bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adjuvant treatment of coronary heart disease angina pectoris with Chinese patent medicine
Authors: Liu Yijia , Li Zhu , Shen Dandan , Song Yanqi , Huang Mengnan , Xue Xiaoxue , Xie Jing , Jiao Ziyi , Gao Shuming , Xu Yilan , Gao Shan , Wang Xianliang , Xu Qiang , Gao Sheng , Li Chunjie , Li Lin , Niu Kaijun , Yu Chunquan 
Published: August 2019

Abstract

Background:
Patients with coronary heart disease (CHD) angina pectoris are in critical condition, which can cause sudden death, myocardial infarction, and other adverse events, and bring serious burden to families and society. Timely treatment should be given to improve the condition. Western medicine treatment of angina pectoris failed to meet the demand of angina symptom control.

Objective:
It is hoped that the research method with higher evidential value will be adopted to compare the short-term, medium-term, and long-term effects of Chinese patent medicine combined with conventional western medicine and conventional western medicine alone in the treatment of CHD angina pectoris, so as to tap the clinical efficacy advantages of traditional Chinese medicine (TCM) and provide reliable data support for its clinical application.

Methods:
A prospective cohort study was conducted among patients with CHD angina pectoris who were treated with oral Chinese patent medicine and conventional western medicine. The patients were divided into exposed group and nonexposed group according to whether or not the patients with CHD angina pectoris were treated with Chinese patent medicine. The exposed group was treated with TCM combined with conventional western medicine, while the nonexposed group was treated with conventional western medicine alone. Patients need to be hospitalized for 2 weeks as the introduction period and whether to enter the group is determined according to the treatment and medication conditions of the patients. The follow-up time points were 0th, 4th, 12th, 24th, and 48th weeks. The main events and secondary events were used as the evaluation criteria for clinical efficacy of CHD angina pectoris. In the experimental study, we will use strict indicators to detect standard operation procedure for multinomics and bacterial flora detection.

Conclusion:
This study will provide evidence for the clinical efficacy advantages of Chinese patent medicine and reliable support for its clinical application through test data.
Recurrent fever of unknown fungal infection in a low-risk patient
Authors: Guo Tang-meng , Ye Yu , Huang Li-li , Cheng Bei 
Published: August 2019

Abstract

Rationale:
Fungal infectious disease does not usually occur in low-risk patients. Clinicians tend to ignore the role of fungi in the fevers of low-risk patients. If there is not timely control of fungal infections and associated fever, the disease will continue to worsen, resulting in physical dysfunction or death.

Patient concerns:
Recurrent fever continued for 1 month in a young adult.

Diagnoses and interventions:
Non-albicans Candida (NAC) species probably was the main pathogen in this case based on the resolution of fever after capsofungin administration.

Outcomes:
The fever and the associated indicators, including white blood cell count, C-reaction protein, erythrocyte sedimentation rate, and BDG levels, showed improvement quickly. The patient left the hospital successfully after 18 days of caspofungin treatment. There was no recurrent fever at a follow-up of 1 year.

Lessons:
Clinicians should be aware that the incidence of fungal infection is increasing in low-risk patients. The BDG assay is still an effective tool used to diagnose invasive fungal diseases. Caspofungin is an effective drug for the treatment of some unknown fungal infections.
Is Disruptive Behavior Inherent to the Surgeon or the Environment? Analysis of 314 Events at a Single Academic Medical Center
Authors: Heslin Martin J. , Singletary Brandon A. , Benos Kaitlin C. , Lee Laura Read , Fry Charles , Lindeman Brenessa 
Published: August 2019

Objective:
In 2009, the Joint Commission mandated a process to manage disruptive behavior, as evidence suggests it undermines a culture of safety. This process often reviews only the reporter's side of the story as the truth. In this study, we compared both reporter account (RA) and involved party (IP) responses to determine if disruptive behavior was inherent to the surgeon or the hospital environment and its relationship to patient safety.

