bluuebunny/crossref_metadata_2025_split huggingface dataset:
Guide tree optimization with genetic algorithm to improve multiple protein 3D-structure alignment
Authors: Shegay Maksim V , Švedas Vytas K , Voevodin Vladimir V , Suplatov Dmitry A , Popova Nina N 
Published: November 2021

Abstract

Motivation
With the increasing availability of 3D-data, the focus of comparative bioinformatic analysis is shifting from protein sequence alignments toward more content-rich 3D-alignments. This raises the need for new ways to improve the accuracy of 3D-superimposition.

Results
We proposed guide tree optimization with genetic algorithm (GA) as a universal tool to improve the alignment quality of multiple protein 3D-structures systematically. As a proof of concept, we implemented the suggested GA-based approach in popular Matt and Caretta multiple protein 3D-structure alignment (M3DSA) algorithms, leading to a statistically significant improvement of the TM-score quality indicator by up to 220–1523% on ‘SABmark Superfamilies’ (in 49–77% of cases) and ‘SABmark Twilight’ (in 59–80% of cases) datasets. The observed improvement in collections of distant homologies highlights the potentials of GA to optimize 3D-alignments of diverse protein superfamilies as one plausible tool to study the structure–function relationship.

Availability and implementation
The source codes of patched gaCaretta and gaMatt programs are available open-access at https://github.com/n-canter/gamaps.

Supplementary information
Supplementary data are available at Bioinformatics online.
Socioeconomic status effects on health vary between rural and urban Turkana
Authors: Lea Amanda J , Waigwa Charles , Muhoya Benjamin , Lotukoi Francis , Peng Julie , Henry Lucas P , Abhyankar Varada , Kamau Joseph , Martins Dino , Gurven Michael , Ayroles Julien F 
Published: November 2021

AbstractBackground and objectivesUnderstanding the social determinants of health is a major goal in evolutionary biology and human health research. Low socioeconomic status (often operationalized as absolute material wealth) is consistently associated with chronic stress, poor health and premature death in high-income countries. However, the degree to which wealth gradients in health are universal—or are instead made even steeper under contemporary, post-industrial conditions—remains poorly understood.MethodologyWe quantified absolute material wealth and several health outcomes among a population of traditional pastoralists, the Turkana of northwest Kenya, who are currently transitioning toward a more urban, market-integrated lifestyle. We assessed whether wealth associations with health differed in subsistence-level versus urban contexts. We also explored the causes and consequences of wealth-health associations by measuring serum cortisol, potential sociobehavioral mediators in early life and adulthood, and adult reproductive success (number of surviving offspring).ResultsHigher socioeconomic status and greater material wealth predicts better self-reported health and more offspring in traditional pastoralist Turkana, but worse cardiometabolic health and fewer offspring in urban Turkana. We do not find robust evidence for either direct biological mediators (cortisol) or indirect sociobehavioral mediators (e.g. adult diet or health behaviors, early life experiences) of wealth–health relationships in either context.Conclusions and implicationsWhile social gradients in health are well-established in humans and animals across a variety of socioecological contexts, we show that the relationship between wealth and health can vary within a single population. Our findings emphasize that changes in economic and societal circumstances may directly alter how, why and under what conditions socioeconomic status predicts health.Lay SummaryHigh socioeconomic status predicts better health and more offspring in traditional Turkana pastoralists, but worse health and fewer offspring in individuals of the same group living in urban areas. Together, our study shows that under different economic and societal circumstances, wealth effects on health may manifest in very different ways.
Comparative Investigation of the Stems, Leaves, Flowers, and Roots of Centipeda Minima Based on Fingerprinting–Multivariate Classification Techniques
Authors: Liu Meiqi , Zhao Xiaoran , Qiu Ziying , Sun Lili , Deng Yanru , Ren Xiaoliang , Mou Jiajia 
Published: November 2021

Abstract

Background
Centipeda minima (L.) A. Br. et Aschers, known as Ebushicao (EBSC) in Chinese, has long been used in traditional Chinese medicine for dispelling wind, clearing orifices, detoxification, and swelling. Although the traditional use of EBSC involves the whole plant, during harvesting and processing, separation of the stems, leaves, flowers, and roots often occurs. However, there are few studies on its medicinal parts.

