bluuebunny/crossref_metadata_2025_split huggingface dataset:
Creation and implementation of a novel clinical workflow based on the AAST uniform anatomic severity grading system for emergency general surgery conditions
Authors: Bessoff Kovi E , Choi Jeff , Bereknyei Merrell Sylvia , Nassar Aussama Khalaf , Spain David , Knowlton Lisa Marie 
Published: September 2020

ObjectiveEmergency general surgery (EGS) conditions encompass a variety of diseases treated by acute care surgeons. The heterogeneity of these diseases limits infrastructure to facilitate EGS-specific quality improvement (QI) and research. A uniform anatomic severity grading system for EGS conditions was recently developed to fill this need. We integrated this system into our clinical workflow and examined its impact on research, surgical training, communication, and patient care.MethodsThe grading system was integrated into our clinical workflow in a phased fashion through formal education and a written handbook. A documentation template was also deployed in our electronic medical record to prospectively assign severity scores at the time of patient evaluation. Mixed methods including a quantitative survey and qualitative interviews of trainees and attending surgeons were used to evaluate the impact of the new workflow and to identify obstacles to its adoption.ResultsWe identified 2291 patients presenting with EGS conditions during our study period. The most common diagnoses were small bowel obstruction (n=470, 20.5%), acute cholecystitis (n=384, 16.8%), and appendicitis (n=370, 16.1%). A total of 21 qualitative interviews were conducted. Twenty interviewees (95.2%) had a positive impression of the clinical workflow, citing enhanced patient care and research opportunities. Fifteen interviewees (75.0%) reported the severity grading system was a useful framework for clinical management, with five participants (25.0%) indicating the system was useful to facilitate clinical communication. Participants identified solutions to overcome barriers to adoption of the clinical workflow.ConclusionsThe uniform anatomic severity grading system can be readily integrated into a clinical workflow to facilitate prospective data collection for QI and research. The system is perceived as valuable by users. Educational initiatives that focus on increasing familiarity with the system and its benefits will likely improve adoption of the classification system and the clinical workflow that uses it.Level of evidenceLevel III.
Dietary restriction and/or exercise training impairs spermatogenesis in normal rats
Authors: Li Yinlam , Zhang Li , Zheng Xiaoguo , Qian Jianing , Li Yanquan , Xie Chong , Zhang Xuelian , Zhou Yuchuan , Huang Hefeng 
Published: September 2020

Dietary restriction and/or exercise has been shown to have multiple benefits for health. However, its effects on reproductive health and the mechanisms by which it regulates reproductive function remain unclear. Here, to evaluate its effects on spermatogenesis and sperm function, rats were divided into 4 groups: ad libitum-fed sedentary control, dietary restriction (DR), exercise training (ET), and dietary restriction plus exercise training (DR+ET) groups. Results indicated that body weight, epididymal fat pad weight, and sperm counts were significantly reduced in the DR, ET, and DR+ET groups. Moreover, sperm motility and capacitation-associated protein tyrosine phosphorylation were suppressed in the DR and DR+ET groups, but not the ET group. Microarray analysis revealed that the number of downregulated genes was higher than that of upregulated genes in the DR and/or ET groups. About half of the downregulated genes are common after exercise training and/or diet restriction. Gene ontology analysis showed that downregulated genes in the DR, ET, and DR+ET groups affected spermatogenesis through overlapping pathways, including glucocorticoid, corticosteroid, extracellular structure organization, and estradiol responses. Our findings suggest that diet restriction and/or exercise training may present potential risks to male reproductive dysfunction by disrupting normal gene expression patterns in the testis. Novelty: Dietary restriction and/or exercise can lead to the damage of spermatogenesis as well as sperm maturation. Sperm functional changes are more sensitive to dietary restriction than exercise training. Dietary restriction and exercise impair spermatogenesis through overlapping biological pathways in the testis.
Effects of oral bovine lactoferrin on a mouse model of inflammation associated colon cancer
Authors: Tanaka Hajime , Gunasekaran Sivagami , Saleh Dina Mourad , Alexander William T. , Alexander David B. , Ohara Hirotaka , Tsuda Hiroyuki 
Published: September 2020

