bluuebunny/crossref_metadata_2025_split huggingface dataset:
Temporal expression of polysaccharide biosynthesis genes in the leaves of Cyclocarya paliurus at different developmental stages
Authors: Lin Weida , Chen Huanwei , Wang Jianmei , Zhen Yongli , Lu Qiuwei , Li Yueling , Jin Zexin , Lv Hongfei , Li Junmin 
Published: September 2019

Abstract
Background: Cyclocarya paliurus (Batal.) Iljinskaja is a common endemic tree species. The leaves of C. paliurus are used as a Chinese medicine and the main active components are polysaccharides. However, the temporal pattern of polysaccharide synthesis at different leaf developmental stages has not been reported to date. Results: With the development of leaves, the content of polysaccharides increased first and the highest content was found at the F3 stage (the third larger full expanded leaf). A total of 499710194 clean reads were obtained using C. paliurus genomic data and were assembled into 296593 unigenes. Among 4708 identified DEGs, 429 DEGs were up-regulated and 451 DEGs were down-regulated from F1 stage (the smallest full expanded leaf) to F2 stage (the second larger full expanded leaf), 630 DEGs were up-regulated and 60 DEGs were down-regulated from F2 stage to F3 stage, and 1833 up-regulated and 1816 down-regulated DEGs from F3 stage to F4 stage. Forty DEGs associated with GT belong to 13 GT families. Among them, only one gene was down-regulated from F1 stage to F2 stage, two genes were down-regulated from F2 to F3 stages, and 23 genes were down-regulated and 15 genes were up-regulated from F3 stage to F4 stage, respectively. A significant correlation exists between the five unigenes and the polysaccharide content. UDP-glucose 4-epimerase gene was significantly positively correlated with the polysaccharide content. A pathway map for the biosynthesis of C. paliurus polysaccharide was proposed. Among 150 transcription factors identified from DEGs, the majority was members of the AP2/ERF family (21, 14%), followed by the C2H2 family (14, 9.33%), the MYB family (12, 8%), the C2C2-GATA family (10, 6.67%), the GRAS family (9, 6%), and the zf-HD family (7, 4.67%). Conclusions: These results identified genes involved in the biosynthesis of Cyclocarya paliurus polysaccharides during different leaf developmental stages and provided evidence for the change of polysaccharide content during the development of C. paliurus leaves. Possible synthetic pathways and related transcription factors were suggested. This study provides information for the screening of polysaccharide biosynthesis related genes and elucidates the mechanism underlying polysaccharide biosynthesis in C. paliurus.
Designing a Framework of Technical Hospital Information Systems Requirements and Evaluating the Systems Implemented through this Framework
Authors: Farzandipour Mehrdad , Meidani Zahra , Nabovati Ehsan , Jabali Monireh Sadeqi , Banadaki Razieh Dehghan 
Published: September 2019

Abstract
Background Hospital Information System (HIS) implementation is complex and costly compared to other information systems. Therefore, the present study was conducted with the aim of designing and evaluating technical HIS requirements.Methods This study was conducted in 2016 in two parts: designing technical requirements and evaluating the HIS. The first part of the study was performed through the Delphi technique. In the second part of the study, evaluation of systems was done using a checklist based on the approved requirements.Results In the first part of the study, the final list of technical HIS requirements was designed with 73 items in four domains including ‘communication service’, ‘system architecture’, ‘security service’, and ‘system response time’. In the second part, the results of the evaluation indicated that the approved requirements had been observed in 63.8%, 65.5%, 72.4%, and 76.3% of the HIS software programs in the dimensions of ‘communication service’, ‘system architecture’, ‘security service’, and ‘system response time’, respectively.Conclusions The technical HIS evaluation tool was designed to be used in the evaluation and selection of the system. The evaluation results also indicated that the studied HISs were weaker in ‘communication service’ and ‘system architecture’ domains compared to the other two domains under study.
Development and Implementation of a clinical pathway to reduce inappropriate admissions among patients with Community acquired pneumonia in a private health system in Brazil: An observational cohort study and a promising tool for efficiency improvement.
Authors: Moreira Rodrigo , Mendonça Hugo T. F. , Farias Ayla M. , Sznejder Henry , Lang Eddy , Wilson Margaret M. 
Published: September 2019