Objective
A strategy combining high-performance liquid chromatography (HPLC) fingerprinting and multivariate classification techniques are here proposed for the comparison of roots, stems, leaves, and flowers of EBSC.

Method
The roots, stems, leaves, and flowers of EBSC samples were analyzed and compared based on HPLC fingerprints combined with chemometrics, including hierarchical cluster analysis (HCA), principal component analysis (PCA), partial least-squares discriminant analysis (PLS-DA), and back propagation artificial neural network (BP-ANN). Chemical markers were screened using PLS-DA, and the contents of representative ingredients were determined by an HPLC method.

Results
The HCA and PCA provided clear discrimination of roots, stems, leaves, and flowers. Moreover, the PLS-DA model and BP-ANN were established to verify the classification results and showed a greater ability to predict new samples. Four representative chemical markers were screened out, and the content of these markers in flowers and leaves was higher than that in stems and roots, and the difference was significant.

Conclusions
Combining HPLC fingerprinting and multicomponent chemical pattern recognition technology can be used to distinguish different parts of EBSC. The results indicated that brevilin A, quercetin, rutin, and chlorogenic acid, the important active components of EBSC, were mainly present in the leaves and flowers. This is of great significance for the differentiation and identification of the different medicinal parts of EBSC, as well as for the effectiveness of drug usage in clinical practice.

Highlights
HP LC was used to quickly obtain chemical for fingerprint analysis. HCA, P CA, P LS-DA were used to visualize the discrimination of roots, stems, leaves and flowers of EBSC. P LS-DA model was established to verify the classification results and obtained the chemical marker. BP-ANN model was used to further improve the discrimination accuracy.
The New Reform of the Penal Law of the Catholic Church: Resuscitating a Forgotten Pastoral Instrument?
Authors: Zambrana-Tévar Nicolás 
Published: November 2021

Abstract
The new reform of the penal law of the Catholic Church, amending Book VI of the Code of Canon Law of the Latin Church, as well as other recent canon law norms, aims at making sure that local bishops can punish more straightforwardly and with less discretion those conducts which are considered as most harmful for the church as a community. The drafters of this reform have made it clear that, in the past, many believed that penal laws should only exceptionally be applied. Now, however, this area of canon law should actually be considered one more instrument of pastoral governance. Although the Vatican has underlined that the new Book VI will be useful in the fight against the crime of sex abuse by clergy, this reform partly codifies norms and punitive mechanisms which had been progressively introduced and had already been in place, sometimes for decades.
Identification and expression assay of calcium-dependent protein kinase family genes in Hevea brasiliensis and determination of HbCDPK5 functions in disease resistance
Authors: Zhang Bei , Song Yufeng , Zhang Xiaodong , Wang Qiannan , Li Xiuqiong , He Chaozu , Luo Hongli 
Published: November 2021

