bluuebunny/crossref_metadata_2025_split huggingface dataset:
miRNASNP-v3: a comprehensive database for SNPs and disease-related variations in miRNAs and miRNA targets
Authors: Liu Chun-Jie , Fu Xin , Xia Mengxuan , Zhang Qiong , Gu Zhifeng , Guo An-Yuan 
Published: September 2020

Abstract
MicroRNAs (miRNAs) related single-nucleotide variations (SNVs), including single-nucleotide polymorphisms (SNPs) and disease-related variations (DRVs) in miRNAs and miRNA-target binding sites, can affect miRNA functions and/or biogenesis, thus to impact on phenotypes. miRNASNP is a widely used database for miRNA-related SNPs and their effects. Here, we updated it to miRNASNP-v3 (http://bioinfo.life.hust.edu.cn/miRNASNP/) with tremendous number of SNVs and new features, especially the DRVs data. We analyzed the effects of 7 161 741 SNPs and 505 417 DRVs on 1897 pre-miRNAs (2630 mature miRNAs) and 3′UTRs of 18 152 genes. miRNASNP-v3 provides a one-stop resource for miRNA-related SNVs research with the following functions: (i) explore associations between miRNA-related SNPs/DRVs and diseases; (ii) browse the effects of SNPs/DRVs on miRNA-target binding; (iii) functional enrichment analysis of miRNA target gain/loss caused by SNPs/DRVs; (iv) investigate correlations between drug sensitivity and miRNA expression; (v) inquire expression profiles of miRNAs and their targets in cancers; (vi) browse the effects of SNPs/DRVs on pre-miRNA secondary structure changes; and (vii) predict the effects of user-defined variations on miRNA-target binding or pre-miRNA secondary structure. miRNASNP-v3 is a valuable and long-term supported resource in functional variation screening and miRNA function studies.
Mechanism of efficient double-strand break repair by a long non-coding RNA
Authors: Thapar Roopa , Wang Jing L , Hammel Michal , Ye Ruiqiong , Liang Ke , Sun Chengcao , Hnizda Ales , Liang Shikang , Maw Su S , Lee Linda , Villarreal Heather , Forrester Isaac , Fang Shujuan , Tsai Miaw-Sheue , Blundell Tom L , Davis Anthony J , Lin Chunru , Lees-Miller Susan P , Strick Terence R , Tainer John A 
Published: September 2020

AbstractMechanistic studies in DNA repair have focused on roles of multi-protein DNA complexes, so how long non-coding RNAs (lncRNAs) regulate DNA repair is less well understood. Yet, lncRNA LINP1 is over-expressed in multiple cancers and confers resistance to ionizing radiation and chemotherapeutic drugs. Here, we unveil structural and mechanistic insights into LINP1’s ability to facilitate non-homologous end joining (NHEJ). We characterized LINP1 structure and flexibility and analyzed interactions with the NHEJ factor Ku70/Ku80 (Ku) and Ku complexes that direct NHEJ. LINP1 self-assembles into phase-separated condensates via RNA–RNA interactions that reorganize to form filamentous Ku-containing aggregates. Structured motifs in LINP1 bind Ku, promoting Ku multimerization and stabilization of the initial synaptic event for NHEJ. Significantly, LINP1 acts as an effective proxy for PAXX. Collective results reveal how lncRNA effectively replaces a DNA repair protein for efficient NHEJ with implications for development of resistance to cancer therapy.
Blood Dehydroepiandrosterone and Dehydroepiandrosterone Sulfate as Pathophysiological Correlates of Chronic Pain: Analyses Using a National Sample of Midlife Adults in the United States
Authors: Li Rui , Chapman Benjamin P , Smith Shannon M 
Published: September 2020

Abstract

Objective
Identifying biomarkers is a priority in translational chronic pain research. Dehydroepiandrosterone (DHEA) and its sulfated form, DHEA-S, are adrenocortical steroids in the blood with neuroprotective properties that also produce sex hormones. They may capture key sex-specific neuroendocrine mechanisms of chronic pain.

Design
Cross-sectional study.

