bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Effect of Antenatal Vaginal Progesterone Administration on Uterine, Umbilical, and Fetal Middle Cerebral Artery Doppler Flow: A Cohort Study
Authors: Maged Ahmed M. , Shoab Amira Y. , Hussein Eman A. , Alsawaf Ahmed H. , Mahmoud Doaa S. , AbdAllah Ameer A. , Dahab Sherif , Darwish Mohamed , Ali Yahia Z. , Badran Haitham 
Published: March 2019

Objective This study aimed to evaluate the effect of vaginal progesterone (P) administration during the second and third trimesters of pregnancy on Doppler velocimetry of uterine, umbilical, and middle cerebral vessels.
Study Design A prospective cohort study conducted on 80 women at risk for preterm labor. Uterine artery, umbilical artery, and middle cerebral artery (MCA) Doppler indices were measured before and after 1 week of administration of 200 mg twice daily vaginal P. The primary outcome parameter was the change of MCA pulsatility index (PI) after P administration. Secondary outcomes included changes in uterine artery and umbilical artery Doppler measurement.
Results There was no significant changes of umbilical artery resistance index (RI) (0.69 ± 0.049 vs. 0.68 ± 0.041), umbilical artery PI (1.14 ± 0.118 vs. 1.11 ± 0.116), uterine artery RI (0.66 ± 0.12 vs. 0.66 ± 0.107), uterine artery PI (1.00 ± 0.26 vs. 1.016 ± 0.24), and MCA PI (1.27 ± 0.18 vs. 1.26 ± 0.23) measurements before and after 1 week of P administration, respectively.
Conclusion Administration of vaginal P has no significant effects on uterine artery, umbilical artery, and MCA Doppler indices.
Growth and morphogenesis of the gastropod shell
Authors: Johnson Adam B. , Fogel Nina S. , Lambert J. David 
Published: March 2019

Significance
Mollusc shells are emblematic of the morphological diversity in nature. They are important models for understanding the evolution of form; they are all variations on the same basic geometrical groundplan, their shapes can be directly related to various adaptations, and they have an exquisite fossil record. Despite these advantages, the developmental mechanisms that control shell development are unknown. We examined cell division patterns in the shell-secreting epithelium and found striking asymmetries in proliferation rate and division orientation that correlate with key aspects of shell morphogenesis in two gastropods with different shell shapes. This work provides a foundation for understanding the cellular and developmental mechanisms that generate gastropod shell form and suggest how such mechanisms might evolve to generate new morphologies.
Using a system’s equilibrium behavior to reduce its energy dissipation in nonequilibrium processes
Authors: Tafoya Sara , Large Steven J. , Liu Shixin , Bustamante Carlos , Sivak David A. 
Published: March 2019

Significance
Biomolecular machines implement many vital activities in cells and must operate quickly and in functional directions, requiring energy dissipation. Recent experiments reveal that some evolved machines are quite energetically efficient, engendering interest in design principles that achieve such high efficiency. Recent theory predicts how to use equilibrium measurements (in the absence of driving) to design ways to drive a system to minimize energy dissipation. Here, we experimentally demonstrate the utility of this theory for designing efficient driving processes (“protocols”) by rapidly unfolding and folding single DNA hairpins. We show that such designed protocols systematically and significantly reduce energy dissipation over large variations of driving speed and DNA hairpin friction. Similar protocols may underlie the high efficiency observed in molecular machines.
Second language speakers’ awareness of their own comprehensibility
Authors: Strachan Lauren , Kennedy Sara , Trofimovich Pavel 
Published: March 2019

