bluuebunny/crossref_metadata_2025_split huggingface dataset:
A comparative study of the stress-dependence of dynamic and static moduli for sandstones
Authors: Wang Yang , Han De-Hua , Li Hui , Zhao Luanxiao , Ren Jiali , Zhang Yonghao 
Published: March 2020

Understanding the differences between the static and dynamic elastic moduli of reservoir rocks is essential for the successful exploration and production of hydrocarbon reservoirs. However, the controlling factors on the dynamic-static discrepancy for sandstones remain ambiguous. Consequently, we have purposely selected three outcrop sandstone samples with large porosity contrast to investigate the effects of the stress state, magnitude, and load-unload history on the dynamic and static moduli through laboratory measurements. The results suggest that the dynamic moduli are systematically larger than the static moduli at almost any hydrostatic or deviatoric stress magnitude. In contrast, the static moduli are much more sensitive to the stress variations than the dynamic ones, leading to the decreasing dynamic-static difference upon hydrostatic loading and the increasing dynamic-static difference upon deviatoric loading. When the maximum stress in a cycle is initially reversed, the dynamic-static ratio tends to approach one, whatever the bulk modulus under hydrostatic pressure condition or the Young’s modulus under triaxial stress condition. Under the subsequent unloading process, the static bulk modulus is always higher than that derived during loading. However, the unloading static Young’s modulus is larger than the loading Young’s modulus only at a relatively high deviatoric stress magnitude greater than 30 MPa, while showing an opposite trend at a low-stress condition of less than 25 MPa. From the microstructural viewpoint, it is believed that the static tests accumulate the elastic, viscoelastic, and nonelastic properties within a certain stress or strain range. In contrast to the dynamic modulus, the static modulus exhibits greater sensitivity to the pressure or stress changes under hydrostatic and deviatoric stress conditions. The strong stress dependence makes it important to consider the in situ stress conditions when establishing dynamic-static modulus relations.
Racial, Ethnic, and Gender Diversity in Pediatric Anesthesiology Fellowship and Anesthesiology Residency Programs in the United States: Small Reservoir, Leaky Pipeline
Authors: Nafiu Olubukola O. , Leis Aleda M. , Wang Wendy , Wixson Matthew , Zisblatt Lara 
Published: March 2020

BACKGROUND:
The critical question of racial and gender diversity in pediatric anesthesia training programs has not been previously explored. The primary objective of this study was to evaluate trends by race/ethnicity and gender in pediatric anesthesiology fellowship training programs in the United States for the years 2000 to 2018.

METHODS:
Demographic data on pediatric anesthesiology fellows and anesthesiology residents were obtained from the self-reported data collected for the Journal of the American Medical Association’s annual report on Graduate Medical Education for the years 2000 to 2018. Diversity was assessed by calculating the proportions of trainees per year by gender and racial/ethnic groups in pediatric anesthesiology fellowship and anesthesiology residency programs. Logistic regression equations were developed to estimate the annual growth rate of each racial/ethnic groups.

RESULTS:
The number of pediatric anesthesiology fellows increased from 57 trainees in 2000–2001 to 202 in 2017–2018 at an average rate of 9 fellows per year (95% confidence interval [CI], 8–10). These increases were primarily due to white trainees (54.4%–63.4%) as the proportions of black (7.0%–4.5%), Asian (26.3%–21.3%), and other minority (12.3%–10.9%) trainees have remained low. The number of anesthesiology residents increased from 3950 trainees in 2000–2001 to 5940 in 2017–2018 at an average rate of 99 residents per year (95% CI, 88–111). Within all anesthesiology trainees, these increases were due to white trainees (55.7%–61.3%) as the proportion of black (5.0%–6.0%), Asian (25.8%–24.1%), and other minority trainees (8.2%–8.5%) has remained fairly constant over the time period. Despite the overall lower proportion of female anesthesiology residents (range: 27.0%–37.5%), a steady increase in the number of women in pediatric anesthesiology fellowship programs has reversed the gender imbalance in this population as of 2010.

