Miracle-dz/UniFAR-FTUs huggingface dataset:
Transformation of identity in substance use as a pathway to recovery and the potential of treatment for hepatitis C: a systematic review

Abstract Background and aim People who inject drugs are at high risk of contracting hepatitis C (HCV). The introduction of direct acting antiviral (DAA) drugs to treat HCV has the potential to transform care; however, uptake of DAAs has been slower than anticipated. The strong link between HCV and injecting drug use frames HCV as a shameful, stigmatising disease, reinforcing an ‘addict’ identity. Linking HCV care to a recovery journey, ‘clean’ identity and social redemption may provide compelling encouragement for people to engage with treatment and re‐evaluate risk and behaviours, reducing the incidence of HCV re‐infection. The aim of this review was to identify actions, interventions and treatments that provide an opportunity for a change in identity and support a recovery journey and the implications for HCV care. Methods Databases (MEDLINE, EMBASE, PsycINFO, ProQuest Public Health, ProQuest Sociological Abstracts, CINAHL and Web of Science) were searched following our published strategy and a grey literature search conducted. A narrative synthesis was undertaken to collate themes and identify common threads and provide an explanation of the findings. Results Thirty‐two studies fulfilled the inclusion criteria. The narrative synthesis of the studies identified five over‐arching analytical themes: social factors in substance use and recovery, therapeutic communities, community treatment, online communities, and finally women and youth subsets. The change from an ‘addict’ identity to a ‘recovery’ identity is described as a key aspect of a recovery journey, and this process can be supported through social support and turning point opportunities. Conclusions Recovery from addiction is a socially mediated process. Actions, interventions and treatments that support a recovery journey provide social connections, a recovery identity and citizenship (reclaiming a place in society). There is a gap in current literature describing how pathways of care with direct acting antivirals can be designed to promote recovery, as part of hepatitis C care.
Image variability and face matching

This study investigates whether variability in perceived trait judgements disrupts our ability to match unfamiliar faces. In this preregistered study, 174 participants completed a face matching task where they were asked to indicate whether two ambient face images belonged to the same person or different people (17,748 total data points). Participants completed 51 match trials consisting of images of the same person that differed substantially on one trait (either trustworthiness, dominance or attractiveness) with minimal differences in the alternate traits. Participants also completed 51 mismatch trials which contained two photos of similar-looking individuals. We hypothesised that participants would make more errors on match trials when images differed in terms of attractiveness ratings than when they differed on trustworthiness or dominance. Contrary to expectations, images that differed in terms of attractiveness were matched most accurately, and there was no relationship between the extent of differences in attractiveness ratings and accuracy. There was some evidence that differences in perceived dominance and, to a lesser extent, trustworthiness were associated with lower face matching performance. However, these relationships were not significant when alternate traits were accounted for. The findings of our study suggest that face matching performance is largely robust against variation in trait judgements.
Persistence of Residual Submicroscopic P. falciparum Parasitemia following Treatment of Artemether-Lumefantrine in Ethio-Sudan Border, Western Ethiopia

The emergence of artemisinin-resistant parasites in Africa has had a devastating impact, causing most malaria cases and related deaths reported on the continent. In Ethiopia, artemether-lumefantrine (AL) is the first-line drug for the treatment of uncomplicated falciparum malaria. ABSTRACT The emergence of artemisinin-resistant parasites in Africa has had a devastating impact, causing most malaria cases and related deaths reported on the continent. In Ethiopia, artemether-lumefantrine (AL) is the first-line drug for the treatment of uncomplicated falciparum malaria. This study is one of the earliest evaluations of artemether-lumefantrine (AL) efficacy in western Ethiopia, 17 years after the introduction of this drug in the study area. This study aimed at assessing PCR- corrected clinical and parasitological responses at 28 days following AL treatment. Sixty uncomplicated falciparum malaria patients were enrolled, treated with standard doses of AL, and monitored for 28 days with clinical and parasitological assessments from September 15 to December 15, 2020. Microscopy was used for patient recruitment and molecular diagnosis of P. falciparum was performed by Var gene acidic terminal sequence (varATS) real-time PCR on dried blood spots collected from each patient from day 0 and on follow-up days 1, 2, 3, 7, 14, 21, and 28. MspI and msp2 genotyping was done to confirm occurrence of recrudescence. Data entry and analysis were done by using the WHO-designed Excel spreadsheet and SPSS version 20 for Windows. A P value of less or equal to 0.05 was considered significant. From a total of 60 patients enrolled in this efficacy study, 10 were lost to follow-up; the results were analyzed for 50 patients. All the patients were fever-free on day 3. The asexual parasite positivity rate on day 3 was zero. However; 60% of the patients were PCR positive on day 3. PCR positivity on day 3 was more common among patients <15 years old as compared with those ≥15 years old (AOR = 6.44, P = 0.027). Only two patients met the case definition of treatment failure. These patients were classified as a late clinical failure as they showed symptoms of malaria and asexual stages of the parasite detected by microscopy on day 14 of their follow-ups. Hence, the Kaplan-Meier analysis of PCR- corrected adequate clinical and parasitological response (ACPR) rate of AL among study participants was 96% (95% CI: 84.9–99). In seven patients, the residual submicroscopic parasitemia persists from day 0 to day 28 of the follow-up. In addition, 16% (8/50) of patients were PCR– and then turned PCR+ after day 7 of the follow-up. AL remains efficacious for the treatment of uncomplicated falciparum malaria in the study area. However, the persistence of PCR-detected residual submicroscopic parasitemia following AL might compromise this treatment and need careful monitoring.
The epidemiology of diphtheria in Haiti, December 2014–June 2021: A spatial modeling analysis

