bluuebunny/crossref_metadata_2025_split huggingface dataset:
Piloting an Automated Clinical Trial Eligibility Surveillance and Provider Alert System based on Artificial Intelligence and Standard Data Models
Authors: Meystre Stéphane M. , Heider Paul M. , Cates Andrew , Bastian Grace , Pittman Tara , Gentilin Stephanie , Kelechi Teresa J. 
Published: June 2022

Abstract
Background: To advance new therapies into clinical care, clinical trials must recruit enough participants. Yet, many trials fail to do so, leading to delays, early trial termination, and wasted resources. Under-enrolling trials make it impossible to draw conclusions about the efficacy of new therapies. An oft-cited reason for insufficient enrollment is lack of study team and provider awareness about patient eligibility. Automating clinical trial eligibility surveillance and study team and provider notification could offer a solution. Methods: To address this need for an automated solution, we conducted an observational pilot study of our TAES (TriAl Eligibility Surveillance) system. We tested the hypothesis that an automated system based on natural language processing and machine learning algorithms could detect patients eligible for specific clinical trials by linking the information extracted from trial descriptions to the corresponding clinical information in the electronic health record (EHR). To evaluate the TAES information extraction and matching prototype (i.e., TAES prototype), we selected five open cardiovascular and cancer trials at the Medical University of South Carolina and created a new reference standard of 21,974 clinical text notes from a random selection of 400 patients (including at least 100 enrolled in the selected trials), with a small subset of 20 notes annotated in detail. We also developed a simple web interface for a new database that stores all trial eligibility criteria, corresponding clinical information, and trial-patient match characteristics using the Observational Medical Outcomes Partnership (OMOP) common data model. Finally, we investigated options for integrating an automated clinical trial eligibility system into the EHR and for notifying health care providers promptly of potential patient eligibility without interrupting their clinical workflow.Results: Although the rapidly implemented TAES prototype achieved only moderate accuracy (recall: 0.000-0.778; precision: 0.000-1.000), it enabled us to assess options for integrating an automated system successfully into the clinical workflow at a healthcare system.Conclusions: Once optimized, the TAES system could exponentially enhance identification of patients potentially eligible for clinical trials, while simultaneously decreasing the burden on research teams of manual EHR review. Through timely notifications, it could also raise physician awareness of patient eligibility for clinical trials.
Circulating cytokines reflect the etiology-specific immune environment in cirrhosis and HCC
Authors: Beudeker Boris J.B. , Groothuismink Zwier M.A. , Eijk Annemiek A. , Debes Jose D. , Boonstra Andre 
Published: June 2022

Abstract
Background and AimsChronic liver disease -from any etiology- can progress to fibrosis, cirrhosis and hepatocellular carcinoma (HCC). The progression of liver cirrhosis to the end stages of disease is influenced by a variety of factors, including inflammatory cytokines (soluble inflammatory mediators of cell communication). We pursued a study of cytokine-mediated inflammatory responses in hepatitis B (HBV), hepatitis C (HCV), alcoholic liver disease (ALD) and non-alcoholic fatty liver disease (NAFLD) patients with liver cirrhosis. MethodsImmune profiles were determined through serum multiplex profiling of >100 cytokines in a 188 cirrhotic patients, 35 healthy controls and 198 early-stage HCC patients.ResultsPatients with liver cirrhosis exhibited vast upregulation of proinflammatory cytokines (p<0.0001), including those with pro-oncogenic features, when compared to healthy individuals. In contrast to prevailing assumptions, each etiological cause of cirrhosis exhibited a unique cytokine profile in blood. Regardless of antiviral therapy, HBV cirrhosis patients had the largest number of upregulated proinflammatory mediators, compared to HCV, ALD and NAFLD (p<0.0001). To further evaluate the etiology-dependent modulation of cytokine response in relation to liver cancer, we studied cytokine profiles in early-stage HCC patients strictly stratified by underlying liver disease. We observed unique sets of differentially expressed cytokines in each cohort of early-stage HCC patients of different cirrhosis etiologies. ConclusionsOur findings, therefore, underscore the importance of stratification by etiological cause of liver cirrhosis in immune-based studies.
A blood DNA methylation biomarker for predicting short-term risk of cardiovascular events
Authors: Cappozzo Andrea , McCrory Cathal , Robinson Oliver , Sterrantino Anna Freni , Sacerdote Carlotta , Krogh Vittorio , Panico Salvatore , Tumino Rosario , Iacoviello Licia , Ricceri Fulvio , Sieri Sabina , Chiodini Paolo , Kenny Rose Anne , O’Halloran Aisling , Polidoro Silvia , Solinas Giuliana , Vineis Paolo , Ieva Francesca , Fiorito Giovanni 
Published: June 2022

