bluuebunny/crossref_metadata_2025 huggingface dataset:
Bismuth Containing Quadruple Therapy versus Tailored Therapy as first-line treatments for Helicobacter pylori infection in a high clarithromycin resistance area
Authors: Bang Byoung Wook , Shin Jong Beom , Ko Eun Jung , Kwon Kye Sook , Shin Yong Woon , Suh Young Ju , Kim Hyungkil , Ko Weonjin
Published: October 2019

Background Increasing clarithromycin resistance has led to the need for an alternative first-line therapy for the eradication of Helicobacter pylori (H. pylori) in Korea, and bismuth containing quadruple therapy (BQT) and tailored therapy (TT) have been proposed as alternative regimens. The aim of this study was to compare the eradication rates of BQT and TT as first-line H. pylori eradication therapies. Methods H. pylori infection was diagnosed using the rapid urease test or dual-priming oligonucleotide-based multiplex polymerase chain reaction (DPO-PCR) during endoscopy. Patients positive for H. pylori were divided into two groups; those tested using the rapid urease test received empirical BQT (the BQT group) whereas those tested by DPO-PCR received TT (the TT group). Eradication rates, adverse events, and overall medical costs, which included diagnostic test and eradication regimen costs, were compared. Results Three hundred and sixty patients were included in the study (TT group 178, BQT group 182). The modified intention-to-treat eradication rates of BQT and TT were 88.2% (142/161) and 80.3% (118/147), respectively (p=0.055), and corresponding eradication rates in the per-protocol population were 88.8% (142/160) and 81.4% (118/145) (p=0.07). Compliance and adverse event rates were similar in the two groups. Average medical costs were $ 90.3 per patient in the TT group and $ 75.5 in the BQT group (p=0.000). Conclusions Empirical BQT and tailored therapy were similar in terms of H. pylori eradication rate, safety, and tolerability, but BQT was more cost-effective.
Long-term, Sustained Feeding by Asian citrus psyllid Disrupts Salicylic Acid Homeostasis in Sweet Orange
Authors: Ibanez Freddy , Suh Joon Hyuk , Wang Yu , Stelinski Lukasz L.
Published: October 2019

Abstract
Background
Phloem-feeding insects are known to modulate the salicylic acid (SA) signaling pathway in various plant-insect interaction models. Diaphorina citri is a phloem feeding vector of the deadly phytopathogens, Candidatus Liberibacter americanus and Candidatus Liberibacter asiaticus, and the interactions of D. citri with its host that may modulate plant defenses are not well understood. The objectives of this study were to investigate the molecular mechanisms involved in transcriptional regulation of SA modification and activation of defense-associated responses in sweet orange (Citrus sinensis) exposed to various durations (7-, 14- and 150- days) of continuous feeding by D. citri.
Results
We quantified expression of genes involved in SA pathway activation and subsequent modification, as well as, associated SA metabolites (SA methyl ester, 2,3-Dihydroxybenzoic acid and SA 2-O-β-D-glucoside). NPR1 and PR-1 expression was upregulated in plants exposed to continuous feeding by D. citri for 14 days. Expression of BSMT-like, MES1-like and DMR6-like oxygenase, as well as, accumulation of their respective SA metabolites (SA methyl ester, 2,3-Dihydroxybenzoic acid) was significantly higher in plants exposed to continuous feeding by D. citri for 150 days than in those without D. citri infestation. Concomitantly, expression of UGT74F2-like was significantly downregulated and its metabolite, salicylic acid 2-β-D-glucoside, was highly accumulated in trees exposed to 150 d of feeding compared to control trees without D. citri.
Conclusions
D. citri herbivory differentially regulated transcription and SA-metabolite accumulation in citrus leaves, depending on duration of insect feeding. Our results suggest that prolonged and uninterrupted exposure (150 d) of citrus to D. citri feeding suppressed plant immunity and inhibited growth, which may highlight the importance of vector suppression as part of huanglongbing (HLB) management in citrus.

Keywords: salicylic acid, Diaphorina citri, plant defense, metabolomics, gene expression, vector-host interaction, huanglongbing.
The Distribution of Preputial Vessels in Different Severity of Rat Congenital Hypospadias Model: Imaging study using Micro-Computerized Tomograph
Authors: Lin Defu , Liu Pei , Wang Guannan , Zhang Weiping , Sun Ning
Published: October 2019

