Moussab/ORKG-training-evaluation-set huggingface dataset:
Research field: Bioinformatics
Title: Relationship between Resilience, Psychological Distress and Physical Activity in Cancer Patients: A Cross-Sectional Observation Study
Abstract: Objective Psychological distress remains a major challenge in cancer care. The complexity of psychological symptoms in cancer patients requires multifaceted symptom management tailored to individual patient characteristics and active patient involvement. We assessed the relationship between resilience, psychological distress and physical activity in cancer patients to elucidate potential moderators of the identified relationships. Method A cross-sectional observational study to assess the prevalence of symptoms and supportive care needs of oncology patients undergoing chemotherapy, radiotherapy or chemo-radiation therapy in a tertiary oncology service. Resilience was assessed using the 10-item Connor-Davidson Resilience Scale (CD-RISC 10), social support was evaluated using the 12-item Multidimensional Scale of Perceived Social Support (MSPSS) and both psychological distress and activity level were measured using corresponding subscales of the Rotterdam Symptom Checklist (RSCL). Socio-demographic and medical data were extracted from patient medical records. Correlation analyses were performed and structural equation modeling was employed to assess the associations between resilience, psychological distress and activity level as well as selected socio-demographic variables. Results Data from 343 patients were included in the analysis. Our revised model demonstrated an acceptable fit to the data (χ2(163) = 313.76, p = .000, comparative fit index (CFI) = .942, Tucker-Lewis index (TLI) = .923, root mean square error of approximation (RMSEA) = .053, 90% CI [.044.062]). Resilience was negatively associated with psychological distress (β = -.59), and positively associated with activity level (β = .20). The relationship between resilience and psychological distress was moderated by age (β = -0.33) but not social support (β = .10, p = .12). Conclusion Cancer patients with higher resilience, particularly older patients, experience lower psychological distress. Patients with higher resilience are physically more active. Evaluating levels of resilience in cancer patients then tailoring targeted interventions to facilitate resilience may help improve the effectiveness of psychological symptom management interventions.
Extracted statement — uses: SPSS
Research field: Bioinformatics
Title: Prevalence and Predictors of Depression among Pregnant Women in Debretabor Town, Northwest Ethiopia
Abstract: Background Depression during pregnancy is a major health problem because it is prevalent and chronic, and its impact on birth outcome and child health is serious. Several psychosocial and obstetric factors have been identified as predictors. Evidence on the prevalence and predictors of antenatal depression is very limited in Ethiopia. This study aims to determine prevalence and associated factors with antenatal depression. Methods Community based cross-sectional study was conducted among 527 pregnant women recruited in a cluster sampling method. Data were collected by face-to-face interviews on socio-demographic, obstetric, and psychosocial characteristics. Depression symptoms were assessed using the Edinburgh Postnatal Depression Scale (EPDS). The List of Threatening Experiences questionnaire (LTE-Q) and the Oslo Social Support Scale (OSS-3) were used to assess stressful events and social support, respectively. Data were entered into Epi-info and analyzed using SPSS-20. Descriptive and logistic regression analyses were carried out. Results The prevalence of antenatal depression was found to be 11.8%. Having debt (OR = 2.79, 95% CI = 1.33, 5.85), unplanned pregnancy (OR = 2.39, 95% CI = (1.20, 4.76), history of stillbirth (OR = 3.97, 95% CI = (1.67,9.41), history of abortion (OR = 2.57, 95% CI = 1.005, 6.61), being in the third trimester of pregnancy (OR = 1.70, 95% CI = 1.07,2.72), presence of a complication in the current pregnancy (OR = 3.29, 95% CI = 1.66,6.53), and previous history of depression (OR = 3.48, 95% CI = 1.71,7.06) were factors significantly associated with antenatal depression. Conclusion The prevalence of antenatal depression was high, especially in the third trimester. Poverty, unmet reproductive health needs, and obstetric complications are the main determinants of antenatal depression. For early detection and appropriate intervention, screening for depression during the routine antenatal care should be promoted.