Abstract
Background: Recent evidence highlights the epidemiological value of blood DNA methylation (DNAm) as surrogate biomarker for exposures to risk factors for non-communicable diseases (NCD). DNAm surrogate of exposures predict diseases and longevity better than self-reported or measured exposures in many cases. Consequently, disease prediction models based on blood DNAm surrogates may outperform current state-of-art prediction models. This study aims to develop novel DNAm surrogates for cardiovascular diseases (CVD) risk factors and develop a composite biomarker predictive of CVD risk. We compared the prediction performance of our newly developed risk score with the state-of-art DNAm risk scores for cardiovascular diseases, the ‘next-generation’ epigenetic clock DNAmGrimAge, and the prediction model based on traditional risk factors SCORE2.Results: Using data from the EPIC Italy cohort, we derived novel DNAm surrogates for BMI, blood pressure, fasting glucose and insulin, cholesterol, triglycerides, and coagulation biomarkers. We validated them in four independent datasets from Europe and the US. Further, we derived a DNAmCVDscore predictive of the time-to-CVD event as a combination of several DNAm surrogates. ROC curve analyses show that DNAmCVDscore outperforms previously developed DNAm scores for CVD risk and SCORE2 for short-term CVD risk. Interestingly, the performance of DNAmGrimAge and DNAmCVDscore was comparable (slightly lower for DNAmGrimAge, although the differences were not statistically significant).Conclusions: We described novel DNAm surrogates for CVD risk factors useful for future molecular epidemiology research, and we described a blood DNAm-based composite biomarker, DNAmCVDscore, predictive of short-term cardiovascular events. Our results highlight the usefulness of DNAm surrogate biomarkers of risk factors in epigenetic epidemiology to identify high-risk populations. In addition, we provide further evidence on the effectiveness of prediction models based on DNAm surrogates and discuss methodological aspects for further improvements. Finally, our results encourage testing this approach for other NCD diseases by training and developing DNAm surrogates for disease-specific risk factors and exposures.
Different treatments of pearl millet for cellulose recovery: effects on lignocellulosic composition
Authors: Dresch Aline Perin , Cavali Matheus , Santos David F. , Fogolari Odinei Odinei , Tironi Siumar Pedro , Pinto Vânia Z. , Mibielli Guilherme Martinez , Bender João Paulo 
Published: June 2022

Abstract
Pretreatment is the main step that must be performed in order to isolate the cellulose, hemicellulose, and lignin contained in the lignocellulosic biomass. The objective of this study was to recover cellulose from pearl millet biomass through chemical (alkali and acid), physical (vapor explosion and size reduction) and combined treatments. The cellulosic fraction was characterized by Fourier transform spectroscopy (FTIR-ATR), X-ray diffraction (XRD), and Raman spectroscopy. The cellulose-rich fraction presented 100% and 99.86% of lignin and hemicellulose removal, respectively, and a high crystallinity index of 82.43% after two 4-hour alkaline extractions with 4% NaOH followed by 2 hours extraction with C2H2O4 5% in autoclave at a temperature of 125.6°C and 1.4 bar. Based on the analysis of FTIR-ATR, XRD, and Raman spectroscopy, it was possible to confirm the removal of hemicellulose and lignin from pearl millet biomass, highlighting the efficiency of the treatments evaluated in the process of solubilization of these compounds. The results presented in this study should contribute to improve the efficiency of the fractionation processes of lignocellulosic biomasses.
RNA polymerase inaccuracy underlies SARS-CoV-2 variants and vaccine heterogeneity
Authors: Herman Christophe , Bradley Catherine , Gordon Alasdair , Wang Chen , Cooke Matthew , Kohrn Brendan , Kennedy Scott , Lichtarge Olivier , Ronca Shannon 
Published: June 2022

