operon. Moreover, the QS genes (abaI/abaR) were among the most upregulated in theabaM::T26 mutant.A. baumannii lux-basedabaMreporter gene fusions revealed thatabaMexpression is positively regulated by QS but negatively auto-regulated. Overall, the data presented in this work demonstrates thatabaMplays a central role in regulatingA. baumanniiQS, virulence, surface motility and biofilm formation.IMPORTANCEAcinetobacter baumanniis a multi-antibiotic resistant pathogen of global healthcare importance. UnderstandingAcinetobactervirulence gene regulation could aid the development of novel anti-infective strategies. InA. baumannii, theabaRandabaIgenes that code for the receptor and synthase components of anN-acylhomoserine (AHL) lactone-dependent quorum sensing system (QS) are separated byabaM. Here we show that although mutation ofabaMincreased AHL production, surface motility and biofilm development, it resulted in the attenuation of virulence.abaMwas found to control both QS-dependent and QS-independent genes. The significance of this work lies in the identification ofabaM, an RsaM ortholog known to control virulence in plant pathogens, as a modulator of virulence in a human pathogen.
Accuracy, Clinical Utility and Usability Study of a Wireless Self-Guided Fetal Heart Rate Monitor
Authors: Porter Paul , Muirhead Fleur , Brisbane Joanna , Schneider Brooke , Choveaux Jennifer , Bear Natasha , Carson Jennie , Jones Kym , Silva Desiree , Neppe Cliff 
Published: November 2020

AbstractObjectiveTo evaluate the accuracy, reliability, clinical utility, and usability of HeraBEAT, a wireless fetal and maternal heart rate monitor (HBM) when used by clinicians and pregnant women to monitor fetal heart rate (FHR).MethodsWe recruited women aged 18 years or older with a singleton pregnancy of ≥12 weeks gestation. FHR recordings were performed using the HBM and cardiotocography (CTG) to determine comparative accuracy. The HBM was then used by clinicians and participants in the antenatal clinic with the latter then using the device unassisted to record at home. The women rated the HBM using the System Usability Scale (SUS).ResultsA total of 81 participants provided 126 recordings for analysis. The accuracy of the HBM was excellent compared with CTG, with limits of agreement (95%) between −1.5 and +0.9 beats per minute (bpm) and a mean difference of −0.29 bpm. The FHR was detected on 100% of occasions by clinicians (52 recordings) and participants when used in the clinic (42 recordings) and at home (32 recordings). Home users took an average of 1.1 minutes to detect the FHR and recorded a continuous trace of >1 minute in 94% of occasions, with an average total trace time of 4.4 minutes. The FHR trace was deemed to be clinically useful in 100% of clinician recordings and 97% of home recordings. There was no effect from body mass index, gestational age, pregnancy history, or placental position. The HBM ranked in the 96–100th percentile on the SUS for usability and learnability.ConclusionsThe HBM was accurate and easy for clinicians and participants to use. The data recorded at home was equivalent to that obtained in the clinic using current assessment protocols for low-risk pregnancies, allowing the device to be used in telehealth consultations.Clinical Trial RegistrationAustralian New Zealand Clinical Trial Registry, https://www.anzctr.org.au ACTRN12620000739910.