Background: Micro-computerized tomography (micro-CT) is considered as an innovative non-invasive and high-resolution imaging technology. The current research aims to reconstruct the distribution of preputial vessels in different severity of rat congenital hypospadias model by micro-CT, and to provide an anatomic basis for the selection of preputial vessel pedicle flaps in surgery.
Methods: Pregnant rats were exposed to finasteride from gestational day 12 to 17. Depending on the position of the urethral meatus, the pups were divided into normal, mild hypospadias and severe hypospadias groups. Six months after birth, the preputial blood vessels were observed in vascular perfusion with Microfil (a silicone-based polymer) and scanned by micro-CT. CTvox and NRecon were utilized to reconstruct 3-dimentional(3D) images. A pathological analysis of the specimen was taken in order to determine the position of Microfil.
Results: The normal group and the mild hypospadias group had similar preputial image characteristics. At the junction of the inner and outer prepuce, the deep layer vessels of the superficial fascia were transversely distributed and formed a vascular ring-like structure. Among the severe hypospadias group, five had sufficient blood circulation while six had insufficient blood circulation. In sufficient blood circulation type, the ring-like vessels were found at the junction of the inner and outer prepuce similar to that of the normal and mild hypospadias group. However, only a small amount of capillary supply to this area in the insufficient type.
Conclusion: The junction of the inner and outer prepuce with abundant blood circulation was suitable to be a vascular pedicle flap. The tubularized preputial island flaps were consistent with the ring-like vessels area, and the original blood supply was retained to the greatest extent.
Suicidal ideation, attempt, and determinants among medical students
Authors: desalegn getachew tesfaw , Wondie Mesele , Dereje Saron , Addisu Adanech
Published: October 2019

Background: Suicidal ideation and attempts are highly prevalent among medical students compared to the general population and negatively impacts the quality of life, physical, and mental well being of students. However, research into suicidal ideation and attempts among medical students in low and middle-income countries are limited. Therefore, this study aimed to explore the suicidal ideation and attempts and associated factors among medical students in Ethiopia.
Methods : An institution based cross-sectional study was conducted on 393 medical students from March to June 2019 at the University of Gondar in Ethiopia. A simple random sampling technique used to get study units by their identification card. Suicidal ideation and attempts were assessed by using World Health Organization Composite International Diagnostic Interview (CIDI) to assess lifetime suicidal ideation and attempt during medical school. Data were collected using self-administered questionnaires. Bi-variable and multivariable logistic regression analyses were used to identify associated factors between suicidal ideation and attempts with the explanatory variables at P-value <0.05 was considered statistically significant.
Results: A total of 393 study participants were interviewed with a response rate of 92.9%. The prevalence of suicidal ideation and attempts among study participants were found to be 14% and 7.4% with 95% CI (10.9, 18.1) and (5.1, 10.2), respectively. In multivariate logistic regression; female sex (AOR: 5.21, 95% CI: 2.42, 11.20), depression (AOR: 10.12, 95% CI; 4.80, 21.52), current khat chewing (AOR: 4.46, 95% CI; 132, 15.02), and poor social support (AOR: 4.46, 95% CI: 1.43, 13.87) were factors significantly associated with suicidal ideation. Being female (AOR: 8.08, 95% CI: 3.04, 21.39), depression (AOR: 10.66, 95% CI; 4.01, 28.01 ), and history of mental illness (AOR: 5.53, 95% CI; 1.20, 25.50) were factors significantly associated with suicide attempts.
Conclusions : In the current study, the prevalence of suicidal ideation among medical students was low compared to other studies, but the suicide attempt was high. Ethiopian medical students better to instate a screening program for every medical student for early detection and intervention of suicidal ideation and attempt.
Keywords: Suicidal Ideation, Attempt, Medical Students, Prevalence, Ethiopia
Glucose 6 Phosphate Dehydrogenase Deficiency and Hemoglobinopathy in South Western Region Nepal: A Boon or Burden
Authors: Gautam Narayan , Gaire Bhagwati , Manandhar Trishna , Marasini Bishnu P , Parajuli Niranjan , Lekhak Sunil P , Nepal Monica
Published: October 2019

Objectives: The study was carried out to optimize the phenotypic method to characterize the sickle cell trait (SCT), sickle cell anaemia (SCA) and β-thalassemia (β-TT) suspected sample from tharu community of South Western province-5, Nepal. SCT and SCA were further evaluated by genotypic method employing amplification refractory mutation system (ARMS PCR). Moreover, Glucose 6 Phosphate Dehydrogenase (G6PD) was estimated in those hemoglobinopathy to observe its prevalence. The accurate and reliable method can play an important role in reduction of morbidity and mortality rate.
Results: The 100 suspected cases were subjected to phenotypic method adopting cellulose acetate electrophoresis and genotypic metod using ARMS PCR which portraits (5%) SCA positive test showing HBS/HBS, (38%) SCT positive trait HBA/HBS and (36%) cases normal HBA/HBA. β-TT (21%) cases were confirmed by electropherogram. G6PD deficiency was observed in (40%) of SCA, (18.4%) of SCT, (4.8%) of β-TT and (2.8%) in normal cases. Increased G6PD were developed only in SCT (5.3 %) and β-TT (4.8%). The study highlighted sickle cell disorder (SCD) and β-TT as the most common hemoglobinopathy coexisting with G6PD deficiency. Though hemoglobinopathy sometime could be protective in malaria but G6PD deficiency can cause massive hemolysis which may exacerbate the condition.
Seasonal variations in the occurrence of acute appendicitis and their relationship with the presence of fecaliths in children
Authors: Hsu Yao-Jen , Fu Yu-Wei , Chin Taiwai
Published: October 2019