Patients with ulcerative colitis or colonic Crohn’s disease have a significantly increased risk of developing colorectal cancer. Bovine lactoferrin (bLF) reportedly inhibited the development of colon cancer in rats and mice, and in a placebo controlled trial, ingestion of bLF inhibited the growth of intestinal polyps. In addition, in a case study, a patient with Crohn’s disease was reported to have remained in remission for over 7 years while ingesting 1 g of bLF daily. Thus, bLF has an inhibitory effect on colon carcinogenesis, and it may also promote remission of Crohn’s disease. The purpose of this study was to investigate the effects of bLF in a mouse model of colorectal cancer related to irritable bowel disease (IBD). The mice were divided into 4 groups: (i) no treatment; (ii) treated with bLF only; (iii) treated with azoxymethane plus dextran sulfate sodium (AOM + DSS); and (iv) treated with AOM + DSS + bLF. AOM was used to initiate intestinal cancer, and DSS was used to induce IBD-like inflammation in the intestine of the C57BL/6 mice. At the end of the study, the mice treated with AOM + DSS + bLF had a better fecal score, fewer lesions in the colon, and less weight loss than the mice treated with AOM + DSS without bLF. However, there were no statistically significant differences between the two groups with respect to tumor burden.
A Deep Learning Framework Identifies Pathogenic Noncoding Somatic Mutations from Personal Prostate Cancer Genomes
Authors: Wang Cheng , Li Jingjing 
Published: September 2020

Abstract

Our understanding of noncoding mutations in cancer genomes has been derived primarily from mutational recurrence analysis by aggregating clinical samples on a large scale. These cohort-based approaches cannot directly identify individual pathogenic noncoding mutations from personal cancer genomes. Therefore, although most somatic mutations are localized in the noncoding cancer genome, their effects on driving tumorigenesis and progression have not been systematically explored and noncoding somatic alleles have not been leveraged in current clinical practice to guide personalized screening, diagnosis, and treatment. Here, we present a deep learning framework to capture pathogenic noncoding mutations in personal cancer genomes, which perturb gene regulation by altering chromatin architecture. We deployed the system specifically for localized prostate cancer by integrating large-scale prostate cancer genomes and the prostate-specific epigenome. We exhaustively evaluated somatic mutations in each patient's genome and agnostically identified thousands of somatic alleles altering the prostate epigenome. Functional genomic analyses subsequently demonstrated that affected genes displayed differential expression in prostate tumor samples, were vulnerable to expression alterations, and were convergent onto androgen receptor–mediated signaling pathways. Accumulation of pathogenic regulatory mutations in these affected genes was predictive of clinical observations, suggesting potential clinical utility of this approach. Overall, the deep learning framework has significantly expanded our view of somatic mutations in the vast noncoding genome, uncovered novel genes in localized prostate cancer, and will foster the development of personalized screening and therapeutic strategies for prostate cancer.

Significance:
This study's characterization of the noncoding genome in prostate cancer reveals mutational signatures predictive of clinical observations, which may serve as a powerful prognostic tool in this disease.
Abstract MP23: Vascular Smooth Muscle Rho-related Btb Domain Containing Protein 1 In Hypertension And Arterial Stiffness
Authors: Fang Shi , Wu Jing , Donato Silva Sebastiao , Lu Ko-ting , Sigmund Curt D 
Published: September 2020

