Moussab/ORKG-training-evaluation-set huggingface dataset:
Research field: Bioinformatics
Title: The neuroelectric dynamics of the emotional anticipation of other people’s pain
Abstract: When we observe a dynamic emotional facial expression, we usually automatically anticipate how that expression will develop. Our objective was to study a neurocognitive biomarker of this anticipatory process for facial pain expressions, operationalized as a mismatch effect. For this purpose, we studied the behavioral and neuroelectric (Event-Related Potential, ERP) correlates, of a match or mismatch, between the intensity of an expression of pain anticipated by the participant, and the intensity of a static test expression of pain displayed with the use of a representational momentum paradigm. Here, the paradigm consisted in displaying a dynamic facial pain expression which suddenly disappeared, and participants had to memorize the final intensity of the dynamic expression. We compared ERPs in response to congruent (intensity the same as the one memorized) and incongruent (intensity different from the one memorized) static expression intensities displayed after the dynamic expression. This paradigm allowed us to determine the amplitude and direction of this intensity anticipation by measuring the observer’s memory bias. Results behaviorally showed that the anticipation was backward (negative memory bias) for high intensity expressions of pain (participants expected a return to a neutral state) and more forward (memory bias less negative, or even positive) for less intense expressions (participants expected increased intensity). Detecting mismatch (incongruent intensity) led to faster responses than detecting match (congruent intensity). The neuroelectric correlates of this mismatch effect in response to the testing of expression intensity ranged from P100 to LPP (Late Positive Potential). Path analysis and source localization suggested that the medial frontal gyrus was instrumental in mediating the mismatch effect through top-down influence on both the occipital and temporal regions. Moreover, having the facility to detect incongruent expressions, by anticipating emotional state, could be useful for prosocial behavior and the detection of trustworthiness.
Extracted statement — uses: PROCESS
Research field: Bioinformatics
Title: PSICIC: Noise and Asymmetry in Bacterial Division Revealed by Computational Image Analysis at Sub-Pixel Resolution
Abstract: Live-cell imaging by light microscopy has demonstrated that all cells are spatially and temporally organized. Quantitative, computational image analysis is an important part of cellular imaging, providing both enriched information about individual cell properties and the ability to analyze large datasets. However, such studies are often limited by the small size and variable shape of objects of interest. Here, we address two outstanding problems in bacterial cell division by developing a generally applicable, standardized, and modular software suite termed Projected System of Internal Coordinates from Interpolated Contours (PSICIC) that solves common problems in image quantitation. PSICIC implements interpolated-contour analysis for accurate and precise determination of cell borders and automatically generates internal coordinate systems that are superimposable regardless of cell geometry. We have used PSICIC to establish that the cell-fate determinant, SpoIIE, is asymmetrically localized during Bacillus subtilis sporulation, thereby demonstrating the ability of PSICIC to discern protein localization features at sub-pixel scales. We also used PSICIC to examine the accuracy of cell division in Esherichia coli and found a new role for the Min system in regulating division-site placement throughout the cell length, but only prior to the initiation of cell constriction. These results extend our understanding of the regulation of both asymmetry and accuracy in bacterial division while demonstrating the general applicability of PSICIC as a computational approach for quantitative, high-throughput analysis of cellular images.
Extracted statement — creates: PSICIC
Research field: Bioinformatics
Title: PSICIC: Noise and Asymmetry in Bacterial Division Revealed by Computational Image Analysis at Sub-Pixel Resolution
Abstract: Live-cell imaging by light microscopy has demonstrated that all cells are spatially and temporally organized. Quantitative, computational image analysis is an important part of cellular imaging, providing both enriched information about individual cell properties and the ability to analyze large datasets. However, such studies are often limited by the small size and variable shape of objects of interest. Here, we address two outstanding problems in bacterial cell division by developing a generally applicable, standardized, and modular software suite termed Projected System of Internal Coordinates from Interpolated Contours (PSICIC) that solves common problems in image quantitation. PSICIC implements interpolated-contour analysis for accurate and precise determination of cell borders and automatically generates internal coordinate systems that are superimposable regardless of cell geometry. We have used PSICIC to establish that the cell-fate determinant, SpoIIE, is asymmetrically localized during Bacillus subtilis sporulation, thereby demonstrating the ability of PSICIC to discern protein localization features at sub-pixel scales. We also used PSICIC to examine the accuracy of cell division in Esherichia coli and found a new role for the Min system in regulating division-site placement throughout the cell length, but only prior to the initiation of cell constriction. These results extend our understanding of the regulation of both asymmetry and accuracy in bacterial division while demonstrating the general applicability of PSICIC as a computational approach for quantitative, high-throughput analysis of cellular images.