Background
Acute appendicitis (AA) is the most common surgical condition in children. Although a higher incidence of AA in summer has been reported, the reason for this observation remains unclear. The purpose of this study was to compare the clinical findings of AA patients who underwent appendectomies during the summer months with those who underwent the procedure during the non-summer months.
Methods
The clinical data of 171 patients who underwent appendectomy from January 2013 to December 2016 were reviewed. The patients were divided into a summer group (from May to October) and a non-summer group (from November to April) based on the month when appendectomy was performed. All patients were under 18 years of age at the time of surgery. Laboratory data, computed tomography scans, pathology reports and operative records were reviewed.
Results
The number of patients with AA was higher in the summer group than in the non-summer group (101 vs. 70 patients). No significant differences in the laboratory results between the two groups of patients were observed. The percentage of AA patients who presented with a fecalith was significantly lower in the summer group (33.6%) than in the non-summer group (55.7%). No significant differences in the incidence of appendiceal perforations and abscesses were observed between the two groups.
Conclusions
The percentage of AA patients with fecaliths in summer was lower than that in the non-summer months. The increase in the number of AA patients in summer may be due to the increased occurrence of lymphoid hyperplasia, which may be correlated with the yearly outbreak of enterovirus infection during this period.
C1GALT1 expression is associated with galactosylation of IgA1 in peripheral B lymphocyte in immunoglobulin A nephropathy
Authors: Xing Yue , Li Lina , Zhang Yaru , Wang Fanghao , He Dandan , Liu Youxia , Jia Junya , Yan Tiekun , Lin Shan
Published: October 2019

Background More and more studies demonstrated that genetic variation at C1GALT1 influences Gd-IgA1 level in IgAN. However, whether the expression of β1, 3-galactosyltransferase (β1, 3Gal-T) was influenced may provide insights into how Gd-IgA1 levels are controlled in IgAN. Methods Thirty IgAN patients diagnosed in Tianjin Medical University General Hospital from April to September 2018 and 30 healthy volunteers whose age and gender matched with patients were enrolled in this study. Total Gd-IgA1 levels in plasma were determined by ELISA and C1GALT1 levels were determined by RT-PCR. Four databases (PubMed, EMBASE, CNKI, WanFang Medical Network) were searched to identify eligible studies that evaluated a difference in the expression of C1GALT1 in IgAN patients compared with total controls (non-IgAN and health controls). The C1GALT1C1 expression levels, which was indispensable to β1, 3Gal-T of IgA1, was also been compared. Results Gd-IgA1 levels were remarkable higher in IgAN patients compared with healthy control. The expression levels of C1GALT1 gene were remarkably down-regulated in IgAN patients compared with healthy control. And the mRNA level of C1GALT1 was inversely correlated to Gd-IgA1 levels. In meta-analysis, six articles including 316 participants that analyzed the expression of β1, 3Gal-T were met inclusion criteria. There was no significant difference in the expression of C1GALT1 between IgAN patients compared with controls. And we found patients with IgAN had lower levels of C1GALT1 gene expression in the B cells compared to controls. The C1GALT1C1 levels in the IgAN patients were not different from the levels in the control group, which were unchanged no matter according to different ethnic population, different control group and different cell source. Two studies including 46 persons compared enzymatic activity of β1, 3Gal-T in B cells, and the result showed the β1, 3Gal-T activity was decreased in B cells. Conclusions We found expression levels of C1GALT1 were remarkably downregulated in IgAN patients and negatively correlated with higher levels of Gd-IgA1. Subsequent meta-analysis validated the low expression and activity of β1, 3Gal-T in B cells in patients with IgAN. However, there was no apparent disparity in the aspect of C1GALT1C1 expression between IgAN and control groups.
Establishment of a sentinel surveillance network for sexually transmissible infections and blood borne viruses in Aboriginal primary care services across Australia: the ATLAS project
Authors: Bradley Clare , Hengel Belinda , Crawford Katy , Elliott Salenna , Donovan Basil , Mak Donna B , Nattabi Barbara , Johnson David , Guy Rebecca , Fairley Christopher K , Wand Handan , Ward James
Published: October 2019

Background Sexually transmissible infection (STI) and blood-borne virus (BBV) notification data is a mainstay of the Australian National Notifiable Diseases Surveillance System (NNDSS) and is a mandatory requirement in all Australian jurisdictions. The system focuses on STI and BBV diagnoses alone, without testing, treatment or management data, leaving major gaps in the understanding of epidemics, especially among priority populations like Aboriginal and Torres Strait Islander peoples. Further information is required to supplement the NNDSS to better understand epidemics, the impact of interventions and health care delivery against clinical guidelines. Here we describe the rationale, processes and expected outcomes of establishing a national STI and BBV sentinel surveillance network in Aboriginal primary care services—known as the ATLAS network.Methods Researchers invited participation and consultation with Aboriginal Community-Controlled Health Services (ACCHS) clustered in five clinical hubs across four jurisdictions, representative of urban, regional and remote regions. Site-specific participation agreements were developed for each clinical hub and individual ACCHS. De-identified electronic medical record (EMR) data relating to STI and BBV testing, treatment and care are collected passively from each health service via the GRHANITE tm data extraction tool. These data are analysed centrally to inform 12 performance indicators which are included in surveillance reports generated for each health service and clinical hub.Results The ATLAS network currently involves 29 ACCHS representing all five clinical hubs. The ATLAS network provides detailed surveillance reports to individual ACCHS as well as contributing to aggregate comparative analyses at the clinical hub, jurisdictional and national levels. Data derived from the ATLAS network is used to assess clinical practice within each site. Aggregated data will inform clinical guidelines and extend the research potential of participating ACCHS sites. The ATLAS infrastructure can be expanded to include other health services and potentially linked to other data sources using GRHANITE.Conclusions The ATLAS network will supplement the NNDSS and contribute to improved understanding of local, regional and national patterns of clinical care of STI and BBV to inform clinical practice, policy, and program-planning.
Assessing the youth-friendliness of youth clinics in northern Sweden: the perspective of the youth
Authors: Waenerlund Anna-Karin , Sebastian Miguel San , Hurtig Anna-Karin , Wiklund Maria , Christianson Monica , Goicolea Isabel
Published: October 2019

