bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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.