Extracted statement — deposits: PSICIC
Research field: Bioinformatics
Title: PSICIC: Noise and Asymmetry in Bacterial Division Revealed by Computational Image Analysis at Sub-Pixel Resolution
Abstract: Live-cell imaging by light microscopy has demonstrated that all cells are spatially and temporally organized. Quantitative, computational image analysis is an important part of cellular imaging, providing both enriched information about individual cell properties and the ability to analyze large datasets. However, such studies are often limited by the small size and variable shape of objects of interest. Here, we address two outstanding problems in bacterial cell division by developing a generally applicable, standardized, and modular software suite termed Projected System of Internal Coordinates from Interpolated Contours (PSICIC) that solves common problems in image quantitation. PSICIC implements interpolated-contour analysis for accurate and precise determination of cell borders and automatically generates internal coordinate systems that are superimposable regardless of cell geometry. We have used PSICIC to establish that the cell-fate determinant, SpoIIE, is asymmetrically localized during Bacillus subtilis sporulation, thereby demonstrating the ability of PSICIC to discern protein localization features at sub-pixel scales. We also used PSICIC to examine the accuracy of cell division in Esherichia coli and found a new role for the Min system in regulating division-site placement throughout the cell length, but only prior to the initiation of cell constriction. These results extend our understanding of the regulation of both asymmetry and accuracy in bacterial division while demonstrating the general applicability of PSICIC as a computational approach for quantitative, high-throughput analysis of cellular images.
Extracted statement — uses: PSICIC
Research field: Bioinformatics
Title: Estimating genetic kin relationships in prehistoric populations
Abstract: Archaeogenomic research has proven to be a valuable tool to trace migrations of historic and prehistoric individuals and groups, whereas relationships within a group or burial site have not been investigated to a large extent. Knowing the genetic kinship of historic and prehistoric individuals would give important insights into social structures of ancient and historic cultures. Most archaeogenetic research concerning kinship has been restricted to uniparental markers, while studies using genome-wide information were mainly focused on comparisons between populations. Applications which infer the degree of relationship based on modern-day DNA information typically require diploid genotype data. Low concentration of endogenous DNA, fragmentation and other post-mortem damage to ancient DNA (aDNA) makes the application of such tools unfeasible for most archaeological samples. To infer family relationships for degraded samples, we developed the software READ (Relationship Estimation from Ancient DNA). We show that our heuristic approach can successfully infer up to second degree relationships with as little as 0.1x shotgun coverage per genome for pairs of individuals. We uncover previously unknown relationships among prehistoric individuals by applying READ to published aDNA data from several human remains excavated from different cultural contexts. In particular, we find a group of five closely related males from the same Corded Ware culture site in modern-day Germany, suggesting patrilocality, which highlights the possibility to uncover social structures of ancient populations by applying READ to genome-wide aDNA data. READ is publicly available from https://bitbucket.org/tguenther/read.
Extracted statement — deposits: READ
Research field: Bioinformatics
Title: Examining individual and geographic factors associated with social isolation and loneliness using Canadian Longitudinal Study on Aging (CLSA) data
Abstract: Background A large body of research shows that social isolation and loneliness have detrimental health consequences. Identifying individuals at risk of social isolation or loneliness is, therefore, important. The objective of this study was to examine personal (e.g., sex, income) and geographic (rural/urban and sociodemographic) factors and their association with social isolation and loneliness in a national sample of Canadians aged 45 to 85 years. Methods The study involved cross-sectional analyses of baseline data from the Canadian Longitudinal Study on Aging that were linked to 2016 census data at the Forward Sortation Area (FSA) level. Multilevel logistic regression analyses were conducted to examine the association between personal factors and geographic factors and social isolation and loneliness for the total sample, and women and men, respectively. Results The prevalence of social isolation and loneliness was 5.1% and 10.2%, respectively, but varied substantially across personal characteristics. Personal characteristics (age, sex, education, income, functional impairment, chronic diseases) were significantly related to both social isolation and loneliness, although some differences emerged in the direction of the relationships for the two measures. Associations also differed somewhat for women versus men. Associations between some geographic factors emerged for social isolation, but not loneliness. Living in an urban core was related to increased odds of social isolation, an effect that was no longer significant when FSA-level factors were controlled for. FSAs with a higher percentage of 65+ year old residents with low income were consistently associated with higher odds of social isolation. Conclusion The findings indicate that socially isolated individuals are, to some extent, clustered into areas with a high proportion of low-income older adults, suggesting that support and resources could be targeted at these areas. For loneliness, the focus may be less on where people live, but rather on personal characteristics that place individuals at risk.
