bluuebunny/crossref_metadata_2025_split huggingface dataset:
The feasibility of pragmatic influenza vaccine randomized controlled real-world trials in Denmark and England
Authors: Nealon Joshua , Modin Daniel , Ghosh Rebecca E. , Rudin Deborah , Gislason Gunnar , Booth Helen P. , Jensen Jens Ulrik Stæhr , Williams Rachael , Shepherd Hilary , Yelland Eleanor , Bricout Helene , Chaves Sandra S. , Biering-Sørensen Tor 
Published: February 2022

AbstractWe estimated the frequency of non-specific influenza-associated clinical endpoints to inform the feasibility of pragmatic randomized controlled trials (RCT) assessing relative vaccine effectiveness (rVE). Hospitalization rates of respiratory, cardiovascular and diabetic events were estimated from Denmark and England’s electronic databases and stratified by age, comorbidity and influenza vaccination status. We included a seasonal average of 4.5 million Danish and 7.2 million English individuals, 17 and 32% with comorbidities. Annually, approximately 1% of Danish and 0.5% of English individuals were hospitalized for selected events, ~50% of them respiratory. Hospitalization rates were 40–50-fold and 2–10-fold higher in those >50 years and with comorbidities, respectively. Our findings suggest that a pragmatic RCT using non-specific endpoints is feasible. However, for outcomes with rates <2.5%, it would require randomization of ~100,000 participants to have the power to detect a rVE difference of ~13%. Targeting selected groups (older adults, those with comorbidities) where frequency of events is high would improve trial efficiency.
Ancient DNA and deep population structure in sub-Saharan African foragers
Authors: Lipson Mark , Sawchuk Elizabeth A. , Thompson Jessica C. , Oppenheimer Jonas , Tryon Christian A. , Ranhorn Kathryn L. , de Luna Kathryn M. , Sirak Kendra A. , Olalde Iñigo , Ambrose Stanley H. , Arthur John W. , Arthur Kathryn J. W. , Ayodo George , Bertacchi Alex , Cerezo-Román Jessica I. , Culleton Brendan J. , Curtis Matthew C. , Davis Jacob , Gidna Agness O. , Hanson Annalys , Kaliba Potiphar , Katongo Maggie , Kwekason Amandus , Laird Myra F. , Lewis Jason , Mabulla Audax Z. P. , Mapemba Fredrick , Morris Alan , Mudenda George , Mwafulirwa Raphael , Mwangomba Daudi , Ndiema Emmanuel , Ogola Christine , Schilt Flora , Willoughby Pamela R. , Wright David K. , Zipkin Andrew , Pinhasi Ron , Kennett Douglas J. , Manthi Fredrick Kyalo , Rohland Nadin , Patterson Nick , Reich David , Prendergast Mary E. 
Published: February 2022

AbstractMultiple lines of genetic and archaeological evidence suggest that there were major demographic changes in the terminal Late Pleistocene epoch and early Holocene epoch of sub-Saharan Africa1–4. Inferences about this period are challenging to make because demographic shifts in the past 5,000 years have obscured the structures of more ancient populations3,5. Here we present genome-wide ancient DNA data for six individuals from eastern and south-central Africa spanning the past approximately 18,000 years (doubling the time depth of sub-Saharan African ancient DNA), increase the data quality for 15 previously published ancient individuals and analyse these alongside data from 13 other published ancient individuals. The ancestry of the individuals in our study area can be modelled as a geographically structured mixture of three highly divergent source populations, probably reflecting Pleistocene interactions around 80–20 thousand years ago, including deeply diverged eastern and southern African lineages, plus a previously unappreciated ubiquitous distribution of ancestry that occurs in highest proportion today in central African rainforest hunter-gatherers. Once established, this structure remained highly stable, with limited long-range gene flow. These results provide a new line of genetic evidence in support of hypotheses that have emerged from archaeological analyses but remain contested, suggesting increasing regionalization at the end of the Pleistocene epoch.
Designing of two dimensional lanthanum cobalt hydroxide engineered high performance supercapacitor for longer stability under redox active electrolyte
Authors: Bailmare Deepa B. , Tripathi Prashant , Deshmukh Abhay D. , Gupta Bipin Kumar 
Published: February 2022