Background Haiti has been experiencing a resurgence of diphtheria since December 2014. Little is known about the factors contributing to the spread and persistence of the disease in the country. Geographic information systems (GIS) and spatial analysis were used to characterize the epidemiology of diphtheria in Haiti between December 2014 and June 2021. Methods Data for the study were collected from official and open-source databases. Choropleth maps were developed to understand spatial trends of diphtheria incidence in Haiti at the commune level, the third administrative division of the country. Spatial autocorrelation was assessed using the global Moran’s I. Local indicators of spatial association (LISA) were employed to detect areas with spatial dependence. Ordinary least squares (OLS) and geographically weighted regression (GWR) models were built to identify factors associated with diphtheria incidence. The performance and fit of the models were compared using the adjusted r-squared (R2) and the corrected Akaike information criterion (AICc). Results From December 2014 to June 2021, the average annual incidence of confirmed diphtheria was 0.39 cases per 100,000 (range of annual incidence = 0.04–0.74 per 100,000). During the study period, diphtheria incidence presented weak but significant spatial autocorrelation (I = 0.18, p<0.001). Although diphtheria cases occurred throughout Haiti, nine communes were classified as disease hotspots. In the regression analyses, diphtheria incidence was positively associated with health facility density (number of facilities per 100,000 population) and degree of urbanization (proportion of urban population). Incidence was negatively associated with female literacy. The GWR model considerably improved model performance and fit compared to the OLS model, as indicated by the higher adjusted R2 value (0.28 v 0.15) and lower AICc score (261.97 v 267.13). Conclusion This study demonstrates that GIS and spatial analysis can support the investigation of epidemiological patterns. Furthermore, it shows that diphtheria incidence exhibited spatial variability in Haiti. The disease hotspots and potential risk factors identified in this analysis could provide a basis for future public health interventions aimed at preventing and controlling diphtheria transmission.
CTCF shapes chromatin structure and gene expression in health and disease

CCCTC‐binding factor (CTCF) is an eleven zinc finger (ZF), multivalent transcriptional regulator, that recognizes numerous motifs thanks to the deployment of distinct combinations of its ZFs. The great majority of the ~50,000 genomic locations bound by the CTCF protein in a given cell type is intergenic, and a fraction of these sites overlaps with transcriptional enhancers. Furthermore, a proportion of the regions bound by CTCF intersect genes and promoters. This suggests multiple ways in which CTCF may impact gene expression. At promoters, CTCF can directly affect transcription. At more distal sites, CTCF may orchestrate interactions between regulatory elements and help separate eu‐ and heterochromatic areas in the genome, exerting a chromatin barrier function. In this review, we outline how CTCF contributes to the regulation of the three‐dimensional structure of chromatin and the formation of chromatin domains. We discuss how CTCF binding and architectural functions are regulated. We examine the literature implicating CTCF in controlling gene expression in development and disease both by acting as an insulator and a factor facilitating regulatory elements to efficiently interact with each other in the nuclear space.
Testing Positive on a Multigene Panel Does Not Suffice to Determine Disease Risks

See the Notes section for the full list of authors’ affiliations. Correspondence to: Hormuzd A. Katki, PhD, Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Dr., Room 7E592, Bethesda, MD 20892 (e-mail: katkih@mail.nih.gov); or Maria Isabel Achatz, MD, Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Dr., Room 6E508, Bethesda, MD 20892 (e-mail: mariaisabel.achatz@nih.gov).
The impact of comorbid spinal pain in depression on work participation and clinical remission following brief or short psychotherapy. Secondary analysis of a randomized controlled trial with two-year follow-up

