bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of sustained virological response after direct-acting antivirals on liver fibrosis in patients with chronic HCV infection
Authors: Agwa Ramy H. , Elgazzar Mohamed H. , El-Zayyadi Islam A. , Saed Ahmed M. , Ghannam Mayada A. , Saleh Ahmed 
Published: February 2022

Abstract
Background
Direct-acting antivirals (DAAs) have revolutionized the therapy of HCV infection with higher sustained virological response (SVR) rates. Fibrosis regression after achieving SVR to DAA remains to be evaluated in chronic hepatitis C patients. One of the main inquiries here is what occurs with liver fibrosis after achieving a SVR, albeit the current DAA was not intended to be antifibrotic. Liver biopsy was replaced by various non-invasive methods, like FIB4 score and fibroscan. The aim of the study was to evaluate the impact of SVR following DAAs on liver fibrosis in chronic HCV patients.

Results
Five hundred of 1170 F4 treated patients (42.7%) improved and became 190 F3, 90 F2, and 220 F1. Also, 40 of 60 F3 patients improved and became 10 F2 and 30 F1. Also, 350 of 1230 treated patients (28.4%) transited from significant fibrosis (≥F3) to non-significant fibrosis (≤F2). There was a significant improvement of FIB-4 (p<0.001) in the improved group after DAAs were proved by liver stiffness measurement.

Conclusion
Treatment of chronic HCV with DAAs is associated with regression of liver fibrosis as about 28% of patients improved from significant fibrosis (≥F3) to non-significant fibrosis (≤F2) after treatment.
Developing a Prediction Model for Pathologic Complete Response Following Neoadjuvant Chemotherapy in Breast Cancer: A Comparison of Model Building Approaches
Authors: Basmadjian Robert B. , Kong Shiying , Boyne Devon J. , Jarada Tamer N. , Xu Yuan , Cheung Winson Y. , Lupichuk Sasha , Quan May Lynn , Brenner Darren R. 
Published: February 2022

PURPOSE The optimal characteristics among patients with breast cancer to recommend neoadjuvant chemotherapy is an active area of clinical research. We developed and compared several approaches to developing prediction models for pathologic complete response (pCR) among patients with breast cancer in Alberta. METHODS The study included all patients with breast cancer who received neoadjuvant chemotherapy in Alberta between 2012 and 2014 identified from the Alberta Cancer Registry. Patient, tumor, and treatment data were obtained through primary chart review. pCR was defined as no residual invasive tumor at surgical excision in breast or axilla. Two types of prediction models for pCR were built: (1) expert model: variables selected on the basis of oncologists' opinions and (2) data-driven model: variables selected by trained machine. These model types were fit using logistic regression (LR), random forests (RF), and gradient-boosted trees (GBT). We compared the models using area under the receiver operating characteristic curve and integrated calibration index, and internally validated using bootstrap resampling. RESULTS A total of 363 cases were included in the analyses, of which 86 experienced pCR. The RF and GBT fits yielded higher optimism-corrected area under the receiver operating characteristic curves compared with LR for the expert (RF: 0.70; GBT: 0.69; LR: 0.65) and data-driven models (RF: 0.71; GBT: 0.68; LR: 0.64). The LR fit yielded the lowest integrated calibration indices for the expert (LR: 0.037; GBT: 0.05; RF: 0.10) and data-driven models (LR: 0.026; GBT: 0.06; RF: 0.099). CONCLUSION Our models demonstrated predictive ability for pCR using routinely collected clinical and demographic variables. We show that machine learning fit methods can be used to optimize models for pCR prediction. We also show that additional variables beyond clinical expertise do not considerably improve predictive ability and may not be of value on the basis of the burden of data collection.
Genome Nexus: A Comprehensive Resource for the Annotation and Interpretation of Genomic Variants in Cancer
Authors: de Bruijn Ino , Li Xiang , Sumer Selcuk Onur , Gross Benjamin , Sheridan Robert , Ochoa Angelica , Wilson Manda , Wang Avery , Zhang Hongxin , Lisman Aaron , Abeshouse Adam , Zhang Emily , Thum Alice , Sadagopan Ananthan , Heins Zachary , Kandoth Cyriac , Rodenburg Sander , Tan Sander , Lukasse Pieter , van Hagen Sjoerd , Fijneman Remond J. A. , Meijer Gerrit A. , Schultz Nikolaus , Gao Jianjiong 
Published: February 2022