Methods
Using data from 1,216 community-dwelling adults aged 34–84 from the Midlife in the United States (MIDUS) cohort, we examined blood DHEA and DHEA-S levels in association with chronic pain in men and women, adjusting for demographics, chronic diseases, medications including opioids, and psychosocial factors. If an association was found, we further explored dose-response relationships by the number of pain locations and the degree of pain interference.

Results
In women, chronic pain was associated with 0.072 lower (95% confidence interval [CI], –0.127 to –0.017) log10 DHEA-S µg/dL, with pain in one to two locations associated with 0.068 lower (95% CI, –0.131 to –0.006) and in three or more locations 0.071 lower (95% CI, –0.148 to 0.007) log10 DHEA-S (P for trend = 0.074). Furthermore for women, low-interference pain was associated with 0.062 lower (95% CI, –0.125 to –0.000), whereas high-interference pain was associated with 0.138 lower (95% CI, –0.233 to –0.043) log10 DHEA-S (P for trend = 0.004). Chronic pain was not associated with DHEA or DHEA-S levels in men or DHEA levels in women.

Conclusions
Chronic pain and its functional interference correspond to lower blood DHEA-S levels in women.
A novel phage display vector for selection of target-specific peptides
Authors: Chang Alex , Ting Joey P , Espada Alfonso , Broughton Howard , Molina-Martin Manuel , Afshar Sepideh 
Published: September 2020

Abstract
Intrinsic low display level of polypeptides on phage is a fundamental and limiting hurdle in successful isolation of target-specific binders by phage display technology. To circumvent this challenge, we optimized the copy number of peptides displayed on the phage surface using type 33 phage vector. We randomized the first 67 amino acids of the wild type PIII to identify mutants that would result in its reduced expression. Consequently, the display level was improved by 30-fold due to higher incorporation of the synthetic PIII–peptide fusion protein on the phage surface. Utilization of this novel phage vector should provide a solid basis for the discovery of therapeutic peptides.
Perceiving actions before they happen: psychological dimensions scaffold neural action prediction
Authors: Thornton Mark A , Tamir Diana I 
Published: September 2020

Abstract
The social world buzzes with action. People constantly walk, talk, eat, work, play, snooze and so on. To interact with others successfully, we need to both understand their current actions and predict their future actions. Here we used functional neuroimaging to test the hypothesis that people do both at the same time: when the brain perceives an action, it simultaneously encodes likely future actions. Specifically, we hypothesized that the brain represents perceived actions using a map that encodes which actions will occur next: the six-dimensional Abstraction, Creation, Tradition, Food(-relevance), Animacy and Spiritualism Taxonomy (ACT-FAST) action space. Within this space, the closer two actions are, the more likely they are to precede or follow each other. To test this hypothesis, participants watched a video featuring naturalistic sequences of actions while undergoing functional magnetic resonance imaging (fMRI) scanning. We first use a decoding model to demonstrate that the brain uses ACT-FAST to represent current actions. We then successfully predicted as-yet unseen actions, up to three actions into the future, based on their proximity to the current action’s coordinates in ACT-FAST space. This finding suggests that the brain represents actions using a six-dimensional action space that gives people an automatic glimpse of future actions.
Inferring the Effect of Species Interactions on Trait Evolution
Authors: Xu Liang , Van Doorn Sander , Hildenbrandt Hanno , Etienne Rampal S 
Published: September 2020