AbstractRedox active electrolyte supercapacitors differ significantly from the conventional electrolytes based storage devices but face a long term stability issue which requires a different approach while designing the systems. Here, we show the change in layered double hydroxides (LDHs) systems with rare earth elements (lanthanum) can drastically influence the stability of two dimensional LDH systems in redox electrolyte. We find that the choice of rare earth element (lanthanum) having magnetic properties and higher thermal and chemical stability has a profound effect on the stability of La–Co LDHs electrode in redox electrolyte. The fabricated hybrid device with rare earth based positive electrode and carbon as negative electrode having redox electrolyte leads to long stable high volumetric/gravimetric capacity at high discharge rate, demonstrates the importance of considering the rare earth elements while designing the LDH systems for redox active supercapacitor development.
Survival Genie, a web platform for survival analysis across pediatric and adult cancers
Authors: Dwivedi Bhakti , Mumme Hope , Satpathy Sarthak , Bhasin Swati S. , Bhasin Manoj 
Published: February 2022

AbstractThe genomics data-driven identification of gene signatures and pathways has been routinely explored for predicting cancer survival and making decisions related to targeted treatments. A large number of packages and tools have been developed to correlate gene expression/mutations to the clinical outcome but lack the ability to perform such analysis based on pathways, gene sets, and gene ratios. Furthermore, in this single-cell omics era, the cluster markers from cancer single-cell transcriptomics studies remain an underutilized prognostic option. Additionally, no bioinformatics online tool evaluates the associations between the enrichment of canonical cell types and survival across cancers. Here we have developed Survival Genie, a web tool to perform survival analysis on single-cell RNA-seq (scRNA-seq) data and a variety of other molecular inputs such as gene sets, genes ratio, tumor-infiltrating immune cells proportion, gene expression profile scores, and tumor mutation burden. For a comprehensive analysis, Survival Genie contains 53 datasets of 27 distinct malignancies from 11 different cancer programs related to adult and pediatric cancers. Users can upload scRNA-seq data or gene sets and select a gene expression partitioning method (i.e., mean, median, quartile, cutp) to determine the effect of expression levels on survival outcomes. The tool provides comprehensive results including box plots of low and high-risk groups, Kaplan–Meier plots with univariate Cox proportional hazards model, and correlation of immune cell enrichment and molecular profile. The analytical options and comprehensive collection of cancer datasets make Survival Genie a unique resource to correlate gene sets, pathways, cellular enrichment, and single-cell signatures to clinical outcomes to assist in developing next-generation prognostic and therapeutic biomarkers. Survival Genie is open-source and available online at https://bbisr.shinyapps.winship.emory.edu/SurvivalGenie/.
High stability microwave discharge ion sources
Authors: Neri L. , Celona L. 
Published: February 2022

AbstractA new plasma heating mechanism for Microwave Discharge Ion Sources (MDIS) was discovered. Unprecedented beam stability was observed during the commissioning of the Proton Source for the European Spallation Source (PS-ESS) where several thousand source configurations were tested using a custom software tool. Data analysis and plasma simulation revealed that the new behaviour is generated by a completely new plasma heating schema activated by a precise magnetic configuration peculiarity. The stability showed in this configuration, denominated High Stability Microwave Discharge Ion Source (HSMDIS), is excellent and the emittance of the produced beam is lower than produced by standard MDIS configuration. High linearity between power and beam current was observed making easier the use of the source. This new mode of operation can be easily implemented in all existing sources.
Segmentation of pancreatic ductal adenocarcinoma (PDAC) and surrounding vessels in CT images using deep convolutional neural networks and texture descriptors
Authors: Mahmoudi Tahereh , Kouzahkanan Zahra Mousavi , Radmard Amir Reza , Kafieh Raheleh , Salehnia Aneseh , Davarpanah Amir H. , Arabalibeik Hossein , Ahmadian Alireza 
Published: February 2022

