Miracle-dz/UniFAR-FTUs huggingface dataset:
Nonparametric methods for analyzing recurrent gap time data with application to infections after hematopoietic cell transplant

Infection is one of the most common complications after hematopoietic cell transplantation. Many patients experience infectious complications repeatedly after transplant. Existing statistical methods for recurrent gap time data typically assume that patients are enrolled due to the occurrence of an event of interest, and subsequently experience recurrent events of the same type; moreover, for one‐sample estimation, the gap times between consecutive events are usually assumed to be identically distributed. Applying these methods to analyze the post‐transplant infection data will inevitably lead to incorrect inferential results because the time from transplant to the first infection has a different biological meaning than the gap times between consecutive recurrent infections. Some unbiased yet inefficient methods include univariate survival analysis methods based on data from the first infection or bivariate serial event data methods based on the first and second infections. In this article, we propose a nonparametric estimator of the joint distribution of time from transplant to the first infection and the gap times between consecutive infections. The proposed estimator takes into account the potentially different distributions of the two types of gap times and better uses the recurrent infection data. Asymptotic properties of the proposed estimators are established.
Seeing the Forest for the Trees? An Investigation of Network Knowledge

This paper assesses the empirical content of one of the most prevalent assumptions in the economics of networks literature, namely the assumption that decision makers have full knowledge about the networks they interact on. Using network data from 75 villages, we ask 4,554 individuals to assess whether five randomly chosen pairs of households in their village are linked through financial, social, and informational relationships. We find that network knowledge is low and highly localized, declining steeply with the pair's network distance to the respondent. 46% of respondents are not even able to offer a guess about the status of a potential link between a given pair of individuals. Even when willing to offer a guess, respondents can only correctly identify the links 37% of the time. We also find that a one-step increase in the social distance to the pair corresponds to a 10pp increase in the probability of misidentifying the link. We then investigate the theoretical implications of this assumption by showing that the predictions of various models change substantially if agents behave under the more realistic assumption of incomplete knowledge about the network. Taken together, our results suggest that the assumption of full network knowledge (i) may serve as a poor approximation to the real world and (ii) is not innocuous: allowing for incomplete network knowledge may have first-order implications for a range of qualitative and quantitative results in various contexts.
Maternal SSRI discontinuation, use, psychiatric disorder and the risk of autism in children: a meta‐analysis of cohort studies

We undertook an exclusive meta-analysis of cohort studies investigating the possible link between prenatal selective serotonin reuptake inhibitor (SSRI) exposure and autism spectrum disorders (ASD) in children to further investigate our previous suggestion of confounding by indication. The point estimates regarding the following cohorts were extracted and pooled: (1) pregnant women who discontinued SSRI until 3 months before pregnancy; (2) pregnant women who were exposed to SSRI during pregnancy; and (3) pregnant women with maternal psychiatric disorder but no exposure to SSRI during pregnancy. Although the pooled point estimate of the first cohort showed a trend for increase, it did not reach significance. The pooled point estimates of the latter cohorts showed a significant association with ASD which strengthens our previous suggestion of confounding by indication. Future studies should be adequately designed to differentiate whether the previously suggested association is a result of maternal psychiatric disorder or SSRI exposure or both.
Development and Preliminary Validation of the Salzburg Emotional Eating Scale

Existing self-report questionnaires for the assessment of emotional eating do not differentiate between specific types of emotions and between increased or decreased food intake in response to these emotions. Therefore, we developed a new measure of emotional eating—the Salzburg Emotional Eating Scale (SEES)—for which higher scores indicate eating more than usual in response to emotions and lower scores indicate eating less than usual in response to emotions. In study 1, a pool of items describing 40 emotional states was used. Factor analysis yielded four factors, which represented both positive (happiness subscale) and negative emotions (sadness, anger, and anxiety subscales). Subsequently, the scale was reduced to 20 items (5 items for each subscale) and its four-factor structure was replicated in studies 2 and 3. In all three studies, internal consistencies of each subscale were α > 0.70 and mean subscale scores significantly differed from each other such that individuals reported the strongest tendency to eat more than usual when being sad and the strongest tendency to eat less than usual when being anxious (sadness > happiness > anger > anxiety). Higher scores on the happiness subscale related to lower scores on the negative emotions subscales, lower body mass index (BMI), and lower eating pathology. In contrast, higher scores on the negative emotions subscales related to lower scores on the happiness subscale, higher BMI, and higher eating pathology. The SEES represents a useful measure for the investigation of emotional eating by increasing both specificity (differentiation between specific emotional states) and breadth (differentiation between increase and decrease of food intake) in the assessment of the emotion–eating relationship.
Alcohol and older people: A systematic review of barriers, facilitators and context of drinking in older people and implications for intervention design

