bluuebunny/crossref_metadata_2025_split huggingface dataset:
CSVS, a crowdsourcing database of the Spanish population genetic variability
Authors: Peña-Chilet María , Roldán Gema , Perez-Florido Javier , Ortuño Francisco M , Carmona Rosario , Aquino Virginia , Lopez-Lopez Daniel , Loucera Carlos , Fernandez-Rueda Jose L , Gallego Asunción , García-Garcia Francisco , González-Neira Anna , Pita Guillermo , Núñez-Torres Rocío , Santoyo-López Javier , Ayuso Carmen , Minguez Pablo , Avila-Fernandez Almudena , Corton Marta , Moreno-Pelayo Miguel Ángel , Morin Matías , Gallego-Martinez Alvaro , Lopez-Escamez Jose A , Borrego Salud , Antiñolo Guillermo , Amigo Jorge , Salgado-Garrido Josefa , Pasalodos-Sanchez Sara , Morte Beatriz ,   The Spanish Exome Crowdsourcing Consortium, Al-Shahrour Fátima , Artuch Rafael , Benitez Javier , Castaño Luis Antonio , Castillo Ignacio del , Delmiro Aitor , Espinos Carmina , González Roser , Grinberg Daniel , Guillén Encarnación , Lapunzina Pablo , Lopez Esther , Martí Ramón , Milá Montserrat , Millán José Mª , Nunes Virginia , Palau Francesc , Perez Belen , Jurado Luis Pérez , Perona Rosario , Pujol Aurora , Ramos Feliciano , Ribes Antonia , Rosell Jordi , Rovira Eulalia , Surrallés Jordi , Tejada Isabel , Ugarte Magdalena , Carracedo Ángel , Alonso Ángel , Dopazo Joaquín 
Published: September 2020

AbstractThe knowledge of the genetic variability of the local population is of utmost importance in personalized medicine and has been revealed as a critical factor for the discovery of new disease variants. Here, we present the Collaborative Spanish Variability Server (CSVS), which currently contains more than 2000 genomes and exomes of unrelated Spanish individuals. This database has been generated in a collaborative crowdsourcing effort collecting sequencing data produced by local genomic projects and for other purposes. Sequences have been grouped by ICD10 upper categories. A web interface allows querying the database removing one or more ICD10 categories. In this way, aggregated counts of allele frequencies of the pseudo-control Spanish population can be obtained for diseases belonging to the category removed. Interestingly, in addition to pseudo-control studies, some population studies can be made, as, for example, prevalence of pharmacogenomic variants, etc. In addition, this genomic data has been used to define the first Spanish Genome Reference Panel (SGRP1.0) for imputation. This is the first local repository of variability entirely produced by a crowdsourcing effort and constitutes an example for future initiatives to characterize local variability worldwide. CSVS is also part of the GA4GH Beacon network.CSVS can be accessed at: http://csvs.babelomics.org/.
Current situation and perspectives of ready-to-eat food/meal suppliers
Authors: Sakata Takashi ,   for Working Group 2 of the Healthy Diet Research Committee of International Life Sciences Institute, Japan
Published: September 2020

Abstract
Working Group 2 of the Healthy Diet Research Committee of International Life Sciences Institute Japan (WG2) assessed the concept and practice of healthy eating in the ready-to-eat food/meal industry in Japan. WG2 interviewed 14 arbitrarily selected member companies that included “health” or “nutrition” in their management policy, and sent a questionnaire to 338 member companies of the Japan Ready-Made Meal Association. Ready-to-eat food/meal suppliers mainly referred to Dietary Reference Intakes for Japanese, the Japanese Food Guide, and/or Healthy Japan 21 for their menu construction. They increased dietary fiber, variety, vegetables, whole-grain cereals, millet rice, and soy bean products; and reduced energy, carbohydrates, and salt in “healthy” food. They tended to avoid making direct appeals to health. Many companies reduced the salt content without drawing attention to the practice. They continually strive to improve flavor as the single most important factor for selling healthy food. The cycling of menus is used to increase diversity in food consumption. These industries require both academia and the government to define priorities for increasing and decreasing particular nutrients as the main targets and to establish the maximum time for balancing each nutrient.
What is the scientific definition of the Japanese diet from the viewpoint of nutrition and health?
Authors: Sasaki Satoshi ,   for Working Group 1 of the Healthy Diet Research Committee of International Life Sciences Institute, Japan
Published: September 2020