Abstract
Background: Patients with community-acquired pneumonia (CAP) at low risk of death by CURB-65 scoring system are usually unnecessarily treated as inpatients generating additional economic and clinical burden. We aimed to implement an evidence based clinical pathway to reduce hospital admissions of low risk CAP and investigate factors related to mortality and readmissions within 30 days.Methods: From November 2015 to August 2017 a clinical pathway was implemented at twenty hospitals. We included patients aged >18 years, with a diagnosis of CAP by the attendant physician. The main outcome was the monthly proportion of low risk CURB-65 admission after implementation of the clinical pathway. Logistic regression models were performed to assess variables associated with mortality and readmission in the admitted population within 30 days.Results: We included 10909 participants with suspected CAP. The proportion of low risk CAP admitted decreased from 22.1% to 12.8% in the period. Among participants with low risk, there has been no perceptible increase in deaths (0.80%) or readmissions (6.92%). Regression analysis identified that CURB-65 variables, presence of pleural effusion (OR= 1.74; 95%IC=1.08-2.8; p=0.02) and leucopenia (OR= 2.47; 95%IC=1.11-5.48;p=0.02) were independently associated with 30-day mortality whereas a prolonged hospital stay (OR= 2.09; 95%=1.14-3.83;p=0.01) were associated with 30-day readmission in the low risk population.Conclusion: The implementations of a clinical pathway diminished the proportion of low risk CAP admissions with no apparent increase of clinical outcomes within 30 days. Nonetheless, additional factors influences the clinical decision about site of care management in low risk CAP.
Comparisons of cryptococcal meningitis caused by Cryptococcus neoformans between HIV-negative patients with and without lung infection in two Chinese university hospitals
Authors: Yang Ming , Sun Fengjun , Liu Fu , Feng Wei , Yuan Qian , Wang Yu , Cheng Lin , Xia Peiyuan 
Published: September 2019

Abstract
Background Lung infection may cause many symptoms, such as fever and headache, that may be confused with cryptococcal meningitis (CM) symptoms. This study aimed to investigate the discrepancy in clinical features and outcomes of CM between HIV-negative patients with and without lung infection.Methods We retrospectively reviewed the medical records of patients with CM admitted to two hospitals in Southwest China from 1 January 2014 to 31 December 2018.Results A total of 71 patients was included during the 5 years, among which 35 (49.3%) patients had lung disease. CM occurred more frequently in male (62.9% vs. 44.4%, P=0.12) and young (≤30 years, 31.4% vs. 16.7%, P=0.30) patients with lung infection than in the patients without lung infection, with more fever (77.1% vs. 30.6%, P=0.001) and less central nervous system symptoms (5.7% vs. 16.7%, P=0.28) and vomiting (25.0% vs. 14.3%, P=0.26). In addition, patients with lung infection presented higher percentages of white blood cell (WBC) counts ˂20×106/L (45.7% vs. 22.2%, P=0.036) and lower percentages of ethmoid sinusitis, maxillary sinusitis, paranasal sinusitis, and otitis media than patients without lung infection (8.6% vs. 30.6%, P=0.02). The Cryptococcus neoformans isolates were sensitive to itraconazole, voriconazole, fluconazole, and amphotericin B but resistant to flucytosine. Patients with lung infection had higher mortality at discharge compared with patients without lung infection (8.6% vs. 0, P=0.12). Multivariable analyses showed that WBC counts ˂20×106/L was significantly associated with treatment outcome (OR=0.01, 95% CI=0-0.833, P=0.041).Conclusions There were significant discrepancies in clinical features between CM patients with and without lung infection. Clinicians must consider the divergences in the diagnosis of CM in patients with lung infection.
Ultraconserved non-coding DNA within insect phyla
Authors: Brody Thomas , Yavatkar Amar , Kuzin Alexander , Odenwald Ward F. 
Published: September 2019