CONCLUSIONS:
While historic gains have been made in gender diversity in pediatric anesthesiology, there is persistent underrepresentation of black and Hispanic trainees in pediatric anesthesiology. It appears that their low numbers in anesthesiology residency programs (the reservoir) may be partly responsible. Efforts to increase ethnic/racial diversity in pediatric anesthesiology fellowship and anesthesiology residency training programs are urgently needed.
Baseline imbalance about depressive symptoms may overestimate the effectiveness of mindfulness-based cognitive therapy for anxiety disorders.
Authors: Oka Takuya , Watanabe Jun , Tsujimoto Yasushi 
Published: March 2020

We read the article by Ninomiya et al. with great interest and appreciate the author's efforts to analyze the effect of primary mindfulness-based cognitive therapy (MBCT) in patients with anxiety disorder in secondary-care settings, compared with a waiting-list group. However, we have concerns about baseline imbalance of depressive symptoms that may influence the conclusion of the trial.
Comorbid major depressive disorder can have caused an underestimation of anxiety symptoms in the waiting-list group and distort effectiveness of MBCT. The wait-list group had more severe depressive symptoms than the intervention group, about 7 points more in the Center for Epidemiologic Studies Depression Scale (CES-D) scores, and that group might have more major depressive disorder. Indeed, the rate of antidepressant use in the wait-list group was 25% higher than the intervention group.
It is well known that major depressive disorder is associated with cognitive errors and underestimation of self-report outcomes. Baseline imbalance of depressive symptoms may therefore weaken the conclusion of the study, because all outcome measures were self-report questionnaires.
The authors should acknowledge the limitation and provide information about the diagnosis of major depressive disorder.
Comparison of the Efficacy of Buspirone and Placebo in Childhood Functional Abdominal Pain: A Randomized Clinical Trial
Authors: Badihian Negin , Yaghini Omid , Badihian Shervin , Shahsanai Armindokht , Saneian Hossein 
Published: March 2020

INTRODUCTION:
Pharmacological interventions have not been successful in the treatment of childhood functional abdominal pain (FAP) hitherto. Buspirone is suggested to be efficacious in some of the abdominal pain–related functional gastrointestinal disorders based on evidences from the studies on adults. We aim to investigate the efficacy of buspirone on childhood FAP.

METHODS:
This randomized clinical trial was conducted on 117 patients with childhood FAP aged 6–18 years. We randomly assigned patients to receive buspirone or placebo for 4 weeks, with the adjusted dosage for age. Participants completed the questionnaires assessing pain, depression, anxiety, somatization, and sleep disturbances at baseline, at the end of the 4-week therapy (first follow-up), and at 8 weeks after medication discontinuation (second follow-up). The primary outcome was treatment response rate, defined as reduced pain score of ≥2 or reporting no pain at the follow-up assessments.

RESULTS:
Ninety-five patients completed the 4-week therapy (48 and 47 in buspirone and placebo groups, respectively). Both buspirone and placebo reduced pain after 4 weeks of treatment, and these effects were persistent 8 weeks after medication discontinuation (P < 0.001 for both groups at weeks 4 and 12). Treatment response rates for buspirone and placebo were 58.3% and 59.6% at week 4 (P = 0.902) and 68.1% and 71.1% at week 12 (P = 0.753), respectively.