AbstractFully automated and volumetric segmentation of critical tumors may play a crucial role in diagnosis and surgical planning. One of the most challenging tumor segmentation tasks is localization of pancreatic ductal adenocarcinoma (PDAC). Exclusive application of conventional methods does not appear promising. Deep learning approaches has achieved great success in the computer aided diagnosis, especially in biomedical image segmentation. This paper introduces a framework based on convolutional neural network (CNN) for segmentation of PDAC mass and surrounding vessels in CT images by incorporating powerful classic features, as well. First, a 3D-CNN architecture is used to localize the pancreas region from the whole CT volume using 3D Local Binary Pattern (LBP) map of the original image. Segmentation of PDAC mass is subsequently performed using 2D attention U-Net and Texture Attention U-Net (TAU-Net). TAU-Net is introduced by fusion of dense Scale-Invariant Feature Transform (SIFT) and LBP descriptors into the attention U-Net. An ensemble model is then used to cumulate the advantages of both networks using a 3D-CNN. In addition, to reduce the effects of imbalanced data, a multi-objective loss function is proposed as a weighted combination of three classic losses including Generalized Dice Loss (GDL), Weighted Pixel-Wise Cross Entropy loss (WPCE) and boundary loss. Due to insufficient sample size for vessel segmentation, we used the above-mentioned pre-trained networks and fine-tuned them. Experimental results show that the proposed method improves the Dice score for PDAC mass segmentation in portal-venous phase by 7.52% compared to state-of-the-art methods in term of DSC. Besides, three dimensional visualization of the tumor and surrounding vessels can facilitate the evaluation of PDAC treatment response.
Prognostic signature based on m6A-related lncRNAs to predict overall survival in pancreatic ductal adenocarcinoma
Authors: Wu Qiong , Chen Lei , Miao Dongliu , Jin Yiqi , Zhu Zhigang 
Published: February 2022

AbstractA growing body of evidence indicates that N6-methyladenosine (m6A) and long non-coding RNAs (lncRNAs) play crucial roles in the progression of PDAC and the treatment response of patients with pancreatic ductal adenocarcinoma (PDAC). In this study, we identified m6A-related lncRNAs to reveal their association with PDAC in prognosis and tumor immune environment. A prognostic signature based on 9 m6A-related lncRNAs was established, and the high-risk patients exhibited a significantly worse prognosis than low-risk patients. The predictive capacity was confirmed by receiver operating characteristic (ROC) curve analysis and an independent validation cohort. Correlation analyses revealed that m6A-related lncRNA signature was significantly associated with the number of somatic mutations, immunocyte infiltration, immune function, immune checkpoints, tumor microenvironment (TME) score, and sensitivity to chemotherapeutic drugs. Consequently, we constructed a highly accurate nomogram for improving clinical applicability of signature and exhibited superior predictive accuracy than both the signature and tumor stage. In conclusion, our proposed m6A-related lncRNA signature is a potential indicator predictive of prognosis and immunotherapeutic responses in PDAC patients.
Ibrutinib reverses IL-6-induced osimertinib resistance through inhibition of Laminin α5/FAK signaling
Authors: Li Li , Li Zhujun , Lu Conghua , Li Jianghua , Zhang Kejun , Lin Caiyu , Tang Xiaolin , Liu Zhulin , Zhang Yimin , Han Rui , Wang Yubo , Feng Mingxia , Zhuang Yuan , Hu Chen , He Yong 
Published: February 2022

AbstractOsimertinib, a 3rd generation epidermal growth factor receptor tyrosine kinase inhibitor (EGFR-TKI), is the first-line standard-of-care for EGFR-mutant non-small cell lung cancer (NSCLC) patients, while acquired drug resistance will inevitably occur. Interleukin-6 (IL-6) is a keystone cytokine in inflammation and cancer, while its role in osimertinib efficacy was unknown. Here we show that clinically, plasma IL-6 level predicts osimertinib efficacy in EGFR mutant NSCLC patients. Highly increased IL-6 levels are found in patients with acquired resistance to osimertinib. Addition of IL-6 or exogenous overexpression of IL-6 directly induces osimertinib resistance. Proteomics reveals LAMA5 (Laminin α5) and PTK2, protein tyrosine kinase 2, also called focal adhesion kinase (FAK), are activated in osimertinib-resistant cells, and siRNA knockdown of LAMA5 or PTK2 reverses IL-6-mediated osimertinib resistance. Next, using a large-scale compound screening, we identify ibrutinib as a potent inhibitor of IL-6 and Laminin α5/FAK signaling, which shows synergy with osimertinib in osimertinib-resistant cells with high IL-6 levels, but not in those with low IL-6 levels. In vivo, this combination inhibits tumor growth of xenografts bearing osimertinib-resistant tumors. Taken together, we conclude that Laminin α5/FAK signaling is responsible for IL-6-induced osimertinib resistance, which could be reversed by combination of ibrutinib and osimertinib.
Simultaneous dimensionality reduction and integration for single-cell ATAC-seq data using deep learning
Authors: Kopp Wolfgang , Akalin Altuna , Ohler Uwe 
Published: February 2022

