Miracle-dz/UniFAR-FTUs huggingface dataset:
Burden of Infectious Diseases, Substance Use Disorders, and Mental Illness among Ukrainian Prisoners Transitioning to the Community

Background The epidemics of incarceration, substance use disorders (SUDs), and infectious diseases are inextricably intertwined, especially in the Former Soviet Union (FSU). Few objective data documenting this relationship regionally are available. We therefore conducted a comprehensive, representative country-wide prison health survey in Ukraine, where one of the world’s most volatile HIV epidemics persists, in order to address HIV prevention and treatment needs. Methods A nation-wide, multi-site randomly sampled biobehavioral health survey was conducted in four Ukrainian regions in 13 prisons among individuals being released within six months. After consent, participants underwent standardized health assessment surveys and serological testing for HIV, viral hepatitis, and syphilis. Results Of the 402 participants (mean age = 31.9 years), 20.1% were female. Prevalence of HIV, HCV, HBV, and syphilis was 19.4% (95% CI = 15.5%–23.3%), 60.2% (95% CI = 55.1%–65.4%), 5.2% (95% CI = 3.3%–7.2%), and 10% (95% CI = 7.4%–13.2%), respectively, with regional differences observed; HIV prevalence in the south was 28.6%. Among the 78 HIV-infected inmates, 50.7% were unaware of their HIV status and 44 (56.4%) had CD4<350 cells/mL, of which only five (11%) antiretroviral-eligible inmates were receiving it. Nearly half of the participants (48.7%) reported pre-incarcertion drug injection, primarily of opioids, yet multiple substance use (31.6%) and alcohol use disorders (56.6%) were common and 40.3% met screening criteria for depression. Conclusions This is the only such representative health study of prisoners in the FSU. This study has important implications for regional prevention and treatment because, unlike elsewhere, there is no recent evidence for reduction in HIV incidence and mortality in the region. The prevalence of infectious diseases and SUDs is high among this sample of prisoners transitioning to the community. It is critical to address pre- and post-release prevention and treatment needs with the development of linkage programs for the continuity of care in the community after release.
LEXICAL BUNDLES IN L 1 AND L 2 ACADEMIC WRITING

Yu-Hua Chen and Paul Baker Lancaster University This paper adopts an automated frequency-driven approach to identify frequently-used word combinations (i.e., lexical bundles) in academic writing. Lexical bundles retrieved from one corpus of published academic texts and two corpora of student academic writing (one L1, the other L2), were investigated both quantitatively and qualitatively. Published academic writing was found to exhibit the widest range of lexical bundles whereas L2 student writing showed the smallest range. Furthermore, some high-frequency expressions in published texts, such as in the context of, were underused in both student corpora, while the L2 student writers overused certain expressions (e.g., all over the world) which native academics rarely used. The findings drawn from structural and functional analyses of lexical bundles also have some pedagogical implications.
Real-time Detection and Recognition of Machine-Readable Zones with Mobile Devices

Many security documents contain machine readable zones (MRZ) for automatic inspection. An MRZ is intended to be read by dedicated machinery, which often requires a stationary setup. Although MRZ information can also be read using camera phones, current solutions require the user to align the document, which is rather tedious. We propose a real-time algorithm for MRZ detection and recognition on off-the-shelf mobile devices. In contrast to state-of-the-art solutions, we do not impose position restrictions on the document. Our system can instantly produce robust reading results from a large range of viewpoints, making it suitable for document verification or classification. We evaluate the proposed algorithm using a large synthetic database on a set of off-the-shelf smartphones. The obtained results prove that our solution is capable of achieving good reading accuracy despite using largely unconstrained viewpoints and mobile devices.
On-line preconcentration employing a tannin resin for copper determination in plant material and food stuff by atomic absorption spectrometry

A flow system for copper on-line preconcentration, employing a tannin resin prepared from Eucalyptus Saligna Sm, with determination by flame atomic absorption spectrometry is proposed. The manifold was designed by assembling an automatic injector-commutator and a set of three-way solenoid valves which were controlled by a microcomputer with a PCL-711 interface card running a software written in QuickBASIC 4.5. The analyte was concentrated by pumping the sample solution through the resin column during 60 s, followed by elution with a 1.0 mol L-1 hydrochloric acid solution. Accuracy was assessed by analyzing acidic digests of certificate reference materials and no significant difference at 95% confidence level was observed. Other profitable features such as throughput of 48 determinations per hour, reagent consumption of 67 mL per determination, relative standard deviation of 3% (n=10) for a typical sample presenting concentration of 21.75 ng mL-1 Cu, detection limit of 1 ng mL-1 and enrichment factor of 10 times were also achieved.
African Trypanosoma infection in a dog in France