Abstract
Both the SARS-CoV-2 virus and its mRNA vaccines depend on RNA polymerases (RNAP)1,2; however, these enzymes are inherently error-prone and can introduce variants into the RNA3. To understand SARS-CoV-2 evolution and vaccine efficacy, it is critical to identify the extent and distribution of errors introduced by the RNAPs involved in each process. Current methods lack the sensitivity and specificity to measure de novo RNA variants in low input samples like viral isolates3. Here, we determine the frequency and nature of RNA errors in both SARS-CoV-2 and its vaccine using a targeted Accurate RNA Consensus sequencing method (tARC-seq). We found that the viral RNA-dependent RNAP (RdRp) makes ~1 error every 10,000 nucleotides – higher than previous estimates4. We also observed that RNA variants are not randomly distributed across the genome but are associated with certain genomic features and genes, such as S (Spike). tARC-seq captured a number of large insertions, deletions and complex mutations that can be modeled through non-programmed RdRp template switching. This template switching feature of RdRp explains many key genetic changes observed during the evolution of different lineages worldwide, including Omicron. Further sequencing of the Pfizer-BioNTech COVID-19 vaccine revealed an RNA variant frequency of ~1 in 5,000, meaning most of the vaccine transcripts produced in vitro by T7 phage RNAP harbor a variant. These results demonstrate the extraordinary genetic diversity of viral populations and the heterogeneous nature of an mRNA vaccine fueled by RNAP inaccuracy. Along with functional studies and pandemic data, tARC-seq variant spectra can inform models to predict how SARS-CoV-2 may evolve. Finally, our results may help improve future vaccine development and study design as mRNA therapies continue to gain traction.
Addition of the nuclear export inhibitor selinexor to standard intensive treatment for elderly patients with AML and high risk MDS
Authors: Janssen Jeroen , Löwenberg Bob , Manz Markus , Biemond Bart , Westerweel Peter , Klein Saskia , Fehr Martin , Sinnige Harm , Efthymiou Anna , Legdeur M , Pabst Thomas , Gregor Michael , Poel Marjolein van der , Deeren Dries , Tick Lidwine , Jongen-Lavrencic Mojca , Obbergh Florence , Boersma Rinske , de Weerdt Okke , Chalandon Yves , Heim Dominik , spertini Olivier , Sluis Geerte van , Graux Carlos , Stuessi Georg. , Norden Yvette van , Ossenkoppele Gert 
Published: June 2022

Abstract
Treatment results of AML in elderly patients are unsatisfactory. In an open label randomized phase II study, we investigated whether addition of the XPO1 inhibitor selinexor to intensive chemotherapy would improve outcome in this population. 102 AML patients > 65 years of age (median 69 (65–80)) were randomly assigned to standard chemotherapy (3 + 7) with or without oral selinexor 60 mg twice weekly (both arms n = 51), days 1–24. In the second cycle, cytarabine 1000 mg/m2 twice daily, days 1–6 with or without selinexor was given. CR/CRi rates were significantly higher in the control arm than in the investigational arm (80% (95% C.I. 69–91%) vs. 59% (45–72%; p = 0.018), respectively). At 18 months, event-free survival was 45% for the control arm versus 26% for the investigational arm (Cox-p = 0.012) and overall survival 58% vs. 33%, respectively (p = 0.009). AML and infectious complications accounted for an increased death rate in the investigational arm. Irrespective of treatment, MRD status after two cycles appeared to be correlated with survival. We conclude that the addition of selinexor to standard chemotherapy does negatively affect the therapeutic outcome of elderly AML patients. (Netherlands Trial Registry number NL5748 (NTR5902), www.trialregister.nl).
Association between lignan intake from different types of plant-based foods and obesity indicators in the Netherlands
Authors: Zaki Umi Kalsum Hussain , Trijsburg Laura , Feskens Edith J.M. 
Published: June 2022