Methods:
From 1/1/2015 through 12/31/2017, we prospectively recorded the RA and the IP response. This resulted in 314 reports involving 204 IPs. Four reviewers scored issues, interactions, modifiable stressors, and patient safety. Logistic regression determined factors associated with patient harm. Significance defined as P < 0.05.

Results:
Surgical, medical, and other specialties were IPs 43%, 35%, and 22%, respectively; 73% had only one event. High-intensity environments (OR, ICU, etc.) made up 56% of the total. Perceived unprofessional or lack of communication was present in 70% and 44% of events. A significant direct relationship existed between the stress of the clinical situation and the egregiousness of the behavior (P < 0.0001). Logistic regression revealed that unclear hospital policies, the IP being a surgeon, and urgent competing responsibilities were associated with potential patient harm (P < 0.05).

Conclusions:
Unclear policies and urgent competing responsibilities in the surgical environment create stress, leading to conflict. Single events for the majority suggest the environment as the primary contributor. Tactics to improve stressful environments and clearly communicated policies may be more effective and sustainable than individually targeted interventions in enhancing patient safety.
An R package for divergence analysis of omics data
Authors: Dinalankara Wikum , Ke Qian , Geman Donald , Marchionni Luigi 
Published: August 2019

AbstractGiven the ever-increasing amount of high-dimensional and complex omics data becoming available, it is increasingly important to discover simple but effective methods of analysis. Divergence analysis transforms each entry of a high-dimensional omics profile into a digitized (binary or ternary) code based on the deviation of the entry from a given baseline population. This is a novel framework that is significantly different from existing omics data analysis methods: it allows digitization of continuous omics data at the univariate or multivariate level, facilitates sample level analysis, and is applicable on many different omics platforms. The divergence package, available on the R platform through the Bioconductor repository collection, provides easy-to-use functions for carrying out this transformation. Here we demonstrate how to use the package with data from the Cancer Genome Atlas.
Sorting motifs target the movement protein of ourmia melon virus to the trans-Golgi network and plasmodesmata
Authors: Ozber Natali , Margaria Paolo , Anderson Charles T. , Turina Massimo , Rosa Cristina 
Published: August 2019

AbstractPlants have a highly sophisticated endomembrane system targeted by plant viruses for cell-to-cell movement. The movement protein (MP) of ourmia melon virus (OuMV) is delivered to plasmodesmata (PD) and forms tubules to facilitate cell-to-cell movement. Although several functionally important regions for correct subcellular localization of OuMV MP have been identified, little is known about the pathways OuMV MP hijacks to reach the PD. Here, we demonstrate that OuMV MP localizes to the trans-Golgi network (TGN), but not to the multivesicular body/prevacuolar compartment or Golgi, and carries two putative sorting motifs, a tyrosine (Y) and a dileucine (LL) motif, near its N-terminus. Glycine substitutions in these motifs result in loss of OuMV infectivity in Nicotiana benthamiana and Arabidopsis. Live cell imaging of GFP-labeled sorting motif mutants shows that Y motif mutants fail to localize to the TGN, plasma membrane, and PD. Mutations in the LL motif do not impair plasma membrane targeting of MP but affect its ability to associate with callose deposits at the PD. Taken together, these results suggest that both motifs are indispensable for targeting OuMV MP to PD and for efficient systemic infection but show differences in functionality. Co-immunoprecipitation assays coupled with mass spectrometry identified a series of host factors that could interact with the OuMV MP and link the MP with various pathways, in particular vesicle trafficking and membrane lipids. This study provides new insights into the intracellular targeting of MPs and pathways that plant viruses hijack for cell-to-cell movement.
Genome Report: A highly contiguous reference genome for Northern Bobwhite (Colinus virginianus)
Authors: Salter Jessie F. , Johnson Oscar , Stafford Norman J. , Herrin William F. , Schilling Darren , Cedotal Cody , Brumfield Robb T. , Faircloth Brant C. 
Published: August 2019

