bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantum machine learning of large datasets using randomized measurements
Authors: Haug Tobias , Self Chris N , Kim M S 
Published: January 2023

Abstract
Quantum computers promise to enhance machine learning for practical applications. Quantum machine learning for real-world data has to handle extensive amounts of high-dimensional data. However, conventional methods for measuring quantum kernels are impractical for large datasets as they scale with the square of the dataset size. Here, we measure quantum kernels using randomized measurements. The quantum computation time scales linearly with dataset size and quadratic for classical post-processing. While our method scales in general exponentially in qubit number, we gain a substantial speed-up when running on intermediate-sized quantum computers. Further, we efficiently encode high-dimensional data into quantum computers with the number of features scaling linearly with the circuit depth. The encoding is characterized by the quantum Fisher information metric and is related to the radial basis function kernel. Our approach is robust to noise via a cost-free error mitigation scheme. We demonstrate the advantages of our methods for noisy quantum computers by classifying images with the IBM quantum computer. To achieve further speedups we distribute the quantum computational tasks between different quantum computers. Our method enables benchmarking of quantum machine learning algorithms with large datasets on currently available quantum computers.
Indian heatwaves in a future climate with varying hazard thresholds
Authors: Rao K Koteswara , Jyoteeshkumar Reddy P , Chowdary Jasti S 
Published: January 2023

Abstract
India has experienced remarkable changes in temperature extremes in recent decades due to rapid global warming leading to extreme heat events with disastrous societal impacts. In response to continuing global warming, this study investigates summertime (March–June) heatwave characteristics over India in the present and future climate. During 1951–2020, India Meteorological Department observational data show rising trends in heatwave characteristics such as frequency, intensity, duration, and season length, mainly over India’s northwest, central, and south peninsular regions. Further, the present study explores the changes in future heatwave characteristics using the state-of-the-art statistically downscaled bias-corrected climate models data from Coupled Model Intercomparison Project Phase 6 (CMIP6) of the Shared Socioeconomic Pathway scenario. This study uses varying hazard thresholds, namely fixed (time-invariant historical climatological threshold) and decadal moving thresholds (time-varying future climatological threshold), to define heatwaves and examine the future changes in heatwave characteristics over India. Results show a significant increase in mean summertime heatwaves defined using fixed thresholds in terms of their frequency, duration, number, amplitude, cumulative magnitude, and season length in the near future (NF) (2025–2054) and the far future (FF) (2065–2094) compared to the baseline period (1985–2014) over much of India, with the most substantial increases seen in the FF. However, heatwaves defined using the decadal moving thresholds show no significant changes in their characteristics during the NF but a substantial change in the FF over many parts of India. This work is the first attempt to use bias-corrected CMIP6 models data to project heatwave characteristics utilising the concept of the varying hazard thresholds across India. Overall, this study provides a comprehensive assessment of climate change’s impact on Indian heatwaves, which can help in planning better adaptation and mitigation strategies.
GlobeCorr: interactive globe-based visualization for correlation datasets
Authors: Arab Mariam , Woods Nolan , Garlock Emma S , Winsor Geoffrey L , Parks Jaclyn P , Jia Baofeng , Doiron Dany , Takaro Tim K , Brook Jeffrey R , Brinkman Fiona S L 
Published: January 2023

Abstract

Motivation
Increasingly complex omics datasets are being generated, along with associated diverse categories of metadata (environmental, clinical, etc.). Looking at the correlation between these variables can be critical to identify potential confounding factors and novel relationships. To date, some correlation globe software has been developed to aid investigations; however, they lack secure, dynamic visualization capability.

Results
GlobeCorr.ca is a web-based application designed to provide user-friendly, interactive visualization and analysis of correlation datasets. Users load tabular data listing pairwise variables and their correlation values, and GlobeCorr creates a dynamic visualization using ribbons to represent positive and negative correlations, optionally grouped by domain/category (such as microbiome taxa against other metadata). GlobeCorr runs securely (locally on a user’s computer) and provides a simple method for users to visualize and summarize complex datasets. This tool is applicable to a wide range of disciplines and domains of interest, including the bioinformatics/microbiome and metadata examples provided within.