Extracted statement — uses: SAS
Research field: Bioinformatics
Title: Infectious Disease and Grouping Patterns in Mule Deer
Abstract: Infectious disease dynamics are determined, to a great extent, by the social structure of the host. We evaluated sociality, or the tendency to form groups, in Rocky Mountain mule deer (Odocoileus hemionus hemionus) from a chronic wasting disease (CWD) endemic area in Saskatchewan, Canada, to better understand factors that may affect disease transmission. Using group size data collected on 365 radio-collared mule deer (2008–2013), we built a generalized linear mixed model (GLMM) to evaluate whether factors such as CWD status, season, habitat and time of day, predicted group occurrence. Then, we built another GLMM to determine factors associated with group size. Finally, we used 3 measures of group size (typical, mean and median group sizes) to quantify levels of sociality. We found that mule deer showing clinical signs of CWD were less likely to be reported in groups than clinically healthy deer after accounting for time of day, habitat, and month of observation. Mule deer groups were much more likely to occur in February and March than in July. Mixed-sex groups in early gestation were larger than any other group type in any season. Groups were largest and most likely to occur at dawn and dusk, and in open habitats, such as cropland. We discuss the implication of these results with respect to sociobiology and CWD transmission dynamics.
Extracted statement — uses: SAS
Research field: Bioinformatics
Title: SCOTTI: Efficient Reconstruction of Transmission within Outbreaks with the Structured Coalescent
Abstract: Exploiting pathogen genomes to reconstruct transmission represents a powerful tool in the fight against infectious disease. However, their interpretation rests on a number of simplifying assumptions that regularly ignore important complexities of real data, in particular within-host evolution and non-sampled patients. Here we propose a new approach to transmission inference called SCOTTI (Structured COalescent Transmission Tree Inference). This method is based on a statistical framework that models each host as a distinct population, and transmissions between hosts as migration events. Our computationally efficient implementation of this model enables the inference of host-to-host transmission while accommodating within-host evolution and non-sampled hosts. SCOTTI is distributed as an open source package for the phylogenetic software BEAST2. We show that SCOTTI can generally infer transmission events even in the presence of considerable within-host variation, can account for the uncertainty associated with the possible presence of non-sampled hosts, and can efficiently use data from multiple samples of the same host, although there is some reduction in accuracy when samples are collected very close to the infection time. We illustrate the features of our approach by investigating transmission from genetic and epidemiological data in a Foot and Mouth Disease Virus (FMDV) veterinary outbreak in England and a Klebsiella pneumoniae outbreak in a Nepali neonatal unit. Transmission histories inferred with SCOTTI will be important in devising effective measures to prevent and halt transmission.
Extracted statement — creates: SCOTTI
Research field: Bioinformatics
Title: Comparisons between different elements of reported burden and common mental disorder in caregivers of ethnically diverse people with dementia in Trinidad
Abstract: Objective Culture plays a significant role in determining family responsibilities and possibly influences the caregiver burden associated with providing care for a relative with dementia. This study was carried out to determine the elements of caregiver burden in Trinidadians regarding which interventions will provide the most benefit. Methods Seventy-five caregivers of patients diagnosed with dementia participated in this investigation. Demographic data were recorded for each caregiver and patient. Caregiver burden was assessed using the Zarit Burden Interview (ZBI), and the General Health Questionnaire (GHQ) was used as a measure of psychiatric morbidity. Statistical analyses were performed using Stata and SPSS software. Associations between individual ZBI items and GHQ-28 scores in caregivers were analyzed in logistic regression models; the above-median GHQ-28 scores were used a binary dependent variable, and individual ZBI item scores were entered as 5-point ordinal independent variables. Results The caregiver sample was composed of 61 females and 14 males. Caregiver burden was significantly associated with the participant being male; there was heterogeneity by ethnic group, and a higher burden on female caregivers was detected at borderline levels of significance. Upon examining the associations between different ZBI items and the above-median GHQ-28 scores in caregivers, the strongest associations were found with domains reflecting the caregiver’s health having suffered, the caregiver not having sufficient time for him/herself, the caregiver’s social life suffering, and the caregiver admitting to feeling stressed due to caregiving and meeting other responsibilities. Conclusions In this sample, with a majority of female caregivers, the factors of the person with dementia being male and belonging to a minority ethnic group were associated with a greater degree of caregiver burden. The information obtained through the association of individual ZBI items and above-median GHQ-28 scores is a helpful guide for profiling Trinidadian caregiver burden.