ABSTRACTNorthern bobwhites (Colinus virginianus) are small quails in the New World Quail family (Odontophoridae) and are one of the most phenotypically diverse avian species. Despite extensive research on bobwhite ecology, genomic studies investigating the evolution of phenotypic diversity in this species are lacking. Here, we present a new, highly contiguous assembly for bobwhites using tissue samples from a vouchered, wild, female bird collected in Louisiana. Using Dovetail Chicago and HiC libraries with the HiRise assembly pipeline, we produced an 866.8 Mbp assembly including 1,512 scaffolds with a contig N50 of 66.8 Mbp, a scaffold L50 of four, and a BUSCO completeness score of 90.8%. This new assembly greatly improves scaffold lengths and contiguity compared to an existing draft bobwhite genome and provides an important tool for future studies of evolutionary and functional genomics in bobwhites.
MIR3607regulates cerebral cortex development via activation of Wnt/βCat signaling
Authors: Chinnappa Kaviya , Márquez-Galera Ángel , Prieto-Colomina Anna , Nomura Yuki , Cárdenas Adrián , López-Atalaya José P. , Borrell Víctor 
Published: August 2019

AbstractThe evolutionary expansion of the mammalian cerebral cortex is recapitulated during embryonic development in large mammals, but the underlying genetic mechanisms remain mostly unknown. Previous transcriptomic analyses of the developing ferret cortex identify candidate genes related to the expansion of germinal layers and cortex size. Here we focused onMIR3607, a microRNA differentially expressed between germinal layers of the large human and ferret cortex, not expressed in the small mouse cortex. Expression ofMIR3607in mouse embryos at E14.5 leads to increased progenitor cell proliferation. This is reflected in transcriptomic changes, which also reveal increased Wnt/βCatenin signaling. Expression ofMIR3607at E12.5, when progenitor cells expand, causes amplification and severe delamination of apical progenitors, leading to rosette formation. This is rescued by co-expressing Adenomatous Polyposis Coli, inhibitor of canonical Wnt signaling. A similar phenotype is produced in human cerebral organoids. Our findings demonstrate thatMIR3607expands and delaminates apical progenitor cells via activating Wnt/βCatenin, and suggest that a secondary loss of expression in mouse may underlie their reduction in cortex size during recent evolution.
Targeted cell ablation in zebrafish using optogenetic transcriptional control
Authors: Mruk Karen , Ciepla Paulina , Piza Patrick A. , Alnaqib Mohammad A. , Chen James K. 
Published: August 2019

ABSTRACTCell ablation is a powerful method for elucidating the contributions of individual cell populations to embryonic development and tissue regeneration. Targeted cell loss in whole organisms has been typically achieved through expression of a cytotoxic or prodrug-activating gene product in the cell type of interest. This approach depends on the availability of tissue-specific promoters, and it does not allow further spatial selectivity within the promoter-defined region(s). To address this limitation, we have developed ablative methods that combine genetically encoded toxins, the tissue specificity afforded bycis-regulatory elements, and the conditionality of optogenetics. Using this integrative approach, we have ablated cells in zebrafish embryos with spatial and temporal precision.
IRG1 and iNOS act redundantly with other interferon gamma-induced factors to restrict intracellular replication ofLegionella pneumophila
Authors: Price Jordan V. , Russo Daniel , Ji Daisy X. , Chavez Roberto , DiPeso Lucian , Lee Angus Yiu-Fai , Coers Jörn , Vance Russell E. 
Published: August 2019