Abstract
This study aimed to assess whether lignan intake is associated with lower body mass index (BMI) and waist circumference in a Dutch population. Data on lignan content of foods was extracted from a lignan database of Dutch plant-based foods and complemented with three other references to estimate lignan intake in 1012 Dutch men and women participating in the NQ-plus prospective cohort study. The association between lignan intake and BMI and waist circumference was assessed using linear regression analysis. Three multivariate models were used to investigate the association of BMI and waist circumference with total lignan intake. Model 1 included adjustments for lifestyle variables, in model 2 adjustments were made for energy intake and nutrients, and in model 3 these adjustment were combined. The median lignan intake was 3226 µg/day (mean 4763 µg/day, SD 5386 µg/day). Lignan intake was strongly skewed towards higher values, ranging from 40-50500 µg/day. The major sources of lignans were bread, which contributed 52%, nuts, seeds, and snacks (21%), and vegetables (12%) to the lignan intake. After adjustments lignan intake was associated with a lower waist circumference (-0.93 cm, 95% CI: -0.88; -1.00). No association between BMI and lignan intake was observed. A higher lignan intake is significantly associated with a smaller waist circumference in Dutch adults. To what extent a high lignan intake can reduce waist circumference in obese patients or can prevent onset of abdominal obesity remains to be tested in future intervention studies.
Social Reception and Inclusion of Refugees From Ukraine
Authors: Isański Jakub , Marek Nowak , Michalski Michał A. , Sereda Victoria , Vakhitova Hanna 
Published: June 2022

Abstract
Our research aimed to study the ongoing phenomena of cross-border displacement of the Ukrainian population resulting from the Russian aggression that started on the 24th of February 2022. In the first stage of this research, we managed to get the opinions of over 500 refugees with a focus on their needs, concerns, plans, and expectations. Collected data also allowed a reconstruction of social-demographic profiles of fleeing Ukrainian refugees. The preliminary outcomes are presented in the report.
Clinical Effect of Post-rewarming Fever after Targeted Temperature Management in Cardiac Arrest Patients: A Systematic Review and Meta-Analysis
Authors: Guo Guangqi , Ma Yannan , Xu Shuang , Zhang Hongrong , Sun Peng 
Published: June 2022

Abstract
Aim: To characterize and summarize the studies regarding the influence of post-rewarming fever on neurological outcome and mortality in cardiac arrest patients. Methods: Two investigators separately screened relevant articles in EMBASE, PubMed, and Cochrane Central databases. Randomized clinical trials (RCTs) and cohort studies that evaluated the influence of post-rewarming fever (PRF) and normothermia in cardiac arrest patients were included. The meta-analysis was performed using a random effects model or a fixed effects model to calculate the pooled odds ratios (ORs) and corresponding 95% confidence intervals (CIs). The primary outcome was the unfavorable neurological outcome and the secondary outcome was the mortality. Results: The meta-analysis included 12 studies involving 2,991 patients. Results of quantitative analysis suggested that PRF (body temperature >37.5°C) did not affect the unfavorable neurological outcome of patients with cardiac arrest (OR, 0.82; 95% CI, 0.54-1.25; I2, 81%). Also, PRF (body temperature >37.8°C) was not related to higher mortality of patients with cardiac arrest (OR, 0.86; 95% CI, 0.55-1.34; I2, 74%). However, PRF with higher body temperature (>38.5℃) was associated with higher mortality (OR, 2.22; 95%CI, 1.40- 3.35; I2, 0%). Conclusions: This study suggests that PRF (body temperature >37.5°C) is not related to neurological outcome. And no significant association is found between PRF (body temperature >37.8°C) and mortality. However, PRF is associated with higher mortality when PRF was defined as >38.5℃.
Research on Perception and Control Technology for Robot Dexterous Operation
Authors: Zhang Tengteng , Mo Hongwei 
Published: June 2022

Abstract
In an unstructured environment, multiple objects are closely arranged, which leads to the complexity of robot grasping. Deep reinforcement learning(DRL) can take long-term reasoning, and make better and more robust decisions in a series of decisions, allowing the robot to continuously learn from its own experience. In this paper, we demonstrate that a new deep reinforcement learning algorithm based on Q-learning and attention mechanisms can effectively solve the robot grasping problem. In addition, we present a grasp and move strategy that reduces complexity by replacing hand-designed features with data-driven ones. The robot is used to move the objects to create a larger grasping space when the objects are densely distributed to improve the grasping success rate. The application of the proposed model on a simulated UR5 robot manipulator demonstrates the effectiveness and stability of the model. The results show that our proposed method outperforms the baseline framework in terms of grasping accuracy and efficiency.
Design and Implementation of Power-Efficient Cryptography Scheme Using a Novel Multiplication Technique
Authors: Srik B. , Ravindra JVR. , Ramakrishna P. , Ajitha D. 
Published: June 2022

