bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative analysis of basic helix–loop–helix gene family among Brassica oleracea, Brassica rapa, and Brassica napus
Authors: Miao Liming , Gao Yingying , Zhao Kun , Kong Lijun , Yu Shubo , Li Rongrong , Liu Kaiwen , Yu Xiaolin 
Published: September 2019

Abstract
Background: The basic helix–loop–helix (bHLH) transcription factors exist widely in eukaryotes and play important roles in development and stress response regulation in plants. The bHLH gene family has been identified in many species, except for Brassica oleracea and Brassica napus thus far. This study aims to identify the bHLH family members in B. oleracea, Brassica rapa, and B. napus and elucidate the expression, duplication, phylogeny and evolution characters of these genes.
Result: A total of 268 bHLH genes in B. oleracea, 440 genes in B. napus, and 251 genes in B. rapa, including 21 new bHLH members, have been identified. Subsequently, the analysis of the phylogenetic tree, conserved motifs and gene structures showed that the members in the same subfamily were highly conserved. Most Ka/Ks values of the homologous gene were <1, which indicated that the homologous genes suffered from strong purifying selection for retention. The Ks values of the three Brassica crops were concentrated in the range of 0.3–0.5. Hence, the divergence time of the bHLH gene family between Brassica crops and Arabidopsis thaliana is approximately 10–18 MYA. The retention rates of BrabHLH and BolbHLH genes were 51.6% and 55.1%, respectively. A total of 182 genes were lost in B. napus after tetraploid. GO annotations of BolbHLH genes showed that most genes focused on DNA-binding transcription factor, DNA-binding, and protein dimerization activities. The temporal and spatial expression patterns of 50 BolbHLH genes were diverse, some of which showing high expression in the reproduction tissue, while some had high expression in the root. The comparison of expression patterns between B. rapa and B. napus showed that they had similar expression patterns in the root and contrasting patterns in the stems, leaves, and reproduction tissues. However, the expression patterns of B. oleracea and B. napus were different.
Conclusion: This study is the first to report about the gene family analysis of the bHLH gene in B. oleracea and B. napus. Our results not only offer useful information on the functional analysis of the bHLH gene but also provide new insights into the evolution of Brassica spp.
Evaluating the impact of the weather conditions on the influenza propagation
Authors: Singh David E. , Marinescu Maria-cristina , Carretero Jesus , Delgado-Sanz Concepcion , Gomez-Barroso Diana , Larrauri Amparo 
Published: September 2019

Abstract
Background: Predicting the details of how an epidemic evolves is highly valuable as health institutions need to better plan towards limiting the infection propagation effects and optimizing their prediction and response capabilities. Simulation is a cost- and time-effective way of predicting the evolution of the infection as the joint influence of many different factors: interaction patterns, personal characteristics, travel patterns, meteorological conditions, previous vaccination, etc. The work presented in this paper extends EpiGraph, our influenza epidemic simulator, by introducing a meteorological model as a modular component that interacts with the rest of EpiGraph's modules to refine our previous simulation results. Our goal is to estimate the effects of changes in temperature and relative humidity on the patterns of epidemic influenza based on data provided by the Spanish Influenza Sentinel Surveillance System (SISSS) and the Spanish Meteorological Agency (AEMET).

Methods: Our meteorological model is based on the regression model developed by Barreca and Shimshack, and it is tuned with influenza surveillance data obtained from SISSS. After pre-processing this data to clean it and reconstruct missing samples, we obtain new values for the reproduction number of each urban region in Spain, every 10 minutes during 2011. We simulate the propagation of the influenza by setting the date of the epidemic onset and the initial influenza-illness rates for each urban region.

Results: We show that the simulation results have the same propagation shape as the weekly influenza rates as recorded by SISSS. We perform experiments for a realistic scenario based on actual meteorological data from 2010-2011, and for synthetic values assumed under simplified predicted climate change conditions. Results show that a diminishing relative humidity of 10\% produces an increment of about 1.6\% in the final infection rate. The effect of temperature changes on the infection spread is also noticeable, with a decrease of 1.1\% per extra degree.