Objectives This explorative study analyses the influence of baseline comorbid long-lasting spinal pain (CSP) on improvement of long term work participation and clinical remission of mental health illness following either brief coping-focussed or short-term psychotherapy for depression. Whether type of treatment modifies outcome with or without CSP is also analysed. Design A secondary post hoc subgroup analysis of a pragmatic randomised controlled trial. Interventions Brief or standard short psychotherapy. Methods Based on baseline assessment, the sample was subdivided into a subgroup with and a subgroup without CSP. Work participation and clinical remission of depression and anxiety were assessed as treatment outcome at two-year follow-up. Simple and multivariate logistic regression analyses, across the intervention arms, were applied to evaluate the impact of CSP on treatment outcome. Selected baseline variables were considered as potential confounders and included as variates if relevant. The modifying effect of CSP on treatment outcome was evaluated by including intervention modality as an interaction term. Main results Among the 236 participants with depressive symptoms, 83 participants (35%) were identified with CSP. In simple logistic regression analysis, CSP reduced improvements on both work participation and clinical remission rate. In the multivariate analysis however, the impact of CSP on work participation and on clinical remission were not significant after adjusting for confounding variables. Reduction of work participation was mainly explained by the higher age of the CSP participants and the reduced clinical remission by the additional co-occurrence of anxiety symptoms at baseline. The occurrence of CSP at baseline did not modify long term outcome of brief compared to short psychotherapy. Conclusions CSP at baseline reduced work participation and worsened remission of mental health symptoms two-year following psychotherapy. Older age and more severe baseline anxiety are associated to reduced effectiveness. Type of psychotherapy received did not contribute to differences.
Identification of technology frontiers of artificial intelligence-assisted pathology based on patent citation network

Objectives This paper aimed to identify the technology frontiers of artificial intelligence-assisted pathology based on patent citation network. Methods Patents related to artificial intelligence-assisted pathology were searched and collected from the Derwent Innovation Index (DII), which were imported into Derwent Data Analyzer (DDA, Clarivate Derwent, New York, NY, USA) for authority control, and imported into the freely available computer program Ucinet 6 for drawing the patent citation network. The patent citation network according to the citation relationship could describe the technology development context in the field of artificial intelligence-assisted pathology. The patent citations were extracted from the collected patent data, selected highly cited patents to form a co-occurrence matrix, and built a patent citation network based on the co-occurrence matrix in each period. Text clustering is an unsupervised learning method, an important method in text mining, where similar documents are grouped into clusters. The similarity between documents are determined by calculating the distance between them, and the two documents with the closest distance are combined. The method of text clustering was used to identify the technology frontiers based on the patent citation network, which was according to co-word analysis of the title and abstract of the patents in this field. Results 1704 patents were obtained in the field of artificial intelligence-assisted pathology, which had been currently undergoing three stages, namely the budding period (1992–2000), the development period (2001–2015), and the rapid growth period (2016–2021). There were two technology frontiers in the budding period (1992–2000), namely systems and methods for image data processing in computerized tomography (CT), and immunohistochemistry (IHC), five technology frontiers in the development period (2001–2015), namely spectral analysis methods of biomacromolecules, pathological information system, diagnostic biomarkers, molecular pathology diagnosis, and pathological diagnosis antibody, and six technology frontiers in the rapid growth period (2016–2021), namely digital pathology (DP), deep learning (DL) algorithms—convolutional neural networks (CNN), disease prediction models, computational pathology, pathological image analysis method, and intelligent pathological system. Conclusions Artificial intelligence-assisted pathology was currently in a rapid development period, and computational pathology, DL and other technologies in this period all involved the study of algorithms. Future research hotspots in this field would focus on algorithm improvement and intelligent diagnosis in order to realize the precise diagnosis. The results of this study presented an overview of the characteristics of research status and development trends in the field of artificial intelligence-assisted pathology, which could help readers broaden innovative ideas and discover new technological opportunities, and also served as important indicators for government policymaking.
Rocking and rolling down an incline : the dynamics of nested cylinders on a ramp

