bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole Exome Sequencing of Nigerian Prostate Tumors from the Prostate Cancer Transatlantic Consortium (CaPTC) Reveals DNA Repair Genes Associated with African Ancestry
Authors: White Jason , Kaninjing Ernest T , Adeniji Kayode A , Jibrin Paul , Obafunwa John O , Ogo Chidiebere N , Faruk Mohammed , Popoola Ademola , Fatiregun Omolara A , Oluwole Olabode P , Karanam Balasubramanyam , Elhussin Isra , Ambs Stefan , Tang Wei , Davis Melissa , Polak Paz , Campbell Moray J , Francis Damian K , Gibbs Denise Y , Brignole Kathryn R , Rotimi Solomon , Odedina Folake T , Martin Damali N , Yates Clayton 
Published: February 2022

AbstractIn this study, we used whole-exome sequencing of a cohort of 45 advanced-stage, treatment-naïve Nigerian (NG) primary prostate cancer (PCa) tumors and 11 unmatched non-tumor tissues to compare genomic alterations with African American (AA) and European American (EA) TCGA PCa. NG samples were collected from 6 sites in central and southwest Nigeria. After whole-exome sequencing, samples were processed using GATK best practices. BRCA1 (100%), BARD1 (45%), BRCA2 (27%), and PMS2(18%) had germline alterations in at least two NG non-tumor samples. Across 111 germline variants, the AA cohort reflected a pattern [BRCA1 (68%), BARD1 (34%), BRCA2 (28%), and PMS2 (16%)] similar to NG samples. Of the most frequently mutated genes, BRCA1 showed a statistically (p ≤ 0.05) higher germline mutation frequency in men of African ancestry (MAA) and increasing variant frequency with increased African ancestry. Disaggregating gene level mutation frequencies by variants revealed both ancestry-linked and NG-specific germline variant patterns. Driven by rs799917 (T>C), BRCA1 showed an increasing mutation frequency as African admixture increased. BRCA2_rs11571831 was present only in MAAs, and BRCA2_rs766173 was elevated in NG men. 133 somatic variants were present in 26 PCa-associated genes within the NG tumor cohort. BRCA2 (27%), APC (20%), ATM (20%), BRCA1 (13%), DNAJC6 (13%), EGFR (13%), MAD1L1 (13%), MLH1 (11%), and PMS2 (11%) showed mutation frequencies > 10%. Compared to TCGA cohorts, NG tumors showed statistically significant elevated frequencies of BRCA2, APC, and BRCA1. The NG cohort variant pattern shared similarities (cosign similarities ≥ 0.734) with COSMIC signatures 5 and 6, and mutated genes showed significant (q < 0.001) GO and functional enrichment in mismatch repair and non-homologous repair deficiency pathways. Here, we showed that alterations in DNA damage response (DDR) genes were higher in NG PCa samples and that a portion of those alterations correlate with African ancestry. Moreover, we identified variants of unknown significance that may contribute to population-specific routes of tumorigenesis and treatment. These results present the most comprehensive characterization of the NG PCa exome to date and highlight the need to increase diversity of study populations.
Quantitative Radiomic Features from Computed Tomography Can Predict Pancreatic Cancer up to 36 Months Before Diagnosis
Authors: Chen Wansu , Zhou Yichen , Asadpour Vahid , Parker Rex A , Lustigova Eva , Puttock Eric J. , Wu Bechien U 
Published: February 2022