Conclusions: Using a tool like ours could help predict the shape of developing epidemics and its peaks, and would permit to quickly run scenarios to determine the evolution of the epidemic under different conditions. We make EpiGraph source code and epidemic data publicly available.
Chronic Hypersensitivity Pneumonitis In The Southeastern United States: An Assessment Of How Clinicians Reached The Diagnosis
Authors: Gu Jessie , Tsai Chen-Liang , Wysham Nicholas , Huang Yuh-Chin Tony 
Published: September 2019

Abstract
Background: Chronic hypersensitivity pneumonitis (cHP) is a disease caused by exposure to inhaled environmental antigens. Diagnosis of cHP is influenced by the awareness of the disease prevalence, which varies significantly in different regions, and how clinicians utilize relevant clinical information. We conducted a retrospective study to evaluate how clinicians in the Southeast United States, where the climate is humid favoring mold growth, diagnosed cHP using items identified in the international modified Delphi survey of experts, i.e., environmental exposure, CT imaging and lung pathology,
Methods: We searched Duke University Medical Center database for patients over the age of 18 with a diagnosis of cHP (ICD-9 code: 495) between Jan. 1, 2008 to Dec. 31, 2013 using a query tool, Duke Enterprise Data Unified Content Explorer (DEDUCE).
Results: Five hundred patients were identified and 261 patients had cHP confirmed in clinic notes by a pulmonologist or an allergist. About half of the patients lived in the Research Triangle area where our medical center is located, giving an estimated prevalence rate of 6.5 per 100,000 persons. An exposure source was mentioned in 69.3% of the patient. The most common exposure sources were environmental molds (43.1%) and birds (26.0%). We used Venn diagram to evaluate how the patients met the three most common cHP diagnostic criteria: evidence of environmental exposures (history or precipitin) (E), chest CT imaging (C) and pathology from lung biopsies (P). Eighteen patients (6.9%) met none of three criteria. Of the remaining 243 patients, 135 patients (55.6%) had one (E 35.0%, C 3.3%, P 17.3%), 81 patients (33.3%) had two (E+C 12.3%, E+P 17.3%, C+P 4.9%), and 27 patients (11.1%) had all three criteria (E+C+P). Overall, 50.6% of patients had pathology from lung biopsy compared to 31.6% with CT scan.
Conclusions: Environmental mold was the most common exposure for cHP in the Southeast United States. Lung pathology was available in more than half of cHP cases in our tertiary care center, perhaps reflecting the complexity of referrals. Differences in exposure sources and referral patterns should be considered in devising future diagnostic pathways or guidelines for cHP.
Protocol of 4-plex N,N-Dimethyl Leucine Isobaric Labeling Based Proteome Quantitation by LC-MS/MS
Authors: Cui Yusi , Yu Qing , Li Lingjun 
Published: September 2019

Abstract
Isobaric labeling is one of the wide-spread high throughput proteome quantification strategies, where enzymatically digested protein extracts from different experimental groups are labeled with chemical tags and yield identical mass shift for individual peptides in MS precursor scan, whereas quantitation can be achieved by comparing reporter ion ratios upon fragmentation in tandem MS scan. In addition to commercial tags such as TMT and iTRAQ, we developed 4-plex and 12-plex N,N-dimethyl leucine (DiLeu) tags as cost-effective alternatives with comparable performance 1,2. DiLeu labeling methods allow multiplexing of samples and enable comparative analysis of acetyl-CoA flux regulated proteomes from different mouse models in the same LC-MS runs, providing statistically reliable data that avoids run-to-run variations. This protocol describes steps including 40 hrs of sample preparation of lysis, tryptic digestion, tag labeling, SCX purification and high pH fractionation, as well as details about LC-MS/MS analysis and data processing. The protocol can be applied to other proteome quantitation systems.
Construction of a novel quinoxaline as a new class of Nrf2 activator
Authors: Kandasamy Murugesh , Mak Kit-Kay , Devadoss Thangaraj , Thanikachalam Punniyakoti Veeraveedu , Sakirolla Raghavendra , Choudhury Hira , Pichika Malllikarjuna Rao 
Published: September 2019

