bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bat Coronavirus of Pteropus alecto from Gorontalo Province, Indonesia
Authors: Febriani Wenty Dwi , Saepuloh Uus , Ayuningsih Ellis Dwi , Saputra R. Suryo , Purbatrapsila Azhari , Nangoy Meis Jacinta , Ransaleh Tiltje Andretha , Wahyuni Indyah , Dako Safriyanto , Noviana Rachmitasari , Iskandriati Diah , Tumbelaka Ligaya ITA , Pamungkas Joko 
Published: August 2019

Bats have been known as natural reservoirs for potential emerging infectious viruses, such as Lyssaviruses, Coronaviruses, Ebola viruses, Nipah virus, and many others. Because of their abudance in population, wide distribution and mobility, bats have a greater risk as source for zoonotic transmission than other animals. Despite the facts of their role as reservoirs for many pathogens, not until an epidemic of Severe Acute Respiratory Coronavirus (SARS-CoV) in 2003 and Middle-East Respiratory Syndrome Coronavirus (MERS-CoV) in 2012, that people pay much attention about coronavirus in bats. SARS-like virus also found in bats with a higher prevalence rate. This study aims to detect the coronavirus of bats in Gorontalo province Indonesia, characterization at the molecular level of the coronavirus genome and determining the level of kinship (through trees filogenetic). This study was conducted as part of bigger PREDICT Indonesia project, in particular to examine coronavirus in bats from Gorontalo province, Indonesia. As many as 95 rectal swab samples collected from flying foxes (Pteropus alecto) were analyzed in the laboratory using Consensus Polymerase Chain Reaction (PCR) technique to amplify the target sequence from RNA-dependent RNA Polymerase (RdRp) gene with 434 basepair product, resulted 24 samples determined as presumptive positive. Eight out of 24 presumptive positive samples by PCR were analyzed further by nucleotide sequencing and confirmed coronavirus positive. Phylogenetic tree analyses to the eight coronavirus confirmed-sequences were constructed with MEGA-6.0 . The conclusion was 24 out of 95 samples suggested as presumptive positive to Bat CoV. Eight out of 24 samples were analyzed further by nucleotide sequencing and have similarities in the kinship. Three samples had the 98% nucleotide identity to BatCoV from Indonesia and five samples were 85-88% nucleotide identity to BatCoV from Thailand.
Concentration Of Cortisol Metabolites In Captive Sumatran Elephants At Elephant Conservation Facilities In Aceh
Authors: Wahyuni Rosa Rika , Wahyuni Sri , Azhar Al , Gholib Gholib 
Published: August 2019

This study was conducted to validate the DRG Cortisol ELISA EIA-1887 Germany kit for measure the concentration of stress hormone metabolites (cortisol) from the feces and its correlation to the stressor factor in captive elephants in PKG and CRU of Aceh. These factors are location, diet and presence of livestock. There is no special treatment, observation based on the activity, behavior or natural condition of the animals. The sampling technique was non invasive, fresh dung samples of each (±20 gram) were collected from 25 elephants in CRU and PKG. Feces taken in the morning (before the animals are bathed) along with the observation of animal behavior. All samples were collected and stored at -200C until the analysis process. The validation test are analytic (parallelilmsm) and biological validation test. The analytic test result (paralillsm), showed that the sample curve was not parallel to the standard curve, but crossed the standard curve. While the results of biological validation test, DRG Cortisol ELISA EIA-1887 Germany kit can measure the concentration of cortisol hormone feces of Sumatran elephant and able to describe the difference of cortisol concentration relation to physiological events (stress vs non-stress). The mean values of cortisol metabolite concentrations from PKG Saree (Komplek PKG and Hutan Seunapet), Sampoiniet CRU, Cot Girek, Das Peusangan, Meulaboh and Aceh Timur were (577 ng/g and 400 ng/g), 435ng /g, 419ng /g, 517ng / g, 401ng/g and 425ng /g. The measurement results correlate with the physiological conditions and observed factors.
Potentially functional genetic variants in the c-Myb signaling pathway genes are associated with survival of non-small cell lung cancer patients in the PLCO Cancer Screening Trial
Authors: Guo Yi , Feng Yun , Liu Hongliang , Luo Sheng , Moorman Patricia G. , Patz Edward F. , Su Li , Shen Sipeng , Christiani David C. , Wei Qingyi 
Published: August 2019

Abstract
Background

The c-Myb signaling pathway plays a critical role in regulating expression of genes involved in differentiation, proliferation of cells and cell death, which are related to cancer progression and metastasis.