Abstract
The threat application has been increased a lot in the digital application; hence, protecting the data and the digital application is very important. Several crypto algorithms were already implemented with different sub-module to secure the data from the malicious event. However, the harmfulness of the malicious events has broken the security in many cases. This has resulted in high data theft, less confidential range and data loss So, the present article has designed a novel Bernoulli Data-encryption-standard (B-DES) for securing the digital communication in the wireless environment. Here, the Bernoulli function has been performed after the XOR process, and then during the decryption process, the function of the novel B-DES has been reversed. Moreover, the designed encryption approach is checked with the brute force attack. Here, the gained power usage by the designed scheme is 193 mW, compared to other models; it has diminished the power usage by 7%. Moreover, the earned memory utilization is 0.6 kB, compared to other compared models, it has reduced the memory utilization is 3%. The delay rated recorded by the designed model is 3.43 ns, compared to other models it has minimized the delay score by 3%.
Ranking of suitable concrete mix parameter based on splitting tensile strength of partially set concrete subjected to delays in casting using Multi-criteria decision making approach
Authors: Gayake Sudhir Bhaskarrao , Desai Atul K. , Kute Sunil Y. 
Published: June 2022

Abstract
Delays in casting of freshly prepared concrete mix is always uncertain and cannot be predicted in the initial time. The interval of time t between the preparation of dry mix including the water addition i.e. t = 0 and casting of the same concrete where required at some elapsed time t is called as time lag. In this paper, attempt is made to correlate the experimental splitting tensile strength variation of partially set concrete (PSC) with the analytical model developed earlier for selfing and the correlation factors are estimated. Also as the success of any task is always contingent on the ability to make decisions and recognize to select the best feasible option from a variety of options. Therefore a multi criteria decision making (MCDM) tool is implemented for ascertaining the suitable concrete mix of PSC. Three different types of concrete mix were tried and compared to the normal mix to check the variation in splitting strength. The experimental and analytical values of tensile strength are validated and the average correlation factor is observed 0.998. Furthermore, using the Analytical Hierarchy Process (AHP) for ranking, normal PSC (Type-1) and PSC with 1% synthetic fibers (Type-4) showed maximum splitting tensile strength at 75 minutes time lag, whereas PSC with 20% fly ash (Type-2) and PSC with 25% fly ash (Type-3) showed maximum splitting tensile strength at 100 minutes time lag, indicating that the addition of fly ash retarded setting time and kept PSC more workable.The AHP model also suggested 1% synthetic fibers (Type-4) as the most suitable concrete mix parameter among four alternatives experimented.
Genome-wide Analysis of the bHLH Transcription Factor Family and Functional Identification of bHLH Genes Related to Puerarin Biosynthesis in Pueraria lobata var. thomsonii (Benth.)
Authors: Xiao Liang , Huang Ding , Wu Zhengdan , Shang Xiaohong , Cao Sheng , Zeng Wendan , Lu Liuying , Shi Pingli , Yan Huabing 
Published: June 2022

Abstract

Plant basic helix-loop-helix (bHLH) transcription factors are involved in diverse biological process. Several bHLH transcription factors have been functionally characterized in various crop species. However, no systematic and comprehensively identification of bHLH members has been in Pueraria lobata var. thomsonii (Benth.) (P. thomsonii), a traditional Chinese herb that is an excellent source of puerarin. Phylogenetic analysis showed that 219 bHLH genes were identified in the P. thomsonii and classified into 13 subfamilies. All the PlbHLH genes were distributed on the 11 chromosomes unevenly and the number of PlbHLH genes on each chromosome varied from 12 to 44. Both of tandem and segmental duplications were key factors driving bHLH gene family expansion in P. thomsonii. The gene structure analysis indicated that 20 conserved motifs were found in PlbHLH gene family, 185 PlbHLH members contain more than two introns, and genes within the same subfamily appeared to share similar intron-exon gene structures. The Ka/Ks analysis indicated PlbHLH gene family undergo purifying selection during evolution. The hierarchical clustering analysis indicated that 41 PlbHLHs showed root-specific expression patterns, and seven of them exhibited up-regulated expression pattern after MeJA treatment within 24 h. Using qRT-PCR validation, five puarian synthesis genes had a similar expression pattern with the seven PlbHLH genes in response to MeJA within 24 h. Together, our study provided a good foundation for further research into the regulatory mechanism of the seven candidate PlbHLH proteins for pueraria biosynthesis in P. thomsonii.