Extracted statement — uses: SPSS
Research field: Bioinformatics
Title: Women’s autonomy and men's involvement in child care and feeding as predictors of infant and young child anthropometric indices in coffee farming households of Jimma Zone, South West of Ethiopia
Abstract: Background Most of child mortality and under nutrition in developing world were attributed to suboptimal childcare and feeding, which needs detailed investigation beyond the proximal factors. This study was conducted with the aim of assessing associations of women’s autonomy and men’s involvement with child anthropometric indices in cash crop livelihood areas of South West Ethiopia. Methods Multi-stage stratified sampling was used to select 749 farming households living in three coffee producing sub-districts of Jimma zone, Ethiopia. Domains of women’s Autonomy were measured by a tool adapted from demographic health survey. A model for determination of paternal involvement in childcare was employed. Caring practices were assessed through the WHO Infant and young child feeding practice core indicators. Length and weight measurements were taken in duplicate using standard techniques. Data were analyzed using SPSS for windows version 21. A multivariable linear regression was used to predict weight for height Z-scores and length for age Z-scores after adjusting for various factors. Results The mean (sd) scores of weight for age (WAZ), height for age (HAZ), weight for height (WHZ) and BMI for age (BAZ) was -0.52(1.26), -0.73(1.43), -0.13(1.34) and -0.1(1.39) respectively. The results of multi variable linear regression analyses showed that WHZ scores of children of mothers who had autonomy of conducting big purchase were higher by 0.42 compared to children's whose mothers had not. In addition, a child whose father was involved in childcare and feeding had higher HAZ score by 0.1. Regarding age, as for every month increase in age of child, a 0.04 point decrease in HAZ score and a 0.01 point decrease in WHZ were noted. Similarly, a child living in food insecure households had lower HAZ score by 0.29 compared to child of food secured households. As family size increased by a person a WHZ score of a child is decreased by 0.08. WHZ and HAZ scores of male child was found lower by 0.25 and 0.38 respectively compared to a female child of same age. Conclusion Women’s autonomy and men’s involvement appeared in tandem with better child anthropometric outcomes. Nutrition interventions in such setting should integrate enhancing women’s autonomy over resource and men’s involvement in childcare and feeding, in addition to food security measures.
Extracted statement — uses: SPSS
Research field: Bioinformatics
Title: Personality and social support as determinants of entrepreneurial intention. Gender differences in Italy
Abstract: The interest in the promotion of entrepreneurship is significantly increasing, particularly in those countries, such as Italy, that suffered during the recent great economic recession and subsequently needed to revitalize their economy. Entrepreneurial intention (EI) is a crucial stage in the entrepreneurial process and represents the basis for consequential entrepreneurial actions. Several research projects have sought to understand the antecedents of EI. This study, using a situational approach, has investigated the personal and contextual determinants of EI, exploring gender differences. In particular, the mediational role of general self-efficacy between internal locus of control (LoC), self-regulation, and support from family and friends, on the one hand, and EI, on the other hand, has been investigated. The study involved a sample of 658 Italian participants, of which 319 were male and 339 were female. Data were collected with a self-report on-line questionnaire and analysed with SPSS 23 and Mplus 7 to test a multi-group structural equation model. The results showed that self-efficacy totally mediated the relationship between internal LoC, self-regulation and EI. Moreover, it partially mediated the relationship between support from family and friends and EI. All the relations were significant for both men and women; however, our findings highlighted a stronger relationship between self-efficacy and EI for men, and between support from family and friends and both self-efficacy and EI for women. Findings highlighted the role of contextual characteristics in addition to personal ones in influencing EI and confirmed the key mediational function of self-efficacy. As for gender, results suggested that differences between men and women in relation to the entrepreneur role still exist. Practical implications for trainers and educators are discussed.