Methods

To test the hypothesis that genetic variants in the c-Myb pathway genes are associated with survival of non-small cell lung cancer (NSCLC) patients, we used genotyping data from 1,185 NSCLC patients in the Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial as the discovery dataset and 984 NSCLC patients in the Harvard Lung Cancer Susceptibility (HLCS) Study as the validation dataset. With genotyping data for 8587 SNPs in 83 genes of the c-Myb pathway from the PLCO dataset, we performed Cox proportional hazards regression analysis to evaluate association between each SNP and survival, and resultant significant SNPs were validated in the HLCS dataset and further evaluated for their functional relevance.

Results

Specifically, we found that ETS1 rs11606640 GA+AA and ZFHX3 rs62053220 CG+GG genotypes were associated with a favorable overall survival in NSCLC patients (Pdom=0.004 and 0.001, respectively) in a multivariable Cox model. These two validated SNPs were predicted by the RegulomeDB score to be potentially functional. In addition, ETS1 and ZFHX3 mRNA expression levels in lung cancer tissues were significantly lower than that in adjacent normal lung tissues (P<0.05 for both SNPs). Furthermore, the TCGA-based expression quantitative trait loci (eQTL) analysis showed that ETS1 rs11606640 genotypes were significantly associated with their corresponding mRNA expression levels in lung cancer tissues in both additive and recessive models (Padd=0.045 and Prec=0.042), but such a phenotype-genotype correlation for ZFHX3 rs62053220 genotypes was found in only a dominant model (Pdom=0.048).

Conclusion

We identified two potentially functional SNPs (ETS1 rs11606640 G>A and ZFHX3 rs62053220 C>G) that are associated with survival in NSCLC patients. Additional larger studies are needed to validate our findings.
Phenotypic and genotypic detection of metallo-β-lactamases in A. baumanii strains isolated in the teaching hospitals Shahrekord, southwest Iran
Authors: Khaledi Mansoor , Abadi Milad Shahini Shams , Validi Majid , Zamanzad Behnam , Vafapour Rezvan , Gholipour Abolfazl 
Published: August 2019

Abstract
Objective

Acinetobacter baumanii is a pathogenic bacterium that is the cause of many nosocomial infections. This study aimed to determine metallo-β-lactamases produced by the A. baumanii strains isolated in the teaching hospitals in Shahrekord, southwest Iran.

Results

A total of 100 A. baumanii isolates were isolated from 250 clinical samples between June 2013 and June 2014. Then, the strains were identified by biochemical tests and MBL screening conducted by the phenotypic tests modified Hodge, EDTA-disk synergy (EDS), combined disk (CD) and AmpC disc after antibiotic sensitivity test, and the bla (IMP) and bla (VIM) genes detected by PCR. Eighty five (85%) isolates were resistant to meropenem and imipenem. Phenotypic tests showed that out of the 100 isolates, 46, 59, 50, 65 and 65 isolates were positive: AmpC disk, CD, EDS, Modified Hodge and Etest MBL, suggesting MBL production, respectively. Gene detection by PCR showed that 23 isolates carried the VIM-1 gene and only three isolates carried the IMP-1 gene. The prevalence of metallo-β-lactamases-containing A. baumanii isolates is increasing, and the coexistence of various carbapenemases is a problem. Continuous monitoring of the infections due to these bacteria should be taken into account in planning for alternative and new therapeutic strategies.
Trends in maternal use of snus and smoking tobacco in pregnancy. A register study in Southern Norway
Authors: Rygh Ellen , Gallefoss Frode , Grøtvedt Liv 
Published: August 2019