DISCUSSION:
Buspirone effectively improves pain and associated psychological symptoms including depressive symptoms, anxiety, somatization, and sleep disturbances in childhood FAP but has no superiority over placebo. Further studies, with the higher doses of buspirone and longer follow-ups are recommended.
Distinctive Features and Outcomes of Hepatocellular Carcinoma in Patients With Alcohol-Related Liver Disease: A US Multicenter Study
Authors: deLemos Andrew , Patel Milin , Gawrieh Samer , Burney Heather , Dakhoul Lara , Miller Ethan , Scanga Andrew , Kettler Carla , Liu Hao , Roche Patrick , Wattacheril Julia , Chalasani Naga 
Published: March 2020

Introduction:
The burden of hepatocellular carcinoma (HCC) occurring in patients with alcoholic liver disease (ALD) is increasing at an alarming rate. The aims of this study were to compare the patient and tumor characteristics of HCC occurring in ALD-alone relative to and in addition to other chronic liver diseases.

Methods:
Patients diagnosed with HCC between 2000 and 2014 were identified at 5 US clinical centers. The patients were categorized as ALD-alone, ALD plus viral hepatitis, or a non-ALD etiology. Clinical and tumor characteristics among the 3 groups were compared, and survival probability was estimated by the Kaplan-Meier method. The frequency of noncirrhotic HCC was compared across the 3 groups.

Results:
A total of 5,327 patients with HCC were analyzed. Six hundred seventy (12.6%) developed HCC due to underlying ALD. Ninety-one percent of ALD-related HCC arose in men, in contrast to non-ALD etiologies where men accounted for 70% of HCCs cases (P < 0.001). Patients with ALD-alone-related HCC were older at diagnosis and had tumors less likely to be detected as part of routine surveillance. The ALD-alone cohort was least likely to be within the Milan criteria and to undergo liver transplantation. Overall survival in the ALD-alone HCC cohort was lower than the other 2 groups (1.07 vs 1.31 vs 1.41 years, P < 0.001). HCC in the noncirrhotic ALD cohorts occurred in only 3.5% of the patients compared with 15.7% in patients with non-ALD etiologies (P < 0.001).

DISCUSSION:
HCC occurring in patients with ALD occurred mostly in older men and almost exclusively in a cirrhotic background. They present with advanced tumors, and their survival is lower than HCCs occurring in non-ALD.
The State of Integrated Computer-Aided Manufacturing/Computer Numerical Control: Prior Development and the Path Toward a Smarter Computer Numerical Controller
Authors: Lynn Roby , Helu Moneer , Sati Mukul , Tucker Tommy , Kurfess Thomas 
Published: March 2020

AbstractCurrent industrial practice in automated manufacturing operations relies on low fidelity data transmission methods between computer numerical control (CNC) machine tools and the computer-aided manufacturing (CAM) systems used to program them. The typical language used to program CNC machines, known as G-Code, has been in existence for nearly sixty years and offers limited resolution for command data. In addition, the proprietary nature of industrial CNC systems hampers the ability of manufacturers to expand and improve upon the capability of existing machine tools. G-Code was not designed to support transmission of feedback data, and thus both the CAM system and higher level organizational control systems are frequently blind to the state of the production process. In response, separate standards that enable data exchange with machine tools have been used by industry, such as MTConnect and Open Platform Communications Unified Architecture. However, these standards enable data pathways that are independent of the G-Code command data pathway, and thus they provide practically no means to affect the state of a process on receipt of feedback data. As a result, control and data acquisition exist in separate realms, which makes the implementation of self-optimizing smart CNC systems challenging. This state-of-the-art review surveys existing methods for data transmission to and from machine tools and explores the current state of so-called integrated CAM/CNC systems that enable more thorough control of the machining process using intelligence built into the CAM system. The literature survey reveals that integrated CAM/CNC systems are impeded both by the data exchange methods used to interface with CNC systems in addition to the proprietary and closed architecture of the CNC systems themselves. Future directions in integrated CAM/CNC research are identified based on the requirements identified for such systems.
Whole Genome Sequences of 23 Species from the Drosophila montium Species Group (Diptera: Drosophilidae): A Resource for Testing Evolutionary Hypotheses
Authors: Bronski Michael J , Martinez Ciera C , Weld Holli A , Eisen Michael B 
Published: March 2020