Extracted statement — uses: SPSS
Research field: Bioinformatics
Title: Knowledge, attitude and perceived stigma towards tuberculosis among pastoralists; Do they differ from sedentary communities? A comparative cross-sectional study
Abstract: Background Ethiopia is ninth among the world high tuberculosis (TB) burden countries, pastoralists being the most affected population. However, there is no published report whether the behavior related to TB are different between pastoralist and the sedentary communities. Therefore, the main aim of this study is to assess the pastoralist community knowledge, attitude and perceived stigma towards tuberculosis and their health care seeking behavior in comparison to the neighboring sedentary communities and this may help to plan TB control interventions specifically for the pastoralist communities. Method A community-based cross-sectional survey was carried out from September 2014 to January 2015, among 337 individuals from pastoralist and 247 from the sedentary community of Kereyu district. Data were collected using structured questionnaires. Three focus group discussions were used to collect qualitative data, one with men and the other with women in the pastoralist and one with men in the sedentary groups. Data were analyzed using Statistical Software for Social Science, SPSS V 22 and STATA. Results A Lower proportion of pastoralists mentioned bacilli (bacteria) as the cause of PTB compared to the sedentary group (63.9% vs. 81.0%, p<0.01), respectively. However, witchcraft was reported as the causes of TB by a higher proportion of pastoralists than the sedentary group (53.6% vs.23.5%, p<0.01), respectively. Similarly, a lower proportion of pastoralists indicated PTB is preventable compared to the sedentary group (95.8% vs. 99.6%, p<0.01), respectively. Moreover, majority of the pastoralists mentioned that most people would reject a TB patient in their community compared to the sedentary group (39.9% vs. 8.9%, p<0.001), respectively, and the pastoralists expressed that they would be ashamed/embarrassed if they had TB 68% vs.36.4%, p<0.001), respectively. Conclusion The finding indicates that there is a lower awareness about TB, a negative attitude towards TB patients and a higher perceived stigma among pastoralists compared to their neighbor sedentary population. Strategic health communications pertinent to the pastoralists way of life should be planned and implemented to improve the awareness gap about tuberculosis.
Extracted statement — uses: STATA
Research field: Bioinformatics
Title: Complete Mitochondrial DNA Analysis of Eastern Eurasian Haplogroups Rarely Found in Populations of Northern Asia and Eastern Europe
Abstract: With the aim of uncovering all of the most basal variation in the northern Asian mitochondrial DNA (mtDNA) haplogroups, we have analyzed mtDNA control region and coding region sequence variation in 98 Altaian Kazakhs from southern Siberia and 149 Barghuts from Inner Mongolia, China. Both populations exhibit the prevalence of eastern Eurasian lineages accounting for 91.9% in Barghuts and 60.2% in Altaian Kazakhs. The strong affinity of Altaian Kazakhs and populations of northern and central Asia has been revealed, reflecting both influences of central Asian inhabitants and essential genetic interaction with the Altai region indigenous populations. Statistical analyses data demonstrate a close positioning of all Mongolic-speaking populations (Mongolians, Buryats, Khamnigans, Kalmyks as well as Barghuts studied here) and Turkic-speaking Sojots, thus suggesting their origin from a common maternal ancestral gene pool. In order to achieve a thorough coverage of DNA lineages revealed in the northern Asian matrilineal gene pool, we have completely sequenced the mtDNA of 55 samples representing haplogroups R11b, B4, B5, F2, M9, M10, M11, M13, N9a and R9c1, which were pinpointed from a massive collection (over 5000 individuals) of northern and eastern Asian, as well as European control region mtDNA sequences. Applying the newly updated mtDNA tree to the previously reported northern Asian and eastern Asian mtDNA data sets has resolved the status of the poorly classified mtDNA types and allowed us to obtain the coalescence age estimates of the nodes of interest using different calibrated rates. Our findings confirm our previous conclusion that northern Asian maternal gene pool consists of predominantly post-LGM components of eastern Asian ancestry, though some genetic lineages may have a pre-LGM/LGM origin.