Background Sweden has nearly 300 youth clinics that have been offering services since the 1970s. However, no evaluation has been done to assess their youth-friendliness. This study aims to assess: i) to what extent youth clinics are perceived as youth-friendly by the young people using them; and ii) if the level of youth friendliness is equally perceived across different sociodemographic groups of users.Methods The four northernmost counties of Sweden were included in the study. Of the total identified 22 youth clinics, 20 participated by giving out questionnaires to the youth after their visits to the respective youth clinics. In total 1,110 youth participated in the study and answered questions according to the World Health Organization’s criteria of accessibility, equity, respect, privacy and confidentiality, no judgement, and quality. Means and frequencies were calculated, and t-test and ANOVA were used to compare means by sociodemographic variables.Results Participants perceived the youth clinics as very youth friendly across the measured domains, with scores as high as 4.8 and 4.9 (of a maximum of 5) in the studied domains. Youth clinics were perceived in a similar way regardless of gender, but other sociodemographic factors influenced some of the domains, especially ethnic background.Conclusions The perception of youth friendliness in youth clinics was very high. Nonetheless, younger users; users who did not categorize themselves as either heterosexual, homosexual, or bisexual; users with trans-experiences; and users with migrant backgrounds gave youth clinics lower scores for certain domains.
Bioinformatic Analysis of Peripheral Blood miRNA of Breast Cancer Patients in Relation With Anthracycline Cardiotoxicity
Authors: Yadi Wang , Shurui Chen , Tong Zhang , Suxian Chen , Qing Tong , Dongning He
Published: October 2019

The current diagnostic methods and treatments still fail to lower the incidence of anthracycline-induced cardiotoxicity effectively. In this study, we aimed to (1) analyze the cardiotoxicity-related genes after breast cancer chemotherapy in gene expression database and (2) carry out bioinformatic analysis to identify cardiotoxicity-related abnormal expressions, the biomarkers of such abnormal expressions, and the key regulatory pathways after breast cancer chemotherapy. Cardiotoxicity-related gene expression data (GSE40447) after breast cancer chemotherapy was acquired from the GEO database. The biomarker expression data of women with chemotherapy-induced cardiotoxicity (group A), chemotherapy history but no cardiotoxicity (group B), and confirmatory diagnosis of breast cancer but normal ejection fraction before chemotherapy (group C) were analyzed to obtain the mRNA with differential expressions and predict the miRNAs regulating the differential expressions. The miRanda formula and functional enrichment analysis were used to screen abnormal miRNAs. Then, the gene ontology (GO) analysis was adapted to further screen the miRNAs related to cardiotoxicity after breast cancer chemotherapy. The data of differential analysis of biomarker expression of groups A, B, and C using the GSE40447-related gene expression profile database showed that there were 30 intersection genes. The differentially expressed mRNAs were predicted using the miRanda and TargetScan software, and a total of 2978 miRNAs were obtained by taking the intersections. Further, the GO analysis and targeted regulatory relationship between miRNA and target genes were used to establish miRNA-gene interaction network to screen and obtain 7 cardiotoxicity-related miRNAs with relatively high centrality, including hsa-miR-4638-3p, hsa-miR-5096, hsa-miR-4763-5p, hsa-miR-1273g-3p, hsa-miR6192, hsa-miR-4726-5p and hsa-miR-1273a. Among them, hsa-miR-4638-3p and hsa-miR-1273g-3p had the highest centrality. The PCR verification results were consistent with those of the chip data. There are differentially expressed miRNAs in the peripheral blood of breast cancer patients with anthracycline cardiotoxicity. Among them, hsa-miR-4638-3p and hsa-miR-1273g-3p are closely associated with the onset of anthracycline cardiotoxicity in patients with breast cancer. Mining, integrating, and validating effective information resources of biological gene chips can provide a new direction for further studies on the molecular mechanism of anthracycline cardiotoxicity.
Strategic priorities for TB control in Bangladesh, Indonesia, and the Philippines – Comparative Analysis of National TB Prevalence Surveys
Authors: Kak Neeraj , Chakraborty Krishnapada , Sadaphal Swati , AlMossawi Hala Jassim , Calnan Marianne , Vikarunnessa Begum
Published: October 2019