Background Harmful alcohol consumption in older people has increased and effective approaches to understanding and addressing this societal concern are needed. Methods Systematic review of qualitative studies in older populations (55+ years) to identify barriers, facilitators or context of drinking in older people. Multiple databases (MEDLINE, EMBASE, PsycINFO, CINAHL, CENTRAL, Social Sciences Citation Index, York Centre for Reviews and Dissemination, Cochrane database and grey literature) were searched from 2000 to February 2017 for studies in English, from OECD countries using MeSH terms and text words relating to alcohol combined with older age terms. Study quality was assessed using NICE methodology. The review is reported according to PRISMA. Results Drinking in older people is strongly linked to social engagement and there is scepticism about the health risks of alcohol. Drinking was also linked to difficulties such as social isolation, illness or bereavement. Alcohol can be related to routines and identity. However, older people often regulate their own drinking and strategies that emphasise the life experience of older people to drink wisely could be helpful. Conclusions To be effective societal approaches need to take into account contexts of risks for harmful drinking. The evidence supports a strong social role for drinking alcohol which should be taken into account in any policy development with the potential benefits of social participation for cognitive health. Approaches to reducing alcohol use in older people need to avoid paradoxical harm, with a need for approaches that reduce harm from drinking alcohol but retain the benefit of socialising.
Use and misuse of alcohol and psychotropic drugs among older people: Is that an issue when services are planned for and implemented?

BACKGROUND To investigate health personnel's perceptions and experiences of alcohol and psychotropic drug use among older people (65 years and above) and to what extent this is an issue when services are planned for and implemented. METHOD Qualitative interviews with 16 health professionals who work with older patients, 13 registered district nurses, two occupational therapists and one physiotherapist, were performed during 2013. The sample included informants aged 34-62 years from 14 municipalities, four were male. FINDINGS Two main categories emerged: state of practice and a desire to improve services. The first category details the informants' perceptions of legitimacy and attention to substance use and misuse among older people in need of healthcare, and their competence and knowledge on the topic. The topic was experienced as demanding to bring up. Health personnel described a lack of attention and competence how to handle use and misuse of alcohol and psychotropic drugs. The category is described in the subcategories legitimacy and attention to substance use and misuse and competence and knowledge in practice. The second category demonstrates the informants' desire to improve services so it better can contribute to detect misuse among older people and contribute to treatment. The variation is contained in the subcategories improving collaboration and changing routines. CONCLUSION Use and misuse of alcohol and psychoactive drugs among older people had little attention when the community health service is planned for and implemented. The participating health professionals had a desire to improve routines and collaboration in the healthcare services, but were also in need of improved competence about use and misuse of alcohol and psychoactive drugs.
Ground beetles in city forests: does urbanization predict a personality trait?