AbstractThis study investigated whether second language (L2) speakers are aware of and can manipulate aspects of their speech contributing to comprehensibility. Forty Mandarin speakers of L2 English performed two versions of the same oral task. Before the second task, half of the speakers were asked to make their speech as easy for the interlocutor to understand as possible, while the other half received no additional prompt. Speakers self-assessed comprehensibility after each task and were interviewed about how they improved their comprehensibility. Native-speaking listeners evaluated speaker performances for five dimensions, rating speech similarly across groups and tasks. Overall, participants did not become more comprehensible from task 1 to task 2, whether prompted or not, nor did speakers’ self-assessments become more in line with raters’, indicating speakers may not be aware of their own comprehensibility. However, speakers who did demonstrate greater improvement in comprehensibility received higher ratings of flow, and speakers’ self-ratings of comprehensibility were aligned with listeners’ assessments only in the second task. When discussing comprehensibility, speakers commented more on task content than linguistic dimensions. Results highlight the roles of task repetition and self-assessment in speakers’ awareness of comprehensibility.
IgM-PRODUCING TUMORS IN THE BALB/c MOUSE
Authors: Andersson Jan , Buxbaum Joel , Citronbaum Ronald , Douglas Steven , Forni Luciana , Melchers Fritz , Pernis Benvenuto , Stott David 
Published: March 2019

Left side from top to bottom: e, d, c, b, a
Bottom from left to right: C, B, A.
Measuring the Issue Content of Supreme Court Opinions
Authors: Rice Douglas 
Published: March 2019

AbstractThe opinions of the US Supreme Court are central to volumes of research on law, courts, and politics. To understand these complex and often-lengthy documents, scholars frequently rely on dichotomous indicators of opinion content. While sometimes appropriate, for many research settings this simplification of opinion content systematically omits important information. Using all US Supreme Court opinions from 1803 to 2010 in association with structural topic models, I instead demonstrate the value of representing the Court’s attention in opinions in terms of topic proportions.
SodaPop: a forward simulation suite for the evolutionary dynamics of asexual populations on protein fitness landscapes
Authors: Gauthier Louis , Di Franco Rémicia , Serohijos Adrian W R 
Published: March 2019

Abstract

Motivation
Protein evolution is determined by forces at multiple levels of biological organization. Random mutations have an immediate effect on the biophysical properties, structure and function of proteins. These same mutations also affect the fitness of the organism. However, the evolutionary fate of mutations, whether they succeed to fixation or are purged, also depends on population size and dynamics. There is an emerging interest, both theoretically and experimentally, to integrate these two factors in protein evolution. Although there are several tools available for simulating protein evolution, most of them focus on either the biophysical or the population-level determinants, but not both. Hence, there is a need for a publicly available computational tool to explore both the effects of protein biophysics and population dynamics on protein evolution.

Results
To address this need, we developed SodaPop, a computational suite to simulate protein evolution in the context of the population dynamics of asexual populations. SodaPop accepts as input several fitness landscapes based on protein biochemistry or other user-defined fitness functions. The user can also provide as input experimental fitness landscapes derived from deep mutational scanning approaches or theoretical landscapes derived from physical force field estimates. Here, we demonstrate the broad utility of SodaPop with different applications describing the interplay of selection for protein properties and population dynamics. SodaPop is designed such that population geneticists can explore the influence of protein biochemistry on patterns of genetic variation, and that biochemists and biophysicists can explore the role of population size and demography on protein evolution.

Availability and implementation
Source code and binaries are freely available at https://github.com/louisgt/SodaPop under the GNU GPLv3 license. The software is implemented in C++ and supported on Linux, Mac OS/X and Windows.

Supplementary information
Supplementary data are available at Bioinformatics online.
Lemon: a framework for rapidly mining structural information from the Protein Data Bank
Authors: Fine Jonathan , Chopra Gaurav 
Published: March 2019

Abstract

Motivation
The Protein Data Bank (PDB) currently holds over 140 000 biomolecular structures and continues to release new structures on a weekly basis. The PDB is an essential resource to the structural bioinformatics community to develop software that mine, use, categorize and analyze such data. New computational biology methods are evaluated using custom benchmarking sets derived as subsets of 3D experimentally determined structures and structural features from the PDB. Currently, such benchmarking features are manually curated with custom scripts in a non-standardized manner that results in slow distribution and updates with new experimental structures. Finally, there is a scarcity of standardized tools to rapidly query 3D descriptors of the entire PDB.