Background: Philippines, Indonesia, and Bangladesh are three high TB burden countries in Asia which account for 18% of the estimated global TB incidence (1.787m) and 15% of TB related deaths (192,000). In 2017 alone, approximately 785,000 of the incident TB cases in these countries remained missing including diagnosed but not notified. Methods: We reviewed the published data from the most recent TB prevalence surveys conducted in Bangladesh, Indonesia, and the Philippines. The prevalence rates established by the surveys were used to estimate the disease burden of these countries for 2017. The Global TB Report 2017 and WHO’s global TB database were sourced for collection of incidence and notification data by age groups and types of TB to estimate prevalence to notification gaps 2017. Results: According to the surveys, the estimated prevalence rates of bacteriologically confirmed TB and smear-positive TB are 287 and 113 for Bangladesh (2015-16), 759 and 256 for Indonesia (2013-14) and 1159 and 434 for the Philippines (2016) per 100,000 population over the age of 15 years. The overall national TB prevalence estimates for all forms is 260 for Bangladesh, 660 for Indonesia, and 970 for the Philippines (2016). Compared with the incidence rate, the proportion of total notified cases is 67% Bangladesh, 52% for Indonesia, and 55% for Philippines. Bangladesh has been able to detect almost 100% of the prevalent pulmonary TB, while Indonesia and Philippines have detected only 30% and 22% of these infectious cases respectively. Although notification has been improving over the years, there is no impact on the incidence rate since a large proportion of the undiagnosed cases, and delayed diagnosis continue to feed the transmission process. Conclusion: The surveys have provided data that is critical for developing realistic strategies for the countries to eliminate TB. In general, this paper recommends interventions for strengthening diagnosis of pulmonary TB, targeted communication programs and active case finding to reduce patient level delays, expanding public-private mix to increase access to TB services, use of rapid diagnostics, and social protection for vulnerable populations, to accelerate the countries’ progress towards achieving End TB goals.
Evaluation of condylar cortical bone thickness in patients with different vertical facial dimensions using cone-beam computed tomography.
Authors: Giudice Antonino Lo , Rustico Lorenzo , Caprioglio Alberto , Bellocchio Angela Mirea , Gatto Elda , Portelli Marco , Militi Angela , Dolci Carolina , Spinuzza Paola , Leonardi Rosalia , Nucera Riccardo
Published: October 2019

Background The aim of this study is to evaluate through computed tomography differences in cortical plate thickness of condyle in patients with different facial vertical skeletal pattern.Methods The final sample of this retrospective study included CBCT exams of 60 adult subjects (mean age 33.2 ± 5.6), selected from the digital archive of a private practice. The subjects were assigned to 3 different groups according to the values of the Frankfurt-mandibular plane angle: hyper- normo- and hypodivergent group. The volume rendering of the mandible was obtained and three condylar points were marked on it: median pole, lateral pole and the most cranial point. For each considered reference point the minimum distance between external and internal cortical surface was measured, obtaining three different outcomes: median pole, lateral pole and cranial point cortical bone thickness. The measurement was executed by means of Mimics software by the same expert operator in specific scan views.Results The cortical bone thickness of hyperdivergent patients was found to be statistically thicker than normodivergent patients and hypodivergent patients. Cortical bone thickness of normodivergent patients was found thicker than hypodivergent patients. All the differences were statistically significant (p<0.05). The Person correlation coefficient showed a statistically significant correlation (p<.001) between the Frankfurt-mandibular plane angle and the evaluated cortical bone thickness outcomes.Conclusion Facial biotype characteristics that define vertical facial skeletal pattern affect the cortical bone thickness of mandibular condyle.
Clinical study of Endoscopic treatment of a sellar pituitary adenomas with sellar diaphragm defect
Authors: Jin Zhuoru , Wu Xinyu , Wang Yibao
Published: October 2019

Purpose: Invasive growth of pituitary macroadenomas to the suprasellar region occurs commonly. Pituitary adenomas show varying growth patterns when the sellar diaphragm is absent, and they are often confused with other common tumors in the sellar region. This article explores the clinical features of suprasellar pituitary adenomas with defects of the sellar diaphragm (SPADSD) and evaluates the efficacy of the endoscopic endonasal approach (EEA) for treatment of such tumors. Methods: We performed a detailed examination of records from 19 patients collected prior to surgery. After relevant diseases were excluded, the tumor properties were evaluated according to imaging characteristics. Diagnoses were verified using EEA surgery. The concept of SPADSD was put forward. Postoperative recovery was followed to determine whether EEA is suitable for the treatment of such tumors. Results: In the 19 patients with SPADSD, we found that the tumors were less stressed on the pituitary, and tumors in the suprasellar region often had irregular shapes. During surgery, we took extended supra-saddle approaches and confirmed that unrestricted growth of the tumor was caused by defects in the diaphragm of the sella turcica to the suprasellar region. Recovery was good after surgery, confirming the efficacy of EEA for treatment of these tumors. Conclusion: SPADSD has different clinical features from those of other pituitary tumors and requires careful screening prior to surgery. Endoscopic surgery is the preferred procedure for this type of tumor.
Investigation of candidate biomarkers and prognostic values in endometrial cancer based on bioinformatics analysis
Authors: Li Yaowei , Li Li
Published: October 2019