Background Urbanization leads to substantial changes in natural habitats with profound effects on wildlife. Understanding behavioural responses to such environmental change is essential for identifying which organisms may adapt, as behaviour is often the first response to altered conditions. Individuals in more urbanized habitats may be expected to be more exploratory and bolder than their conspecifics in less urbanized habitats as they may be better able to cope with novel challenges. Methods In a two-year field study we tested ground beetles from differently urbanized forests for their exploratory behaviour (in a novel environment) and their risk-taking (death-feigning). In total, we tested ca. 3,000 individuals of four forest-dwelling ground beetle species from eight within-city forest patches. In the second year, we also transferred ca. 800 tested individuals of two species to the laboratory to test for consistent behavioural differences (i.e. personality differences) under standardised conditions. Results Individuals were generally more exploratory in more urbanized than in less urbanized areas but only in one year of the study. Exploratory behaviour was not predicted by population density but increased with temperature or showed a temperature optimum. Exploration was consistent over time and individuals that were more exploratory also took higher risks. Discussion We demonstrated that species which are generally less directly exposed to human activities (e.g., most invertebrates) show behavioural responses to urbanization. Effects of urbanization were year-dependent, suggesting that other environmental conditions interacted with effects of urbanization on beetle behaviour. Furthermore, our results indicate that different personality compositions might cause behavioural differences among populations living in differently urbanized habitats.
Human mitochondrial cytochrome P450 27C1 is localized in skin and preferentially desaturates trans-retinol to 3,4-dehydroretinol

Recently, zebrafish and human cytochrome P450 (P450) 27C1 enzymes have been shown to be retinoid 3,4-desaturases. The enzyme is unusual among mammalian P450s in that the predominant oxidation is a desaturation and in that hydroxylation represents only a minor pathway. We show by proteomic analysis that P450 27C1 is localized to human skin, with two proteins of different sizes present, one being a cleavage product of the full-length form. P450 27C1 oxidized all-trans-retinol to 3,4-dehydroretinol, 4-hydroxy (OH) retinol, and 3-OH retinol in a 100:3:2 ratio. Neither 3-OH nor 4-OH retinol was an intermediate in desaturation. No kinetic burst was observed in the steady state; neither the rate of substrate binding nor product release was rate-limiting. Ferric P450 27C1 reduction by adrenodoxin was 3-fold faster in the presence of the substrate and was ∼5-fold faster than the overall turnover. Kinetic isotope effects of 1.5–2.3 (on kcat/Km) were observed with 3,3-, 4,4-, and 3,3,4,4-deuterated retinol. Deuteration at C-4 produced a 4-fold increase in 3-hydroxylation due to metabolic switching, with no observable effect on 4-hydroxylation. Deuteration at C-3 produced a strong kinetic isotope effect for 3-hydroxylation but not 4-hydroxylation. Analysis of the products of deuterated retinol showed a lack of scrambling of a putative allylic radical at C-3 and C-4. We conclude that the most likely catalytic mechanism begins with abstraction of a hydrogen atom from C-4 (or possibly C-3) initiating the desaturation pathway, followed by a sequential abstraction of a hydrogen atom or proton-coupled electron transfer. Adrenodoxin reduction and hydrogen abstraction both contribute to rate limitation.
Patient Satisfaction and Associated Factors among Clients Admitted to Obstetrics and Gynecology Wards of Public Hospitals in Mekelle Town, Ethiopia: An Institution-Based Cross-Sectional Study

Background To improve the quality of services, satisfying patients is the primary goal of the Ethiopian reform programme. Objectives To assess patient satisfaction and associated factors among clients admitted to obstetrics and gynecology wards of public hospitals in Mekelle town. Method: Institution-based cross-sectional study design was conducted on 413 participants using systematic sampling methods. Data were collected from March 9 to May 8, 2016, using structured questionnaires. Data were entered and cleaned in Epidata 3.1 and analysed using SPSS V20 with binary logistic regression model. Result. The observed satisfaction rate was 79.7% at 95% CI (75.8%, 83.6%). Clients were dissatisfied towards well-describing side effects of medication, informing what the medication is used for before prescribing and administering, cleanness of toilet and washroom, and access to drinking water, latrine, and hand-washing facility. Respondents live in rural area, stayed < 4 days, admitted for the first time, admitted in Mekelle General Hospital, and who reported their feeling on ways privacy was assured were more likely satisfied than their counterparts. Conclusions The observed satisfaction rate is high. So, policymakers, Regional Health Bureau, hospital managers, caregivers, and researchers should plan and work together to keep track of patient satisfaction. Areas patients are dissatisfied should also improve.
Influence of vitreomacular interface on anti-vascular endothelial growth factor treatment outcomes in neovascular age-related macular degeneration