ABSTRACTObjectivesPancreatic cancer (PC) is the 3rdleading cause of cancer deaths. We aimed to detect early changes on computed tomography (CT) images associated with pancreatic ductal adenocarcinoma (PDAC) based on quantitative imaging features (QIF).MethodsAdults 18+ years of age diagnosed with PDAC in 2008-2018 were identified. Their CT scans 3 months-3 years prior to the diagnosis date were matched to up to two scans of controls. Pancreas was automatically segmented using a previously developed algorithm. 111 QIF were extracted. The dataset was randomly split for training/validation. Neighborhood and principal component analyses were applied to select the most important features. Conditional support vector machine was used to develop prediction algorithms. The computer labels were compared with manually reviewed CT images 2-3 years prior to the index date in 19 cases and 19 controls.Results227 scans from cases (stages: 35% I-II, 44% III-IV, 21% unknown) and 554 matched scans of healthy controls were included (average age 71 years; 51% females). In the validation dataset, accuracy measures were 94%-95%, and area under the curve (AUC) measures were 0.98-0.99. Sensitivity, specificity, positive predictive value, and negative predictive values were in the ranges of 88-91%, 96-98%, 91-95%, and 94-96%. QIF on CT examinations within 2-3 years prior to index date also had very high predictive accuracy (accuracy 95-98%; AUC 0.99-1.00). The QIF-based algorithm outperformed manual re-review of images for determination of PDAC-risk.ConclusionsQIF can accurately predict PDAC on CT imaging and represent promising biomarkers for early detection of pancreatic cancer.WHAT IS KNOWNPancreatic cancer is the 3rdleading cause of cancer deaths.Early detection of pancreatic ductal adenocarcinoma (PDAC) is difficult owing to lack of specific symptoms or established screening.WHAT IS NEW HEREQuantitative imaging features (QIF) of pre-diagnostic CT scans can accurately predict PDAC in 3-36 months prior to diagnosis (accuracy 94-95% and AUC 0.98-0.99).QIF on CT examinations within 2-3 years prior to cancer diagnosis also had very high predictive accuracy (accuracy 95-98%; AUC 0.99-1.00).The QIF-based algorithm outperformed manual re-review of images for determination of PDAC risk.
Insights on Telemedicine Use by Physiatrists Before, During, and Beyond the COVID-19 Pandemic
Authors: Sobrepera M. J. , Weseloh A. , Chaudhri D. , Johnson M. J. 
Published: February 2022

ABSTRACTPurposeTo determine if physiatrists increased their use of telemedicine during the first 11 months of the COVID-19 pandemic and if changes are expected to persist post-pandemic. And to identify key tasks which require video for telemedicine.Materials and MethodsA survey containing questions about the telemedicine tools used before, during, and after (planned) the COVID-19 pandemic was distributed to physiatrists. Analysis was conducted to evaluate the change in usage of telemedicine due to the pandemic and predict whether the pandemic will lead to a durable change in usage. Tasks which physiatrists have/believe they can complete with different modes of interaction were explored.ResultsResponses from 56 physiatrists showed a 105% increase in video-based telemedicine use during the pandemic. The use of phone and video communications for care delivery significantly increased. 79% of respondents planned to use video-based telemedicine post-pandemic, a significant increase from pre-pandemic use. Motor assessments, cognitive assessments, stretching, strength building, and orthotics assessment and prescription were identified as key tasks that require video for telemedicine.ConclusionThis study confirms increased use of telemedicine by physiatrists during the pandemic and suggests this shift will be durable. Key tasks where video is necessary for telemedicine were identified.
Changes in nanomechanical properties of single neuroblastoma cells as a model for oxygen and glucose deprivation (OGD)
Authors: Zieliński Tomasz , Pabijan Joanna , Zapotoczny Bartłomiej , Zemła Joanna , Wesołowska Julita , Pera Joanna , Lekka Małgorzata 
Published: February 2022

AbstractThe biological processes underlying ischemic stroke, although complex, are better known than those related to biomechanical alterations of single cells. Mechanisms of biomechanical changes and their relations to the molecular processes are crucial for understanding the function and dysfunction of the brain. In our study, we applied atomic force microscopy (AFM) to quantify the alterations in biomechanical properties in neuroblastoma SH-SY5Y cells subjected to oxygen and glucose deprivation (OGD) and reoxygenation (RO). Obtained results reveal several characteristics. Cell viability remained at the same level, regardless of the OGD and RO conditions, but, in parallel, the metabolic activity of cells decreased with OGD duration. 24h RO did not recover the metabolic activity fully. Cells subjected to OGD appeared softer than control cells. Cell softening was strongly present in cells after 1h of OGD and, with longer OGD duration and in RO conditions, cells recovered their mechanical properties. Changes in the nanomechanical properties of cells were attributed to the remodelling of actin filaments, which was related to cofilin-based regulation and impaired metabolic activity of cells. The presented study shows the importance of nanomechanics in research on ischemic-related pathological processes such as stroke.
Post-COVID-19 tele-survey for persistent symptoms in a single center hospital cohort in India along with a parallel country-wide web-survey
Authors: Chaudhuri Kausik , Sarkar Jit , Das Tirthankar , Paul Shekhar Ranjan , Basu Rajita , Gangopadhyay Supratik , Gangopadhyay Devyani , Manna Asis , Haldar Anima , Ray Yogiraj , Banerjee Sayantan , Ganguly Dipyaman 
Published: February 2022