In this thesis, I report the results of a combined experimental and theoretical investigation of a journal bearing, specifically, a cylinder suspended in a viscous fluid housed within a cylindrical shell, rolling down an incline under the influence of gravity. Particular attention is given to rationalizing the distinct modes of motion observed. We performed a series of experiments in which the inner cylinder density and the fluid viscosity were varied. Three distinct types of behavior were observed. First, in what we shall call the "rocking" mode, after an initial settling period, the shell rocks back and forth without moving down the ramp. Second, we observed "slow, quasi-steady rolling"; this mode is characterized by the system proceeding down the hill at essentially a constant velocity. Finally, the cylinders roll down the incline with constant acceleration; we shall call this mode "unbounded acceleration. " An accompanying theoretical model is developed and enables us to rationalize the rocking and accelerating modes. In the rocking solutions, potential and kinetic energy are dissipated in the fluid as the inner cylinder approaches the bottom of the outer cylinder. In the accelerating solutions, the whole system moves as a solid body so that no dissipation occurs and potential energy is continually converted into kinetic energy. In order to understand the quasi-steady motion, we analyze the motion of a similar system: a metal cylinder is placed inside a larger plastic cylinder filled with fluid and attached to a motor which fixes the larger cylinder's rotation rate. Our observations of this system, specifically, the differences betweeen experiments and theory lead us to consider the effect of internal friction due to surface roughness. The resulting model's predictions are well supported by our observations. Finally, to rationalize the slow, quasi-steady rolling motion of the system, we incorporate surface roughness and cavitation into the theoretical model. These effects provide a restoring force on the inner cylinder; however, we find that surface roughness is the dominant effect. Thesis Supervisor: John W. M. Bush Title: Associate Professor
Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution

Chromosomal inversions have been shown to play a major role in a local adaptation by suppressing recombination between alternative arrangements and maintaining beneficial allele combinations. However, so far, their importance relative to the remaining genome remains largely unknown. Understanding the genetic architecture of adaptation requires better estimates of how loci of different effect sizes contribute to phenotypic variation. Here, we used three Swedish islands where the marine snail Littorina saxatilis has repeatedly evolved into two distinct ecotypes along a habitat transition. We estimated the contribution of inversion polymorphisms to phenotypic divergence while controlling for polygenic effects in the remaining genome using a quantitative genetics framework. We confirmed the importance of inversions but showed that contributions of loci outside inversions are of similar magnitude, with variable proportions dependent on the trait and the population. Some inversions showed consistent effects across all sites, whereas others exhibited site‐specific effects, indicating that the genomic basis for replicated phenotypic divergence is only partly shared. The contributions of sexual dimorphism as well as environmental factors to phenotypic variation were significant but minor compared to inversions and polygenic background. Overall, this integrated approach provides insight into the multiple mechanisms contributing to parallel phenotypic divergence.
The Journey of Resveratrol from Vineyards to Clinics

Abstract With rising technological advancements, several factors influence the lifestyle of people and stimulate chronic inflammation that severely affects the human body. Chronic inflammation leads to a broad range of physical and pathophysiological distress. For many years, non-steroidal drugs and corticosteroids were most frequently used in treating inflammation and related ailments. However, long-term usage of these drugs aggravates the conditions of chronic diseases and is presented with morbid side effects, especially in old age. Hence, the quest for safe and less toxic anti-inflammatory compounds of high therapeutic potential with least adverse side effects has shifted researchers’ attention to ancient medicinal system. Resveratrol (RSV) − 3,4,5′ trihydroxystilbene is one such naturally available polyphenolic stilbene derivative obtained from various plant sources. For over 2000 years, these plants have been used in Asian medicinal system for curing inflammation-associated disorders. There is a wealth of in vitro, in vivo and clinical evidence that shows RSV could induce anti-aging health benefits including, anti-cancer, anti-inflammatory, anti-oxidant, phytoesterogenic, and cardio protective properties. However, the issue of rapid elimination of RSV through the metabolic system and its low bio-availability is of paramount importance which is being studied extensively. Therefore, in this article, we scientifically reviewed the molecular targets, biological activities, beneficial and contradicting effects of RSV as evinced by clinical studies for the prevention and treatment of inflammation-mediated chronic disorders.
Complex optimal transport and the pluripotential theory of K\"ahler-Ricci solitons

Let (X,L) be a (semi-) polarized complex projective variety and T a real torus acting holomorphically on X with moment polytope P. Given a probability density g on P we introduce a new type of Monge-Ampere measure on X, defined for singular T-invariant metrics on the line bundle L, generalizing the ordinary Monge-Ampere of global pluripotential theory, which corresponds to the case when T is trivial (or g=1). In the opposite extreme case when T has maximal rank, i.e. (X,L,T) is a toric variety, the solution of the corresponding Monge-Ampere equation with right hand side \mu corresponds to the convex Kantorovich potential for the optimal transport map in the Monge-Kantorovich transport problem betweeen \mu and g (for a quadratic cost function). Accordingly, our general setting can be seen as a complex version of optimal transport theory. Our main complex geometric applications concern the pluripotential study of singular (shrinking) Kahler-Ricci solitons. In particular, we establish the uniqueness of such solitons, modulo automorphisms, and explore their relation to a notion of modified K-stability inspired by the work of Tian-Zhu. The quantization of this setup, in the sense of Donaldson, is also studied.