Results
Our solution is the Lemon framework, a C++11 library with Python bindings, which provides a consistent workflow methodology for selecting biomolecular interactions based on user criterion and computing desired 3D structural features. This framework can parse and characterize the entire PDB in &lt;10 min on modern, multithreaded hardware. The speed in parsing is obtained by using the recently developed MacroMolecule Transmission Format to reduce the computational cost of reading text-based PDB files. The use of C++ lambda functions and Python bindings provide extensive flexibility for analysis and categorization of the PDB by allowing the user to write custom functions to suite their objective. We think Lemon will become a one-stop-shop to quickly mine the entire PDB to generate desired structural biology features.

Availability and implementation
The Lemon software is available as a C++ header library along with a PyPI package and example functions at https://github.com/chopralab/lemon.

Supplementary information
Supplementary data are available at Bioinformatics online.
ECOGEMS: efficient compression and retrieve of SNP data of 2058 rice accessions with integer sparse matrices
Authors: Yao Wen , Huang Fangfang , Zhang Xuehai , Tang Jihua 
Published: March 2019

Abstract

Summary
We proposed to store large-scale genotype data as integer sparse matrices, which consumed much fewer computing resources for storage and analysis than traditional approaches. In addition, the raw genotype data could be readily recovered from integer sparse matrices. Utilizing this approach, we stored the genotype data of 1612 Asian cultivated rice accessions and 446 Asian wild rice accessions across 8 584 244 SNP sites in the ECOGEMS database with 310 MB of disk usage. Graphical interface for visualization, analysis and download of SNP data were implemented in ECOGEMS, which made it a valuable resource for rice functional genomic studies.

Availability and implementation
The code and data of ECOGEMS are freely available at https://github.com/venyao/ECOGEMS. ECOGEMS is deployed at http://ecogems.ncpgr.cn and http://150.109.59.144: 3838/ECOGEMS/ for online use.

Supplementary information
Supplementary data are available at Bioinformatics online.
In utero Exposure to Anesthetics Alters Neuronal Migration Pattern in Developing Cerebral Cortex and Causes Postnatal Behavioral Deficits in Rats
Authors: Gluncic V , Moric M , Chu Y , Hanko V , Li J , Lukić I K , Lukić A , Edassery S L , Kroin J S , Persons A L , Perry P , Kelly L , Shiveley T J , Nice K , Napier C T , Kordower J H , Tuman K J 
Published: March 2019

Abstract
During fetal development, cerebral cortical neurons are generated in the proliferative zone along the ventricles and then migrate to their final positions. To examine the impact of in utero exposure to anesthetics on neuronal migration, we injected pregnant rats with bromodeoxyuridine to label fetal neurons generated at embryonic Day (E) 17 and then randomized these rats to 9 different groups receiving 3 different means of anesthesia (oxygen/control, propofol, isoflurane) for 3 exposure durations (20, 50, 120 min). Histological analysis of brains from 54 pups revealed that significant number of neurons in anesthetized animals failed to acquire their correct cortical position and remained dispersed within inappropriate cortical layers and/or adjacent white matter. Behavioral testing of 86 littermates pointed to abnormalities that correspond to the aberrations in the brain areas that are specifically developing during the E17. In the second set of experiments, fetal brains exposed to isoflurane at E16 had diminished expression of the reelin and glutamic acid decarboxylase 67, proteins critical for neuronal migration. Together, these results call for cautious use of anesthetics during the neuronal migration period in pregnancy and more comprehensive investigation of neurodevelopmental consequences for the fetus and possible consequences later in life.
Successful Treatment of Antibiotic-resistant, Poly-microbial Bone Infection With Bacteriophages and Antibiotics Combination
Authors: Nir-Paz Ran , Gelman Daniel , Khouri Ayman , Sisson Brittany M , Fackler Joseph , Alkalay-Oren Sivan , Khalifa Leron , Rimon Amit , Yerushalmy Ortal , Bader Reem , Amit Sharon , Coppenhagen-Glazer Shunit , Henry Matthew , Quinones Javier , Malagon Francisco , Biswas Biswajit , Moses Allon E , Merril Greg , Schooley Robert T , Brownstein Michael J , Weil Yoram A , Hazan Ronen 
Published: March 2019