Rho-related BTB domain containing protein 1 (RhoBTB1) is a transcriptional target of peroxisome proliferator activated receptor γ (PPARγ), but its physiological and molecular function in blood pressure (BP) control remains unclear. We showed that aortic RhoBTB1 expression was decreased in mice expressing vascular smooth muscle (VSM) specific dominant negative PPARγ mutation (S-P467L). Genetic complementation of VSM RhoBTB1 reversed the hypertension, vascular dysfunction, and arterial stiffness in S-P467L mice; and suppressed the elevated enzymatic activity of phosphodiesterase 5 (PDE5) in S-P467L mice. In HEK293 cells, RhoBTB1 increases PDE5 ubiquitination in a Cullin-3-dependent manner. We concluded that VSMC RhoBTB1 mediates the anti-hypertensive effect of PPARγ.
RhoBTB1 expression was decreased in aorta from mice treated with angiotensin II (AngII, 490ng/kg/min, 2-weeks). We hypothesized that restoration of VSM RhoBTB1 would reverse established AngII-mediated hypertension, vascular dysfunction, and arterial stiffness. Transgenic mice expressing inducible VSM-specific RhoBTB1 (S-RhoBTB1) were treated with AngII (490ng/kg/min, 6-weeks) and the transgene was activated by Tamoxifen (Tx) during week 3. ISM-Cre mice expressing VSM Cre-recombinase were similarly treated as controls. AngII equally increased BP, as measured by radiotelemetry in both ISM-Cre and S-RhoBTB1 mice. The vasodilatory and vasoconstrictor responses in the carotid artery were not different in AngII-treated S-RhoBTB1 and ISM-Cre mice. RhoBTB1 did not affect pulse wave velocity (PWV), a measure of arterial stiffness, in mice without AngII (ISM-Cre vs S-RhoBTB1: 2.64±0.08 vs 2.48±0.06 mm/ms, p>0.05, n=6); and AngII increased PWV similarly in both strains before Tx (ISM-Cre vs S-RhoBTB1: 3.54±0.22 vs 3.52±0.18 mm/ms, p>0.05, n=7-9). PWV of S-RhoBTB1 mice started to decrease after the first week whereas it continued to rise in ISM-Cre mice. By the second week of Tx, VSMC RhoBTB1 expression significantly attenuated AngII induced arterial stiffness (ISM-Cre vs S-RhoBTB1: 4.21±0.37 vs 3.17±0.16 mm/ms, p=0.02, n=7-9). These data suggest a mechanism where RhoBTB1 improves vascular compliance independently from BP and is protective against arterial stiffness.
Abstract P023: Relationship Between TNF-α And SBP In The Baseline Cohort Of The Dietary Approaches To Stop Hypertension (DASH)-Sodium Trial
Authors: Farhan Khalid , Drugge Elizabeth D , Zhou Hong , Graham Lesley , Hao Shoujin , Ferreri Nicholas R 
Published: September 2020

Hypertension (HTN) is a leading global noncommunicable cause of mortality and dietary salt is the most common modifiable risk factor for HTN. Evidence suggests that tumor necrosis factor alpha (TNF-α) modulates mechanisms that may contribute to salt-sensitive hypertension (SSHT). We conducted a secondary analysis of the baseline cohort of the DASH-Sodium trial, to explore the relationship between TNF-α and systolic blood pressure (SBP) in subjects categorized by race, sex, and baseline blood pressure.
Urinary TNF-α levels adjusted for creatinine (pg/mg) were measured in (91%) (374 of 412) subjects ingesting high salt (150 mmol) and control diet for 2 weeks prior to randomization. Descriptive analyses were used to determine the sample prevalence of demographic, laboratory, and outcome variables, and bivariate analyses were used to check for highly correlated variables. Robust multiple linear regression was used to evaluate the association of TNF-α and SBP with and without covariates, p < 0.05.
SBP, urinary sodium and potassium adjusted for creatinine, and 24-hour urine volume were positively associated with TNF-α, whereas African American, male, and increasing waist circumference exhibited negative associations with TNF-α, p < 0.05. Predicted TNF-α increased from 22.7 (19.3,26.8) to 33.2 (26.9,41.0) pg/mg with increasing SBP (100 to 180 mm Hg). TNF-α was 25.4 (23.7, 27.1) pg/mg for AA vs. 28.9 (27.2, 30.8) pg/mg for non-AA, and 24.2 (22.6, 25.9) for males vs. (27.3, 30.7) pg/mg for females, respectively. TNF-α increased from 22.3 (20.3, 24.5) to 46.8 (36.1, 60.7) pg/mg as urinary potassium increased from 10 to 100 mg/g, and from 22.7 (20.3, 25.5) to 33.1 (29.0, 37.8) pg/mg as urinary sodium increased from 10 to 250 mg/g. There was a statistically significant interaction between urinary sodium and potassium: TNFα increased to a greater extent with increasing urinary potassium at a lower level of urinary sodium (-1 SD),16.7 (14.0, 20.2) to 38.1 (31.3, 47.3) pg/mg compared to that at higher urinary sodium levels (+1SD), 24.4 (21.0, 28.4) to 35.2 (30.9, 40.1) pg/mg.
These results suggest that TNF-α may regulate ion transport mechanisms that contribute to differences in potassium handling and changes in sodium and potassium excretion observed in SSHT.
Abstract P031: Reduced Augmentation Of The Intrarenal Renin-angiotensin System (ras), Lower Systolic Blood Pressure, And Preserved Renal Function In Female Compared To Male Rats With Unilateral Renal Artery Stenosis
Authors: Bell Annie L , Shao Weijian A , Katsurada Akemi , Sato Ryosuke , NAVAR L Gabriel G 
Published: September 2020