Abstract
Large groups of species with well-defined phylogenies are excellent systems for testing evolutionary hypotheses. In this paper, we describe the creation of a comparative genomic resource consisting of 23 genomes from the species-rich Drosophila montium species group, 22 of which are presented here for the first time. The montium group is well-positioned for clade genomics. Within the montium clade, evolutionary distances are such that large numbers of sequences can be accurately aligned while also recovering strong signals of divergence; and the distance between the montium group and D. melanogaster is short enough so that orthologous sequence can be readily identified. All genomes were assembled from a single, small-insert library using MaSuRCA, before going through an extensive post-assembly pipeline. Estimated genome sizes within the montium group range from 155 Mb to 223 Mb (mean = 196 Mb). The absence of long-distance information during the assembly process resulted in fragmented assemblies, with the scaffold NG50s varying widely based on repeat content and sample heterozygosity (min = 18 kb, max = 390 kb, mean = 74 kb). The total scaffold length for most assemblies is also shorter than the estimated genome size, typically by 5–15%. However, subsequent analysis showed that our assemblies are highly complete. Despite large differences in contiguity, all assemblies contain at least 96% of known single-copy Dipteran genes (BUSCOs, n = 2,799). Similarly, by aligning our assemblies to the D. melanogaster genome and remapping coordinates for a large set of transcriptional enhancers (n = 3,457), we showed that each montium assembly contains orthologs for at least 91% of D. melanogaster enhancers. Importantly, the genic and enhancer contents of our assemblies are comparable to that of far more contiguous Drosophila assemblies. The alignment of our own D. serrata assembly to a previously published PacBio D. serrata assembly also showed that our longest scaffolds (up to 1 Mb) are free of large-scale misassemblies. Our genome assemblies are a valuable resource that can be used to further resolve the montium group phylogeny; study the evolution of protein-coding genes and cis-regulatory sequences; and determine the genetic basis of ecological and behavioral adaptations.
Identifying Small Molecules That Promote Quasipalindrome-Associated Template-Switch Mutations inEscherichia coli
Authors: Klaric Julie A , Perr Eli L , Lovett Susan T 
Published: March 2020

AbstractDNA can assemble into non-B form structures that stall replication and cause genomic instability. One such secondary structure results from an inverted DNA repeat that can assemble into hairpin and cruciform structures during DNA replication. Quasipalindromes (QP), imperfect inverted repeats, are sites of mutational hotspots. Quasipalindrome-associated mutations (QPMs) occur through a template-switch mechanism in which the replicative polymerase stalls at a QP site and uses the nascent strand as a template instead of the correct template strand. This mutational event causes the QP to become a perfect or more perfect inverted repeat. Since it is not fully understood how template-switch events are stimulated or repressed, we designed a high-throughput screen to discover drugs that affect these events. QP reporters were engineered in the Escherichia coli lacZ gene to allow us to study template-switch events specifically. We tested 700 compounds from the NIH Clinical Collection through a disk diffusion assay and identified 11 positive hits. One of the hits was azidothymidine (zidovudine, AZT), a thymidine analog and DNA chain terminator. The other ten were found to be fluoroquinolone antibiotics, which induce DNA-protein crosslinks. This work shows that our screen is useful in identifying small molecules that affect quasipalindrome-associated template-switch mutations. We are currently assessing more small molecule libraries and applying this method to study other types of mutations.
Evaluation of STAR and Kallisto on Single Cell RNA-Seq Data Alignment
Authors: Du Yuheng , Huang Qianhui , Arisdakessian Cedric , Garmire Lana X 
Published: March 2020