Abstract
The Japanese people have enjoyed longevity for several decades, and Japanese dietary habits are considered to contribute to this longevity. The scientific definition of the Japanese diet, however, is not yet fully established. The Working Group 1 of the Healthy Diet Research Committee of the International Life Sciences Institute Japan reviewed the literature to collect definitions of the Japanese diet appearing in articles in the fields of diet, nutrition, foods, and human health. This report addresses the definitions and the questions raised by these definitions. Among 283 relevant articles identified, 116 were carefully screened and included in the analysis. In most of the articles, the authors self-defined the Japanese diet; some studies used a government-proposed definition. This review revealed no systematic approach to define the Japanese diet from the viewpoints of nutrition and health. Before conducting studies to determine whether the Japanese diet is healthy, it is important to address the question of what the Japanese diet is from the viewpoint of human nutrition rather than culinary culture.
Personalized nutrition and healthy aging
Authors: Ordovas Jose M , Berciano Silvia 
Published: September 2020

AbstractThe human lifespan and quality of life depend on complex interactions among genetic, environmental, and lifestyle factors. Aging research has been remarkably advanced by the development of high-throughput “omics” technologies. Differences between chronological and biological ages, and identification of factors (eg, nutrition) that modulate the rate of aging can now be assessed at the individual level on the basis of telomere length, the epigenome, and the metabolome. Nevertheless, the understanding of the different responses of people to dietary factors, which is the focus of precision nutrition research, remains incomplete. The lack of reliable dietary assessment methods constitutes a significant challenge in nutrition research, especially in elderly populations. For practical and successful personalized diet advice, big data techniques are needed to analyze and integrate the relevant omics (ie, genomic, epigenomic, metabolomics) with an objective and longitudinal capture of individual nutritional and environmental information. Application of such techniques will provide the scientific evidence and knowledge needed to offer actionable, personalized health recommendations to transform the promise of personalized nutrition into reality.
Grapevine U-Box E3 Ubiquitin Ligase VlPUB38 Negatively Regulates Fruit Ripening by Facilitating Abscisic-Aldehyde Oxidase Degradation
Authors: Yu Yihe , Meng Xiangxuan , Guo Dalong , Yang Shengdi , Zhang Guohai , Liang Zhenchang 
Published: September 2020

AbstractThe plant U-box E3 ubiquitin ligase-mediated ubiquitin/26S proteasome degradation system plays a key role in plant growth and development. Previously identified as a member of the grape PUB gene family, PUB38 was shown to participate in the berry-ripening progress. Here, we demonstrate that the E3 ligase VlPUB38 mediates abscisic acid (ABA) synthesis via 26S proteasome degradation and its involvement in regulating fruit-ripening processes. Strawberry-overexpressing VlPUB38 lines displayed obvious inhibition of mature phenotype, and this was rescued by exogenous ABA treatment and MG132. Post-ABA treatment, expression levels of ABA response-related genes in VlPUB38-overexpressed Arabidopsis significantly exceeded controls. Strawberry and Arabidopsis ectopic expression assays suggest that VlPUB38 negatively regulates fruit ripening in an ABA-dependent manner. Moreover, VlPUB38 has ubiquitin ligase activity, which depends on the U-box-conserved domain. VlPUB38 interacts with abscisic-aldehyde oxidase (VlAAO), targeting VlAAO proteolysis via the 26S proteasome system. These results indicate that VlPUB38 negatively regulates grape fruit ripening by mediating the degradation of key factor VlAAO in the ABA synthesis pathway.
The Role of Identity Prioritization
Authors: Hickel Flavio R , Alamillo Rudy , Oskooii Kassra A R , Collingwood Loren 
Published: September 2020