AbstractAdvances in single-cell technologies enable the routine interrogation of chromatin accessibility for tens of thousands of single cells, elucidating gene regulatory processes at an unprecedented resolution. Meanwhile, size, sparsity and high dimensionality of the resulting data continue to pose challenges for its computational analysis, and specifically the integration of data from different sources. We have developed a dedicated computational approach: a variational auto-encoder using a noise model specifically designed for single-cell ATAC-seq (assay for transposase-accessible chromatin with high-throughput sequencing) data, which facilitates simultaneous dimensionality reduction and batch correction via an adversarial learning strategy. We showcase its benefits for detailed cell-type characterization on individual real and simulated datasets as well as for integrating multiple complex datasets.
Non-target impacts of fungicide disturbance on phyllosphere yeasts in conventional and no-till management
Authors: Noel Zachary A , Longley Reid , Benucci Gian Maria Niccolò , Trail Frances , Chilvers Martin I , Bonito Gregory 
Published: February 2022

Abstract
Fungicides reduce fungal pathogen populations and are essential to food security. Understanding the impacts of fungicides on crop microbiomes is vital to minimizing unintended consequences while maintaining their use for plant protection. However, fungicide disturbance of plant microbiomes has received limited attention, and has not been examined in different agricultural management systems. We used amplicon sequencing of fungi and prokaryotes in maize and soybean microbiomes before and after foliar fungicide application in leaves and roots from plots under long-term no-till and conventional tillage management. We examined fungicide disturbance and resilience, which revealed consistent non-target effects and greater resiliency under no-till management. Fungicides lowered pathogen abundance in maize and soybean and decreased the abundance of Tremellomycetes yeasts, especially Bulleribasidiaceae, including core microbiome members. Fungicide application reduced network complexity in the soybean phyllosphere, which revealed altered co-occurrence patterns between yeast species of Bulleribasidiaceae, and Sphingomonas and Hymenobacter in fungicide treated plots. Results indicate that foliar fungicides lower pathogen and non-target fungal abundance and may impact prokaryotes indirectly. Treatment effects were confined to the phyllosphere and did not impact belowground microbial communities. Overall, these results demonstrate the resilience of no-till management to fungicide disturbance, a potential novel ecosystem service provided by no-till agriculture.
Interface temperature evolution exposed to arc discharges occurred on the uniform moist pollution layer of composite insulators based on interface fibre Bragg gratings
Authors: Hao Yanpeng , Bi Jikai , Wang Quan , Yang Lin 
Published: February 2022

AbstractArc discharges of moist polluted composite insulators pose a serious threat to the stable operation of transmission line. However, there is no effective detection technology for arc discharges. The evolution mechanism of interface temperature accompanied by arc discharges is not clear. In this paper, a 10 kV composite insulator with quasi‐distributed fibre Bragg gratings (FBGs) embedded at the insulator core‐housing interface was developed. The temperature calibration experiment of interface FBGs, and the arc discharges experiment of the uniform moist polluted composite insulator were conducted. Applied voltage was controlled to get the continuous arc with an arc time of 46 s and the intermittent arc with an arc time of 8 s. Exposed to the two types of surface arcs, the interface temperature evolution was explored. A new phenomenon of the sharp drop of the interface temperature was observed: the interface temperature first drops sharply and then rises rapidly during the continuous arc. Test results show that quasi‐distributed FBGs are valid for detecting the two types of surface arcs by interface temperature rise. This paper provides a technical means to evaluate the state of surface discharges and insulating properties of composite insulators.
Treatment of Atypical Clots
Authors: Ageno Walter 
Published: February 2022

AbstractThe term unusual site thrombosis refers to the occurrence of venous thromboembolism outside of the lower limbs and the pulmonary arteries. Unusual site thrombosis can virtually affect any venous segment, with the most common and/or clinically relevant sites including the upper limbs veins, the retinal veins, the splanchnic veins and the cerebral veins. Clinical features are obviously heterogeneous, while many predisposing factors are common, though with different prevalence among the various disorders. Antithrombotic therapy is prescribed to most patients, but the type, intensity, and duration of treatment vary both within and among patient groups. Increasing evidence is supporting the use of the direct oral anticoagulants in patients with upper limb deep vein thrombosis, cerebral vein thrombosis, and with splanchnic vein thrombosis. This article will review available evidence on the treatment of venous thrombosis occurring in unusual sites.
Sport mit Knieprothese – Wieviel Sport ist möglich und was gilt es zu beachten ?
Authors: Hanreich Carola , Springer Bernhard , Waldstein Wenzel , Rueckl Kilian , Bechler Ulrich , Boettner Friedrich 
Published: February 2022