AbstractModels of trait evolution form an important part of macroevolutionary biology. The Brownian motion model and Ornstein–Uhlenbeck models have become classic (null) models of character evolution, in which species evolve independently. Recently, models incorporating species interactions have been developed, particularly involving competition where abiotic factors pull species toward an optimal trait value and competitive interactions drive the trait values apart. However, these models assume a fitness function rather than derive it from population dynamics and they do not consider dynamics of the trait variance. Here, we develop a general coherent trait evolution framework where the fitness function is based on a model of population dynamics, and therefore it can, in principle, accommodate any type of species interaction. We illustrate our framework with a model of abundance-dependent competitive interactions against a macroevolutionary background encoded in a phylogenetic tree. We develop an inference tool based on Approximate Bayesian Computation and test it on simulated data (of traits at the tips). We find that inference performs well when the diversity predicted by the parameters equals the number of species in the phylogeny. We then fit the model to empirical data of baleen whale body lengths, using three different summary statistics, and compare it to a model without population dynamics and a model where competition depends on the total metabolic rate of the competitors. We show that the unweighted model performs best for the least informative summary statistic, while the model with competition weighted by the total metabolic rate fits the data slightly better than the other two models for the two more informative summary statistics. Regardless of the summary statistic used, the three models substantially differ in their predictions of the abundance distribution. Therefore, data on abundance distributions will allow us to better distinguish the models from one another, and infer the nature of species interactions. Thus, our framework provides a conceptual approach to reveal species interactions underlying trait evolution and identifies the data needed to do so in practice. [Approximate Bayesian computation; competition; phylogeny; population dynamics; simulations; species interaction; trait evolution.]
Analysis of the different locomotive wireless multi-traction synchronous control systems for heavy-haul combined trains and their performance
Authors: Li Wei , Chen Chunyang , Li Hui , Wang Kai , Xie Liang , Zhang Wenlu 
Published: September 2020

Abstract
This paper looks at the heavy-haul combined train composed of different types of locomotives and its distributed power control system with a combination of 800 MHz and TD-LTE wireless communication. It analyses some key characteristic parameters that affect the synchronism and communication of the differential wireless multi-traction synchronous control systems for heavy-haul combined trains. At the same time, in order to reduce the latency of instruction and information transfer between different types of locomotives, improve the time-limit certainty of wireless transmission and optimize the control quality of multi-traction control systems for heavy-haul combined trains, a synchronism optimization strategy based on the Markov decision process on the basis of Petri networkconstruction is proposed. Relevant experiments and tests are carried out to verify the effectiveness of the synchronism optimization of the control system, which provides a guarantee for improving the differential wireless multi-traction synchronous control system for combined trains and optimizing train control.
“There Is a Lot of Change Afoot”: A Qualitative Study of Faculty Adaptation to Elimination of Tiered Grades With Increased Emphasis on Feedback in Core Clerkships
Authors: McDonald Jordan A. , Lai Cindy J. , Lin Matthew Y.C. , O’Sullivan Patricia S. , Hauer Karen E. 
Published: September 2020

Purpose
Medical schools responding to challenges with fairness, equity, learning environments, and student wellness have reconsidered clerkship grades. This study used the Concerns-Based Adoption Model (CBAM) to explore how faculty responded to a change in the approach to assessment from focus on grades toward focus on feedback.

Method
This qualitative study used an inductive approach to analyze data from semistructured interviews with teaching faculty and education leaders at University of California, San Francisco, School of Medicine 6 months following the elimination of traditional tiered clerkship grades. Participants were recruited in 2019 using purposive sampling. Interview questions addressed participants’ perceptions of the new approach to assessment and grading that emphasizes assessment for learning, including advantages and concerns. The authors analyzed data using thematic analysis informed by sensitizing concepts from CBAM.

Results
Nineteen faculty participated (11 medicine, 8 surgery). Faculty expressed optimism about the impact of the change on their clinical educator roles and sought faculty development to enhance feedback and assessment skills. Perceived benefits to students addressed learning and wellness, with concern for students’ motivation and professional development. Faculty shared uncertainty about their roles and larger systemic consequences involving the residency match and institutional reputation. Participants acknowledged that traditional grading is imperfect, yet felt a departure from this system represented significant culture change.

Conclusions
Faculty perceptions of the assessment and grade change in 2 large departments demonstrated tensions around grading. Their descriptions of change as an ongoing process aligned with CBAM and required them to consider new approaches and perspectives. While discourse about assessment and grading frequently focuses on learners, these findings support institutional consideration of the impact of changes in assessment on teaching faculty.
Standardized Criteria for Review of Perinatal Suicides and Accidental Drug-Related Deaths
Authors: Smid Marcela C. , Maeda Jewel , Stone Nicole M. , Sylvester Heidi , Baksh Laurie , Debbink Michelle P. , Varner Michael W. , Metz Torri D. 
Published: September 2020

OBJECTIVE:
To estimate the proportion of accidental drug-related deaths and suicides classified as pregnancy-related from 2013 to 2014 (preimplementation of standardized criteria) and 2015 to 2016 (postimplementation).