PURPOSE Interpretation of genomic variants in tumor samples still presents a challenge in research and the clinical setting. A major issue is that information for variant interpretation is fragmented across disparate databases, and aggregation of information from these requires building extensive infrastructure. To this end, we have developed Genome Nexus, a one-stop shop for variant annotation with a user-friendly interface for cancer researchers and clinicians. METHODS Genome Nexus (1) aggregates variant information from sources that are relevant to cancer research and clinical applications, (2) allows high-performance programmatic access to the aggregated data via a unified application programming interface, (3) provides a reference page for individual cancer variants, (4) provides user-friendly tools for annotating variants in patients, and (5) is freely available under an open source license and can be installed in a private cloud or local environment and integrated with local institutional resources. RESULTS Genome Nexus is available at https://www.genomenexus.org . It displays annotations from more than a dozen resources including those that provide variant effect information (variant effect predictor), protein sequence annotation (Uniprot, Pfam, and dbPTM), functional consequence prediction (Polyphen-2, Mutation Assessor, and SIFT), population prevalences (gnomAD, dbSNP, and ExAC), cancer population prevalences (Cancer hotspots and SignalDB), and clinical actionability (OncoKB, CIViC, and ClinVar). We describe several use cases that demonstrate the utility of Genome Nexus to clinicians, researchers, and bioinformaticians. We cover single-variant annotation, cohort analysis, and programmatic use of the application programming interface. Genome Nexus is unique in providing a user-friendly interface specific to cancer that allows high-performance annotation of any variant including unknown ones. CONCLUSION Interpretation of cancer genomic variants is improved tremendously by having an integrated resource for annotations. Genome Nexus is freely available under an open source license.
exTREEmaTIME: a method for incorporating uncertainty into divergence time estimates
Authors: Carruthers Tom , Scotland Robert W. 
Published: February 2022

ABSTRACT
We present a method of divergence time estimation (exTREEmaTIME) that aims to effectively account for uncertainty in divergence time estimates. The method requires a minimal set of assumptions, and, based on these assumptions, estimates the oldest possible divergence times and youngest possible divergence times that are consistent with the assumptions. We use a series of simulations and empirical analyses to illustrate that exTREEmaTIME is effective at representing uncertainty. We then describe how exTREEmaTIME can act as a basis to determine the implications of the more stringent assumptions that are incorporated into other methods of divergence time estimation that produce more precise estimates. This is critically important given that many of the assumptions that are incorporated into these methods are highly complex, difficult to justify biologically, and as such can lead to estimates that are highly inaccurate.
This article has an associated First Person interview with the first author of the paper.
RAS-mediated tumor stress adaptation and the targeting opportunities it presents
Authors: Redding Alexandra , Aplin Andrew E. , Grabocka Elda 
Published: February 2022

ABSTRACT
Cellular stress is known to function in synergistic cooperation with oncogenic mutations during tumorigenesis to drive cancer progression. Oncogenic RAS is a strong inducer of a variety of pro-tumorigenic cellular stresses, and also enhances the ability of cells to tolerate these stresses through multiple mechanisms. Many of these oncogenic, RAS-driven, stress-adaptive mechanisms have also been implicated in tolerance and resistance to chemotherapy and to therapies that target the RAS pathway. Understanding how oncogenic RAS shapes cellular stress adaptation and how this functions in drug resistance is of vital importance for identifying new therapeutic targets and therapeutic combinations to treat RAS-driven cancers.
Convolutional neural network-based reconstruction for acceleration of prostate T2 weighted MR imaging: a retro- and prospective study
Authors: Jung Woojin , Kim Eu Hyun , Ko Jingyu , Jeong Geunu , Choi Moon Hyung 
Published: February 2022