Availability and Implementation
See https://GlobeCorr.ca; Code provided under an open source MIT license: https://github.com/brinkmanlab/globecorr.
Lifestyle trajectories and ischaemic heart diseases: a prospective cohort study in UK Biobank
Authors: Gao Yinyan , Chen Yancong , Hu Mingyue , Song Jinlu , Zhang Zixuan , Sun Hui , Wang Jiali , Lin Yijuan , Wu Irene X Y 
Published: January 2023

AbstractAimsTo evaluate the associations of baseline and long-term trajectories of lifestyle with incident ischaemic heart diseases (IHDs).Methods and results29 164 participants in the UK Biobank who had at least one follow-up assessment and were free of IHD at the last follow-up assessment were included. We constructed a weighted unhealthy lifestyle score though summing five lifestyle factors [smoking, physical activity, diet, body mass index, and sleep duration]. Lifestyle assessed at baseline (2006–09), the first follow-up assessment (2012–13), and the second follow-up assessment (since 2014) were used to derive the trajectories of each individual. The joint categories were created through cross-classifying the three baseline lifestyle categories (ideal, intermediate, and poor) by the three lifestyle trajectory categories (improve, maintain, and decline). During a median follow-up period of 4.2 years, 868 IHD events were recorded. The hazard ratio (HR) of incident IHD associated with per unit increase in unhealthy lifestyle trajectory was 1.08 [95% confidence interval (CI): 0.99–1.17]. Subgroup analyses indicated such association was stronger among individuals with hypertension (HR: 1.13, 95% CI: 1.03–1.24), diabetes (HR: 1.23, 95% CI: 0.96–1.58), or hyperlipidaemia (HR: 1.09, 95% CI: 0.97–1.22). Compared with participants consistently adhering to an ideal lifestyle (ideal–maintain), the HRs of incident IHD were 1.30 (1.07–1.58) for intermediate–maintain, 1.52 (1.23–1.88) for poor–maintain, 1.25 (0.93–1.68) for intermedia–improve, 1.48 (1.17–1.88) for poor–improve, 1.46 (1.08–1.99) for intermedia–decline, and 1.77 (1.21–2.59) for poor–decline.ConclusionsA declined lifestyle trajectory increased the risk of incident IHD, irrespective of baseline lifestyle levels. Individuals with hypertension, diabetes, or hyperlipidaemia were more predisposed to the influence of lifestyle change.
Ethanolic leaf extract ofDatura stramoniumattenuates methotrexate-induced biochemical alterations in Wistar Albino rats
Authors: Alum Esther U , Inya Joseph E , Ugwu Okechukwu P C , Obeagu Emmanuel I , Aloke Chinyere , Aja Patrick M , Okpata Mmesoma G , John Esther C , Orji Manasseh O , Onyema Ozioma 
Published: January 2023

AbstractObjectivesMethotrexate (MTX) is a commonly used anti-cancer drug. However, its usage could lead to various biochemical dysregulations culminating in organ toxicity. Globally, most plant products have been used for the treatment of several diseases. Thus, we investigated the effect of Datura stramonium ethanolic leaf extract (DSELE) supplementation in MXT-induced biochemical alterations in rats.MethodsRats were divided into four groups: Group 1 received normal saline (5 mg/kg b. w), Group 2 received DSELE (200 mg/kg), Group 3 received 20 mg/kg MXT while rats in Group 4 received 200 mg/kg + MTX 20 mg/kg. Normal saline and DSELE were administered per os for 21 days while MXT single injection was given intraperitoneally on day 18 and the rats were sacrificed after 3 days. Thereafter, biochemical parameters were evaluated.Key findingsMTX caused a significant (P &lt; 0.05) increase in serum activities of liver enzymes (AST, ALT and ALP) and levels of total cholesterol and low-density lipoprotein while the levels of total protein and albumin decreased significantly relative to the normal control. Interestingly, DSELE administration favourably modulated MXT-induced biochemical alterations to levels comparable to normal control.ConclusionsDSELE can be a useful combinatorial natural product in MTX chemotherapy since it mitigates MXT-induced biochemical alterations in rats.
Secure reconstruction after pancreaticoduodenectomy: Review and improved our continuous duct-to-mucosa anastomosis
Authors: Hwang Tsann-Long , Kao Hao-Wei , Hsu Chih-Po , Hsu Jun-Te , Yeh Chun-Nan , Yeh Ta-Sen 
Published: January 2023