Background: Endometrial cancer is a common gynecological cancer whose incidence is increasing annually worldwide. However, the biomarkers that provide the prognosis and progression of endometrial cancer are still lacking. Methods: The differentially expressed mRNAs and miRNAs were screened out using mRNA and miRNA expression data of endometrial cancer from Gene Expression Omnibus, and then validated in the Cancer Genome Atlas. The Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were conducted using the Database for Annotation,Visualization and Integrated Discovery. A protein–protein interaction network was constructed by STRING and visualized using Cytoscape. OncoLnc was used for studying the prognostic effects of the hub genes. In addition, miRecords were used to predict target genes of differentially expressed miRNAs, and then a miRNA-mRNA regulatory network was constructed. Results: Two eligible human endometrial cancer datasets ( GSE17025 and GSE25405) met the requirement. A total of 520 differentially expressed mRNAs and 30 differentially expressed miRNAs were identified. These differentially expressed mRNAs were mainly enriched in cell cycle, skeletal system development, vasculature development, oocyte maturation, and oocyte meiosis signaling pathways. 160 pairs of differentially expressed miRNAs and mRNAs, including 22 differentially expressed miRNAs and 71 overlapping differentially expressed mRNAs, were validated in endometrial cancer samples using starBase v2.0 project. And the prognosis analysis found that Cyclin E1 (CCNE1, one of the 82 hub genes, which was correlated with hsa-miR-195) was correlated with significantly worse overall survival in endometrial cancer patients. Conclusions: These hub genes and differentially expressed miRNAs might be used as molecular targets for the treatment of endometrial cancer and prognostic biomarkers for endometrial cancer.
Evolution of pathogen response genes associated with increased disease susceptibility during adaptation to an extreme drought in a Brassica rapa plant population
Authors: O'Hara Niamh Breda , Franks Steven J , Kane Nolan C , Tittes Silas , Rest Joshua S
Published: October 2019

Pathogens have dramatic effects in natural and agricultural plant systems. There is evidence of evolutionary changes in disease susceptibility as a consequence of climate change, but we know little about the underlying genetic basis of this evolution. To address this, we took advantage of a historical seed collection of a Brassica rapa population, which we previously demonstrated evolved an increase in disease susceptibility to a necrotrophic fungal pathogen following a drought. Previously, we combined a resurrection experiment with genome-wide sequencing of 124 pooled ancestral and descendant plants. In this study, we found that well-characterized necrotrophic fungal pathogen response (NFPR) genes were differentiated between ancestors and descendants, with several of them identified as extreme F ST outliers. The jasmonic acid (JA) signaling pathway in particular seemed to underlie the evolution of disease susceptibility, in addition to its well characterized role in plastic disease response. Next, we identified a list of 260 genes that are both NFPR genes and are differentially expressed in response to drought, based on publicly available data. We found evidence that five of these genes evolved between ancestors and descendants, suggesting that the drought acted as the evolutionary driver, and that the accompanying increase in disease susceptibility may have been a consequence of genetic pleiotropy. Our study provides evidence that for this population, standing natural variation in NFPR genes is affected by natural selection related to climate change. Our results reveal potentially important candidates that may underlie trait evolution in both crops and natural systems. Additionally, this trade-off between adaptation to biotic and abiotic stresses is an example of how climate change can have diverse and unexpected consequences.
Transcriptome Ortholog Alignment Sequence Tools (TOAST) for Phylogenomic Dataset Assembly
Authors: Dornburg Alex , Wcisel Dustin J. , Howard J. Thomas , Yoder Jeffrey A.
Published: October 2019

Background Advances in next-generation sequencing technologies have reduced the cost of whole transcriptome analyses, allowing characterization of non-model species at unprecedented levels. The rapid pace of transcriptomic sequencing has driven the public accumulation of a wealth of data for phylogenomic analyses, however lack of tools aimed towards phylogeneticists to efficiently identify orthologous sequences currently hinders effective harnessing of this resource.Results We introduce TOAST, an open source R software package that can utilize the ortholog searches based on the software Benchmarking Universal Single-Copy Orthologs (BUSCO) to assemble multiple sequence alignments of orthologous loci from transcriptomes for any group of organisms. By streamlining search, query, and alignment, TOAST automates the generation of locus and concatenated alignments, and also presents a series of outputs from which users can not only explore missing data patterns across their alignments, but also reassemble alignments based on user-defined acceptable missing data levels for a given research question.Conclusions TOAST provides a comprehensive set of tools for assembly of sequence alignments of orthologs for comparative transcriptomic and phylogenomic studies. This software empowers easy assembly of public and novel sequences for any target database of candidate orthologs, and fills a critically needed niche for tools that enable quantification and testing of the impact of missing data. As open-source software, TOAST is fully customizable for integration into existing or novel custom informatic pipelines for phylogenomic inference.
Protein network analysis indicates that Ebola virus, Neisseria meningitidis and Trypanosoma brucei trigger common host defense response pathways
Authors: Gupta Shishir K , Ponte-Sucre Alicia , Bencurova Elena , Dandekar Thomas
Published: October 2019