Abstract
Calcium (Ca2+) signaling is one of the earliest factors to coordinate plant adaptive responses. As direct sensors and activators of Ca2+ signals, calcium-dependent protein kinases (CDPKs) were reported to be widely involved in regulating different biotic and abiotic stress stimuli. In this study, 32 Hevea brasiliensis CDPK (HbCDPK) genes were predicted and classified into four subgroups. Among them, the full-length coding sequences of 28 HbCDPK genes were confirmed by RT-PCR and verified by sequencing. Putative cis-elements assay in the promoters of HbCDPKs showed that most of the HbCDPK genes contained gibberellic acid-responsive element (GARE), abscisic acid-responsive element (ABRE), salicylic acid-responsive element (SARE), defense and stress responsive element (TC-rich repeats) and low-temperature response element (LTR), which could be activated by different biotic and abiotic stresses. Real-time PCR analysis indicated that 28 HbCDPK genes respond to infection of pathogenic fungi and a variety of phytohormones. Subcellular localization was observed with most HbCDPKs located in cell membrane, cytoplasm or organelles. Some HbCDPKs were confirmed to cause reactive oxygen species (ROS) production and accumulation in rubber tree mesophyll protoplast directly. HbCDPK5 was strongly induced by the inoculation with Colletotrichum gloeosporioides and was chosen for further analysis. HbCDPK5 localized to the cell membrane and cytoplasm, and obviously regulated the accumulation of ROS in rubber tree mesophyll protoplast. Overexpression of HbCDPK5 in Arabidopsis enhanced the resistance to Botrytis cinerea. These results indicate that rubber tree CDPK genes play important roles in plant disease resistance.
Race and Ethnicity and Cardiometabolic Risk Profile: Disparities Across Income and Health Insurance in a National Sample of US Adults
Authors: Javed Zulqarnain , Maqsood Muhammad Haisum , Amin Zahir , Nasir Khurram 
Published: November 2021

Context:
Income and health insurance are important social determinants of cardiovascular disease (CVD) and may explain much racial/ethnic variation in CVD burden. However, racial/ethnic disparities in cumulative cardiometabolic (CMB) risk profile by insurance type and income level have not been studied on a national scale.

Objectives:
To test the hypothesis that racial/ethnic minorities experience greater CMB burden at each income level and insurance type than non-Hispanic Whites (NHW).

Setting:
This study used nationally representative data from the National Health Interview Survey (NHIS).

Design:
Observational (cross-sectional).

Participants:
In total, 134661 (weighted N = 197780611) adults, 18 years or older, from the 2013-2017 NHIS.

Primary Outcome:
CMB risk profile.

Intervention/Analysis:
Age-adjusted prevalence of optimal, average, and poor CMB risk profile—defined respectively as self-report of 0, 1-2, and 3 or more risk factors of diabetes, hypertension, obesity, or hypercholesterolemia—was examined for NHW, non-Hispanic Blacks (NHB), and Hispanics. Multivariable ordinal logistic regression models were used to test the association between race and ethnicity and CMB profile overall and separately by household income level and insurance type.

Results:
Overall, 15% of NHB and 11% of Hispanics experienced poor CMB risk profile, compared with 9% for NHW. In fully adjusted models, NHB and Hispanics, respectively had nearly 25%-90% and 10%-30% increased odds of poor CMB profile across insurance types and 45%-60% and 15%-30% increased odds of poor CMB profile across income levels, relative to NHW. The observed disparities were widest for the Medicare group (NHB: OR = 1.90; Hispanics: OR = 1.31) and highest-income level (NHB: OR = 1.62).

Conclusions:
Racial/ethnic minorities experience poor CMB profile at each level of income and insurance. These findings point to the need for greater investigation of unmeasured determinants of minority cardiovascular (CV) health, including structural racism and implicit bias in CV care.
Community-Informed Mobile COVID-19 Testing Model to Addressing Health Inequities
Authors: Jiménez Jonathan , Parra Yury J. , Murphy Katherine , Chen Alexandra Nixxi , Cook Andrew , Watkins Jacob , Baker Melissa D. , Sung Semi , Kaur Guneet , Kress Marielle , Kurien Sarah Joseph , Keeley Chris , Long Theodore 
Published: November 2021

Context:
The New York City (NYC) Test & Trace Corps (Test & Trace), under New York City Health + Hospitals (NYC H+H), set out to provide universal access to COVID-19 testing. Test & Trace partnered with numerous organizations to direct mobile COVID-19 testing from concept through implementation to reduce COVID-19-related health inequities.

Program:
Test & Trace employs a community-informed mobile COVID-19 testing model to deliver testing to the hardest-hit, underserved communities. Community partners, uniquely knowledgeable of the residents they serve, are engaged as decision makers and operational partners in mobile COVID-19 testing delivery.