Abstract
Social Identity Theory suggests that individuals are motivated to support/oppose policies and politicians that benefit/harm members of their ingroup as a means of protecting their social status. Since the Republican Party’s rhetoric against immigrants in recent decades has often been viewed as an assault upon those of Latinx descent, it is not surprising that strong majorities oppose restrictionist immigration policies and support the Democratic Party. However, the existing literature has overlooked why a sizeable minority of Latinx voters express support for restrictionist immigration policies and the politicians who espouse them. Our analysis of Latinx voters with the 2012 and 2016 American National Election Studies (ANES) demonstrates that the degree to which individuals prioritize their US American identity over their Latinx identity has a significant influence over support for conservative immigration policies and GOP candidates. This relationship emerges above and beyond partisanship, ideology, and other key explanatory factors. Such attitudes likely represent an individual social mobility strategy in which members of a social group attempt to “pass” as a member of a higher-status group. Prioritizing a US American identity, supporting the Republican Party, and expressing hostility toward the interests of undocumented immigrants are a means of distinguishing themselves from a social group that has become increasingly associated with negative stereotypes. In contrast, those who are unwilling or unable to make this transition are likely pursuing a collective social mobility strategy (e.g., linked fate) whereby they attempt to enhance their individual status by elevating that of the entire social group.
Exposure totert-Butylphenyl Diphenyl Phosphate, an Organophosphate Ester Flame Retardant and Plasticizer, Alters Hedgehog Signaling in Murine Limb Bud Cultures
Authors: Yan Han , Hales Barbara F 
Published: September 2020

AbstractOrganophosphate esters have become widely used as flame retardants since the phase out of polybrominated diphenyl ethers. Previously, we demonstrated that some organophosphate esters, such as tert-butylphenyl diphenyl phosphate (BPDP), were more detrimental to endochondral ossification in murine limb bud cultures than one of the major polybrominated diphenyl ethers that they replaced, 2,2′,4,4′-tetrabromodiphenyl ether. Here, we used a transcriptomic approach to elucidate the mechanism of action of BPDP in the developing limb. Limb buds collected from gestation day 13 CD1 mouse embryos were cultured for 3 or 24 h in the presence of vehicle, 1 μM, or 10 μM BPDP. RNA sequencing analyses revealed that exposure to 1 µM BPDP for 24 h increased the expression of 5 transcripts, including Ihh, and decreased 14 others, including Gli1, Ptch1, Ptch2, and other targets of Hedgehog (Hh) signaling. Pathway analysis predicted the inhibition of Hh signaling. Attenuation of Hh signaling activity began earlier and reached a greater magnitude after exposure to 10 µM BPDP. Because this pathway is part of the regulatory network governing endochondral ossification, we used a known Hh agonist, purmorphamine, to determine the contribution of Hh signaling inhibition to the negative impact of BPDP on endochondral ossification. Cotreatment of limbs with purmorphamine rescued the detrimental morphological changes in the cartilage template induced by BPDP exposure though it did not restore the expression of key transcription factors, Runx2 and Sp7, to control levels. These data highlight Hh signaling as a developmentally important pathway vulnerable to environmental chemical exposures.
Discrete-Event Simulation Modeling of Critical Care Flow: New Hospital, Old Challenges
Authors: Williams Elizabeth , Szakmany Tamas , Spernaes Izabela , Muthuswamy Babu , Holborn Penny 
Published: September 2020

Objectives:
As the demand for critical care beds rises each year, hospitals must be able to adapt. Delayed transfer of care reduces available critical care capacity and increases occupancy. The use of mathematic modeling within healthcare systems has the ability to aid planning of resources. Discrete-event simulation models can determine the optimal number of critical care beds required and simulate different what-if scenarios.