Background: Sepsis is the most severe final state of infection. Might pathogens belonging to different kingdoms of life and pathogen classes trigger analogous responses pathways in the host? Is there a common denominator or strategy to prevent it? Here we use interactomics and comparative evolutionary analysis of three serious infectious pathogens, spanning viruses, bacteria and parasites: Filovirus ebolavirus (ZE; Zaire ebolavirus , Bundibugyo ebolavirus), Neisseria meningitides (NM), and Trypanosoma brucei (Tb) that target the blood during their infectious life cycle. Results: We analyze 2797 unique human proteins targeted by the pathogens. The comparison resulted in specific and shared protein-protein interactions (PPIs) with each pathogen, derived from orthology searches of experimentally validated PPIs. Furthermore, we narrow down the data set of effected genes of the human (defense) immune response and describe human proteins predicted to participate in at least two of the compared host-pathogen networks. Only four proteins were common to all three host-pathogen interactomes. This interaction clade of four proteins, common to all three host-pathogen networks, suggests a central cluster of host response formed by elongation factor 1-alpha 1 (EF-1-alpha-1), the SWI/SNF complex subunit SMARCC2 (matrix-associated actin-dependent regulator of chromatin subfamily C), the dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1, and the tubulin beta-5 chain. These hub proteins are functionally connected, suggesting according to the collected data including experimental information on VP24 from Ebola virus that these, as well as some joined interaction partners, may orchestrate a common host response to infection.
Comparison of the clinical and MRI features of patients with hepatic hemangioma, epithelioid hemangioendothelioma, or angiosarcoma
Authors: Liu Zhuangsheng , Yi Lilei , Chen Junhao , Li Ruqiong , Liang Keming , Chen Xiangmeng , Li Ronggang , Long Wansheng
Published: October 2019

Background Comparisons of hepatic epithelioid hemangioendothelioma (HEHE), hepatic hemangioma, and hepatic angiosarcoma (HAS) have rarely been reported. The purpose of our study was to analyze the clinical and magnetic resonance imaging (MRI) findings of these conditions.Methods A total of 57 patients (25 with hemangioma, 13 with HEHE, and 19 with HAS) provided hepatic vascular endothelial cell data between June 2006 and May 2017. The measurement data were represented as means±SDs. Between-group comparisons were performed using independent-samples t-tests. Count data were represented as frequencies or rates, and χ2- or Fisher’s exact tests were performed.Results The proportions of cases with circumscribed margins were 88% (22/25), 84.6% (11/3), and 31.6% (6/19) for hemangioma, HEHE, and HAS, respectively (P<0.001). HAS lesions were less likely to have circumscribed margins. The proportions of lesions with hemorrhaging were 4% (1/25), 44.4% (4/13), and 36.8% (7/13) for hemangioma, HEHE, and HAS, respectively (P=0.014). HEHE and HAS cases were more likely to show heterogeneous signals on T1-weighted (T1WI) MRI. HEHE and HAS cases were more likely to show heterogeneous signals on T2-weighted (T2WI) MRI. Centripetal enhancement was the most common pattern in vascular tumors, with proportions of 100%, 46.2% (6/13), and 68.4% (13/19) for hemangioma, HEHE, and HAS, respectively. The difference in enhancement pattern between HEHE and HAS was not significant, but rim enhancement was more common for HEHE (46.2%, 6/13).Conclusions Our study revealed clinical and imaging differences between HEHE and HAS. The platelet count (PLT) and coagulation function of the HAS group decreased, whereas the alpha-fetoprotein (AFP) level increased. The 5-year survival rate for HAS was significantly lower than that of HEHE. A higher malignancy degree indicated a more blurred lesion margin, easier occurrence of hemorrhaging, and more heterogeneous plain T1WI and T2WI signals.
Towards a framework for trust-based management of municipal home care. A realist informed evaluation.
Authors: Eide Tom , Gullslett Monika , Dugstad Janne , Nilsen Etty R. , McCormack Brendan , Eide Hilde
Published: October 2019

Background This study reports on a two-step service innovation project commissioned by the City Council of Oslo, coined as the Trust Model (TM). The aim was to develop a trust-based management model in municipal home care as an alternative to the purchaser-provider split (PPS), which has been the prevalent model in Norwegian and most European health services since the introduction of New Public Management in the 1990s. The TM was developed through a comprehensive participatory process.Methods The objectives were to a) identify important mechanisms facilitating or preventing the development and implementation of the trust model, and b) identify participants perceived outcomes. A realist informed process evaluation using mixed methods was performed in two iterations. The first (autumn 2016) included three districts, three teams and 80 patients. The second (2017) included four districts, eight teams and 160 patients.Results The TM was developed across the four districts. Team members, team leaders and managers found the TM promising, and no one wanted to return to the PPS. Patient satisfaction improved significantly during the first iteration. The TM iterations were complex, involving a series of agents interacting on different levels; interactions which in turn influenced the processes and ongoing interactions. The evaluation displayed a variety of interpretations of the TM and of trust as an organizational value. A series of needs for improvements were identified, including (1) develop a clear description of the model and its managerial principles, (2) develop a culture for trust-based management on all levels, (3) build team leaders’ competence, especially in trust-based management and coaching of team-members (4), clarify roles and responsibilities among team-members, (5) develop common procedures for allocation and distribution of services, and (6) build team-members communication competence in active listening and shared decision-making.Conclusions/implications Complex, values-based organizational innovation and change (like TM) challenge existing institutional logics (like NPM) and an organization’s ability to cope with institutional hybridization. The complexity of organizational innovation in home care and of researching this topic is understudied. The importance of recognizing the complexity of trust-building and the inherent slowness of radical service innovation should be further explored.
In search of universal health coverage – highlighting the accessibility of health services for students with disabilities in Ghana: a qualitative study
Authors: Abodey Eric , Vanderpuye Irene , Mensah Isaac , Badu Eric
Published: October 2019