Abstract
Pancreatic anastomotic leakage is the most common major complication after pancreaticoduodenectomy (PD). The incidence of pancreatic anastomotic leak or fistula has declined to less than 20%, and mortality from this complication has decreased to less than 10% in recent years. The ideal surgical procedures to achieve the most secure pancreaticojejunostomy were compared and reviewed. A single-institution and personal experience was retrogradely compared with two periods between 1988 and 2017, which involved 121 patients who were designed to compare the outcome of complications with or without pancreatic stump by four to six sutures before continuous duct-to-mucosa PD. The surgical reconstruction technique was standardized and unique, and the pancreaticojejunal anastomosis was created using the duct-to-mucosa without (group A, n = 62) and with (group B, n = 59) interrupted stump sutures. The rate of grade A pancreatic fistula was 6.9% in group A and 0% in group B (P < 0.05). Postoperative mortality was 0% in group B. No patient underwent reoperative PD due to pancreatic anastomotic leak. The length of stay during admission and after surgery was significant lower in group B, which was due to less complication after surgery. Interrupted suture of pancreatic stump with a continuous duct-to-mucosa end-to-side pancreaticojejunostomy plus external drainage is the best secure method for pancreaticojejunostomy after PD.
The effects of nuclear DNA mutations on mitochondrial function
Authors: Heuer Beth 
Published: January 2023

ABSTRACT
The multiple functions of mitochondria, including adenosine triphosphate synthesis, are controlled by the coordination of both the mitochondrial DNA (mtDNA) and the nuclear DNA (nDNA) genomes. Mitochondrial disorders manifest because of impairment of energy metabolism. This article focuses on mutations in two nuclear genes and their effect on mitochondrial function. Mutations in the polymerase gamma, or POLG, gene are associated with multisystemic disease processes, including Alpers Syndrome, a severe childhood-onset syndrome. Mutations in the OPA1 gene are associated with autosomal dominant optic atrophy and other neurologic, musculoskeletal, and ophthalmologic symptoms. When assessing for disorders affecting energy metabolism, sequencing of both the mtDNA genome and the nDNA whole exome sequencing is necessary.
Changes in von Willebrand Factor Multimers, Concentration, and Function During Pediatric Extracorporeal Membrane Oxygenation*
Authors: Van Den Helm Suelyn , Letunica Natasha , Barton Rebecca , Weaver Asami , Yaw Hui Ping , Karlaftis Vasiliki , McCafferty Conor , Cai Tengyi , Newall Fiona , Horton Stephen B. , Chiletti Roberto , Johansen Amy , Best Derek , McKittrick Joanne , Butt Warwick , d’Udekem Yves , MacLaren Graeme , Linden Matthew D. , Ignjatovic Vera , Monagle Paul 
Published: January 2023

OBJECTIVES:
To investigate changes in von Willebrand factor (VWF) concentration, function, and multimers during pediatric extracorporeal membrane oxygenation (ECMO) and determine whether routine monitoring of VWF during ECMO would be useful in predicting bleeding.

DESIGN:
Prospective observational study of pediatric ECMO patients from April 2017 to May 2019.

SETTING:
The PICU in a large, tertiary referral pediatric ECMO center.

PATIENTS:
Twenty-five neonates and children (< 18 yr) supported by venoarterial ECMO.

INTERVENTIONS:
None.

MEASUREMENTS AND MAIN RESULTS:
Arterial blood samples were collected within 24 hours pre-ECMO, daily for the first 5 days of ECMO, every second day until decannulation, and 24 hours post-ECMO. The STA R Max analyzer was used to measure VWF antigen (VWF:Ag) and ristocetin cofactor (VWF:RCo) activity. VWF collagen binding (VWF:CB) was measured using an enzyme-linked immunosorbent assay. VWF multimers were measured using the semi-automated Hydragel 11 VWF Multimer assay. Corresponding clinical data for each patient was also recorded. A total of 25 venoarterial ECMO patients were recruited (median age, 73 d; interquartile range [IQR], 3 d to 1 yr). The median ECMO duration was 4 days (IQR, 3–8 d) and 15 patients had at least one major bleed during ECMO. The percentage of high molecular weight multimers (HMWM) decreased and intermediate molecular weight multimers increased while patients were on ECMO, irrespective of a bleeding status. VWF:Ag increased and the VWF:RCo/VWF:Ag and VWF:CB/VWF:Ag ratios decreased while patients were on ECMO compared with the baseline pre-ECMO samples and healthy children.