Abstract The aim of the study was to evaluate the influence of vitreomacular interface configuration on treatment outcomes after intravitreal anti-vascular endothelial growth factor (anti-VEGF) therapy for neovascular age-related macular degeneration (AMD). The Pubmed, Embase, and Cochrane Central Register of Controlled Trials databases were searched to identify relevant prospective or retrospective studies that evaluate the influence of vitreomacular adhesion (VMA) or vitreomacular traction (VMT) on functional and anatomical outcomes in neovascular AMD patients treated with anti-VEGF agents. The outcome measures were the mean change in best corrected visual acuity (BCVA) from baseline, the mean change in central macular thickness (CMT) from baseline, and the mean injection numbers of anti-VEGF treatment from baseline. In total, 9 studies were selected for this meta-analysis, including 2156 eyes (404 eyes in the VMA/VMT group and 1752 eyes in the non-VMA/VMT group). In neovascular AMD patients treated with anti-VEGF agents, the VMA/VMT group was associated with poorer visual acuity gains and CMT reductions at 1 year (WMD [95% CI], −6.17 [−11.91, −0.43] early treatment diabetic retinopathy study (ETDRS) letters, P = . 04; WMD [95% CI], 22.19 [2.01, 42.38] &mgr;m, P = . 03, respectively). There was no significant difference between 2 groups in the mean BCVA change and the CMT change over 2 years (WMD [95% CI], −5.59 [−21.19, 10.01] ETDRS letters, P = .48; WMD [95% CI], 6.56 [−24.78, 37.90] &mgr;m, P = .68, respectively). There was no significant difference in the mean injection numbers between 2 groups at 1 year (WMD [95% CI], 0.36 [−0.19, 0.90], P = .21), whereas the VMA/VMT group had a significantly higher mean injection numbers over 2 years (WMD [95% CI], 1.14 [0.11, 2.16], P = .03). The limited evidence suggests that vitreomacular interface configuration have a significant influence on the visual acuity gain and CMT reduction at 1 year, injection numbers at 2 years in neovascular AMD patients treated with anti-VEGF agents. However, the results of this meta-analysis should be interpreted with caution because of the heterogeneity among study designs. Eyes with VMA/VMT on optical coherence tomography at baseline may require more intensive treatment with decreased response to anti-VEGF agents.
Trends in the incidence of AIDS-defining and non-AIDS-defining cancers in people living with AIDS: a population-based study from São Paulo, Brazil

People living with AIDS are at increased risk of developing certain cancers. Since the introduction of the highly active antiretroviral therapy (HAART), the incidence of AIDS-defining cancers (ADCs) has decreased in high-income countries. The objective of this study was to analyse trends in ADCs and non-AIDS-defining cancers (NADCs) in HIV-positive people with a diagnosis of AIDS, in comparison to the general population, in São Paulo, Brazil. A probabilistic record linkage between the ‘Population-based Cancer Registry of São Paulo’ and the AIDS notification database (SINAN) was conducted. Cancer trends were assessed by annual per cent change (APC). In people with AIDS, 2074 cancers were diagnosed. Among men with AIDS, the most frequent cancer was Kaposi’s sarcoma (469; 31.1%), followed by non-Hodgkin lymphoma (NHL; 304; 20.1%). A decline was seen for ADCs (APC = −14.1%). All NADCs have increased (APC = 7.4%/year) significantly since the mid-2000s driven by the significant upward trends of anal (APC = 24.6%/year) and lung cancers (APC = 15.9%/year). In contrast, in men from the general population, decreasing trends were observed for these cancers. For women with AIDS, the most frequent cancer was cervical (114; 20.2%), followed by NHL (96; 17.0%). Significant declining trends were seen for both ADCs (APC = −15.6%/year) and all NADCs (APC = −15.8%/year), a comparable pattern to that found for the general female population. Trends in cancers among people with AIDS in São Paulo showed similar patterns to those found in developed countries. Although ADCs have significantly decreased, probably due to the introduction of HAART, NADCs in men have shown an opposite upward trend.
The Genetic Structure of Human Populations Studied Through Short Insertion‐Deletion Polymorphisms