Abstract
The transcription factor Nuclear factor erythroid-2-related factor 2 (NRF2) and its principal repressive regulator, the E3 ligase adaptor Kelch-like ECH-associated protein 1 (KEAP1), are critical in the regulation of inflammation, as well as maintenance of homeostasis. Thus, NRF2 activation provides cytoprotection against numerous inflammatory disorders. N-nicotinoylquinoxaline-2-carbohdyrazide (NQC) was designed by combining the important pharmacophoric features of bioactive compounds reported in the literature. NQC was synthesised and characterised using spectroscopic techniques. The compound was tested for its anti-inflammatory effect using LPSEc induced inflammation in mouse macrophages (RAW 264.7 cells). The effect of NQC on inflammatory cytokines was measured using ELISA. The Nrf2 activity of the compound NQC was determined using ‘Keap1:Nrf2 Inhibitor Screening Assay Kit’. To obtain the insights on NQC’s activity on Nrf2, molecular docking studies were performed using Schrodinger suite. The metabolic stability of NQC was determined using mouse, rat and human microsomes. NQC was found to be non-toxic until the dose of 50 µM on RAW 264.7 cells. The NQC showed potent anti-inflammatory effect in an in vitro model of Lipopolysaccharide (LPS) stimulated murine macrophages (RAW 264.7 cells) with an IC50 value 26.13 ± 1.17 µM. The NQC dose-dependently down regulated the pro-inflammatory cytokines (Interleukin (IL)-1β, IL-6 and tumor necrosis factor (TNF)-α) and inflammatory mediator, prostaglandin E2 (PGE2) with IC50 values 13.27 ± 2.37, 10.13 ± 0.58, 14.41 ± 1.83 and 15.23 ± 0.91 µM respectively. Molecular docking studies confirmed the favourable binding of NQC at Kelch domain of Keap-1. It disrupts the Nrf2 interaction with kelch domain of keap 1 and its IC50 value was 4.21 ± 0.89 µM. The metabolic stability studies of NQC in human, rat and mouse liver microsomes revealed that it is quite stable with half-life values; 59.78 ± 6.73, 52.93 ± 7.81, 28.43 ± 8.13 minutes; microsomal intrinsic clearance values; 22.1 ± 4.31, 26.0 ± 5.17 and 47.13 ± 6.34 µL/min/mg protein; respectively. So, rat has comparable metabolic profile with human, thus, rat could be used for predicting the pharmacokinetics and metabolism of NQC in human. NQC is a new class of NRF2 activator with potent in vitro anti-inflammatory activity and good metabolic stability.
Assessment of Drug Related Problems among Type 2 Diabetic Patients on Follow up at Hiwot Fana Specialized University Hospital, Harar, Eastern Ethiopia
Authors: Abdulmalik Haymen , Tadiwos Yohannes , Legesse Nanati 
Published: September 2019

Abstract
Objectives: To assess drug related problem among patients with type 2 diabetes at Hiwot Fana Specialized University HospitalResults: In this study, a total of 148 patient medication records were included. More than half, 83(57.4%) were males and the rest 65(42.6%) were females. The mean age of the study participant’s was 51.26 ± 7.08. Around one third (74.3%) of the participants had urban residency. A total of 127 drug related problems were identified, of which dosage too low was the most common type of DRP encountered, 47(37%), followed by unnecessary drug therapy, 25(19.7%) and ineffective drug therapy, 25(19.7%). 95(64.2%) of the patients had at least one drug related problem. Among patients with DRP, more than half of them, 59 (62.1%) had a single DRP. Out of the total participants, 85(57.4%) of them were taking one anti-diabetic medication and 63(42.6%) of them dual anti-diabetic medications. Only half of the patients have attained the desired FBG level. There was no patient who had experienced more than two types of drug related problems at a time. Less than 10% of patients were taking five or more drugs at a time. Key Words: Diabetes mellitus, Drug therapy problem, Hiwot fana specialized university hospital.
Associations of mental disorders and neurotropic parasitic diseases: a meta-analysis in developing and emerging countries.
Authors: Daré Labanté Outcha , Bruand Pierre-Emile , Gérard Daniel , Marin Benoît , Lameyre Valérie , Boumédiène Farid , Preux Pierre-Marie 
Published: September 2019