Abstract
A patient with a trauma-related left tibial infection associated with extensively drug-resistant Acinetobacter baumannii and multidrug-resistant Klebsiella pneumoniae was treated with bacteriophages and antibiotics. There was rapid tissue healing and positive culture eradication. As a result, the patient’s leg did not have to be amputated and he is undergoing rehabilitation.
Dynamic-SoS: An Approach for the Simulation of Systems-of-Systems Dynamic Architectures
Authors: Manzano Wallace , Graciano Neto Valdemar Vicente , Nakagawa Elisa Yumi 
Published: March 2019

Abstract
Systems-of-Systems (SoS) combine heterogeneous, independent systems to offer complex functionalities for highly dynamic smart applications. Besides their dynamic architecture with continuous changes at runtime, SoS should be reliable and work without interrupting their operation and with no failures that could cause accidents or losses. SoS architectural design should facilitate the prediction of the impact of architectural changes and potential failures due to SoS behavior. However, existing approaches do not support such evaluation. Hence, these systems have been usually built without a proper evaluation of their architecture. This article presents Dynamic-SoS, an approach to predict/anticipate at design time the SoS architectural behavior at runtime to evaluate whether the SoS can sustain their operation. The main contributions of this approach comprise: (i) characterization of the dynamic architecture changes via a set of well-defined operators; (ii) a strategy to automatically include a reconfiguration controller for SoS simulation; and (iii) a means to evaluate architectural configurations that an SoS could assume at runtime, assessing their impact on the viability of the SoS operation. Results of our case study reveal Dynamic-SoS is a promising approach that could contribute to the quality of SoS by enabling prior assessment of its dynamic architecture.
Brain Protein Synthesis Rates in the UM-HET3 Mouse Following Treatment With Rapamycin or Rapamycin With Metformin
Authors: Reid Justin J , Linden Melissa A , Peelor Frederick F , Miller Richard A , Hamilton Karyn L , Miller Benjamin F 
Published: March 2019

Abstract
Treatment with the mechanistic target of rapamycin (mTOR) inhibitor, rapamycin (RAP), alone and in combination with the antidiabetic drug, metformin (RAP+MET), extends lifespan in mice. The mechanisms underlying lifespan extension are unclear. One possibility is improved capacity for proteostatic maintenance. We have previously characterized peripheral protein synthesis rates following treatment with RAP. However, it is unknown if RAP+MET elicits similar changes, or if either treatment affects protein synthesis in the brain. We hypothesized that 8 weeks of treatment with RAP and RAP+MET would alter brain protein synthesis rates to reflect proteostatic processes. Using the stable isotopic tracer, deuterium oxide (D2O), we demonstrate in UM-HET3 mice that protein synthesis rates measured in whole brain were unaffected by treatment in young male mice, whereas RAP+MET decreased mitochondrial protein synthesis in young females. Conversely, RAP increased mitochondrial protein synthesis rates in older females. Activity through the AMPK/mTOR pathway was affected in a sex-specific manner in young mice, and minimal changes were observed in the older cohort. Thus, we establish D2O for measurements of biogenesis in the brain. These results provide initial insights into the effects of RAP and RAP+MET on brain protein synthesis. Additionally, these data emphasize that responses to slowed aging treatments vary with sex and age.
Interface-targeted seismic velocity estimation using machine learning
Authors: Schuba C Nur , Schuba Jonathan P , Gray Gary G , Davy Richard G 
Published: March 2019