METHODS:
Based on Centers for Disease Control and Prevention pregnancy-related death criteria, the Utah Perinatal Mortality Review Committee developed a standardized evaluation tool to assess accidental drug-related death and suicide beginning in 2015. We performed a retrospective case review of all pregnancy-associated deaths (those occurring during pregnancy or 1 year postpartum for any reason) and pregnancy-related deaths (those directly attributable to the pregnancy or postpartum events) evaluated by Utah's Perinatal Mortality Review Committee from 2013 to 2016. We compared the proportion of accidental drug-related deaths and suicides meeting pregnancy-related criteria preimplementation and postimplementation of a standardized criteria checklist tool using Fisher’s exact test. We assessed the change in pregnancy-related mortality ratio in Utah from 2013 to 2014 and 2015 to 2016 using test of trend.

RESULTS:
From 2013 to 2016, there were 80 pregnancy-associated deaths in Utah (2013–2014: n=40; 2015–2016: n=40), and 41 (51%) were pregnancy-related (2013–2014: n=15, 2015–2016: n=26). In 2013–2014 (preimplementation), 12 women died of drug-related deaths or suicides, and only two of these deaths were deemed pregnancy-related (17%). In 2015–2016 (postimplementation), 18 women died of drug-related deaths or suicide, and 94% (n=17/18) of these deaths met one or more of the pregnancy-related criteria on the checklist (P<.001). From 2013 to 2014 to 2015–2016, Utah's overall pregnancy-related mortality ratio more than doubled, from 11.8 of 100,000 to 25.7 of 100,000 (P=.08).

CONCLUSION:
After application of standardized criteria, the Utah Perinatal Mortality Review Committee determined that pregnancy itself was the inciting event leading to the majority of accidental drug-related deaths or suicides among pregnant and postpartum women. Other maternal mortality review committees may consider a standardized approach to assessing perinatal suicides and accidental drug-related deaths.
Characteristics Associated With Consent and Reasons for Declining in a Randomized Trial in Pregnancy
Authors: Mallett Gail , Hill Kim , de Voest Jessica , Bousleiman Sabine Z. , Allard Donna , Harris Stacy , Salazar Ashley , Clark Kelly , Ortiz Felecia , Bartholomew Anna , Dalton Wendy , Craig Jennifer , Bickus Melissa ,   for the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) Maternal-Fetal Medicine Units (MFMU) Network
Published: September 2020

OBJECTIVE:To evaluate the maternal characteristics associated with consent to a randomized trial of labor induction in pregnancy.METHODS:This is a secondary analysis of low-risk nulliparous women randomized to induction of labor at 39 weeks or expectant management. During the trial, the Data and Safety Monitoring Committee requested additional fields on the screening log, which already included race and ethnicity: maternal age, type of insurance, and the reason for declining consent if declined.RESULTS:From August 2016 (start of additional data collection) to August 2017, 1,965 (28%) of the 7,112 eligible women consented to the trial. Consent was more likely for Black women (41%, adjusted odds ratio [aOR] 1.47, 95% CI 1.24–1.74), and less likely for Asian women (15%, aOR 0.64, 95% CI 0.48–0.84), compared with White women (24%). Women without private insurance were more likely to consent (38%, aOR 1.55, 95% CI 1.34–1.79), compared with those with private insurance (22%). Younger women were also more likely to consent. Among eligible women who declined participation and provided a reason (68%), preference to be expectantly managed (85%) was most common, a response more common in Asian women (aOR 1.75, 95% CI 1.31–2.33) and less common in women without private insurance (aOR 0.60, 95% CI 0.51–0.70). Not wanting to participate in research was more common in Asian women (aOR 2.41, 95% CI 1.44–4.03). Declining consent because family or friends objected was more common in Asian women (aOR 2.51, 95% CI 1.27–4.95) and women without private insurance (aOR 1.68, 95% CI 1.10–2.59).CONCLUSION:Frequency of consent and reasons for declining consent were associated with age, type of insurance, and race and ethnicity. These findings should be considered when developing recruitment strategies that promote diverse participant representation.CLINICAL TRIAL REGISTRATION:ClinialTrials.gov, NCT01990612.
Externally Validated Prediction Model of Vaginal Delivery After Preterm Induction With Unfavorable Cervix
Authors: Kawakita Tetsuya , Reddy Uma M. , Huang Jim C. , Auguste Tamika C. , Bauer David , Overcash Rachael T. 
Published: September 2020

OBJECTIVE:
To create and externally validate a predictive model to calculate the likelihood of vaginal delivery after preterm induction with unfavorable cervix.