AbstractInterferon gamma (IFNγ) restricts the intracellular replication of many pathogens, but how IFNγ confers cell-intrinsic pathogen resistance remains unclear. For example, intracellular replication of the bacterial pathogenLegionella pneumophilain macrophages is potently curtailed by IFNγ, but consistent with prior results, no individual genetic deficiency we tested compromised IFNγ-mediated control. Intriguingly, however, we observed that the glycolysis inhibitor 2-deoxyglucose (2DG) partially rescuedL. pneumophilareplication in IFNγ-treated macrophages. 2DG inhibits glycolysis and triggers the unfolded protein response, but unexpectedly, it appears these effects are not responsible for perturbing the antimicrobial activity of IFNγ. Instead, we found that 2DG rescues bacterial replication predominantly by inhibiting the induction of two key antimicrobial factors, inducible nitric oxide synthase (iNOS) and immune responsive gene 1 (IRG1). Using immortalized and primary macrophages deficient in iNOS and IRG1, we confirm that loss of both iNOS and IRG1, but not individual deficiency in each gene, partially reduces IFNγ-mediated restriction ofL. pneumophila. Further, using a combinatorial CRISPR/Cas9 mutagenesis approach, we find that mutation of iNOS and IRG1 in combination with four other genes (CASP11, IRGM1, IRGM3 and NOX2) results in a total loss ofL. pneumophilarestriction by IFNγ in primary bone marrow macrophages. There are few, if any, other examples in which the complete set of cell-intrinsic factors required for IFNγ-mediated restriction of an intracellular bacterial pathogen have been genetically identified. Our results highlight the combinatorial strategy used by hosts to block the exploitation of macrophages by pathogens.ImportanceLegionella pneumophilais one example among many species of pathogenic bacteria that replicate within mammalian macrophages during infection. The immune signaling factor interferon gamma (IFNγ) blocksL. pneumophilareplication in macrophages and is an essential component of the immune response toL. pneumophilaand other intracellular pathogens. However, to date, no study has determined the exact molecular factors induced by IFNγ that are required for its activity. We generated macrophages lacking different combinations of IFNγ-induced genes in an attempt to find a genetic background in which there is a complete loss of IFNγ-mediated restriction ofL. pneumophila. We successfully identified six genes that comprise the totality of the IFNγ-dependent restriction ofL. pneumophilareplication in macrophages. Our results clarify the molecular basis underlying the potent effects of IFNγ and highlight how redundancy downstream of IFNγ is key to prevent exploitation of the macrophage niche by pathogens.
Distinct and shared contributions of diagnosis and symptom domains to cognitive performance in a case-control study of severe mental illness in the Paisa population
Authors: Service Susan K. , Upegui Cristian Vargas , Ramírez Mauricio Castano , Port Allison M. , Moore Tyler M. , Umanes Marfred Munoz , Arango Luis Guillermo Agudelo , Díaz-Zuluaga Ana M. , Espejo Juanita Melo , López María Cecilia , Palacio Juan David , Ruiz Sergio Sánchez , Valencia Johanna , Teshiba Terri , Espinoza Alesandra , Loohuis Loes Olde , De la Hoz Gomez Juan , Brodey Benjamin , Sabatti Chiara , Escobar Javier I. , Reus Victor I. , Jaramillo Carlos Lopez , Gur Ruben C. , Bearden Carrie E. , Freimer Nelson B. 
Published: August 2019

ABSTRACTBackgroundSevere mental illness (SMI) diagnoses display overlapping symptomatology and shared genetic risk, motivating trans-diagnostic investigations of disease-relevant quantitative measures. We analyzed relationships between neurocognitive performance, symptom domains, and diagnoses, in a large sample of SMI cases (ascertained agnostic to diagnosis) and healthy controls from a single, homogeneous population.Methods2,406 participants (1,689 cases, 717 controls; mean age 39 years, 64% female) were assessed for speed and accuracy using the Penn Computerized Neurocognitive Battery (CNB). Cases carried structured-interview based diagnoses of schizophrenia (SCZ, n=160), bipolar-I (BP-I, n=519), bipolar-II (BP-II, n=204) and major depressive disorder (MDD, n=806). Linear mixed models, using CNB tests as repeated measures, modeled neurocognition as a function of diagnosis, sex, and all interactions. Follow-up analyses, in cases, included symptom factor scores obtained from exploratory factor analysis of symptom data, as main effects.FindingsBP-I and SCZ displayed nearly identical impairments in accuracy and speed, across cognitive domains. BP-II and MDD performed similarly to controls, with subtle deficits in executive and social cognition. A three-factor model (psychosis, mania, and depression) best represented symptom data. Controlling for diagnosis, premorbid IQ, and disease severity, high lifetime psychosis scores were associated with reduced accuracy and speed across cognitive domains, while high depression scores were associated with increased social cognition accuracy.InterpretationTrans-diagnostic investigations demonstrated that neurocognitive function in SMI is characterized by two distinct profiles (BP-I/SCZ and BP-II/MDD), and is associated with specific symptom domains. These results suggest the utility of this design for elucidating SMI causes and trajectories.
Wind drives temporal variation in pollinator visitation in a fragmented tropical forest
Authors: Crall James D. , Brokaw Julia , Gagliardi Susan F. , Mendenhall Chase D. , Pierce Naomi E. , Combes Stacey A. 
Published: August 2019