Implementation:
Through several mobile testing methods, community partners choose testing locations and tailor outreach to their community. Test & Trace assumes logistical responsibility for mobile testing but defers critical programmatic decisions and community engagement to partners. Integral to the success of this program is responsive, bidirectional communication.

Evaluation:
During the reporting period of December 1, 2020, to April 30, 2021, Test & Trace's community-informed mobile COVID-19 testing model provided testing to 150351 unique patients and processed 274083 tests in total. The available outcomes data and qualitative feedback provided by community partners illustrate that this intervention, combined with robust governmental investment, successfully ensured that NYC-identified, low-resource neighborhoods had greater access to COVID-19 testing.

Discussion:
Making community partners decision makers reduced inequities in access to testing for communities of color. In addition, the model has served as the framework for Test & Trace's community-informed mobile COVID-19 vaccination program, operated in concert with NYC's Vaccine Command Center, and is a foundation for addressing health inequities at scale, including during public health crises.
Using Public Deliberation to Set Priorities: The Case of COVID-19 Vaccine Access in New York City
Authors: Scherer Maya , Kamler Alexandra , Weiss Linda , Blacksher Erika , Jeavons Jessica , Gold Marthe R. 
Published: November 2021

Context:
The COVID-19 pandemic has resulted in a record number of deaths in the United States and tremendous economic and personal strain. During 2020, in anticipation of a vaccine to slow the spread of disease, local and state governments in the United States developed plans for vaccine prioritization, given a limited initial supply. Recognizing the challenges inherent in prioritization, the New York City (NYC) health department sought guidance from members of the public about the fairest approach to early-stage vaccine distribution.

Objective:
To solicit recommendations from NYC residents on priorities regarding vaccine access for essential worker occupations, considering risk factors and preferred approaches to fairness.

Implementation:
Five public deliberations were conducted with NYC residents (N = 91). Participants heard presentations on the COVID-19 vaccine, the local distribution of illness and death, and approaches to fairness in the context of deliberating on priorities for 6 essential worker occupations and 4 risk factors. Discussions were transcribed, and transcriptions were coded and analyzed using preidentified and emergent themes. Pre- and post-surveys, focused on factors relevant to prioritization, were administered during each public deliberation.

Results:
Recommendations for prioritization emphasized risk of severe morbidity and mortality, and work and neighborhood conditions with fewer protections (eg, in-person work, exposure to many people). Participants prioritized elementary schoolteachers, grocery store workers, and bus drivers, underlying health conditions, and neighborhood of residence. Participants focused on equity, recognizing that those at highest risk were largely low-income populations of color and individuals living in low-resourced neighborhoods.

Conclusions:
Participants' focus on equity, and acknowledgment of racial and ethnic disparities, revealed a nuanced understanding of the broader determinants of health. Recommendations reinforced the NYC health department's approach to vaccine distribution.

Public Health Implications:
Results from these public deliberations confirmed community support for approaches prioritizing health equity, recognizing both societal and personal factors affecting vulnerability to poor health.
ALM Fluid Therapy Shifts Sympathetic Hyperactivity to Parasympathetic Dominance in the Rat Model of Non-Compressible Hemorrhagic Shock
Authors: Letson Hayley L. , Biros Erik , Morris Jodie L. , Dobson Geoffrey P. 
Published: November 2021