AbstractIntroductionA major concern amidst the ongoing coronavirus pandemic has been the longer term persistence of morbidities in individuals recovering from COVID-19 disease, called ‘long COVID’. We aimed at documenting the prevalence and key associations of post-COVID symptoms (PCS) in India in telephonic survey among recovered patients in a single hospital in eastern India as well as a parallel web-survey covering a wider population of the country.MethodsSelf-reported PCS, ranging up to one year since the original COVID-19 diagnosis, were documented in a telephonic survey of subjects (analyzed N=986), treated for acute COVID-19 in Infectious Diseases and Beleghata General Hospital, Kolkata, between April 1, 2020 and April 13, 2021. In parallel, we ran a web-based survey (analyzed N=580), to evaluate concordance.ResultsShortness of breath, fatigue and insomnia were identified to be the most commonly reported PCS in both the surveys, with higher prevalence in females. In the telephonic survey, a 3.65% post-discharge mortality was registered within a median of 39 days since COVID diagnosis. Intensive care during acute disease and hypertension were more often associated with PCS, while fatigue was more often reported by the 20-40 years age-group. The web-survey revealed a gradual decline in PCS with time since COVID-19 diagnosis and type 2 diabetes to be associated with higher prevalence of these symptoms.ConclusionsWe assessed the predominant PCS among Indian COVID-19 patients and identified key demographic and clinical associations in our surveys, which warrants deeper epidemiological and mechanistic studies for guiding management of long-COVID in the country.
Conformational Ensemble of Monomeric α-Synuclein in Aqueous and Crowded Environments as revealed by Markov State Model
Authors: Menon Sneha , Mondal Jagannath 
Published: February 2022

Abstract140-residue intrinsically disordered protein α-synuclein (αS) is known to be susceptible to environmental cues/crowders and adopts conformations that are vastly variable in the extent of secondary structure and tertiary interactions. Depending upon the nature of these interactions, some of the conformations may be suitable for its physiological functions while some may be predisposed to aggregate with other partners into higher ordered species or to phase separate. However, the inherently heterogenous and dynamic nature of αS has precluded a clear demarcation of its monomeric precursor between aggregation-prone and functionally relevant aggregation-resistant states. Here, we optimally characterise a set of metastable conformations of αS by developing a comprehensive Markov state model (MSM) using cumulative 108 µs-long all-atom MD simulation trajectories of monomeric αS. Notably, the dimension of the most populated metastable (85%) state (Rg ∼ 2.59 (±0.45) nm) corroborates PRENMR studies of αS monomer and undergoes kinetic transition at 0.1-150 µs time-scale with weakly populated (0.06%) random-coil like ensemble (Rg ∼ 5.85 (±0.43) nm) and globular protein-like state (14%) (Rg ∼ 1.95 (±0.08) nm). The inter-residue contact maps identify a set of mutually interconverting aggregation-prone β-sheet networks in the NAC region and aggregation-resistant long-range interactions between N- and C-terminus or helical conformations. The presence of crowding agents compacts the MSM-derived metastable conformations in a non-monotonic fashion and skews the ensemble by either introducing new tertiary contacts or reinforcing the innate contacts to adjust to the excluded-volume effects of such environments. These observations of crucial monomeric states would serve as important steps towards rationalising routes that trigger αS-associated pathologies.Significance statementα-synuclein, a neuronal protein, is often associated with neurogenerative diseases due to its tendency to self-assemble into higher ordered aggregates. While the monomeric precursor of this protein is intrinsically disordered, it is also known to be susceptible to biological environmental cues and adopts a wide range of conformations that are either primed for aggregation or remain in auto-inhibitory states. However, the inherently heterogenous nature of the monomeric form has prevented a clear dissection of aggregation-prone and functionally relevant aggregation-resistant states. Here, we resolve this via an atomistic characterisation of an optimal set of crucial metastable monomeric conformations via statistical modelling of computer simulated data. The investigation also sheds light on crowding-induced modulation of the ensemble and eventual fibrillation pathways.
Quantitative sequence basis for the E. coli transcriptional regulatory network
Authors: Qiu Sizhe , Lamoureux Cameron , Akbari Amir , Palsson Bernhard O. , Zielinski Daniel C. 
Published: February 2022