AbstractWind is a critical factor in the ecology of pollinating insects such as bees. However, the role of wind in determining patterns of bee abundance and floral visitation rates across space and time is not well understood. Orchid bees are an important and diverse group of neotropical pollinators that harvest pollen, nectar and resin from plants. In addition, male orchid bees collect volatile scents that they store in special chambers in their hind legs, and for which the wind-based dispersal of odors may play a particularly crucial role. Here we take advantage of this specialized scent foraging behavior to study the effects of wind on orchid bee visitation at scent sources in a fragmented tropical forest ecosystem. We find that temporal changes in wind speed and turbulence are correlated with visitation to scent stations within sites, while local landscape structure is a strong determinant of spatial variation in visitation across nearby sites. These results suggest that the increased dispersal of attractive scents provided by wind and turbulence outweighs any biomechanical or energetic costs that might deter bees from foraging in these conditions. Overall, our results highlight the significance of wind in the ecology of these important pollinators in neotropical forests.
High-throughput analysis of adaptation using barcoded strains ofSaccharomyces cerevisiae
Authors: Fasanello Vincent J. , Liu Ping , Botero Carlos A. , Fay Justin C. 
Published: August 2019

AbstractBackgroundExperimental evolution of microbes can be used to empirically address a wide range of questions about evolution and is increasingly employed to study complex phenomena ranging from genetic evolution to evolutionary rescue. Regardless of experimental aims, fitness assays are a central component of this type of research, and low-throughput often limits the scope and complexity of experimental evolution studies. We created an experimental evolution system inSaccharomyces cerevisiaethat utilizes genetic barcoding to overcome this challenge.ResultsWe first confirm that barcode insertions do not alter fitness and that barcode sequencing can be used to efficiently detect fitness differences via pooled competition-based fitness assays. Next, we examine the effects of ploidy, chemical stress, and population bottleneck size on the evolutionary dynamics and fitness gains (adaptation) in a total of 76 experimentally evolving, asexual populations by conducting 1,216 fitness assays and analyzing 532 longitudinal-evolutionary samples collected from the evolving populations. In our analysis of these data we describe the strengths of this experimental evolution system and explore sources of error in our measurements of fitness and evolutionary dynamics.ConclusionsOur experimental treatments generated distinct fitness effects and evolutionary dynamics, respectively quantified via multiplexed fitness assays and barcode lineage tracking. These findings demonstrate the utility of this new resource for designing and improving high-throughput studies of experimental evolution. The approach described here provides a framework for future studies employing experimental designs that require high-throughput multiplexed fitness measurements.
Flux-based hierarchical organization of Escherichia coli’s metabolic network
Authors: Robaina-Estévez Semidán , Nikoloski Zoran 
Published: August 2019

AbstractBiological networks across scales exhibit hierarchical organization that may constrain network function. Yet, understanding how these hierarchies arise due to the operational constraint of the networks and whether they impose limits to molecular phenotypes remains elusive. Here we show that metabolic networks include a hierarchy of reactions based on a natural flux ordering that holds for every steady state. We find that the hierarchy of reactions is reflected in experimental measurements of transcript, protein and flux levels of Escherichia coli under various growth conditions as well as in the catalytic rate constants of the corresponding enzymes. Our findings point at resource partitioning and a fine-tuning of enzyme levels in E. coli to respect the constraints imposed by the network structure at steady state. Since reactions in upper layers of the hierarchy impose an upper bound on the flux of the reactions downstream, the hierarchical organization of metabolism due to the flux ordering has direct applications in metabolic engineering.