AFRICAN animal trypanosomosis, also known as ‘nagana’ in tropical Africa, is caused by haemoflagellated protozoa, primarily Trypanosoma congolense , Trypanosoma brucei subspecies brucei and Trypanosoma vivax. Trypanosomosis is a serious economic constraint to livestock and agriculture development in sub-Saharan Africa, causing livestock deaths and reduced productivity (Kristjanson 1999, Ilemobade 2009). Dogs are particularly susceptible to T congolense , which is transmitted cyclically by Glossina species (tsetse fly) (Greene 2006). T congolense can be classified into three types: savannah, forest and kilifi (Young and Godfrey 1983, Knowles and others 1988). T congolense savannah type was shown to be the most virulent type in cattle by Bengaly and others (2002). Dogs pose a minimal risk for human infection; however, they seem to be important as a sentinel for infection (Greene 2006). Until now, there has been only one description of a chronically infected dog in Europe, 3.5 years after importation from Africa (Gow and others 2007). This short communication describes a …
TM or not TM: transmembrane protein prediction with low false positive rate using DAS-TMfilter

UNLABELLED Web-based servers implementing the DAS-TMfilter algorithm have been launched at three mirror sites and their usage is described. The underlying computer program is an upgraded and modified version of the DAS-prediction method. The new server is (approximately 1 among 100 unrelated queries) while the high efficiency of the original algorithm locating TM segments in queries is preserved (sensitivity of approximately 95% among documented proteins with helical TM regions). AVAILABILITY The server operates at three mirror sites: http://mendel.imp. univie.ac. at/sat/DAS/DAS.html, http://wooster.bip. bham.ac. uk/DAS.html and http://www.enzim. hu/DAS/DAS.html. The program is available on request.
Role of S100A3 in human colorectal cancer and the anticancer effect of cantharidinate

Colorectal cancer (CRC) is a leading cause of cancer-related mortality. The early diagnosis and treatment of CRC is the key to improving the survival of patients who may benefit from adjuvant chemotherapy. In the present study, the protein expression of S100A3 was observed in a cohort of 20 patients with cancer, which indicated that S100A3 activation was involved in tumorigenesis. In addition, the anticancer activity of cantharidinate was investigated using immunohistochemistry and quantitative polymerase chain reaction (qPCR) analysis. The protein expression of S100A3 was observed to increase by 2.4-fold in human CRC cells compared with the expression level in normal control cells (P<0.01). Cantharidinate inhibited the protein and gene expression of S100A3 in UCT-116 human CRC cells in vitro. These results suggested that S100A3 is important in human CRC. Cantharidinate has the potential to be considered as a novel adjuvant drug for controlling the expression of S100A3 in human CRC as it exhibits preventive effects.
Localized Hough Transform for Human Detection Anonymous CVPR submission

This paper presents a method that uses Hough transform in the localized area for robust visual object recognition. We focus on the human detection problem at different resolutions. The proposed method takes into account orientation information along with spatial information, which is ignored by some dense image descriptors such as the histogram of oriented gradients (HOG). With our method, we capture the linear structure in the image, which renders more discriminative features for object detection than the existing methods. We also discuss in detail as to how each parameter of the localized Hough transform (LHT) affects the robustness of object detection, with experiments done on human detection. Implications of choosing image descriptors versus learning based methods for human detection at various scales are also discussed in this paper, comparing the current state-of-the-art methods for human detection including the convolutional neural networks, the histogram of oriented gradients method and our method. Our experimental results show that the proposed method has the best performance.
Genetic and epigenetic heterogeneity in cancer: A genome‐centric perspective

Genetic and epigenetic heterogeneity (the main form of non‐genetic heterogeneity) are key elements in cancer progression and drug resistance, as they provide needed population diversity, complexity, and robustness. Despite drastically increased evidence of multiple levels of heterogeneity in cancer, the general approach has been to eliminate the “noise” of heterogeneity to establish genetic and epigenetic patterns. In particular, the appreciation of new types of epigenetic regulation like non‐coding RNA, have led to the hope of solving the mystery of cancer that the current genetic theories seem to be unable to achieve. In this mini‐review, we have briefly analyzed a number of mis‐conceptions regarding cancer heterogeneity, followed by the re‐evaluation of cancer heterogeneity within a framework of the genome‐centric concept of evolution. The analysis of the relationship between gene, epigenetic and genome level heterogeneity, and the challenges of measuring heterogeneity among multiple levels have been discussed. Further, we propose that measuring genome level heterogeneity represents an effective strategy in the study of cancer and other types of complex diseases, as emphasis on the pattern of system evolution rather than specific pathways provides a global and synthetic approach. Compared to the degree of heterogeneity, individual molecular pathways will have limited predictability during stochastic cancer evolution where genome dynamics (reflected by karyotypic heterogeneity) will dominate. J. Cell. Physiol. 220: 538–547, 2009. © 2009 Wiley‐Liss, Inc.
Aberrant expression of c‐met and HGF/c‐met pathway provides survival advantage in B‐chronic lymphocytic leukemia