Extracted statement — uses: SPSS
Research field: Bioinformatics
Title: Malaria knowledge and its associated factors among pregnant women attending antenatal clinic of Adis Zemen Hospital, North-western Ethiopia, 2018
Abstract: Introduction In Ethiopia, the burden of malaria during pregnancy remains a public health problem. Having a good malaria knowledge leads to practicing the prevention of malaria and seeking a health care. Researches regarding pregnant women’s knowledge on malaria in Ethiopia is limited. So the aim of this study was to assess malaria knowledge and its associated factors among pregnant woman, 2018. Methods An institutional-basedcross-sectional study was conducted in Adis Zemen Hospital. Data were collected using pre-tested, an interviewer-administered structured questionnaire among 236 mothers. Women’s knowledge on malaria was measured using six malaria-related questions (cause of malaria, mode of transmission, signs and symptoms, complication and prevention of malaria). The collected data were entered using Epidata version 3.1 and exported to SPSS version 20 for analysis. Bivariate and multivariate logistic regressions were computed to identify predictor variables at 95% confidence interval. Variables having P value of <0.05 were considered as predictor variables of malaria knowledge. Result A total of 235 pregnant women participated which makes the response rate 99.6%. One hundred seventy two pregnant women (73.2%) of mothers had good knowledge on malaria.Women who were from urban (AOR; 2.4: CI; 1.8, 5.7), had better family monthly income (AOR; 3.4: CI; 2.7, 3.8), attended education (AOR; 1.8: CI; 1.4, 3.5) were more knowledgeable. Conclusion and recommendation Majority of participants had good knowledge on malaria. Educational status, household monthly income and residence werepredictors of malaria knowledge. Increasing women’s knowledge especially for those who are from rural, have no education, and have low monthly income is still needed.
Extracted statement — uses: SPSS
Research field: Bioinformatics
Title: Quality of Life of Medical Students in China: A Study Using the WHOQOL-BREF
Abstract: Objective The aim of this study was to assess the quality of life (QOL) of medical students during their medical education and explore the influencing factors of the QOL of students. Methods A cross-sectional study was conducted in June 2011. The study population was composed of 1686 medical students in years 1 to 5 at China Medical University. The Chinese version of WHOQOL-BREF instrument was used to assess the QOL of medical students. The reliability and validity of the questionnaire were assessed by Cronbach’s α coefficient and factor analysis respectively. The relationships between QOL and the factors including gender, academic year level, and specialty were examined using t-test or one-way ANOVA followed by Student-Newman–Keuls test. Statistic analysis was performed by SPSS 13.0. Results The overall Cronbach’s α coefficient of the WHOQOL-BREF questionnaire was 0.731. The confirmatory factor analysis provided an acceptable fit to a four-factor model in the medical student sample. The scores of different academic years were significantly different in the psychological health and social relations domains (p<0.05). Third year students had the lowest scores in psychological health and social relations domains. The scores of different specialties had significant differences in psychological health and social relations domains (p<0.05). Students from clinical medicine had the highest scores. Gender, interest in the area of study, confidence in career development, hometown location, and physical exercise were significantly associated with the quality of life of students in some domains (p<0.05). Conclusions The WHOQOL-BREF was reliable and valid in the assessment of the QOL of Chinese medical students. In order to cope with the influencing factors of the QOL, medical schools should carry out curriculum innovation and give the necessary support for medical students, especially for 3rd year students.
Extracted statement — uses: SPSS
Research field: Bioinformatics
Title: Experiences of Social Harm and Changes in Sexual Practices among Volunteers Who Had Completed a Phase I/II HIV Vaccine Trial Employing HIV-1 DNA Priming and HIV-1 MVA Boosting in Dar es Salaam, Tanzania
Abstract: Background Volunteers in phase I/II HIV vaccine trials are assumed to be at low risk of acquiring HIV infection and are expected to have normal lives in the community. However, during participation in the trials, volunteers may encounter social harm and changes in their sexual behaviours. The current study aimed to study persistence of social harm and changes in sexual practices over time among phase I/II HIV vaccine immunogenicity (HIVIS03) trial volunteers in Dar es Salaam, Tanzania. Methods and Results A descriptive prospective cohort study was conducted among 33 out of 60 volunteers of HIVIS03 trial in Dar es Salaam, Tanzania, who had received three HIV-1 DNA injections boosted with two HIV-1 MVA doses. A structured interview was administered to collect data. Analysis was carried out using SPSS and McNemars’ chi-square (χ2) was used to test the association within-subjects. Participants reported experiencing negative comments from their colleagues about the trial; but such comments were less severe during the second follow up visits (χ2 = 8.72; P<0.001). Most of the comments were associated with discrimination (χ2 = 26.72; P<0.001), stigma (χ2 = 6.06; P<0.05), and mistrust towards the HIV vaccine trial (χ2 = 4.9; P<0.05). Having a regular sexual partner other than spouse or cohabitant declined over the two follow-up periods (χ2 = 4.45; P<0.05). Conclusion Participants in the phase I/II HIV vaccine trial were likely to face negative comments from relatives and colleagues after the end of the trial, but those comments decreased over time. In this study, the inherent sexual practice of having extra sexual partners other than spouse declined over time. Therefore, prolonged counselling and support appears important to minimize risky sexual behaviour among volunteers after participation in HIV Vaccine trials.
Extracted statement — uses: SPSS