Abstract
Background Presence of ultra-conserved sequence elements in vertebrate enhancers suggest that transcription factor regulatory interactions are shared across phylogenetically diverse species. To date evidence for similarly conserved elements among evolutionarily distant insects such as flies, mosquitos, ants and bees, has been elusive. This study has taken advantage of the availability of the assembled genomic sequence of these insects to explore the presence of ultraconserved sequence elements in these phylogenetic groups.Results To investigate the integrity of fly regulatory sequences across ~100 million years of evolutionary divergence from the fruitfly Drosophila melanogaster , we compared Drosophila non-coding sequences to those of Ceratitis capitata , the Mediterranean fruit fly and Musca domestica , the domestic housefly. Using various alignment techniques, Blastn, Clustal, Blat, EvoPrinter and Needle, we show that many of the conserved sequence blocks (CSBs) that constitute Drosophila cis -regulatory DNA, recognized by EvoPrinter alignment protocols, are also conserved in Ceratitis and Musca . We term the sequence elements shared among these species ultraconserved CSBs (uCSBs). The position of the uCSBs with respect to flanking genes is also conserved. Blastn alignments also detect putative cis -regulatory sequences shared among evolutionarily distant mosquitos Anopheles gambiae and Culex pipiens and Aedes aegypti. We have also identified conserved sequences shared among bee species. Side by side comparison of bee and ant EvoPrints identify uCSBs shared between the two taxa, as well as more poorly conserved CSBs in either one or the other taxon but not in both.Conclusions The results suggest that CSBs represent the point of interaction of multiple trans-regulators whose functions and interactions are conserved across divergent genera. Analysis of uCSBs in dipterans, mosquitos and bees will lead to a greater understanding of their evolutionary origin and the function of their conserved non-coding sequences.
Characterizing the ribosomal tandem repeat and its utility as a DNA barcode in lichen-forming fungi
Authors: Bradshaw Michael , Grewe Felix , Thomas Anne , Harrison Cody H. , Lindgren Hanna , Muggia Lucia , Clair Larry L. St. , Lumbsch H. Thorsten , Leavitt Steve 
Published: September 2019

Abstract
Background Regions within the nuclear ribosomal operon are a major tool for inferring evolutionary relationships and investigating diversity in fungi. In spite of the prevalent use of ribosomal markers in fungal research, central features of nuclear ribosomal DNA (nrDNA) evolution are poorly characterized for fungi in general, including lichenized fungi. The internal transcribed spacer (ITS) region of the nrDNA has been adopted as the primary DNA barcode identification marker for fungi. However, little is known about intragenomic variation in the nrDNA in symbiotic fungi. In order to better understand evolution of nrDNA and the utility of the ITS region for barcode identification of lichen-forming fungal species, we generated nearly complete nuclear ribosomal operon sequences from approximate nine species in the Rhizoplaca melanophthalma species complex using short reads from high-throughput sequencing.Results We estimated copy numbers for the nrDNA operon, ranging from nine to 48 copies for members of this complex, and found low levels of intragenomic variation in the standard barcode region (ITS). Monophyly of currently described species in this complex was supported in phylogenetic reconstructions of the ITS, 28S, IGS, and some intronic regions; however, phylogenetic reconstructions based on the 18S provided much lower resolution. Phylogenetic analysis of concatenated ITS and intergenic spacer sequence data generated from 496 specimens collected worldwide revealed, previously unrecognized lineages in the nrDNA phylogeny.Conclusions The results from our study support the general assumption that the ITS region of the nrDNA is an effective barcoding marker for fungi. For the R. melanophthalma group, the limited number of potentially polymorphic sites generally do not correspond to fixed diagnostic nucleotide position characters separating taxa within this species complex. Previously unrecognized lineages inferred from ITS sequence data may represent undescribed species-level lineages or reflect uncharacterized aspects of nrDNA evolution.
Evaluation of Tools to Assess Psychological Distress: How to Measure Psychological Stress Reactions in Citizen Responders– A Systematic Review
Authors: Kragh Astrid Rolin , Folke Fredrik , Andelius Linn , Ries Emma Slebsager , Rasmussen Rasmus Vedby , Hansen Carolina Malta 
Published: September 2019