CONCLUSIONS:
Neonates and children on ECMO exhibited a loss of HMWM and lower VWF:CB/VWF:Ag and VWF:RCo/VWF:Ag ratios compared with healthy children, irrespective of major bleeding occurring. Therefore, monitoring VWF during ECMO would not be useful in predicting bleeding in these patients and changes to other hemostatic factors should be investigated to further understand bleeding during ECMO.
Diffusion Weighted MRI could precisely predict the pTERT mutation status of GBM using a residual convolutional neural network
Authors: Hu Congman , Fang Ke , Du Quan , Chen Jiarui , Wang Lin , Li Lanjuan , Zhang Jianmin , Bai Ruiliang , Wang Yongjie 
Published: January 2023

AbstractBackgroundTelomerase reverse transcriptase promoter (pTERT) mutation status plays a key role in the decision-making and prognosis prediction of glioblastoma (GBM). The purpose of this study was to assess the prediction value of diffusion-weighted imaging (DWI) in the pTERT mutation status of GBMMethodsMR imaging data and molecular information of 266 patients with GBM were obtained from the Second Affiliated Hospital of Zhejiang University (n=266). We trained the same residual convolutional neural network (ResNet) for each MR modality, including structural MRIs (T1-weighted, T2-weighted, contrast enhanced T1-weighted) and DWI and its associated ADC map, and their combinations to compare the predictive capacities between DWI and conventional structural MRI. Moreover, we explored the effect of different Region of interests (ROIs) on the outcome of pTERT mutation status prediction: entire tumor (solid tumor, edema and cystic regions), tumor core (solid tumor), and enhanced tumor.ResultsStructural MRI modalities and their combination performed poorly in predicting the pTERT mutation status (accuracy, 51-54%, AUC, 0.545-0.571), while DWI in combination with its ADC maps yielded the best predictive performance (accuracy = 85.2%, AUC= 0.934). The further including of radiological and clinical characteristics could not further improve the predictive performance of pTERT mutation status. Among the three ROI selections, the entire tumor volume yielded the best prediction performance.ConclusionDWI and its associated ADC maps shows promising prediction value in the pTERT mutation in GBM and are suggested to be included into the MRI protocol of GBM in clinical practice.Key PointsThe ResNet model constructed by radiomics provided great help for the prediction of pTERT mutation in glioblastoma.In the ResNet prediction model, conventional structural MRI was of little value while DWI and its associated ADC maps shows excellent value.The model using the whole tumor as ROI showed best predictive capacity and potentiality for future clinical application.
Cancer Cell’s Seven Achilles Heels: Considerations for design of anti-cancer drug combinations
Authors: Gahramanov Valid , Vizeacoumar Frederick S. , Morales Alain Morejon , Bonham Keith , Sakharkar Meena K. , Vizeacoumar Franco J. , Freywald Andrew , Sherman Michael Y. 
Published: January 2023

ABSTRACTLoss of function screens using shRNA and CRISPR are routinely used to identify genes that modulate responses of tumor cells to anti-cancer drugs. Here, by integrating GSEA and CMAP analyses of multiple published shRNA screens, we identified a core set of pathways that affect responses to multiple drugs with diverse mechanisms of action. This suggests that these pathways represent “weak points” or “Achilles heels”, whose mild disturbance should make cancer cells vulnerable to a variety of treatments. These “weak points” include proteasome, protein synthesis, RNA splicing, RNA synthesis, cell cycle, Akt-mTOR, and tight junction-related pathways. Therefore, inhibitors of these pathways are expected to sensitize cancer cells to a variety of drugs. This hypothesis was tested by analyzing the diversity of drugs that synergize with FDA-approved inhibitors of the proteasome, RNA synthesis, and Akt-mTOR pathways. Indeed, the quantitative evaluation indicates that inhibitors of any of these signaling pathways can synergize with a more diverse set of pharmaceuticals, compared to compounds inhibiting targets distinct from the “weak points” pathways. Our findings described here imply that inhibitors of the “weak points” pathways should be considered as primary candidates in a search for synergistic drug combinations.
Spatiotemporal Evolution of SARS-CoV-2 Alpha and Delta Variants during a Large Nationwide Outbreak in Vietnam, 2021
Authors: Tam Nguyen Thi , Anh Nguyen To , Tung Trinh Son , Thach Pham Ngoc , Dung Nguyen Thanh , Trang Van Dinh , Hung Le Manh , Dien Trinh Cong , Ngoc Nghiem My , Van Duyet Le , Cuong Phan Manh , Mai Phuong Hoang Vu , Thai Pham Quang , Nhu Tung Nguyen Le , Huy Man Dinh Nguyen , Phong Nguyen Thanh , Quang Vo Minh , Ngoc Thoa Pham Thi , Truong Nguyen Thanh , Phuong Thao Tran Nguyen , Linh Dao Phuong , Tai Ngo Tan , Bao Ho The , Vuong Vo Trong , Kim Nhung Huynh Thi , Dieu Hong Phan Nu , Phuoc Hanh Le Thi , Chung Le Thanh , Thanh Nhan Nguyen Thi , Thanh Ton That , Hung Do Thai , Mai Huynh Kim , Long Trinh Hoang , Trang Nguyen Thu , Hong Thuong Nguyen Thi , Thu Hong Nguyen Thi , Truc Nhu Le Nguyen , Han Ny Nguyen Thi , Thuy Cao Thu , Thanh Le Kim , Nguyet Lam Anh , Quynh Mai Le Thi , Thuong Tang Chi , Nga Le Hong , Thanh Tran Tan , Thwaites Guy , van Doorn H. Rogier , Van Vinh Chau Nguyen , Kesteman Thomas , Van Tan Le ,   OUCRU COVID-19 research group
Published: January 2023