AbstractThe transcriptional regulatory network (TRN) of E. coli consists of thousands of interactions between regulators and DNA sequences. Inherently the DNA sequence is the primary determinant of the TRN; however, it is well established that the presence of a DNA binding motif does not guarantee a functional regulatory protein binding site. Thus, the extent to which the TRN architecture can be predicted by the genome DNA sequence alone remains unclear. Here, we developed machine learning models that predict the TRN structure of E. coli based on genome sequence. Models were constructed successfully (cross-validation AUROC >= 0.8) for 84% (57/68) of valid E. coli regulons identified from top-down analysis of RNA-seq data. We found that: 1) While regulatory motif strength is the most important sequence feature for determining regulon membership, additional features such as DNA shape substantially influence membership; 2) complex regulons involving multiple interacting regulators could be unraveled by machine learning; 3) investigating regulons where initial ML models failed revealed new regulator-specific sequence features that improved model accuracy. Finally, while regulon structure can appear to be variable across estimation methods and strains, we found that strong regulatory sequence features underlie both the genes that appear most consistently in regulons across estimation methods as well as the core regulon genes in the Fur pan-regulon. This work develops a quantitative understanding of the sequence basis of the TRN and suggests a path towards computationally-guided control of transcriptional regulation for synthetic biology applications.
Directing from the shadows: Women’s experiences of male relative suicide bereavement
Authors: Gordon Evelyn , McElvaney Rosaleen 
Published: February 2022

AbstractSuicide bereavement evokes particular emotions that can hamper recovery processes, if neglected. This Interpretative Phenomenological Analysis (IPA) study explored five women’s experiences of bereavement following the death by suicide of a male relative. One superordinate theme, directing from the shadows, and three interrelated subordinate themes: roller coasting, speaking the unspeakable, and finding meaning and living with suicide were identified. This study highlights that women bereaved by suicide may occupy a complex position in the family when trying to balance caring for themselves and others, sometimes leading them to negate their own support and therapeutic needs. However, women in this study felt supported by timely, flexible and sensitive professional responses and found a proactive outreach approach, peer support groups and counselling helpful at different stages in their bereavement process.
Daily appraisal of commercial real estate a new mixed frequency approach
Authors: Francke Marc , Van De Minne Alex 
Published: February 2022

AbstractWe present a mixed frequency repeat sales model for commercial real estate, taking into account changes in net operating income between the date of buying and selling the property. Moreover, we relate monthly private market index asset returns to lags, up to 1 year, of daily (REIT) index returns. The underlying daily model enables us to interpolate the monthly private market index returns on a daily basis, and to predict the private market index asset returns going forward. The mixed frequency repeat sales model facilitates daily appraisal of commercial real estate portfolios. We apply the model on sale prices (all property types, and apartments only) in the period January 2006–July 2020. We find that the mixed frequency repeat sales model reduces 1‐month‐ahead forecasts errors and index revisions, compared to a benchmark model without daily returns.
What is the best approach for preventing recruitment to terrorism? Findings from ABM experiments in social and situational prevention
Authors: Weisburd David , Wolfowicz Michael , Hasisi Badi , Paolucci Mario , Andrighetto Giulia 
Published: February 2022