Abstract
Background Dispatched citizen responders are increasingly involved in out-of-hospital cardiac arrest (OHCA) resuscitation which can lead to severe stress. It is unknown which psychological assessment tools are most appropriate to evaluate psychological distress in this population. The aim of this systematic review was to identify and evaluate existing assessment tools used to measure psychological distress with emphasis on citizen responders who attempted resuscitation. Methods A systematic literature search conducted by two reviewers was carried out in March 2018 and revised in July 2018. Four databases were searched: PubMed, PsycInfo, Scopus, and The Social Sciences Citation Index. A total of 504 studies examining assessment tools to measure psychological distress reactions after acute traumatic events were identified, and 9 fulfilled the inclusion criteria for further analysis. The selected studies were assessed for methodological quality using the Scottish Intercollegiate Guidelines Network. Results The Impact of Event Scale (IES) and The Impact of Event Scale-Revised (IES-R) were the preferred assessment tools, and were used on diverse populations exposed to various traumatic events. One study included lay rescuers performing bystander cardiopulmonary resuscitation and this study used the IES. The IES and the IES-R also have proven a high validity in various other populations. The Clinical administered PTSD scale (CAPS) was applied in two studies. Though the CAPS is comparable to both the IES-R and the IES, the CAPS assess PTSD symptoms in general and not in relation to a specific experienced event, which makes the scale less suitable when measuring stress due to a specific resuscitation attempt. Conclusions The IES and the IES-R seem to be solid measures for psychological distress among people experiencing an acute psychological traumatic event. However, only one study has assessed psychological distress among citizen responders in OHCA for which the IES-R scale was used, and therefore, further research on this topic is warranted.
(Dis)concordance of comorbidity data across ICD codes, medical charts, and self-reports
Authors: Sheriffdeen Abdullah , Millar Jeremy , Martin Catherine , Evans Melanie , Tikellis Gabriella , Evans Susan 
Published: September 2019

Abstract
Background Benchmarking outcomes across settings commonly requires risk-adjustment for co-morbidities that must be derived from extant sources that were designed for other purposes. A question arises as to the extent to which differing available sources for health data will be concordant when inferring the type and severity of co-morbidities, how close these are to the “truth”. We studied the level of concordance for same-patient comorbidity data extracted from administrative data (coded from International Classification of Diseases, Australian modification,10th edition [ICD-10AM]), from the medical chart audit, and data self-reported by men with prostate cancer who had undergone a radical prostatectomy.Methods We included six hospitals (5 public and 1 private) contributing to the Prostate Cancer Outcomes Registry-Victoria (PCOR-Vic) in the study. We listed eligible patients from the PCOR-Vic who underwent a radical prostatectomy between January 2017 and April 2018 for the Health Information Manager in each hospital, who provided each patient’s associated ICD-10AM comorbidity codes. Medical charts were reviewed to extract comorbidities used to generate the Charlson Comorbidity Index. The self-reported comorbidity questionnaire (SCQ) was distributed through PCOR-Vic to eligible men.Results The percentage agreement between the administrative data, medical charts and self-reports ranged from 92% to 99% in the 122 patients (from 217 eligible participants, 56%), who responded to the questionnaire. The prevalence-adjusted bias-adjusted kappa (PABAK) coefficient was from 0.83 to 0.98 for all conditions aside from cancer, reflecting a strong level of agreement for the absence of comorbidities. Conversely, the presence of comorbidities showed a poor level of agreement between data sources. There was concordance on 213/277 (77%) comorbidities when comparing medical charts and administrative data; 102/238 (30%) comorbidities when comparing medical chart and self-reports; and 34/150 (23%) comorbidities when comparing administrative data and self-reports.Conclusion Relying on a single data source to generate comorbidity indices for risk-modelling purposes may fail to capture the reality of a patient’s disease profile. There does not appear to be a ‘gold-standard’ data source for the collection of data on comorbidities.
A Study of Factors Affecting on Patients’ Length of Stay in a Surgical Ward: Toward Optimization by Technology-based Solutions
Authors: Baniasadi Tayebeh , Ghazisaeedi Marjan , Hassaniazad Mehdi , Kalhori Sharareh R. Niakan , Shahi Mehraban 
Published: September 2019