Abstract
Background Although they are declining worldwide, neurotropic parasitic diseases are still common in developing and emerging countries. The aim of this study was to estimate the pooled prevalence and pooled association measures of comorbidities between mental disorders (anxiety, depression, bipolar disorder, and schizophrenia) and neurotropic parasitic diseases (malaria, cysticercosis, toxoplasmosis, human African trypanosomiasis, Chagas disease, and human toxocariasis) in developing and emerging countries.Methods As the first meta-analysis on this topic, this study was performed in accordance with PRISMA guidelines. The protocol was registered in PROSPERO (N°CRD42017056521). The Medline, Embase, Lilacs, and Institute of Epidemiology and Tropical Neurology databases were used to search for articles without any restriction in language or date. We evaluated the quality of studies independently by two investigators using the Downs and Black assessment grid and pooled estimates using the random-effects method from CMA (Comprehensive Meta Analysis) Version 3.0.Results In total, 18 studies studies published between 1997 and 2016 met our inclusion criteria. We found that the prevalence of anxiety and depression in people suffering from Chagas disease and/or neurocysticercosis was 44.9% (95% CI, 34.4 – 55.9). In 16 pooled studies that included 1,782 people with mental disorders and 1,776 controls, mental disorders (schizophrenia and/or bipolar disorders) were associated with increased risk of toxoplasmosis and/or toxocariasis (odds ratio = 2.3; 95% CI, 1.7 – 3.2). Finally, schizophrenia was associated with an increased risk of the onset of toxocariasis and/or toxoplasmosis (odds ratio = 2.4 / 95% CI, 1.7 – 3.4).Conclusion Our pooled estimates show that the association between neurotropic parasitic diseases among people with related mental disorders, and mental disorders among people with neurotropic parasitic diseases are relatively high in developing and emerging countries even though most studies have been found in Asia. This meta-analysis could prove useful to researchers who want to further explore and understand the associations between mental disorders and neurotropic patristic diseases in developing and emerging countries.
Pregnancy outcomes of dichorionic triamniotic triplet pregnancies after in vitro fertilization-embryo transfer: multifoetal pregnancy reduction versus expectant management
Authors: Cai Pei , Ouyang Yan , Gong Fei , Li Xihong 
Published: September 2019

Abstract
Background: Trichorionic triplet pregnancy reduction to twin pregnancy is associated with a lower risk of preterm delivery but not of miscarriage. However, reports on dichorionic triamniotic (DCTA) triplet pregnancy outcomes are few. This study aimed to compare the pregnancy outcomes of reducing DCTA triplets achieved via in vitro fertilization-embryo transfer (IVF-ET) to monochorionic (MC) singleton or monochorionic diamniotic (MCDA) twin pregnancies at 11-13+6 gestational weeks to the pregnancy outcomes of expectant management.
Method: Two hundred and ninety-eight patients with DCTA triplets via IVF-ET from January 2012 to December 2016 were retrospectively analysed. All foetuses were alive until 11-13+6 gestational weeks. Eighty-four DCTA triplet pregnancies were reduced to MC singleton pregnancies (group A), 149 were reduced to MCDA pregnancies (group B), and 65 were managed expectantly (group C). Each multifoetal pregnancy reduction (MFPR) was performed at 11-13+6 gestational weeks. Pregnancy outcomes were compared among these 3 groups.
Result(s): There were no significant differences in the miscarriage rates (4.8 vs. 2.7 vs. 6.2%, respectively) or live birth rates (90.5 vs. 87.2 vs. 86.2%, respectively) among groups A, B and C (P > 0.05).
Group A had significantly lower preterm delivery (11.9 vs. 89.2%; odds ratio (OR) 0.016, 95% confidence interval (CI) 0.006-0.045) and low birth weight rates (LBW; 9.2 vs. 92.9%; OR 0.008, 95% CI 0.003-0.021) than group C (P < 0.001).
Group B had significantly lower preterm delivery (51.7 vs. 89.2%; OR 0.129, 95% CI 0.055-0.301) and LBW rates (59.0 vs. 92.9%; OR 0.111, 95% CI 0.057-0.214) than group C (P < 0.001).
Group A had significantly lower preterm delivery (11.9 vs. 51.7%; OR 0.126, 95% CI 0.061-0.263; P < 0.001), LBW (9.2 vs. 59.0%; OR 0.071, 95% CI 0.031-0.160; P < 0.001) and perinatal mortality rates (5.0 vs. 13.4%; OR 0.339, 95% CI 0.117-0.978; P = 0.037) than group B.
Conclusion: The MFPR of DCTA triplet pregnancies to singleton or MCDA pregnancies was associated with better pregnancy outcomes than DCTA triplets managed expectantly. The perinatal outcomes of DCTA triplets reduced to singleton pregnancies were better than those of DCTA triplets reduced to MCDA pregnancies.
Effect of maternal birth positions on duration of second stage of labor: Systematic review and meta-analysis
Authors: Badi Marta Berta , Lindgren Helena , Christensson Kyllike , Mekonnen Sollomon , Adefris Mulat 
Published: September 2019