SUMMARY
We present a new approach to estimate 3-D seismic velocities along a target interface. This approach uses an artificial neural network trained with user-supplied geological and geophysical input features derived from both a 3-D seismic reflection volume and a 2-D wide-angle seismic profile that were acquired from the Galicia margin, offshore Spain. The S-reflector detachment fault was selected as the interface of interest. The neural network in the form of a multilayer perceptron was employed with an autoencoder and a regression layer. The autoencoder was trained using a set of input features from the 3-D reflection volume. This set of features included the reflection amplitude and instantaneous frequency at the interface of interest, time-thicknesses of overlying major layers and ratios of major layer time-thicknesses to the total time-depth of the interface. The regression model was trained to estimate the seismic velocities of the crystalline basement and mantle from these features. The ‘true’ velocities were obtained from an independent full-waveform inversion along a 2-D wide-angle seismic profile, contained within the 3-D data set. The autoencoder compressed the vector of inputs into a lower dimensional space, then the regression layer was trained in the lower dimensional space to estimate velocities above and below the targeted interface. This model was trained on 50 networks with different initializations. A total of 37 networks reached minimum achievable error of 2 per cent. The low standard deviation (&lt;300  m s−1) between different networks and low errors on velocity estimations demonstrate that the input features were sufficient to capture variations in the velocity above and below the targeted S-reflector. This regression model was then applied to the 3-D reflection volume where velocities were predicted over an area of ∼400 km2. This approach provides an alternative way to obtain velocities across a 3-D seismic survey from a deep non-reflective lithology (e.g. upper mantle) , where conventional reflection velocity estimations can be unreliable.
Volunteerism as adolescent health promotion asset: a scoping review
Authors: Hernantes Naia , Pumar-Méndez María J , López-Dicastillo Olga , Iriarte Andrea , Mujika Agurtzane 
Published: March 2019

Abstract
The Aim of this scoping review was to explore the available literature on volunteerism in adolescence and the benefits that this activity may report in their healthy development, from a salutogenic perspective. Searches were conducted in Pubmed, Cinahl, PsycINFO and Cochrane Library home databases; 15 articles were selected. Almost all of the studies were conducted in the United States between 1990 and 2000, primarily developed by psychologists and sociologists. The impact of volunteering was reflected in aspects that can be classified based on Lerner's dimensions of the PYD model. Volunteer activities promote an Improved academic, social, cognitive, and vocational competence in adolescents. An increase in conflict resolution capacity, leadership and personal agency, as well as improved pro-social attitudes and relationships with adults and peers, all of which contributed to their self-identification with the community. Moreover, increased positive development of adolescents reduces the rates of risky behaviors. Volunteerism may represent an opportunity for health promotion in adolescence. The concept of volunteering as an asset for health promotion during adolescence evokes the need to adopt and favor this view with regard to key areas of study associated with this stage such as education and health. Teams that work in community health, especially those in primary care, should recognize and value existing volunteer groups as an asset to promote the healthy development of adolescents. Friendlier health services should be encouraged that include comprehensive services from within educational institutions to community actions.
The impact of gardening on nutrition and physical health outcomes: a systematic review and meta-analysis
Authors: Kunpeuk Watinee , Spence William , Phulkerd Sirinya , Suphanchaimat Rapeepong , Pitayarangsarit Siriwan 
Published: March 2019

Abstract
Community gardening has been widely recognized as a multicomponent approach that has affected a broad range of health and well-being outcomes. The objective of this study was to investigate the association between community gardening and nutrition and physical health among adults. A systematic review and meta-analysis were conducted. Five electronic databases were searched systematically. Quality of included studies was appraised by several quality assessment tools related to the study design of each included article. Evidence from 19 articles was included (14 cross-sectional studies, 4 quasi-experimental studies and 1 case–control study). Although the majority of included studies appeared to have moderate quality, there existed weaknesses in the methods used, including low response rate and lack of confounder controls. Due to diversity in the measurement units, only body mass index (BMI) data could be pooled to perform meta-analysis. The results suggest that gardening had a significantly positive effect on BMI reduction. Subgroup analysis showed that quasi-experimental and case–control studies produced greater pooled effect size than those of cross-sectional design. Funnel plot and Egger’s test showed no significant evidence of publication bias. As robust evidence for the effect of community gardening on BMI reduction was found, this intervention should be integrated in health promoting policy to improve population health.