Abstract
Alignment of scRNA-Seq data are the first and one of the most critical steps of the scRNA-Seq analysis workflow, and thus the choice of proper aligners is of paramount importance. Recently, STAR an alignment method and Kallisto a pseudoalignment method have both gained a vast amount of popularity in the single cell sequencing field. However, an unbiased third-party comparison of these two methods in scRNA-Seq is lacking. Here we conduct a systematic comparison of them on a variety of Drop-seq, Fluidigm and 10x genomics data, from the aspects of gene abundance, alignment accuracy, as well as computational speed and memory use. We observe that STAR globally produces more genes and higher gene-expression values, compared to Kallisto, as well as Bowtie2, another popular alignment method for bulk RNA-Seq. STAR also yields higher correlations of the Gini index for the genes with RNA-FISH validation results. Using 10x genomics PBMC 3K scRNA-Seq and mouse cortex single nuclei RNA-Seq data, STAR shows similar or better cell-type annotation results, by detecting a larger subset of known gene markers. However, the gain of accuracy and gene abundance of STAR alignment comes with the price of significantly slower computation time (4 folds) and more memory (7.7 folds), compared to Kallisto.
MYCs and PIFs Act Independently in Arabidopsis Growth Regulation
Authors: Li Chunmei , Nozue Kazunari , Maloof Julin N 
Published: March 2020

AbstractPlants have a variety of strategies to avoid canopy shade and compete with their neighbors for light, collectively called the shade avoidance syndrome (SAS). Plants also have extensive systems to defend themselves against pathogens and herbivores. Defense and shade avoidance are two fundamental components of plant survival and productivity, and there are often tradeoffs between growth and defense. Recently, MYC2, a major positive regulator of defense, was reported to inhibit elongation during shade avoidance. Here, we further investigate the role of MYC2 and the related MYC3 and MYC4 in shade avoidance, and we examine the relationship between MYC2/3/4 and the PIF family of light-regulated transcription factors. We demonstrate that MYC2/3/4 inhibit both elongation and flowering. Furthermore, using both genetic and transcriptomic analysis we find that MYCs and PIFs generally function independently in growth regulation. However, surprisingly, the pif4/5/7 triple mutant restored the petiole shade avoidance response of myc2 (jin1-2) and myc2/3/4. We theorize that increased petiole elongation in myc2/3/4 could be more due to resource tradeoffs or post-translational modifications rather than interactions with PIF4/5/7 affecting gene regulation.
Violencia de pareja contra el hombre en Cali, Colombia
Authors: Floyd-Aristizábal Danielle , Loaiza Osorio Sara Del Pilar , Sierra Ruiz Melibea , López López Juan David , Ricaurte Villota Ana Ínés 
Published: March 2020

Propósito: en Colombia la violencia de pareja es un problema de salud pública que afecta notablemente a la sociedad. Por esto, el propósito de este artículo es caracterizar la violencia intrafamiliar de pareja contra del hombre los casos que se presentaron en Cali, en el año 2014, y que fueron evaluados en la regional suroccidente del Instituto de Medicina Legal. Descripción: se realiza un estudio descriptivo, encontrando 78 casos, los cuales fueron revisados uno a uno; hallando en la muestra una media de edad de 33 años, siendo el grupo más afectado el de adulos jóvenes (88%), con unión libre como estado civil más frecuente (58%). Los meses con más casos fueron diciembre, octubre y febrero (39%), sin una relación clara con las festividades nacionales; y los días predominantes fueron los correspondientes al fin de semana (49% de los eventos). Enfoque: fue llamativo que el 45% de los eventos se desarrollaron en horas no laborales. La principal causa desencadenante fue la intolerancia (63%), y se reportó maltrato previo en 74% de las valoraciones. Conclusiones: este estudio nos permite caracterizar un fenómeno poco descrito que requiere estudios adicionales en la materia, que permitan evaluar patrones de violencia, factores desencadenantes o de riesgo, entre otros. Todo esto sin dejar de lado el verdadero enfoque y atención que se le debe de dar a todas las víctimas de violencia, sin importar su sexo, se debe garantizar el cumplimiento de sus derechos y el lanzamiento de nuevos programas de prevención primaria.