Abstract
Background
The use of tobacco products including Swedish snus (moist snuff) in pregnancy may give adverse health outcomes. While smoking prevalence has decreased among fertile women in Norway, snus use has increased during the last years. We investigated whether these trends were reflected also during pregnancy in a population of women in Southern Norway.
Methods
Data on smoking tobacco and snus use at three time points before and during pregnancy for 20 844 women were retrieved from the electronic birth record for the years 2012-2017. The results for the three-year period 2015-2017 were compared with a previously studied period 2012-2014. Prevalence and quit rates of tobacco use within groups of age, parity and education were reported. Within the same groups adjusted quit rates were analyzed using logistic regression. Mean birthweight and Apgar score of offspring were calculated for tobacco-users and non-users.
Results
There was an increase of snus use before pregnancy from the period 2012-2014 to the period 2015-2017 from 5.1% (CI; 4.6 to 5.5) to 8.4% (CI; 7.8 to 8.9). Despite this, the use of snus during pregnancy did not increase from the first to the second period, but stabilized at 2.8% (CI; 2.5 to 3.2) in first trimester and 2.0% (CI; 1.7 to 2.2) in third trimester. Cigarette smoking decreased significantly both before and during pregnancy. Snus use and smoking during pregnancy gave a reduction in average birthweight, but no significant effects on Apgar scores. Odds ratios for quitting both snus and smoking tobacco during pregnancy were higher for women aged 25-34 years, for the primiparas and for those with a high level of education. Pregnant women were more likely to have quitted tobacco use in the last period compared to the first.

Conclusions
While smoking during pregnancy was decreasing, the use of snus remained constant, levelling off to around 3% in first trimester and 2% in third trimester. Approximately 25% of those that used snus, and 40% that smoked before pregnancy, continued through pregnancy. This implies the need for a continuous watch on the use of snus and other nicotine products during pregnancy.
Utilization, Equity and Determinants of Full Antenatal Care in India: Analysis from the National Family Health Survey 4
Authors: Kumar Gunjan , Choudhary Tarun Shankar , Srivast Akanksha , Updhyay Ravi Praksah , Taneja Sunita , Bahl Rajiv , Martines Jose , Bhan Maharaj Kishan , Bhandari Nita , Mazumder Sarmila 
Published: August 2019

Abstract
Objectives

We estimated the utilisation, determinants and equity of full antenatal care (ANC), defined as 4 or more antenatal visits, at least one tetanus toxoid (TT) injection and consumption of iron folic acid (IFA) for a minimum of 100 days, in India.

Methods

We used data from India’s National Family Health Survey-4. Concentration curves and concentration index were used to assess equity in full ANC utilisation. Multivariable binary logistic regression model was used to examine the factors associated with full ANC utilization.

Results

In India, 21% of pregnant women utilised full ANC, ranging from 2.3% - 65.9% across states. Overall, 51.6% had 4 or more ANC visits, 30.8% consumed IFA for atleast 100 days, and 91.1% had one or more doses of tetanus toxoid. Registration of pregnancy, utilisation of government’s Integrated Child Development Services (ICDS) and health insurance coverage were associated with higher odds of full ANC utilisation. Lower maternal education, lower wealth quintile(s), lack of father’s participation during antenatal visits, higher birth order, teenage and unintended pregnancy were associated with lower odds of full ANC utilisation. Full ANC utilisation was inequitable across area of residence, caste and maternal education.

Conclusions

Full ANC utilization in India was inadequate and inequitable. Although half of the women did not receive the minimum recommended ANC visits, the utilisation of TT immunisation was almost universal. The positive association of full ANC with ICDS utilisation and child’s father involvement may be leveraged for increasing the uptake of full ANC. Strategies to address the socio-demographic factors associated with low and inequitable utilisation of full ANC are imperative for strengthening India’s maternal health program.
Validating a questionnaire to identify women in first trimester of pregnancy during preventive chemotherapy interventions against soil-transmitted helminths in North-western Tanzania
Authors: Mazigo Humphrey Deogratias , Montresor Antonio 
Published: August 2019

Abstract
Background

Women of reproductive age carry a large burden of disease from soil-transmitted helminths infections. Preventive chemotherapy with anthelminthic is an effective treatment to control soil-transmitted helminths morbidity. However, as a precautionary measure, the treatment of pregnant women is recommended only after the first trimester. This has resulted in many women of reproductive age be denied treatment because of doubt on their pregnancy status. The standard assessments of the pregnancy status (i.e. urine pregnancy rapid test or blood test) are too expensive to be used in mass drug administration campaigns. Thus, use of a simple alternative approach is recommended. The present study was conducted to evaluate the performances of a questionnaire in assessing the pregnancy status of women of reproductive age during preventive chemotherapy interventions.