Background: Accessibility to health services for students with disabilities is a global concern. This is no less important in Ghana, however, to date, no study has been undertaken regarding access to health services for students with disabilities. This study, therefore, aims to explore the accessibility of health services for students with disabilities, in the quest of achieving universal health coverage in Ghana. Methods: Qualitative methods, involving in-depth interviews were employed to collect data from 54 participants (29 students with disabilities, 17 health workers and 8 school mothers), selected through purposive sampling. Thematic analysis was used to analyze the data. Results : The study identified three themes – accessibility, adequacy, and affordability. The study findings highlighted that universal health coverage for students with disabilities has not been achieved due to barriers in accessing health services. The barriers faced by students with disabilities are unfriendly physical environments, structures, equipment, limited support services and poor health insurance policy to finance health services. Conclusion : The study concludes that the government should prioritize disability-related issues in health policy formulation, implementation and monitoring. The current provisions and requirements in the disability act should be prioritized, enforced and monitored to ensure adequate inclusion of disability issues in health services. Further, the current exemption policy under the NHIS scheme should be revised to adequately address the needs of people with disabilities.
Can IVIM MRI be used to differentiate patients with placenta accreta spectrum disorders?
Authors: Lu Tao , Pu Hong , Li Kuide , Mei Jie , Huang Meng-wei , Wang Shao-yu
Published: October 2019

Objective The primary aim was to investigate whether the parameters from IVIM can be used to differentiate patients with PAS disorders complicating placenta previa. A second aim was to determine whether these parameters can be used to differentiate different categories of PAS disorders complicating placenta previa. Methods All the patients had placenta previa, including 16 patients with placenta accreta, 51 patients with increta, 8 patients with percreta and 24 patients without PAS disorders between 28+0 and 39+6 weeks. All women underwent MRI examination including an IVIM sequence at 1.5T scanner. The perfusion fraction(f), pseudodiffusion coefficient (D*) and standard diffusion coefficient(D) were calculated. Results Women with PAS disorders had a higher perfusion fraction (P<0.05) than women without the disease. Multiple comparisons showed perfusion fraction in patients without PAS disorders was significantly lower than in patients with placenta accreta and percreta(P<0.05), but was not lower than in patients with increta(p>0.05). Conclusion Patients with placenta accreta and percreta differ in placental perfusion fraction from women with increta and without PAS disorders. The perfusion fraction can be used as a reliable index to evaluate placenta perfusion fraction.
MR Imaging Features of Orbital Langerhans Cell Histiocytosis
Authors: wu chunnan , Mu xuetao , Hei yan , lan pengyu , li kuncheng
Published: October 2019

Background: To investigate the magnetic resonance imaging (MRI) features of orbital Langerhans cell histiocytosis (LCH) to improve diagnostic accuracy. Methods: We retrospectively reviewed clinical manifestations and MRI findings of 23 patients with histopathology-confirmed LCH of the orbit. The findings were evaluated for the following: (a) symptoms, (b) disease duration，(c) location, (d) configuration, (e) margin, (f) MR imaging signal intensity and enhanced performance. Results: Eighteen patients (78%) in our series were male, only five (22%) patients were female, and the mean age at presentation was 6.3 years. The common symptoms include swollen eyelids, exophthalmos, and a palpable mass. Fourteen patients presented with swollen eyelids and/or exophthalmos. Twenty-two cases involved unilateral orbits, and one case involved bilateral orbits. In our study, there was one patient with cough and expectoration, and one patient with polydipsia and polyuria. Lesions were located in the superior or superlateral orbital roof of seventeen patients (74%). Lesions formed masses or irregular shapes. The 12 out of 23 (52.2%)cases appeared heterogeneous isointense and 10 out of 23 (43.5%) cases showed iso-hypointense on T1-weighted imaging, there were 15 out of 23 (65.2%) cases showed hyper-hypointense mixed signals on T2-weighted imaging. 7 cases found patchy hyperintense signal on T1WI, and 11 cases showed markedly hyperintense signal near the edge of lesions on T2WI. After enhancement, 21 out of 23 (91.3%) cases lesions presented marked enhancement at the edges and the surrounding tissues, and with heterogeneous obvious enhancement of the lesion center. Besides, four cases lesions were surrounded by a low circular signal. Conclusion: There were several characteristics MRI features that can provide crucial information for clinicians and improve our understanding and the diagnostic accuracy of the orbital LCH.