Abstract
Background: Understanding each of the factors affecting the length of hospitalization especially in surgery wards can play a major role in planning for the optimal use of hospital resources. This study aims to determine factors affecting the length of stay (LOS) in a surgical ward and then provide technology-based solutions .Methods: In this cross-sectional study, 310 records were selected by systematic random sampling from hospitalized patients in surgery ward of a general teaching hospital in Bandar Abbas, situated in sought of Iran. In order to determine the association of 26 variables (demographic, clinical, and non-clinical) with LOS, analytical and descriptive statistics were used. Then, the researchers reviewed relevant literature in PubMed, Scopus, and Google Scholar to introduce solutions based on health information technology (HIT) toward LOS optimization.Results: Mean and median of patients’ LOS in surgery ward were 3.30±3.71 and 2 days respectively. According to multivariate regression model, factors that exerted higher influence on length of stay includes number of para-clinical tests, surgeries, and consultation as well as type of referral and months of admission(p<0.05). Regarding HIT-based intervention, eleven general categories of suggestions were provided. Based on the findings, more accessible technologies such as hospital information system, picture archiving and communication system, telemedicine especially tele-consultation or tele-visit as well as electronic consultation and discharge planning tools alongside smart dashboards for institutions like the center under study in order to expedite the process of diagnosis and treatment, then optimizing LOS seem appropriate. Conclusions: It is important to move toward optimized LOS though understanding and control influential factors; standardize LOS along with continuous monitoring of performance indicators may help to utilize hospital resources more efficiently. HIT-based interventions may support health care providers and administrators to manage patients` admission, hospitalization, transfer, and discharge processes more properly. Keywords: Index; length of Stay; Hospital; Health Information Technology; Surgery_ward
Catha edulis (Khat) use and Demographic Correlates of Schizophrenia: A Case-Control study.
Authors: Woldemariam Abraha Gosh , Thupayagale-Tshweneagae Gloria , Gebremedihin Misgna Teklay 
Published: September 2019

Abstract
Objective The purpose of this study was to determine the demographic correlates of schizophrenia and the use of Catha edulis.Results Results of the present study shows that variables like age ≤ 30 year ( OR=2.6; 95%CI=1.166,5.821; p=.020 ), single marital status ( OR=4.25; 95%CI=1.86,9.72; p=.001 ), unemployment ( OR=3.82; 95%CI=1.74,8.38; p=.001 ), lifetime Catha edulis (khat) use ( OR=3.89; 95%CI=1.75,8. 64) are significantly correlated with Schizophrenia. Knowledge of the association between demographic variables and the use of Catha edulis would assist in both societal education on the diagnosis and prognosis of schizophrenia.
Pregnancy outcomes with Primary Sjogren's syndrome among Chinese women: a retrospective cohort study
Authors: Xu Jinfeng , Chen Daijuan , Tian Yuan , Peng Bing 
Published: September 2019

Abstract
Background Data on pregnancy outcomes in Primary Sjogren's syndrome (pSS) women are scarce, and results have been conﬂicting. The aim of our study is to analyze the adverse pregnancy outcome in patients with pSS. Methods This was a retrospective cohort study conducted at a tertiary medical center located in Chengdu, Sichuan, China, from May 2013 to November 2018. The relevant medical records of all pregnant women were retrospectively reviewed. Logistic regression analyses were performed to compute crude odds ratios (crude OR) with 95% confidence intervals (CI) for maternal and fetal outcomes. Adjusted odds ratios (aOR) were estimated by logistic regression adjusted for confounders. Results Women with pSS had a significantly higher incidence of pre-eclampsia (aOR 11.49, 95% CI 1.65-79.98), PPROM (aOR 5.09, 95% CI 1.14-22.63). Compared to general population, pregnant women with pSS were at increased risks of fetal loss (aOR 15.06, 95%CI 1.19 to 191.11), and a higher risk of fetal growth restriction (aOR 15.69, 95%CI 1.61 to 153.33), preterm birth (aOR 5.52, 95%CI 1.83 to 16.65), a cesarean section (aOR 6.53, 95%CI 3.18 to 13.42) and a neonatal intensive care unit admission (aOR 12.86, 95%CI 1.88 to 87.82) after adjusting for confounding factors. The rate of congenital heart block in the pSS group was 4.7%. Conclusions Pregnant women with pSS were at increased risk of having adverse pregnancy outcomes. Women with pSS require prenatal counseling to explain the risks involved and well control of pSS condition before conception and a close antenatal monitoring should be performed by both rheumatologists and obstetricians.