Methodology

A questionnaire (20 questions) followed by rapid pregnancy test (RPT) were administered to a group of women of reproductive age in two districts in North-western Tanzania.

Results

A total of 1,217 women of reproductive age participated in the study. Overall, 10.8% of the women reported to be pregnant at the specific question in the questionnaire. The rapid pregnancy test identified 15.1% (184/1217) of the women to be pregnant. In total, 86.4% (114/1,217) of the women who reported to be pregnant during the interview were confirmed to be pregnant using the RPT. The question on pregnancy demonstrated an overall sensitivity of 62% and specificity 98.3%.

Conclusion

The questionnaire can be used to identify pregnant women in first trimester during preventive chemotherapy campaigns. The question on last date of start of menstrual period yield the highest sensitivity and appeared to be the key one to be used in combination with other questions. However, validation of these results in other countries with different cultures are needed to fully evaluate performance of this method.
Electronic data capture for large scale typhoid surveillance, household contact tracing, and health utilisation survey: Strategic Typhoid Alliance across Africa and Asia
Authors: Thindwa Deus , Farooq Yama G , Shakya Mila , Saha Nirod , Tonks Susan , Anokwa Yaw , Gordon Melita A , Hartung Carl , Meiring James E , Pollard Andrew J , Heyderman Robert S 
Published: August 2019

Abstract
Background

Electronic data capture systems (EDCs) have the potential to achieve efficiency and quality in collection of multisite data. We quantify volume, time, accuracy and costs of an EDC using large-scale census data from the STRATAA consortium, a comprehensive programme assessing population dynamics and epidemiology of typhoid fever in Malawi, Nepal and Bangladesh to inform vaccine and public health interventions.

Results

A census form was developed through a structured iterative process and implemented using Open Data Kit Collect running on Android-based tablets. Data were uploaded to Open Data Kit Aggregate, then auto-synced to MySQL-defined database nightly. Data were backed-up daily from 3 sites centrally, and auto-reported weekly. Pre-census materials’ costs were estimated. Demographics of 308,348 individuals from 80,851 households were recorded within average of 14.7 weeks range (13-16) using 65 fieldworkers. Overall, 21.7 errors (95% confidence interval: 21.4, 22.0) per 10,000 data points were found: 13.0 (95% confidence interval: 12.6, 13.5) and 24.5 (95% confidence interval: 24.1, 24.9) errors on numeric and text fields respectively. These values meet standard quality threshold of 50 errors per 10,000 data points. The EDC’s total variable cost was estimated at US$13,791.82 per site.

Conclusions

In conclusion, the EDC is robust, allowing for timely and high volume accurate data collection, and could be adopted in similar epidemiological settings.
Development of a Novel Tool for the Retrieval and Analysis of Hormone Receptor Expression Characteristics in Metastatic Breast Cancer via Data Mining on Pathology Reports
Authors: Chang Kai-Po , Wang John , Liao Cheng-Hsi , Chu Yen-Wei 
Published: August 2019

Abstract
Background

Information about the expression status of hormone receptors such as estrogen receptor (ER), progesterone receptor (PR) and Her-2 is crucial in the management and prognosis of breast cancer. Therefore, the retrieval and analysis of hormone receptor expression characteristics in metastatic breast cancer may be valuable in breast cancer study.

Methods

Herein, we report a text mining tool based on word/phrase matching that retrieves hormone receptor expression data of regional or distant metastatic breast cancer from pathology reports. It was tested on pathology reports at the China Medical University Hospital from 2013 to 2018.

Results

The tool showed specificities of 91.6% and 63.3% for the detection of regional lymph node metastasis and distant metastasis, respectively. Sensitivity in immunohistochemical study result extraction in these cases was 98.6% for distant metastasis and 78.3% for regional lymph node metastasis. Statistical analysis on these retrieved data showed significant differences in PR and Her-2 expression between regional and metastatic breast cancer, which is compatible with previous studies.