Despite growing evidence of sex differences in the progression of hypertension, there are no guidelines that differentiate treatment between men and women. Intrarenal renin-angiotensin system (RAS) activation and tissue injury in 2-kidney, 1-clip (2K1C) hypertensive rats have been characterized in previous studies of male but not female rats.
To evaluate possible sex differences in response to renovascular hypertension, urinary angiotensinogen (uAGT) excretion, systolic blood pressure (BP), urinary protein excretion, and renal function were assessed in female rats.Female (n=8) and male (n=6) rats underwent placement of a 0.2 mm clip on the left renal artery to simulate unilateral renal artery stenosis. BP was measured by tail-cuff plethysmography, and clearance studies were conducted in anesthetized rats to assess renal function. Urine protein concentration was determined by pyrogallol red method. uAGT was measured by ELISA as an index of intrarenal RAS activity.
Systolic BP increased from 120±1 to 176±8 mmHg, and urinary protein excretion reached 20.2±5.6 mg/day in female rats. Although uAGT excretion increased from 13.2±7.7 ng/day to 74.1±29.9 ng/day in female rats, male rats had a significantly higher uAGT excretion of 1572.6±750 ng/day. Nonclipped kidneys exhibited more uAGT excretion compared to clipped kidneys, consistent with previous findings in males. Although 2K1C female rats demonstrate significantly lower renal function than sham females, they show more preserved renal function than male rats. Female rats also demonstrate significantly lower increases in systolic BP and urinary protein excretion compared to male rats.
The data support substantial sex-dependent differences in renal responses to unilateral renal artery stenosis. The results show substantial increases in systolic BP, uAGT, and urinary protein excretion and decreased renal function after renal artery clipping in females, but the magnitude of the changes is markedly lower than in males. Nonclipped kidneys of both sexes exhibit greater uAGT excretion than clipped kidneys. Notably, females show less augmentation of the intrarenal RAS compared to male rats in renovascular hypertension.
Cap and Gap: The Fiscal Effects of Property Tax Levy Limits in New York
Authors: Nguyen-Hoang Phuong , Zhang Pengju 
Published: September 2020

Abstract
This is the first study to examine the fiscal effects of the New York property tax levy limit, using variation from the degree of fiscal stringency across school districts and over time in its first five years of implementation. Based on a difference-in-differences estimator, coupled with an event study specification, we find that the tax limit has imposed a real cap on many school districts; that is, at-limit districts’ total current expenditures per pupil are significantly lower than what they would have spent absent the limit. For those affected school districts, this expenditure gap does not come from spending on teacher salaries or fringe benefits but rather from other instructional salaries/expenses, central administration, transportation, interfund transfers, and undistributed spending. We also find heterogeneity in the constraining effects of the tax limit across different need-based groups of school districts.
Scaling Behavior of a Turbulent Kinetic Energy Closure Scheme for the Stably Stratified Atmosphere: A Steady-State Analysis
Authors: MacDonald Michael , Teixeira João 
Published: September 2020

Abstract
We present a turbulent kinetic energy (TKE) closure scheme for the stably stratified atmosphere in which the mixing lengths for momentum and heat are not parameterized in the same manner. The key difference is that, while the mixing length for heat tends toward the stability independent mixing length for momentum in neutrally stratified conditions, it tends toward one based on the Brunt–Väisälä time scale and square root of the TKE in the limit of large stability. This enables a unique steady-state solution for TKE to be obtained, which we demonstrate would otherwise be impossible if the mixing lengths were the same. Despite the model’s relative simplicity, it is shown to perform reasonably well with observational data from the 1999 Cooperative Atmosphere–Surface Exchange Study (CASES-99) using commonly employed model constants. Analyzing the scaling behavior of the nondimensional velocity and potential temperature gradients, or of the stability (correction) functions, reveals that for large stability the present model scales in the same manner as the first-order operational scheme of Viterbo et al. Alternatively, it appears as a blend of two cases of the TKE closure scheme of Baas et al. Critically, because a unique steady-state TKE can be obtained, the present model avoids the nonphysical behavior identified in one of the cases of Baas et al.
A k–ε Turbulence Model for the Convective Atmosphere
Authors: Zeng Xiping , Wang Yansen 
Published: September 2020