ZusammenfassungMit dem demografischen Wandel der Patientenpopulation, die einen Kniegelenkersatz erhält, verändern sich die Ansprüche der Patienten. Jüngere Patienten möchten sich nach Implantation
einer Knietotalendoprothese (K-TEP) sportlich betätigen und zählen auf die Langlebigkeit des Implantates. Die Literatur zeigt, dass Patienten sowohl prä- als auch postoperativ vorwiegend
Sportarten der Kategorie Low Impact ausüben. Ein gewisser Prozentsatz praktiziert mit entsprechender Vorerfahrung auch High-Impact-Sportarten. In der operativen Versorgung kann durch
konforme Implantate die Punktbelastung der Polyethylenoberfläche verringert werden, durch eine adäquate Komponentenausrichtung erhöhter Stress an der medialen
Knochen-Implantat-Schnittstelle vermieden und durch die Vermeidung eines Retropatellarersatzes eine stärkere Belastung in tiefer Kniebeuge ermöglicht werden.Eine K-TEP sollte heutzutage kein absolutes Hindernis für High-Impact-Sportarten wie Tennis, Golf oder Skifahren sein. Viel mehr als implantatspezifische Faktoren scheinen jedoch
patientenspezifische Faktoren ausschlaggebend zu sein, insbesondere das präoperative Aktivitätslevel und die präoperativen Sportgewohnheiten. Die vorliegende Übersichtsarbeit gibt Einblick
in das tatsächliche Sportverhalten von K-TEP-Patienten, beschreibt die biomechanischen Belastungsmuster am Kniegelenk bei diversen Sportarten und fasst die wichtigsten Aspekte in der
Versorgung von sportlich aktiven Patienten mit einer K-TEP zusammen.
Push-Out Bond Strength of EndoSeal Mineral Trioxide Aggregate and AH Plus Sealers after Using Three Different Irrigation Protocols
Authors: Rifaat Shimaa , Rahoma Ahmed , Alkhalifa Fatimah , AlQuraini Ghofran , Alsalman Zahraa , Alwesaibi Zahraa , Taymour Noha 
Published: February 2022

Abstract
Objective The current study was designed to assess the bonding strength of EndoSeal MTA and AH Plus sealers after using three irrigation protocols as follows: (1) 17% Ethylenediamine tetraacetic acid, (2) 7% maleic acid, and (3) 37% phosphoric acid.
Materials and Methods Push-out bond strength was evaluated for 60 middle root slices of 1-mm thickness each. They were horizontally cut from freshly extracted single-rooted human teeth. A hole in the root canal was made using a carbide round bur of 1.1 mm in diameter in a middle third root slice. Specimens were dipped in 2.5% NaOCl, and then they were grouped into three groups; G1: 17% EDTA, G2: 7% maleic acid, and G3: 37% phosphoric acid as a final irrigant for 3 minutes. Each group was subdivided into two subgroups, according to the type of sealer, either EndoSeal MTA or AH Plus.
Statistical Analysis After the full set of the sealer, the bond strength was evaluated with the push-out test by applying a force to each slice using a plunger with a 1-mm diameter. The one-way Tukey's post hoc test, analysis of variance (ANOVA) test, and Student's t-test were utilized to gather data and statistically evaluate it.
Results The irrigation protocol used exhibited significant influence on the bond strength of EndoSeal MTA and AH Plus sealers. AH Plus sealer subgroups showed the highest bond strength with 7% maleic acid, followed by 37% phosphoric acid, and 17% EDTA. While in the EndoSeal MTA sealer subgroups, the highest bond strength was shown with the 17% EDTA followed by 7% maleic acid and 37% phosphoric acid, respectively.
Conclusion The present study revealed that the type of the final irrigant significantly impacts the bond strength of the sealer used. The AH Plus sealer bond strength was improved by using the 7% maleic acid as a final irrigant. In contrast, the EndoSeal MTA sealer showed the best results with the 17% EDTA as a final irrigant.