ABSTRACTIn 2021, Vietnam experienced a large nationwide outbreak of COVID-19, with over 1.7 million infections and 32,000 deaths. We generated 1,303 SARS-CoV-2 whole-genome sequences, and mapped out the public health measures alongside the evolutionary trajectory of the pathogen. The Alpha variant caused sporadic outbreaks in early 2021 prior to the upsurge in cases associated with the Delta variant from June onward. The Delta variant outbreak was almost entirely confined to the AY.57 lineage, accounting for 99.2% of 1,212 Delta variant sequences, and resulting from a single introduction. Viral dispersal from the north, where it was first introduced into Vietnam, to the south, marked the start of the nationwide outbreak, with the south subsequently seeding the virus back to the other regions. Distinct AY.57 phylogenetic clusters in different regions of Vietnam were documented, pointing to the impact of in-country lockdown. Genomic surveillance is critical to inform pandemic response.
Plasma Microbial Cell-free DNA Sequencing from Over 15,000 Patients Identified a Broad Spectrum of Pathogens
Authors: Park Sarah Y. , Chang Eliza J , Ledeboer Nathan , Messacar Kevin , Lindner Martin S. , Venkatasubrahmanyam Shivkumar , Bercovici Sivan , Wilber Judith C. , Vaughn Marla Lay , Perkins Bradley A. , Nolte Frederick S. 
Published: January 2023

ABSTRACTMicrobial cell-free DNA (mcfDNA) sequencing is an emerging infectious disease diagnostic tool which enables unbiased pathogen detection from plasma. The Karius Test®, a commercial mcfDNA sequencing assay developed by and available since 2017 from Karius, Inc. (Redwood City, CA), detects and quantifies mcfDNA as molecules/μl in plasma. The commercial sample data and results for all tests conducted from April 2018 through mid-September 2021 were evaluated for laboratory performance metrics, reported pathogens, and data from test requisition forms. A total of 18,690 reports were generated from 15,165 patients in a hospital setting among 39 states and the District of Columbia. The median time from sample receipt to reported result was 26 hours (IQR 25–28), and 96% of samples had valid test results. Almost two-thirds (65%) of patients were adults, and 29% at the time of diagnostic testing had ICD10 codes representing a diverse array of clinical scenarios. There were 10,752 (58%) reports that yielded at least one taxon for a total of 22,792 detections spanning 701 unique microbial taxa. The 50 most common taxa detected included 36 bacteria, 9 viruses, and 5 fungi. Opportunistic fungi (374Aspergillusspp., 258Pneumocystis jirovecii, 196Mucorales, and 33 dematiaceous fungi) comprised 861 (4%) of all detections. Additional diagnostically challenging pathogens (247 zoonotic and vector borne pathogens, 144Mycobacteria, 80Legionellaspp., 78 systemic dimorphic fungi, 69Nocardiaspp., and 57 protozoan parasites) comprised 675 (3%) of all detections. We report the largest cohort of patients tested using plasma mcfDNA sequencing. The wide variety of pathogens detected by plasma mcfDNA sequencing reaffirm our understanding of the ubiquity of some infections while also identifying taxa less commonly detected by conventional methods.