AbstractResearch SummaryThis study uses agent‐based models (ABMs) to compare the impacts of three different types of interventions targeting recruitment to terrorism—community workers at community centers; community‐oriented policing; and an employment program for high‐risk agents. The first two programs are social interventions that focus on de‐radicalization and changing the dispositions of agents in the model, whereas the employment program focuses on “deflection” and represents a situational/opportunity reducing approach to prevention. The results show significant impacts of the community worker and community policing interventions on radicalization but no significant impact on recruitment. In contrast, the employment intervention had a strong and significant impact on recruitment, but little impact on radicalization.Policy ImplicationsOur ABM simulations challenge the reliance of existing programs to reduce recruitment to terrorism on counter and de‐radicalization approaches. Instead they suggest that policy makers should focus more attention on deflection and opportunity reduction. At the same time, our ABMs point to the salience of social interventions focusing on risk and protective factors for reducing radicalization in society.
Effect of different alfalfa cultivars on growth and development of the spotted alfalfa aphid, Therioaphis trifolii (Monell)
Authors: Yu Liang‐bin , Lin Ke‐Jian , Xu Lin‐bo , Wang Hui , Cui Jin , Zhang Quan‐yi , Wang Ya‐ping , Yan Li‐ying 
Published: February 2022

AbstractTherioaphis trifolii (Monell) is a well‐known pest in alfalfa cultivation in China. Individuals of T. trifolii were allowed to feed on 10 alfalfa cultivars and their growth, reproduction, and population life table parameters were estimated. Nymphs that fed on Hunter River had the longest development time, whereas nymphs that fed on Defu had the shortest development time. Adults that fed on Debao, Zhongmu No. 2, and Defu had the shortest development time, whereas adults that fed on Golden Empress and Hunter River had the longest development times. Individuals that fed on Zhungeer produced the greatest number of offspring (13.950), and those that fed on Hunter River produced the fewest offspring (6.000). The survival rate of T. trifolii was the highest on Algonquin and lowest on Hunter River, whereas the survival time was the longest on Golden Empress and shortest on Debao. The population that fed on Algonquin had the highest intrinsic growth rate (0.560) and shortest population doubling time (1.237 days), whereas those that fed on Hunter River had the lowest intrinsic growth rate (0.217) and longest population doubling time (3.194 days). The life table parameters of the experimental T. trifolii population were used to quantify the resistance strengths of the cultivars. Results indicate that the Hunter River cultivar may effectively resist damage from T. trifolii. This study provides a theoretical basis for breeding aphid‐resistant alfalfa cultivars, enabling further research into the prevention and control of aphid infestation.
DSWEmod — The Production of High‐Frequency Surface Water Map Composites from Daily MODIS Images
Authors: Soulard Christopher E. , Waller Eric K. , Walker Jessica J. , Petrakis Roy E. , Smith Britt W. 
Published: February 2022

AbstractOptical satellite imagery is commonly used for monitoring surface water dynamics, but clouds and cloud shadows present challenges in assembling complete water time series. To test whether the daily revisit rate of Moderate Resolution Imaging Spectroradiometer (MODIS) satellite imagery can reduce cloud obstruction and improve high‐frequency surface water mapping, we compared map results derived from Landsat (30‐m) and MODIS (250‐m) data across the state of California for 2003–2019. We adapted the Dynamic Surface Water Extent (DSWE) model in Google Earth Engine to generate surface water map composites from MODIS imagery every 5, 10, 15, and 30 days, and compared products to monthly Landsat‐based DSWE maps. Results for DSWEmod (DSWE MODIS) in California suggest that more than 5% data loss (cloud obstruction, etc.) was present in only 2% of the 15‐day time series, as compared to 32% of the monthly Landsat DSWE time series. The five‐day DSWEmod composites averaged 8.4% obscuration in the winter months. Area estimates derived from cloud‐filtered MODIS and Landsat monthly products have the highest linear correlations compared to streamgage discharge records, suggesting that monthly scale analyses best explain the relationship between surface water area and general streamflow dynamics. Shorter‐interval DSWEmod products have lower correlations but utility for understanding the timing of surface water peaks and past flood events.