bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparação entre fixação de fio de Kirschner liso e de parafusos canulados em fraturas deslocadas do côndilo lateral do úmero em crianças
Authors: Vergara Alberto Daniel Navarro , Fretes Alberto Navarro 
Published: October 2022

Resumo
Objetivo Comparar o uso de parafusos canulados e de fios de Kirschner lisos em termos da redução da presença de calo exuberante e de complicações em fraturas pediátricas deslocadas do côndilo lateral do úmero.
Métodos Um estudo analítico transversal de casos consecutivos foi realizado de maio a outubro de 2021 com 30 crianças com fraturas deslocadas de côndilo umeral externo. Os resultados funcionais para dor e amplitude de movimento foram estratificados utilizando o sistema de classificação Dhillon.
Resultados Ao todo, 19 pacientes foram submetidos à fixação de fio Kirschner, e 11 à fixação de parafusos canulados. A fixação realizada foi fechada em 14 casos (47%) e aberta em 16 (53%). Dos casos incluídos, não houve perda no acompanhamento. A amostra continha 21 (70%) pacientes do sexo masculino, e a idade variou de 5 a 15 anos, com média de 6,96 anos. A causa mais frequente de fratura foi queda de altura (50%), e esteve relacionada ao maior deslocamento nas radiografias da linha de base. Complicações que não estavam relacionadas à abordagem de redução ou ao implante utilizado foram observadas em 12 (40%) casos.
Conclusão Este estudo não mostra benefícios em relação ao uso de pinos lisos ou de parafusos canulados para reduzir a presença de calo exuberante na consolidação da fratura. Vemos que as complicações que surgem estão relacionadas à gravidade da lesão, e não é possível identificar benefícios na escolha de um implante ou outro. Pudemos ver que a classificação de Weiss ajuda a definir o comportamento em favor da redução aberta ou fechada sem dar preferência ao pino liso ou ao parafuso canulado para a fixação da fratura.
Retracted: Symbiotic Association Between Ants and Fungus
Authors: Riaz S , Farooq F , Manzoor F 
Published: October 2022

AbstractAnts are eusocial insects belong to family Formicidae and live in symbiotic association with different species of the fungus. Fungi serving them as food and others relationship between fungus and ants is fungi increase the durability of the nest ants living in carton nests in the trees. Our goal was to investigate through literature obvious interactions between ants and common fungi, protection of ants' colonies from pathogens and uses of fungal isolates in sustainable agriculture. Fungal bank in the ants colony is their source of food and colonies of ants (Hymenoptera: Formicidae) are attacked by numerous parasites, pathogens, and parasitoids that exploit entire colonies and their resources. Symbiotic fungi strains belonging to Penicillium found in ants nests are antibiotic producer. High frequency and high diversity of these colonies suggested that insects preferentially sustained this fungus for their survival. Fungal growing ants evolved a close mutualistic relationship with multiple species of Actinobacteria belonging to the genus Pseudonocardia for protection of colony from various diseases. Fungus-growing ants and Pseudonocardia symbionts are novel and significant source of antibiotic and antifungal agents and used as model system due to experimental tractability and well-studied ecology. Beauveria bassiana, Metarhizium anisopliae and Lecanicillium psalliotae are Entomopathogenic fungi found in mutualistic association with Attine ants used in a much smaller scale. Formulation of entomopathogenic fungi-based pesticides biosynthesis of fungal-based nanoparticles at industrial scale is useful in recent sustainable agriculture.
The impact of COVID-19 monoclonal antibodies on clinical outcomes: A retrospective cohort study
Authors: R. Nagler Arielle , Horwitz Leora I , Jones Simon , Petrilli Christopher M , Iturrate Eduardo , Lighter Jennifer L , Phillips Michael , Bosworth Brian P , Polsky Bruce , Volpicelli Frank M , Dapkins Isaac , Viswanathan Anand , François Fritz , Kalkut Gary 
Published: October 2022

Abstract

Purpose
Despite progress in the treatment of coronavirus disease 2019 (COVID-19), including the development of monoclonal antibodies (mAbs), more clinical data to support the use of mAbs in outpatients with COVID-19 is needed. This study is designed to determine the impact of bamlanivimab, bamlanivimab/etesevimab, or casirivimab/imdevimab on clinical outcomes within 30 days of COVID-19 diagnosis.