ABSTRACT
Excessive sympathetic outflow following trauma can lead to cardiac dysfunction, inflammation, coagulopathy, and poor outcomes. We previously reported that buprenorphine analgesia decreased survival after hemorrhagic trauma. Our aim is to examine the underlying mechanisms of mortality in a non-compressible hemorrhage rat model resuscitated with saline or adenosine, lidocaine, magnesium (ALM). Anesthetized adult male Sprague-Dawley rats were randomly assigned to Saline control group or ALM therapy group (both n = 10). Hemorrhage was induced by 50% liver resection. After 15 min, 0.7 mL/kg 3% NaCl ± ALM intravenous bolus was administered, and after 60 min, 0.9% NaCl ± ALM was infused for 4 h (0.5 mL/kg/h) with 72 h monitoring. Animals received 6–12-hourly buprenorphine for analgesia. Hemodynamics, heart rate variability, echocardiography, and adiponectin were measured. Cardiac tissue was analyzed for adrenergic/cholinergic receptor expression, inflammation, and histopathology. Four ALM animals and one Saline control survived to 72 h. Mortality was associated with up to 97% decreases in adrenergic (β-1, α-1A) and cholinergic (M2) receptor expression, cardiac inflammation, myocyte Ca2+ loading, and histopathology, indicating heart ischemia/failure. ALM survivors had higher cardiac output and stroke volume, a 30-fold increase in parasympathetic/sympathetic receptor expression ratio, and higher circulating adiponectin compared to Saline controls. Paradoxically, Saline cardiac adiponectin hormone levels were higher than ALM, with no change in receptor expression, indicating intra-cardiac synthesis. Mortality appears to be a “systems failure” associated with CNS dysregulation of cardiac function. Survival involves an increased parasympathetic dominance to support cardiac pump function with reduced myocardial inflammation. Increased cardiac α-1A adrenergic receptor in ALM survivors may be significant, as this receptor is highly protective during heart dysfunction/failure.
Intravenous administration of mesenchymal stromal cells leads to a dose-dependent coagulopathy and is unable to attenuate acute traumatic coagulopathy in rats
Authors: Wu Xiaowu , Darlington Daniel N. , Christy Barbara A. , Liu Bin , Keesee Jeffrey D. , Salgado Christi L. , Bynum James A. , Cap Andrew P. 
Published: November 2021

BACKGROUND
Mesenchymal stromal cells (MSCs) express surface tissue factor (TF), which may affect hemostasis and detract from therapeutic outcomes of MSCs if administered intravenously. In this study, we determine a safe dose of MSCs for intravenous (IV) administration and further demonstrate the impact of IV-MSC on acute traumatic coagulopathy (ATC) in rats.

METHODS
Tissue factor expression of rat bone marrow–derived mesenchymal stromal cell (BMSC) or adipose-derived mesenchymal stromal cell (AMSC) was detected by immunohistochemistry and enzyme-linked immunosorbent assay. The coagulation properties were measured in MSC-treated rat whole blood, and blood samples were collected from rats after IV administration of MSCs. Acute traumatic coagulopathy rats underwent polytrauma and 40% hemorrhage, followed by IV administration of 5 or 10 million/kg BMSCs (BMSC-5, BMSC-10), or vehicle at 1 hour after trauma.

RESULTS
Rat MSCs expressed TF, and incubation of rat BMSCs or AMSCs with whole blood in vitro led to a significantly shortened clotting time. However, a dose-dependent prolongation of prothrombin time with reduction in platelet counts and fibrinogen was found in healthy rat treated with IV-MSCs. Bone marrow–derived mesenchymal stromal cells at 5 million/kg or less led to minimal effect on hemostasis. Mesenchymal stromal cells were not found in circulation but in the lungs after IV administration regardless of the dosage. Acute traumatic coagulopathy with prolonged prothrombin time was not significantly affected by 5 or 10 million/kg BMSCs. Intravenous administration of 10 million/kg BMSCs led to significantly lower fibrinogen and platelet counts, while significantly higher levels of lactate, wet/dry weight ratio, and leukocyte infiltration in the lung were present compared with BMSC-5 or vehicle. No differences were seen in immune or inflammatory profiles with BMSC treatment in ATC rats, at least in the acute timeframe.

CONCLUSION
Intravenous administration of MSCs leads to a risk of coagulopathy associated with a dose-dependent reduction in platelet counts and fibrinogen and is incapable of restoring hemostasis of rats with ATC after polytrauma and hemorrhagic shock.