Abstract
Background: it is believed that giving birth in an upright position is beneficial for both mother and the infant for several physiologic reasons. An upright positioning helps the uterus to contract more strongly and efficiently, the baby gets in a better position and thus can pass through the pelvis faster. Upright and lateral positions enables flexibility in the pelvis and facilitates the extension of the outlet. Before implementing a change in birthing positions in our clinics we need to review evidences available and context valid related to duration of second stage of labor and birthing positions. Objective: The aim of this review was to examine the effect of maternal flexible sacrum birth position on duration of second stage of labor. Method: The research searched articles using bibliographical Databases: Medline/PUBMED, SCOPUS, Google scholar and Google. All study designs were considered while investigating the impact of maternal flexible sacrum birthing positioning in relation duration of second stage of labor. Studies including laboring mothers with normal labor and delivery. A total of 1,985 women were included in the reviewed studies. We included both qualitative and quantitative analysis. Results: We identified 1,680 potential citations, of which 8 articles assessed the effect of maternal upright birth positioning on the reduction during the duration of second stage of labor. Two studies were excluded because of incomplete reports for meta analysis. The result suggested a reduction in duration of second stage of labor among women in a flexible sacrum birthing position, with a mean duration from 3.2-34.8. The pooled weighted mean difference with random effect model was 21.118(CI: 11.839-30.396) minutes, with the same significant heterogeneity between the studies (I2=96.8%, p<000). Conclusion: The second stage duration was reduced in cases of a flexible sacrum birthing position. Even though the reduction in duration varies across studies with considerable heterogeneity, laboring women should be encouraged to choose her comfortable birth position. Researchers who aim to compare different birthing positions should consider study designs which enable women to choose birthing position. Prospero registration number [CRD42019120618]
Lights and shadows on the last week of life of nursing home residents with advanced dementia: retrospective study
Authors: Toscani Franco , Finetti Silvia , Giunco Fabrizio , Basso Ines , Rosa Debora , Pettenati Francesca , Bussotti Alessandro , Villani Daniele , Gentile Simona , Boncinelli Lorenzo , Monti Massimo , Spinsanti Sandro , Piazza Massimo , Charrier Lorena , Giulio Paola Di 
Published: September 2019

Abstract
Background
Barriers to palliative care still exist in geriatric settings, thus persons with advanced dementia may not receive adequate palliative care in the last days of their life; instead, they may be exposed to aggressive and/or inappropriate treatments. The study aimed at evaluating the palliative appropriateness of clinical interventions and care at end of life in a cohort of NH residents with advanced dementia in a large Italian region (Lombardy Region).
Methods
Retrospective study in a convenience sample of 29 NHs. Data were collected from the clinical records of 482 residents with advanced dementia, who had resided in the NH for at least 6 months before death, mainly focusing on the last week of life.
Results
Most residents (97.1%) died in the NH. In the 7 days before death, 20% were fed and hydrated by mouth, and 13.4% were tube fed. A median of five, often inappropriate, drugs was prescribed. The acknowledgement of worsening condition in clinical records was recorded for 57% of residents, a median of 4 days before death.
Conclusions
A full implementation of palliative care is not yet achieved possibly due to the insufficient acknowledgement of the inappropriateness of some drugs and interventions, and health professionals’ fears and prejudices regarding critical end-of-life decisions. Further studies should focus on how to improve care for NH residents.