Design:
Complex discrete-event simulation model was developed using a warm-up period of 30 days and ran for 30 trials against a 2-year period with the mean calculated for the runs. A variety of different scenarios were investigated to determine the effects of increasing capacity, increasing demand, and reduction of proportion and length of delayed transfer of care out of the ICU.

Setting:
Combined data from two ICUs in United Kingdom.

Patients:
The model was developed using 1,728 patient records and was validated against an independent dataset of 2,650 patients.

Interventions:
None.

Measurements and Main Results:
During model validation, the average bed utilization and admittance rate were equal to the real-world data. In the what-if scenarios, we found that increasing bed numbers from 23 to 28 keeping the arrival rate stable reduces the average occupancy rate to 70%. We found that the projected 4% yearly increase in admissions could overwhelm even the 28-bedded unit, without change in the delayed transfer of care episodes. Reduction in the proportion of patients experiencing delayed transfer of care had the biggest effect on occupancy rates, time spent at full capacity, and average bed utilization.

Conclusions:
Using discrete-event simulation of commonly available baseline patient flow and patient care data produces reproducible models. Reducing the proportion of patients with delayed transfer of care had a greater effect in reducing occupancy levels than simply increasing bed numbers even when demand is increased.
Nurse-driven Clinical Pathway Based on an Innovative Asthma Score Reduces Admission Time for Children
Authors: Sjoerdsma Machtelt H. , Bongaerts Thom H.G. , van Lente Lidy , Kamps Arvid W.A. 
Published: September 2020

Objective:
We recently demonstrated that an innovative asthma score independent of auscultation could accurately predict the requirement for bronchodilator nebulization compared to the physician’s routine clinical judgment to administer bronchodilators. We aimed to standardize inpatient care for children with acute asthma by implementing a clinical pathway based on this innovative asthma score.

Methods:
We designed a nurse-driven clinical pathway. This pathway included standardized respiratory assessments and a protocol for the nursing staff to administer bronchodilators without a specific order from the physician. We compared the length of stay and the number of readmissions to a historical cohort.

Results:
Seventy-nine patients with moderate acute asthma completed the pathway. We obtained a total of 858 Childhood asthma scores in these patients, with a median of 11 scores per patient (interquartile range 8–17). Patients treated according to the nurse-driven protocol were 3.3 times more likely to be discharged earlier (hazard ratio, 3.29; 95% confidence interval, 2.33–4.66; P < 0.05), and length of stay was significantly reduced (median 28 versus 53 h) compared to the historical standard practice. On request, the attending physician assessed the patient’s respiratory status 42 times (4.9% of all childhood asthma score assessments). Patient safety was not compromised, and none of the patients were removed from the pathway. In each group, we readmitted two (2.5%) patients within 1 week after discharge.

Conclusion:
This nurse-driven clinical pathway for children with acute asthma based on an asthma score independent of auscultation findings significantly decreased length of stay without compromising patient safety.
Iterative Ring Artifact Removal Method for Helical Computed Tomography Scans
Authors: Balogh Zsolt Adam , Huszar Tamas , Kis Benedek Janos 
Published: September 2020

Objective
In this article, a statistical-based iterative ring removal (IRR) algorithm that effectively removes ring artifacts generated by defective detector cells is proposed.

Methods
The physical state of computed tomography (CT) detector elements can change dynamically owing to their temperature dependence and the varying irradiation caused by focal spot movements. This variation in the properties of cells may cause false pixel values in sinograms, resulting in rings or segments of rings in reconstructed images. In this article, the proposed algorithm is studied on clinical CT. Two patients were scanned using a clinical CT scanner (AnyScan SPECT/CT, Mediso). Artificial rings and band rings were generated on the real sinogram data to examine the algorithm in different cases. The method was performed also on real ring artifacts.

Results
The IRR can correct both single and band-like ring artifacts with one or more defective pixels. The proposed algorithm can detect the period when pixels contain false signals and only those periods are corrected. The IRR reduces ring artifacts, even in cases where low-contrast rings occur in the reconstructed image.