Extracted statement — uses: STATISTICA
Research field: Bioinformatics
Title: Combined Mitochondrial and Nuclear Markers Revealed a Deep Vicariant History for Leopoldamys neilli, a Cave-Dwelling Rodent of Thailand
Abstract: Background Historical biogeography and evolutionary processes of cave taxa have been widely studied in temperate regions. However, Southeast Asian cave ecosystems remain largely unexplored despite their high scientific interest. Here we studied the phylogeography of Leopoldamys neilli, a cave-dwelling murine rodent living in limestone karsts of Thailand, and compared the molecular signature of mitochondrial and nuclear markers. Methodology/Principal Findings We used a large sampling (n = 225) from 28 localities in Thailand and a combination of mitochondrial and nuclear markers with various evolutionary rates (two intronic regions and 12 microsatellites). The evolutionary history of L. neilli and the relative role of vicariance and dispersal were investigated using ancestral range reconstruction analysis and Approximate Bayesian computation (ABC). Both mitochondrial and nuclear markers support a large-scale population structure of four main groups (west, centre, north and northeast) and a strong finer structure within each of these groups. A deep genealogical divergence among geographically close lineages is observed and denotes a high population fragmentation. Our findings suggest that the current phylogeographic pattern of this species results from the fragmentation of a widespread ancestral population and that vicariance has played a significant role in the evolutionary history of L. neilli. These deep vicariant events that occurred during Plio-Pleistocene are related to the formation of the Central Plain of Thailand. Consequently, the western, central, northern and northeastern groups of populations were historically isolated and should be considered as four distinct Evolutionarily Significant Units (ESUs). Conclusions/Significance Our study confirms the benefit of using several independent genetic markers to obtain a comprehensive and reliable picture of L. neilli evolutionary history at different levels of resolution. The complex genetic structure of Leopoldamys neilli is supported by congruent mitochondrial and nuclear markers and has been influenced by the geological history of Thailand during Plio-Pleistocene.
Extracted statement — uses: STRUCTURE
Research field: Bioinformatics
Title: LAILAPS-QSM: A RESTful API and JAVA library for semantic query suggestions
Abstract: In order to access and filter content of life-science databases, full text search is a widely applied query interface. But its high flexibility and intuitiveness is paid for with potentially imprecise and incomplete query results. To reduce this drawback, query assistance systems suggest those combinations of keywords with the highest potential to match most of the relevant data records. Widespread approaches are syntactic query corrections that avoid misspelling and support expansion of words by suffixes and prefixes. Synonym expansion approaches apply thesauri, ontologies, and query logs. All need laborious curation and maintenance. Furthermore, access to query logs is in general restricted. Approaches that infer related queries by their query profile like research field, geographic location, co-authorship, affiliation etc. require user’s registration and its public accessibility that contradict privacy concerns. To overcome these drawbacks, we implemented LAILAPS-QSM, a machine learning approach that reconstruct possible linguistic contexts of a given keyword query. The context is referred from the text records that are stored in the databases that are going to be queried or extracted for a general purpose query suggestion from PubMed abstracts and UniProt data. The supplied tool suite enables the pre-processing of these text records and the further computation of customized distributed word vectors. The latter are used to suggest alternative keyword queries. An evaluated of the query suggestion quality was done for plant science use cases. Locally present experts enable a cost-efficient quality assessment in the categories trait, biological entity, taxonomy, affiliation, and metabolic function which has been performed using ontology term similarities. LAILAPS-QSM mean information content similarity for 15 representative queries is 0.70, whereas 34% have a score above 0.80. In comparison, the information content similarity for human expert made query suggestions is 0.90. The software is either available as tool set to build and train dedicated query suggestion services or as already trained general purpose RESTful web service. The service uses open interfaces to be seamless embeddable into database frontends. The JAVA implementation uses highly optimized data structures and streamlined code to provide fast and scalable response for web service calls. The source code of LAILAPS-QSM is available under GNU General Public License version 2 in Bitbucket GIT repository: https://bitbucket.org/ipk_bit_team/bioescorte-suggestion