Objective: The aim of this study was to develop a deep neural network (DNN)-based parallel imaging reconstruction for highly accelerated 2D turbo spin echo (TSE) data in prostate MRI without quality degradation compared to conventional scans. Methods: 155 participant data were acquired for training and testing. Two DNN models were generated according to the number of acquisitions (NAQ) of input images: DNN-N1 for NAQ = 1 and DNN-N2 for NAQ = 2. In the test data, DNN and TSE images were compared by quantitative error metrics. The visual appropriateness of DNN reconstructions on accelerated scans (DNN-N1 and DNN-N2) and conventional scans (TSE-Conv) was assessed for nine parameters by two radiologists. The lesion detection was evaluated at DNNs and TES-Conv by prostate imaging-reporting and data system. Results: The scan time was reduced by 71% at NAQ = 1, and 42% at NAQ = 2. Quantitative evaluation demonstrated the better error metrics of DNN images (29–43% lower NRMSE, 4–13% higher structure similarity index, and 2.8–4.8 dB higher peak signal-to-noise ratio; p < 0.001) than TSE images. In the assessment of the visual appropriateness, both radiologists evaluated that DNN-N2 showed better or comparable performance in all parameters compared to TSE-Conv. In the lesion detection, DNN images showed almost perfect agreement (κ > 0.9) scores with TSE-Conv. Conclusions: DNN-based reconstruction in highly accelerated prostate TSE imaging showed comparable quality to conventional TSE. Advances in knowledge: Our framework reduces the scan time by 42% of conventional prostate TSE imaging without sequence modification, revealing great potential for clinical application.
The impact of condom use on the HIV epidemic
Authors: Stover John , Teng Yu 
Published: February 2022

Background: Condom promotion and supply was one the earliest interventions to be mobilized to address the HIV pandemic. Condoms are inexpensive and provide protection against transmission of HIV and other sexually transmitted diseases (STIs) as well as against unintended pregnancy. As many as 16 billion condoms may be used annually in all low- and middle-income countries (LMIC). In recent years the focus of HIV programs as been on testing and treatment and new technologies such as PrEP. Rates of condom use have stopped increasing short of UNAIDS targets and funding from donors is declining. Methods: We applied a mathematical HIV transmission model to 77 high HIV burden countries to estimate the number of HIV infections that would have occurred from 1990 to 2019 if condom use had remained at 1990 levels. Results: The results suggest that current levels of HIV would be five times higher without condom use and that the scale-up in condoms use averted about 117 million HIV infections. Conclusions: HIV programs should ensure that affordable condoms are consistently available and that the benefits of condom use are widely understood.
Behaviour change and physical activity interventions for physical activity engagement in community dwelling adults with chronic obstructive pulmonary disease: protocol for a systematic review
Authors: Hanrahan Ciara , Broderick Julie , O’Connor Terence M. , McVeigh Joseph G. 
Published: February 2022

Background: Chronic obstructive pulmonary disease (COPD) is a complex respiratory disease and the third leading cause of death worldwide. Pulmonary rehabilitation is recognised as the gold standard of care in the management of COPD, however engagement with pulmonary rehabilitation is low and maintenance of a physically active lifestyle in community dwelling adults with COPD is poor. Supporting positive behaviour change in people with COPD could help to increase their engagement with physical activity. This systematic review will examine behaviour change and physical activity interventions delivered to community dwelling adults with COPD with the aim of increasing physical activity engagement. Interventions will be mapped against Michie’s theoretical domains framework (TDF) to inform clinical practice and health policy. Methods: The following databases will be searched from inception until December 2021: Web of Science, CENTRAL, MEDLINE (via EBSCO), EMBASE, APA PsychINFO, CINAHL (via EBSCO), AMED, PROSPERO, Cochrane Airways Trials Register. Reference lists of the relevant studies and grey literature will be searched using Grey Literature Report, Open Grey and Google Scholar search engines. Relevant studies will be systematically reviewed and subject to quality appraisal to determine the impact of behaviour change and physical activity interventions on outcomes of community-dwelling adults with COPD. Interventions will be mapped to Michie’s TDF and a narrative synthesis with respect to nature, effectiveness on target population and setting/environment will be provided. Findings will be reported in relation to the generalisability of the primary results and research question, and will include secondary findings on quality of life, self-reported participation in physical activity, exercise capacity, adverse events and intervention adherence. The review will be presented according to the PRISMA guidelines 2020. Conclusions: This systematic review is necessary to explain the impact of behaviour change and physical activity interventions on outcomes of community dwelling people with COPD. PROSPERO registration: CRD42021264965 (29.06.2021)
Factors associated with Physical Activity Counseling by Health Workers Questionnaire: construction, validation and reliability
Authors: Souza Neto João Miguel de , Silva Sanderson Soares da , Farias Júnior José Cazuza de , Costa Filipe Ferreira da 
Published: February 2022