Conclusion

In conclusion, our study shows that metastatic breast cancer hormone receptor expression characteristics can be retrieved by text mining. Algorithm designed in this study may be useful in future studies about text mining in pathology reports.
Keyword Extraction and Structuralization of Medical Reports
Authors: Tsai Ching-Wei , Wu Pei-Hao , Yu Avon , Koh Jia-Ling , Kuo Chin-Chi , Chen Arbee L.P. 
Published: August 2019

Abstract
In recent years, patients usually accept more accurate and detailed examinations because of the rapid advances in medical technology. Many of the examination reports are not represented in numerical data, but text documents written by the medical examiners based on the observations from the instruments and biochemical tests. If the above-mentioned unstructured data can be organized as a report in a structured form, it will help doctors to understand a patient's status of the various examinations more efficiently. Besides, further association analysis on the structuralized data can be performed to identify potential factors that affect a disease. In this paper, from the pathology examination reports of renal diseases, we applied the POS tagging results of natural language analysis to automatically extract the keyword phrases. Then a medical dictionary for various examination items in an examination report is established, which is used as the basic information for retrieving the terms to construct a structured form of the report. Moreover, a topical probability modeling method is applied to automatically discover the candidate keyword phrases of the examination items from the reports. Finally, a system is implemented to generate the structured form for the various examination items in a report according to the constructed medical dictionary. The results of the experiments showed that the methods proposed in this paper can effectively construct a structural form of examination reports. Furthermore, the keywords of the popular examination items can be extracted correctly. The above techniques will help automatic processing and analysis of medical text reports.
Electronic Medical Records for Discovery Research in Nonalcoholic Fatty Liver Disease
Authors: Kartoun Uri , Aggarwal Rahul , Perer Adam , Park Yoonyoung , Zhang Ping , Luo Heng , Dey Sanjoy , Corey Kathleen , Ng Kenney 
Published: August 2019

Abstract
Background: Nonalcoholic fatty liver disease (NAFLD) is a highly prevalent yet under-diagnosed and under-discussed disease. Given that NAFLD has not been explored sufficiently compared with other diseases, opportunities abound for scientists to discover new biomarkers (such as laboratory observations, current comorbidities, behavioral descriptors) that can be linked to the development of conditions and complications that may develop at a later stage of the patient’s life.

Methods: We analyzed IBM Explorys, a repository that contains electronic medical records (EMRs) of more than 50 million individuals. We used a classification algorithm that members of our group have previously validated to identify patients at a high probability for NAFLD. The algorithm identified more than 80,000 patients with a high probability for NAFLD who had at least 5 years of follow-up. We applied standard statistical methods (such as logistic regression and bootstrapping) and used Clinical Classifications Software (CCS) definitions to identify associations between a variety of covariates and disease outcomes.

Results: Our methodology identified several thousand strongly statistically significant associations between covariates and outcomes in NAFLD. Most of the associations are known, but others may be new and require further investigation in subsequent studies.

Conclusions: A discovery mechanism composed of standard statistical methods applied on a large collection of EMRs, confirmed known associations and identified potentially new associations that can act as biomarkers that might merit further research.
Technical advance articles Composite CDE: modeling composite relationships between common data elements for representing complex clinical data
Authors: Kim Hye Hyeon , Park Yu Rang , Kim Ju Han 
Published: August 2019

Abstract
Background

Semantic interoperability is essential for improving data quality and sharing. The ISO/IEC 11179 Metadata Registry (MDR) standard has been highlighted as a solution for standardizing and registering clinical data elements (DEs). However, the standard model has both structural and semantic limitations, and the number of DEs continues to increase due to poor term reusability. Semantic types and constraints are lacking for comprehensively describing and evaluating DEs on real-world clinical documents.

Methods

We addressed these limitations by defining three new types of semantic relationship (dependency, composite, and variable) in our previous studies. The present study further extended semantic types (hybrid atomic and repeated and dictionary composite common data elements [CDEs]) with four constraints: ordered, operated, required, and dependent. For evaluation, we extracted all atomic and composite CDEs from five major clinical documents from five teaching hospitals in Korea. Metadata reusability and semantic interoperability in real clinical settings were comprehensively evaluated by applying the CDEs with our extended semantic types and constraints.

Results

All of the CDEs (n=1142) extracted from the 25 clinical documents were successfully integrated with a very high CDE reuse ratio (46.9%) into 606 CDEs (259 atomic and 20 unique composite CDEs), which improved the semantic integrity and interoperability without any semantic loss. Moreover, the most complex data structures from two CDE projects were successfully encoded with rich semantics and semantic integrity.

Conclusion

MDR-based extended semantic types and constraints can facilitate comprehensive representation of clinical documents with rich semantics and improved semantic interoperability without semantic loss.