In a landmark study Rosenberg et al. (2002) analyzed human genome diversity with 377 microsatellites in the HGDP‐CEPH Genome Diversity Panel and reported that the populations were structured into five geographical regions: America, Sub‐Saharan Africa, East Asia, Oceania and a cluster composed of Europe, the Middle East and Central Asia. They also observed that the within‐population component accounted for 93–95%, and that the among‐regions portion was only 3.6%, of the total genetic variance. We have also studied the HGDP‐CEPH Diversity Panel (1064 individuals from 52 populations) with a set of 40 biallelic slow‐evolving short insertion‐deletion polymorphisms (indels). We confirmed the partition of worldwide diversity into five genetic clusters that correspond to major geographic regions. Using the indels we have also disclosed an among‐regions component of genetic variance considerably larger (12.1%) than had been estimated using microsatellites. Our study demonstrates that a set of 40 well‐chosen biallelic markers is sufficient for the characterization of human population structure at the global level.
Genomic signatures of rapid adaptive evolution in the bluespotted cornetfish, a Mediterranean Lessepsian invader

Biological invasions are increasingly creating ecological and economical problems both on land and in aquatic environments. For over a century, the Mediterranean Sea has steadily been invaded by Indian Ocean/Red Sea species (called Lessepsian invaders) via the Suez Canal, with a current estimate of ~450 species. The bluespotted cornetfish, Fistularia commersonii, considered a ‘Lessepsian sprinter’, entered the Mediterranean in 2000 and by 2007 had spread through the entire basin from Israel to Spain. The situation is unique and interesting both because of its unprecedented rapidity and by the fact that it took this species c. 130 years to immigrate into the Mediterranean. Using genome scans, with restriction site‐associated DNA (RAD) sequencing, we evaluated neutral and selected genomic regions for Mediterranean vs. Red Sea cornetfish individuals. We found that few fixed neutral changes were detectable among populations. However, almost half of the genes associated with the 47 outlier loci (potentially under selection) were related to disease resistance and osmoregulation. Due to the short time elapsed from the beginning of the invasion to our sampling, we interpret these changes as signatures of rapid adaptation that may be explained by several mechanisms including preadaptation and strong local selection. Such genomic regions are therefore good candidates to further study their role in invasion success.
Impact of Ancestry and Common Genetic Variants on QT Interval in African Americans

Background—Ethnic differences in cardiac arrhythmia incidence have been reported, with a particularly high incidence of sudden cardiac death and low incidence of atrial fibrillation in individuals of African ancestry. We tested the hypotheses that African ancestry and common genetic variants are associated with prolonged duration of cardiac repolarization, a central pathophysiological determinant of arrhythmia, as measured by the electrocardiographic QT interval. Methods and Results—First, individual estimates of African and European ancestry were inferred from genome-wide single-nucleotide polymorphism (SNP) data in 7 population-based cohorts of African Americans (n=12 097) and regressed on measured QT interval from ECGs. Second, imputation was performed for 2.8 million SNPs, and a genome-wide association study of QT interval was performed in 10 cohorts (n=13 105). There was no evidence of association between genetic ancestry and QT interval (P=0.94). Genome-wide significant associations (P<2.5×10–8) were identified with SNPs at 2 loci, upstream of the genes NOS1AP (rs12143842, P=2×10–15) and ATP1B1 (rs1320976, P=2×10–10). The most significant SNP in NOS1AP was the same as the strongest SNP previously associated with QT interval in individuals of European ancestry. Low probability values (P<10–5) were observed for SNPs at several other loci previously identified in genome-wide association studies in individuals of European ancestry, including KCNQ1, KCNH2, LITAF, and PLN. Conclusions—We observed no difference in duration of cardiac repolarization with global genetic indices of African American ancestry. In addition, our genome-wide association study extends the association of polymorphisms at several loci associated with repolarization in individuals of European ancestry to include individuals of Afr.