METHODS:
This was a retrospective cohort study of women with a singleton gestation from a single academic institution who underwent an induction of labor at less than 37 weeks of gestation from January 2009 to June 2018. Women with contraindications for vaginal delivery were excluded. Analyses were limited to women with unfavorable cervix (both simplified Bishop score [dilation, station, and effacement: range 0–9] less than 6 and cervical dilation less than 3 cm). A stepwise logistic regression analysis was used to identify the factors associated with vaginal delivery by considering maternal characteristics and comorbidities as well as fetal conditions. The final model was validated using an external data set of the Consortium on Safe Labor after applying the same inclusion and exclusion criteria. We compared the area under the curve (AUC) of our predictive model and the simplified Bishop score.

RESULTS:
Of the 835 women, 563 (67%) had vaginal delivery. Factors associated with vaginal delivery included later gestational age at delivery, higher parity, more favorable simplified Bishop score, and preterm prelabor rupture of membranes. Factors including older maternal age, non-Hispanic Black race, higher body mass index, and abruption were associated with decreased likelihood of vaginal delivery. In the external validation cohort, 1,899 women were analyzed, of whom 1,417 (75%) had vaginal delivery. The AUCs of simplified Bishop score and the final model were 0.65 (95% CI 0.59–0.66) and 0.73 (95% CI 0.72–0.79), respectively, for the external validation cohort. The online calculator was created and is available at www.medstarapps.org/obstetricriskcalculator/ and in the Obstetric Risk Calculator mobile application in the Apple App Store and Google Play Store.

CONCLUSION:
Our externally validated model was efficient in predicting vaginal delivery after preterm induction with unfavorable cervix.
Outcomes of Subsequent Births After Placenta Accreta Spectrum
Authors: Baldwin Heather J. , Nippita Tanya A. , Torvaldsen Siranda , Ibiebele Ibinabo , Ford Jane B. , Patterson Jillian A. 
Published: September 2020

OBJECTIVE:
To investigate subsequent birth rates, maternal and neonatal outcomes for women with a history of placenta accreta spectrum (placenta accreta, increta, and percreta).

METHODS:
A population-based record linkage study of women who had a first, second, or third birth in New South Wales from 2003 to 2016 was conducted. Data were obtained from birth and hospital records and death registrations. Women with a history of placenta accreta spectrum were matched to women without, on propensity score and parity, to compare outcomes with women who had similar risk profiles. Modified Poisson regression models were used to calculate adjusted relative risk (aRR) for a range of maternal and neonatal outcomes.

RESULTS:
We identified recurrent placenta accreta spectrum in 27/570 (4.7%, 95% CI 3.0–6.5%) of second and 9/119 (7.6%, 95% CI 2.8–12.3%) of third pregnancies after placenta accreta spectrum in the preceding birth, with an overall recurrence rate of 38/689 (5.5%, 95% CI 3.9–7.5%, compared with the population prevalence of 25.5/10,000 births (95% CI 24.6–26.4). Subsequent births after placenta accreta spectrum had higher risk of postpartum hemorrhage (aRR 1.51, 95% CI 1.19–1.92), transfusion (aRR 2.13, 95% CI 1.17–3.90), cesarean delivery (aRR 1.19, 95% CI 1.02–1.37), manual removal of placenta (aRR 6.92, 95% CI 3.81–12.55), and preterm birth (aRR 1.43, 95% CI 1.03–1.98), with lower risk of small for gestational age (aRR 0.64, 95% CI 0.43–0.96), compared with similar-risk births.

CONCLUSION:
Women with a history of placenta accreta spectrum have increased risk of maternal morbidity, preterm birth, and placenta accreta spectrum in the subsequent pregnancy compared with similar-risk women with no previous placenta accreta spectrum, although the absolute risks are generally low. These findings may be used to inform counseling of women on the risks of future pregnancies.