AbstractA k–ε turbulence model for the stable atmosphere is extended for the convective atmosphere. The new model represents the buoyancy-induced increase in the kinetic energy and scale of eddies, and is consistent with the Monin–Obukhov similarity theory for convective atmospheric boundary layers (ABLs). After being incorporated into an ABL model with the Coriolis force, the model is tested by comparing the ABL model results with the Businger–Dyer (BD) relationship. ABL model simulations are carried out to reveal the sensitivity of the vertical wind profile to model parameters (e.g., the Obukhov length, friction velocity, and geostrophic wind). When the friction velocity is consistent with geostrophic wind speed (or the turbulence in the inner regime is in equilibrium with that in the outer regime), the modeled wind profile is close to the BD relationship near the ground surface. Otherwise, the modeled wind profile deviates from the BD relationship, resembling the hockey stick transition model.
Role of Equatorial Cold Tongue in Central Pacific Double-ITCZ Bias in the NCAR CESM1.2
Authors: Song Xiaoliang , Zhang Guang Jun 
Published: September 2020

AbstractWarm SST bias underlying the spurious southern ITCZ has long been recognized as one of the main causes for double-ITCZ bias in coupled GCMs in the central Pacific. This study demonstrates that the NCAR CESM1.2 can still simulate significant double-ITCZ bias even with cold SST bias in the southern ITCZ region, indicating that warm SST bias is not a necessary condition for double-ITCZ bias in the central Pacific. Further analyses suggest that the equatorial cold tongue (ECT) biases play important roles in the formation of double-ITCZ bias in the central Pacific. The severe cold SST biases in the ECT region in the central Pacific may enhance the SST gradient between the ECT and southern ITCZ region, strengthening the lower-troposphere dynamical convergence and hence convection in the southern ITCZ region. The formation mechanism of excessive ECT bias is further investigated. It is shown that the cold SST biases in the ECT region can be largely attributed to the anomalous cooling tendency produced by the upper-ocean zonal advection due to overly strong zonal currents. In the ECT region, the westward ocean surface zonal current is driven by the equatorial easterly surface winds. It is shown that convection bias simulated by the atmospheric model in the equatorial Amazon region may lead to easterly wind bias in the downwind side (west) of convection region. The mean Walker circulation transports these easterly wind momentum anomalies downward and westward to the surface, resulting in the overly strong surface easterly wind in the central equatorial Pacific.
AMSR-E Snow: Can Snowfall Help Improve SWE Estimates?
Authors: Gonzalez Ryan , Kummerow Christian D. 
Published: September 2020

AbstractSnowfall and snowpack are tightly coupled within the snow water cycle and careful monitoring is crucial to better understand snow’s role in Earth’s water and energy cycles. Current and future estimates of the total amount of seasonal snow on the ground are limited by the variability in the initial snowfall and uncertainties in in situ and remote sensing observations. In this study, passive microwave remote sensing estimates of snowfall and snow water equivalent (SWE) from the Advanced Microwave Scanning Radiometer (AMSR-E) instrument are used to assess the consistency in the snow products. A snow evolution model, SnowModel, is employed to simulate snow processes that occur between the initial snowfall and subsequent SWE. AMSR-E is found to have significant discrepancies in both snowfall and SWE compared to MERRA-2 reanalysis and the Canadian Meteorological Centre (CMC) snow product. It is shown that AMSR-E snowfall is currently not a useful metric to estimate SWE without applying large corrections throughout the winter season. Regions of consistency in the AMSR-E snow products occur for reasons that pertain to underestimation in both snowfall and SWE. In addition to snow consistency, microwave brightness temperatures (TBs) are analyzed in response to the snowpack and snowfall physical properties. These experiments indicate significant sensitivity to regime-dependent scattering characteristics that must be accounted for to accurately estimate global snow properties and provide better physical consistency in the snow products from remote sensing platforms.