Extracted statement — creates: LAILAPS-QSM
Research field: Bioinformatics
Title: LAILAPS-QSM: A RESTful API and JAVA library for semantic query suggestions
Abstract: In order to access and filter content of life-science databases, full text search is a widely applied query interface. But its high flexibility and intuitiveness is paid for with potentially imprecise and incomplete query results. To reduce this drawback, query assistance systems suggest those combinations of keywords with the highest potential to match most of the relevant data records. Widespread approaches are syntactic query corrections that avoid misspelling and support expansion of words by suffixes and prefixes. Synonym expansion approaches apply thesauri, ontologies, and query logs. All need laborious curation and maintenance. Furthermore, access to query logs is in general restricted. Approaches that infer related queries by their query profile like research field, geographic location, co-authorship, affiliation etc. require user’s registration and its public accessibility that contradict privacy concerns. To overcome these drawbacks, we implemented LAILAPS-QSM, a machine learning approach that reconstruct possible linguistic contexts of a given keyword query. The context is referred from the text records that are stored in the databases that are going to be queried or extracted for a general purpose query suggestion from PubMed abstracts and UniProt data. The supplied tool suite enables the pre-processing of these text records and the further computation of customized distributed word vectors. The latter are used to suggest alternative keyword queries. An evaluated of the query suggestion quality was done for plant science use cases. Locally present experts enable a cost-efficient quality assessment in the categories trait, biological entity, taxonomy, affiliation, and metabolic function which has been performed using ontology term similarities. LAILAPS-QSM mean information content similarity for 15 representative queries is 0.70, whereas 34% have a score above 0.80. In comparison, the information content similarity for human expert made query suggestions is 0.90. The software is either available as tool set to build and train dedicated query suggestion services or as already trained general purpose RESTful web service. The service uses open interfaces to be seamless embeddable into database frontends. The JAVA implementation uses highly optimized data structures and streamlined code to provide fast and scalable response for web service calls. The source code of LAILAPS-QSM is available under GNU General Public License version 2 in Bitbucket GIT repository: https://bitbucket.org/ipk_bit_team/bioescorte-suggestion
Extracted statement — deposits: LAILAPS-QSM
Research field: Bioinformatics
Title: Acute Lymphoblastic Leukemia Detection from Microscopic Images Using Weighted Ensemble of Convolutional Neural Networks
Abstract: Although automated Acute Lymphoblastic Leukemia (ALL) detection is essential, it is challenging due to the morphological correlation between malignant and normal cells. The traditional ALL classification strategy is arduous, time-consuming, often suffers inter-observer variations, and necessitates experienced pathologists. This article has automated the ALL detection task, employing deep Convolutional Neural Networks (CNNs). We explore the weighted ensemble of deep CNNs to recommend a better ALL cell classifier. The weights are estimated from ensemble candidates' corresponding metrics, such as accuracy, F1-score, AUC, and kappa values. Various data augmentations and pre-processing are incorporated for achieving a better generalization of the network. We train and evaluate the proposed model utilizing the publicly available C-NMC-2019 ALL dataset. Our proposed weighted ensemble model has outputted a weighted F1-score of 88.6%, a balanced accuracy of 86.2%, and an AUC of 0.941 in the preliminary test set. The qualitative results displaying the gradient class activation maps confirm that the introduced model has a concentrated learned region. In contrast, the ensemble candidate models, such as Xception, VGG-16, DenseNet-121, MobileNet, and InceptionResNet-V2, separately produce coarse and scatter learned areas for most example cases. Since the proposed ensemble yields a better result for the aimed task, it can experiment in other domains of medical diagnostic applications.
Extracted statement — dataset: C-NMC-2019