Methods
A retrospective cohort study was conducted at a single academic medical center with 3 campuses in Manhattan, Brooklyn, and Long Island, NY. Patients 12 years of age or older who tested positive for COVID-19 or were treated with a COVID-19–specific therapy, including COVID-19 mAb therapies, at the study site between November 24, 2020, and May 15, 2021, were included. The primary outcomes included rates of emergency department (ED) visit, inpatient admission, intensive care unit (ICU) admission, or death within 30 days from the date of COVID-19 diagnosis.

Results
A total of 1,344 mAb-treated patients were propensity matched to 1,344 patients with COVID-19 patients who were not treated with mAb therapy. Within 30 days of diagnosis, among the patients who received mAb therapy, 101 (7.5%) presented to the ED and 79 (5.9%) were admitted. Among the patients who did not receive mAb therapy, 165 (12.3%) presented to the ED and 156 (11.6%) were admitted (relative risk [RR], 0.61 [95% CI, 0.50-0.75] and 0.51 [95% CI, 0.40-0.64], respectively). Four mAb patients (0.3%) and 2.64 control patients (0.2%) were admitted to the ICU (RR, 01.51; 95% CI, 0.45-5.09). Six mAb-treated patients (0.4%) and 3.37 controls (0.3%) died and/or were admitted to hospice (RR, 1.61; 95% CI, 0.54-4.83). mAb therapy in ambulatory patients with COVID-19 decreases the risk of ED presentation and hospital admission within 30 days of diagnosis.
Burnt Out: Rate of Burnout in Neuropsychology Survey Respondents During the COVID-19 Pandemic, Brief Communication
Authors: Marra David E C , Simons Mary U , Schwartz Eben S , Marston Elizabeth A , Hoelzle James B 
Published: October 2022

AbstractObjectiveDue to the COVID-19 pandemic, burnout among healthcare workers has significantly increased. This study evaluated rates of burnout in neuropsychologists one year into the COVID-19 pandemic.MethodA survey invitation was sent across five neuropsychology-related listservs in April 2021. Burnout was assessed with the Copenhagen Burnout Inventory (CBI; Kristensen, T. S., Borritz, M., Villadsen, E., & Christensen, K. B. (2005). The Copenhagen Burnout Inventory: A new tool for the assessment of burnout. Work & Stress, 19 (3), 192–207) and differences in Personal, Work, and Client burnout scores were evaluated across patient population and work setting.Results57.3% and 51.5% of respondents (N = 130) endorsed moderate-to-high levels of personal and work-related burnout, respectively. In the Personal domain, respondents working with pediatric patients had higher mean scores and a higher proportion of respondents endorsed moderate-to-high levels of burnout.ConclusionMore than half of the survey respondents endorsed elevated levels of personal and work-related burnout. This is concerning as burnout is associated with personal challenges and diminished patient care. Potential organizational interventions are discussed.
ICSDA: a multi-modal deep learning model to predict breast cancer recurrence and metastasis risk by integrating pathological, clinical and gene expression data
Authors: Yao Yuhua , Lv Yaping , Tong Ling , Liang Yuebin , Xi Shuxue , Ji Binbin , Zhang Guanglu , Li Ling , Tian Geng , Tang Min , Hu Xiyue , Li Shijun , Yang Jialiang 
Published: October 2022

AbstractBreast cancer patients often have recurrence and metastasis after surgery. Predicting the risk of recurrence and metastasis for a breast cancer patient is essential for the development of precision treatment. In this study, we proposed a novel multi-modal deep learning prediction model by integrating hematoxylin & eosin (H&E)-stained histopathological images, clinical information and gene expression data. Specifically, we segmented tumor regions in H&E into image blocks (256 × 256 pixels) and encoded each image block into a 1D feature vector using a deep neural network. Then, the attention module scored each area of the H&E-stained images and combined image features with clinical and gene expression data to predict the risk of recurrence and metastasis for each patient. To test the model, we downloaded all 196 breast cancer samples from the Cancer Genome Atlas with clinical, gene expression and H&E information simultaneously available. The samples were then divided into the training and testing sets with a ratio of 7: 3, in which the distributions of the samples were kept between the two datasets by hierarchical sampling. The multi-modal model achieved an area-under-the-curve value of 0.75 on the testing set better than those based solely on H&E image, sequencing data and clinical data, respectively. This study might have clinical significance in identifying high-risk breast cancer patients, who may benefit from postoperative adjuvant treatment.
A systematic assessment of cell type deconvolution algorithms for DNA methylation data
Authors: Song Junyan , Kuan Pei-Fen 
Published: October 2022