Conclusions
This statistical correction method efficiently detects and corrects false pixel values in the projection data without causing new artifacts in the reconstructed image. The algorithm is less sensitive to its parameters.
Timing of invasive mechanic ventilation in critically ill patients with coronavirus disease 2019
Authors: Zhang Qian , Shen Jun , Chen Liangkai , Li Sumeng , Zhang Wenkai , Jiang Cheng , Ma Haoli , Lin Lian , Zheng Xin , Zhao Yan 
Published: September 2020

Background
Invasive mechanical ventilation (IMV) is a lifesaving strategy for critically ill patients with coronavirus disease 2019 (COVID-19). We aim to report the case series of critical patients receiving IMV in Wuhan and to discuss the timing of IMV in these patients.

Methods
Data of 657 patients admitted to emergency intensive care unit of Zhongnan Hospital and isolated isolation wards of Wuhan Union Hospital from January 1 to March 10, 2020, were retrospectively reviewed. All medical records of 40 COVID-19 patients who required IMV were collected at different time points, including baseline (at admission), before receiving IMV, and before death or hospital discharge.

Results
Among 40 COVID-19 patients with IMV, 31 died, and 9 survived and was discharged. The median age was 70 years (interquartile range [IQR], 62–76 years), and nonsurvivors were older than survivors. The median period from the noninvasive mechanic ventilation (NIV) or high-flow nasal cannula oxygen therapy (HFNC) to intubation was 7 hours (IQR, 2–42 hours) in IMV survivors and 54 hours (IQR, 28–143 hours) in IMV nonsurvivors. We observed that, when the time interval from NIV/HFNC to intubation was less than 50 hours (about 2 calendar days), together with Acute Physiology and Chronic Health Evaluation II (APACHE II) score of less than 10 or pneumonia severity index (PSI) score of less than 100, mortality can be reduced to 60% or less. Prolonged interval from NIV/HFNC to intubation and high levels of APACHE II and PSI before intubation were associated with higher mortality in critically ill patients. Multiple organ damage was common among these nonsurvivors in the course of treatment.

Conclusion
Early initial intubation after NIV/HFNC might have a beneficial effect in reducing mortality for critically ill patients meeting IMV indication. Considering APACHE II and PSI scores might help physicians in decision making about timing of intubation for curbing subsequent mortality.

Level of evidence
Therapeutic, level V.
Distinct genetic bases for plant root responses to lipo-chitooligosaccharide signal molecules from distinct microbial origins
Authors: Bonhomme Maxime , Bensmihen Sandra , André Olivier , Amblard Emilie , Garcia Magali , Maillet Fabienne , Puech-Pagès Virginie , Gough Clare , Fort Sébastien , Cottaz Sylvain , Bécard Guillaume , Jacquet Christophe 
Published: September 2020

SummaryLipo-chitooligosaccharides (LCOs) were originally found as symbiotic signals called Nod Factors (Nod-LCOs) controlling nodulation of legumes by rhizobia. More recently LCOs were also found in symbiotic fungi and, more surprisingly, very widely in the kingdom fungi including in saprophytic and pathogenic fungi. The LCO-V(C18:1, Fuc/MeFuc), hereafter called Fung-LCOs, are the LCO structures most commonly found in fungi. This raises the question of how legume plants, such asMedicago truncatula, can perceive and discriminate between Nod-LCOs and these Fung-LCOs.To address this question, we performed a Genome Wide Association Study on 173 natural accessions ofMedicago truncatula, using a root branching phenotype and a newly developed local score approach.Both Nod- and Fung-LCOs stimulated root branching in most accessions but there was very little correlation in the ability to respond to these types of LCO molecules. Moreover, heritability of root response was higher for Nod-LCOs than for Fung-LCOs. We identified 123 loci for Nod-LCO and 71 for Fung-LCO responses, but only one was common.This suggests that Nod- and Fung-LCOs both control root branching but use different molecular mechanisms. The tighter genetic constraint of the root response to Fung-LCOs possibly reflects the ancestral origin of the biological activity of these molecules.