The main purpose of this study is to describe the development, validation and reliability of a questionnaire to measure the associated factors of physical activity counseling by health workers. The development of the questionnaire was carried out in four steps: construction of the analytical matrix; face validation; pilot study; and reliability assessment. The analytical matrix consisted of ten modules with a total of 47 questions. In the second step, 21 Brazilian experts of different knowledge backgrounds gave their opinion on the presentation, clarity and adequacy of each item. In the third step, a pilot study was carried out with 20 professionals (doctors, nurses and community health agents) from the Joao Pessoa, Paraíba Family Health Strategy. In the last step, reliability index was assessed among a sample of 53 health workers from five health units. The final version of the questionnaire was composed of 53 questions distributed in ten modules. Results showed a total validity index of 0.90 ranging from 0.83 to 0.95 in the modules. The clarity and adequacy of the scale showed mean values of 0.93 (ranging from 0.87 to 0.96) and 0.95 (ranging from 0.91 to 0.98), respectively. Eight out of ten modules showed all items with reliability greater than 0.60 (kappa). The questionnaire showed a satisfactory validity and reliability and it is recommended for studies to measure physical activity counseling and other practices in health promotion by health workers in the primary health care.
Building Status in an Online Community
Authors: Smirnova Inna , Reitzig Markus , Sorenson Olav 
Published: February 2022

We argue that the actions for which actors receive recognition vary as they move up the hierarchy. When actors first enter a community, the community rewards them for their easier-to-evaluate contributions to the community. Eventually, however, as these actors rise in status, further increases in stature come increasingly from engaging in actions that are more difficult to evaluate or even impossible to judge. These dynamics produce a positive feedback loop, in which those who have already been accorded some stature garner even greater status through quality-ambiguous actions. We present evidence from Stack Overflow, an online community, and from two online experiments consistent with these expected patterns.Funding: All authors would like to acknowledge funding from the Austrian Science Fund [Grant P 25768-G16].Supplemental Material: The online appendix is available at https://doi.org/10.1287/orsc.2021.1559 .
Getting to the Root of Things: The Role of Epistemic Motivation and Construal Levels in Strategic Problem Formulation
Authors: Park Chan Hyung , Baer Markus 
Published: February 2022

When formulating strategic problems, managers and executives routinely overlook relevant causes. This oversight, in turn, compromises the effectiveness of solutions and strategies. To illuminate the factors determining the success of problem formulation, we develop a model of the individual-level drivers of problem formulation comprehensiveness—the number of nonredundant and relevant causes to a problem that individuals identify. Specifically, we theorize that epistemic motivation—the desire to learn and hold well-informed views of the world—is an important driver of comprehensiveness. Furthermore, we suggest that high construal levels—an abstract thinking style—enhance the benefits of epistemic motivation because they direct individual information processing away from the symptoms of a problem toward its underlying causes. We test this interaction model in two experimental studies involving Chinese top executives and university students in the United States. The results of our two studies are consistent with our theoretical model. High construal levels strengthen the effect of epistemic motivation, resulting in greater comprehensiveness of problem formulation. We discuss the implications of our work for theory and practice.Supplemental Material: The online appendix is available at https://doi.org/10.1287/stsc.2022.0155 .
Prehospital airway management
Authors: Bell Steve , Pennington Elspeth , Hill James , Harrison Joanna 
Published: February 2022

The prehospital emergency airway management is a key moderating factor for patient survival and mortality rates. There has been much debate around the optimum method of prehospital emergency airway management. This commentary critically appraises a recent systematic review which assesses the harms and benefits of three different airway management strategies for a range of emergency clinical scenarios. Commentary on: Carney N, Totten AM, Cheney T et al. Prehospital Airway Management: A Systematic Review. Prehosp Emerg Care. 2021;1–12. https://doi.org/10.1080/10903127.2021.1940400
Phthalate exposure among U.S. college-aged women: Biomonitoring in an undergraduate student cohort (2016-2017) and trends from the National Health and Examination Survey (NHANES, 2005-2016)
Authors: Beckingham Barbara A. , Wischusen Kerry , Walker Joanna P. 
Published: February 2022

Importance
Phthalates are ubiquitous and many are known or suspected human reproductive and endocrine-disrupting toxicants. A data gap exists in reporting on biomonitoring of phthalate biomarkers in college-aged adults.