Abstract
We performed systematic assessment of computational deconvolution methods that play an important role in the estimation of cell type proportions from bulk methylation data. The proposed framework methylDeConv (available as an R package) integrates several deconvolution methods for methylation profiles (Illumina HumanMethylation450 and MethylationEPIC arrays) and offers different cell-type-specific CpG selection to construct the extended reference library which incorporates the main immune cell subsets, epithelial cells and cell-free DNAs. We compared the performance of different deconvolution algorithms via simulations and benchmark datasets and further investigated the associations of the estimated cell type proportions to cancer therapy in breast cancer and subtypes in melanoma methylation case studies. Our results indicated that the deconvolution based on the extended reference library is critical to obtain accurate estimates of cell proportions in non-blood tissues.
A molecular phylogeny of the Persian Gulf and the Gulf of Oman oyster species
Authors: Ghaffari Hamze , Ahmadzadeh Faraham , Saberi-Pirooz Reihaneh , Abtahi Behrooz 
Published: October 2022

Abstract
The taxonomy of oysters along the northern coasts of the Persian Gulf and the Gulf of Oman is not well recognized. We present a phylogenetic analysis of oyster species in these regions. We combined morphological and molecular techniques to obtain the identity of oysters to the lowest taxonomic levels. Analysis of partial nucleotide sequences from mitochondrial cytochrome c oxidase subunit I (COI) was used for the phylogenetic evaluation. Based on our findings, Iranian samples nested within the genus Saccostrea and belonged to Saccostrea mordax and Saccostrea palmula clades. The shell morphology of the studied samples was variable, as in other rock oyster species. The examination of morphological features was in line with the molecular outcomes, but despite some similarities, Iranian S. palmula had well-developed and elongated chomata. The results also showed that S. mordax and S. palmula possessed significant relative abundance as dominant oysters in the Persian Gulf and the Gulf of Oman, respectively. Phylogenetic analysis revealed that Iranian samples of S. palmula formed a separate subclade from the Gulf of California and Panama samples, with large genetic distances (6–7%). Iranian specimens differed morphologically and genetically, suggesting that they could be a new species, although more research is needed.
The emergence of a cryptic lineage and cytonuclear discordance through past hybridization in the Japanese fire-bellied newt,Cynops pyrrhogaster(Amphibia: Urodela)
Authors: Tominaga Atsushi , Yoshikawa Natsuhiko , Matsui Masafumi , Nagata Nobuaki , Sato Yukuto 
Published: October 2022

AbstractDiscrepancies in geographic variation patterns between nuclear DNA and mitochondrial DNA (mtDNA) are the result of the complicated differentiation processes in organisms and are the key to understanding their true evolutionary processes. The genetic differentiation of the northern and Southern-Izu lineages of the Japanese newt, Cynops pyrrhogaster, was investigated through their single nucleotide polymorphism variations obtained via multiplexed ISSR genotyping by sequencing (MIG-seq). We found three genetic groups (Tohoku, N-Kanto and S-Kanto), that were not detected by mtDNA variations, in the northern lineage. N-Kanto has intermediate genetic characteristics between Tohoku and S-Kanto. The genetic groups are now moderately isolated from each other and have unique genetic characteristics. An estimation of the evolutionary history using the approximate Bayesian computation (ABC) approach suggested that Tohoku diverged from the common ancestor of S-Kanto and S-Izu. Then, S-Kanto and S-Izu split, and the recent hybridization between Tohoku and S-Kanto gave rise to N-Kanto. The origin of N-Kanto through the hybridization is relatively young and seems to be related to changes in the distributions of Tohoku and S-Kanto as a result of climatic oscillation in the Pleistocene. We conclude that the mitochondrial genome of S-Kanto was captured in Tohoku and that the original mitochondrial genome of Tohoku was entirely removed through hybridization.
Delineation of functionally essential protein regions for 242 neurodevelopmental genes
Authors: Iqbal Sumaiya , Brünger Tobias , Pérez-Palma Eduardo , Macnee Marie , Brunklaus Andreas , Daly Mark J , Campbell Arthur J , Hoksza David , May Patrick , Lal Dennis 
Published: October 2022

Abstract
Neurodevelopmental disorders (NDDs), including severe paediatric epilepsy, autism and intellectual disabilities are heterogeneous conditions in which clinical genetic testing can often identify a pathogenic variant. For many of them, genetic therapies will be tested in this or the coming years in clinical trials. In contrast to first-generation symptomatic treatments, the new disease-modifying precision medicines require a genetic test-informed diagnosis before a patient can be enrolled in a clinical trial. However, even in 2022, most identified genetic variants in NDD genes are ‘variants of uncertain significance’. To safely enrol patients in precision medicine clinical trials, it is important to increase our knowledge about which regions in NDD-associated proteins can ‘tolerate’ missense variants and which ones are ‘essential’ and will cause a NDD when mutated. In addition, knowledge about functionally indispensable regions in the 3D structure context of proteins can also provide insights into the molecular mechanisms of disease variants.
We developed a novel consensus approach that overlays evolutionary, and population based genomic scores to identify 3D essential sites (Essential3D) on protein structures. After extensive benchmarking of AlphaFold predicted and experimentally solved protein structures, we generated the currently largest expert curated protein structure set for 242 NDDs and identified 14 377 Essential3D sites across 189 gene disorders associated proteins. We demonstrate that the consensus annotation of Essential3D sites improves prioritization of disease mutations over single annotations. The identified Essential3D sites were enriched for functional features such as intermembrane regions or active sites and discovered key inter-molecule interactions in protein complexes that were otherwise not annotated. Using the currently largest autism, developmental disorders, and epilepsies exome sequencing studies including &gt;360 000 NDD patients and population controls, we found that missense variants at Essential3D sites are 8-fold enriched in patients.
In summary, we developed a comprehensive protein structure set for 242 NDDs and identified 14 377 Essential3D sites in these. All data are available at https://es-ndd.broadinstitute.org for interactive visual inspection to enhance variant interpretation and development of mechanistic hypotheses for 242 NDDs genes. The provided resources will enhance clinical variant interpretation and in silico drug target development for NDD-associated genes and encoded proteins.
Hepatitis B Virus (HBV) Replication During Tenofovir Therapy Is Frequent in Human Immunodeficiency Virus/HBV Coinfection
Authors: Hofmann Eveline , Surial Bernard , Boillat-Blanco Noémie , Günthard Huldrych F , Stöckle Marcel , Bernasconi Enos , Schmid Patrick , Calmy Alexandra , Suter-Riniker Franziska , Rauch Andri , Wandeler Gilles , Béguelin Charles ,   for the Swiss HIV Cohort Study, Abela I , Aebi-Popp K , Anagnostopoulos A , Battegay M , Bernasconi E , Braun DL , Bucher HC , Calmy A , Cavassini M , Ciuffi A , Dollenmaier G , Egger M , Elzi L , Fehr J , Fellay J , Furrer H , Fux CA , Günthard HF , Hachfeld A , Haerry D , Hasse B , Hirsch HH , Hoffmann M , Hösli I , Huber M , Kahlert CR , Kaiser L , Keiser O , Klimkait T , Kouyos RD , Kovari H , Kusejko K , Martinetti G , Martinez de Tejada B , Marzolini C , Metzner KJ , Müller N , Nemeth J , Nicca D , Paioni P , Pantaleo G , Perreau M , Rauch A , Schmid P , Speck R , Stöckle M , Tarr P , Trkola A , Wandeler G , Yerly S 
Published: October 2022

AbstractIn the Swiss HIV Cohort Study, 61 of 222 (27%) HIV–suppressed persons with chronic hepatitis B virus (HBV) infection had HBV replication after 2 years on tenofovir, of whom 77% were suppressed thereafter. Self-reported adherence to therapy and HBV viral load at tenofovir initiation were predictors of persistent replication.
When Civilisational Clashes Meet Power Shifts: Rethinking Global Disorder
Authors: Zhang Baohui 
Published: October 2022