Objective
To analyze phthalate exposure in a cross-sectional sample of female college students using urinary phthalate metabolite concentrations and compare to reference populations including college-aged women sampled in the National Health and Nutrition Examination Survey (NHANES).

Methods
Nine monoester phthalate metabolites were analyzed in spot urine collected from 215 female undergraduates (age 18–22, 2016–2017) at a public university in Charleston, SC USA and a subset of participants completed a questionnaire detailing demographics and behaviors including personal care and cosmetic product use (e.g. in the past 6 or 24 hrs). Urine specific gravity was used to assess effect of urine dilution. Phthalate metabolite concentrations were compared to reference populations and the temporal trends of the same age-group in the National Health and Nutrition Examination Survey (NHANES) were analyzed.

Results
Total urinary phthalate metabolite concentrations in individuals ranged three orders of magnitude (geometric mean 56.6 ng/mL, IQR 26.6–114 ng/mL). A third of urine samples had relatively high urine specific gravity levels indicating potential dehydration status. All geometric mean concentrations were similar to the U.S. female population in the most recent NHANES cycle (2015–2016) except for MEP and mono-isobutyl phthalate (MiBP). Relatively low MEP and MiBP may be explained by a time trend of declining MEP in the general U.S. population, the sociocultural character of this cohort, and the time of day of spot sampling in evening. NHANES data indicate a significant effect of sample timing on phthalate metabolite concentrations and decline in most, but not all, phthalate metabolites sampled in women aged 18–22 years over the decade (2005–2016).

Significance
This study reports phthalate metabolites in college-aged women, an understudied group, emphasizes the benefit of survey information for interpreting biomonitoring data, and is a useful case study for communicating phthalate chemical exposure risks to college students.
Evaluation of the effect of the operational parameter on unripe banana (Musa cavendishii) flour production: case study at Arba Minch
Authors: Damota Firew Deneke , Yazie Ketamaw Salelign , Srinivasan Babuskin , Eeranna Ballekallu Chinna 
Published: February 2022

Abstract
In recent times, there are huge postharvest losses in banana production due to low market price, overproduction, lack of proper storage facilities and inadequate supply chain management. The transformation of fresh bananas to Unripe Banana flour has got immense potential to cope up with the postharvest losses of banana and it adds value to fresh bananas. Due to high availability of minerals such as potassium, calcium, iron and also the presence of high dietary fiber and resistant starch in unripe banana, they promote colon health and act as nutritious food source. In relation to this, the effect of the three types of pretreatment techniques on production of flour from unripe banana and their quality characteristics were analyzed. Drying of banana slices was conducted after performing pre-treatments like optimal osmotic solution variables, sodium meta-bisulfite (SMS), and hot water (at 100 °C). Both the untreated (control) and treated samples was oven dried at 45, 60, and 75 °C for a day (24 h). After complete drying, the banana slices were milled into a powder. For the study of optimum osmotic parameters, the design-Expert (software version 7.0.0) at three level full factorial design was employed. The optimum conditions of minimal solid gain percentage (5.66%) at maximum water loss (29.16%) were obtained at 30 °Brix sugar concentration, 60 °C socking temperature and 90 min soaking time.
NiAl – material for the application in gas turbines
Authors: Rosefort Marcel , Fehlbier Martin , Bührig-Polaczek Andreas 
Published: February 2022

Abstract
NiAl alloys are very promising candidates for high-temperature applications such as turbine blades of gas turbines. For such turbine blades, investment casting is the common manufacturing process.
Up to now, the processing of NiAl alloys in general and in particular via investment casting is hardly possible due to the very high melting temperature, hardness, reactivity of the melt, and a characteristic ductile-to-brittle transition
temperature. In this publication, the development of an investment casting technology will be summarised including the shell mould and core development, casting process development, the advancement of numeric simulation tools, and the formulation of a complete data set.