Abstract
Samuel Huntington’s famous prediction in 1993 of “clashes of civilisations”, amid that decade’s rosy expectations of “liberal peace”, sparked wide criticism for its rebutting of the then-conventional wisdom of globalisation, global governance, and democratic peace that defined the so-called “liberal” international politics of the 1990s. However, events in recent decades have corroborated his stark prediction. In particular, conflicts between the West and non-Western rising powers have become a salient feature of international politics—an outcome shaped not only by differences in civilisational identity but also by power shifts that trigger civilisational clashes. In their quest to acquire influence better befitting their expanding material capabilities, rising powers seek to reorder the international system by shaping its rules and institutions according to their civilisational values and norms. This aspiration has generated conflict between non-Western rising powers and the West over ideational incompatibilities, global governance, and the reconfiguration of regional orders. The consequences of such civilisational conflict have led to escalating fragmentation, disorder, and instability in world politics.
CR Loss: Improving Biometric Using ClassRoom Learning Approach
Authors: Prasad Shitala , Chai Tingting , Li Jiahui , Zhang Zhaoxin 
Published: October 2022

Abstract
One of the important factors in deep feature learning is their loss function design which highly influences the network performance. In this paper, we proposed a classroom (CR) learning approach along with arcface loss for contactless palmprint recognition to obtain high-level discriminative features without any extra load made to the network architecture. CR loss allows the network to learn the best possible feature representations for palmprint images. To validate our concept, we performed extensive experimental evaluations on various popular benchmark palmprint databases where our methods outperform the state-of-the-art methods. We also introduced a challenging contactless palmprint database called Harbin Institute of Technology-Network & Information Security Research Center contactless palmprint database version 1.0 (HIT-NIST-V1), as a new contribution to this domain. The result proves that the proposed CR loss consistently outperforms the SOTA methods for all the considered databases and especially for HIT-NIST-V1.
Health-related quality of life following neoadjuvant chemoradiotherapy versus perioperative chemotherapy and esophagectomy for esophageal cancer: a European multicenter study
Authors: Schuring N , Markar S R , Hagens E R C , Jezerskyte E , Sprangers M A G , Lagergren P , Johar A , Gisbertz S S , van Berge Henegouwen M I ,   the LASER study group
Published: October 2022

SummaryCurative treatment for locally advanced esophageal cancer consists of (neo)adjuvant treatment followed by esophagectomy. Both neoadjuvant chemoradiotherapy and perioperative chemotherapy improve the 5-year overall survival rate compared with surgery alone. However, it is unknown whether these treatment strategies are associated with differences in long-term health-related quality of life (HRQL). The aim of this study is to compare long-term HRQL in patients after esophagectomy treated with neoadjuvant chemoradiotherapy or perioperative chemotherapy. Disease-free cancer patients having undergone esophagectomy and (neo)adjuvant treatment in one of the participating lasting symptoms after esophageal resection (LASER) study centers between 2010 and 2016, were identified from the LASER study dataset. Included patients completed the European Organisation for Research and Treatment of Cancer Quality of Life Questionnaire C30 (EORTC QLQ-C30), EORTC QLQ-OG25, and LASER questionnaires at least 1 year after the completion of treatment. Long-term HRQL was compared between patients treated with neoadjuvant chemoradiotherapy or perioperative chemotherapy, using univariable and multivariable regression and presented as differences in mean score. Among the 565 included patients, 349 (61.8%) received neoadjuvant chemoradiotherapy, and 216 (38.2%) perioperative chemotherapy. Patients treated with perioperative chemotherapy reported more symptomatology for diarrhea (difference in means 5.93), reflux (difference in means 7.40), and odynophagia (difference in means 4.66). The differences did not exceed the 10 points to be of clinical relevance. No significant differences for the LASER key symptoms were observed. The observed differences in long-term HRQL are in favor of patients treated with neoadjuvant chemoradiotherapy compared with patients treated with perioperative chemotherapy; however, the differences were small. Patients need to be informed about long-term HRQL when considering allocation of (neo)adjuvant treatment.