B‐chronic lymphocytic leukemia (B‐CLL) is characterized by accumulation of CD5+ B lymphocytes. Decreased VLA‐4 (Cd49d/CD29) and CD11a expression and defective adhesion in B‐CLL have been previously shown, although there was no substantial data about its importance in immunobiology of B‐CLL. The hepatocyte growth factor (HGF) receptor, c‐met, plays a role in adhesion by acting on VLA‐4. c‐met and VLA‐4 share crucial signaling molecules in cell survival. In this study, relationship between expressions of c‐met and CD49d, CD11a, and additional common signaling molecules in B‐CLL was investigated.
Putatively novel serotypes and the potential for reduced vaccine effectiveness: capsular locus diversity revealed among 5405 pneumococcal genomes

The pneumococcus is a leading global pathogen and a key virulence factor possessed by the majority of pneumococci is an antigenic polysaccharide capsule (‘serotype’), which is encoded by the capsular (cps) locus. Approximately 100 different serotypes are known, but the extent of sequence diversity within the cps loci of individual serotypes is not well understood. Investigating serotype-specific sequence variation is crucial to the design of sequence-based serotyping methodology, understanding pneumococcal conjugate vaccine (PCV) effectiveness and the design of future PCVs. The availability of large genome datasets makes it possible to assess population-level variation among pneumococcal serotypes and in this study 5405 pneumococcal genomes were used to investigate cps locus diversity among 49 different serotypes. Pneumococci had been recovered between 1916 and 2014 from people of all ages living in 51 countries. Serotypes were deduced bioinformatically, cps locus sequences were extracted and variation was assessed within the cps locus, in the context of pneumococcal genetic lineages. Overall, cps locus sequence diversity varied markedly: low to moderate diversity was revealed among serogroups/types 1, 3, 7, 9, 11 and 22; whereas serogroups/types 6, 19, 23, 14, 15, 18, 33 and 35 displayed high diversity. Putative novel and/or hybrid cps loci were identified among all serogroups/types apart from 1, 3 and 9. This study demonstrated that cps locus sequence diversity varied widely between serogroups/types. Investigation of the biochemical structure of the polysaccharide capsule of major variants, particularly PCV-related serotypes and those that appear to be novel or hybrids, is warranted.
Cognitive and Brain Consequences of Conflict

Tasks involving conflict between stimulus dimensions have been shown to activate dorsal anterior cingulate and prefrontal areas. It has been proposed that the dorsal anterior cingulate is involved a domain general process of monitoring conflict, while prefrontal areas are involved in resolving conflict. We examine three tasks that all require people to respond based on one stimulus dimension while ignoring another conflicting dimension, but which vary in the source of conflict. One of the tasks uses language stimuli (Stroop effect) and two use nonlanguage spatial conflicts appropriate for children and nonhuman animals. In Experiment 1, 12 participants were studied with event-related functional magnetic resonance imaging (fMRI) while performing each of the three tasks. Reaction times for each of the three tasks were significantly longer in the incongruent condition compared with the congruent condition, demonstrating that each task elicits a conflict. By studying the same people in the same session, we test the hypothesis that conflict activates a similar brain network in the three tasks. Significant activations were found in the anterior cingulate and left prefrontal cortex for all three conflict tasks. Within these regions, the conflict component demonstrated evidence for significant common activation across the three tasks, although the peak activation point and spatial extent were not identical. Other areas demonstrated activation unique to each task. Experiments 2-4 provide behavioral evidence indicating considerable independence between conflict operations involved in the tasks. The behavioral and fMRI results taken together seem to argue against a single unified network for processing conflict, but instead support either distinct networks for each conflict task or a single network that monitors conflict with different sites used to resolve the conflict.
Effect of peers and friends on youth physical activity and motivation to be physically active.

OBJECTIVE To test whether the presence of a peer or a friend increases the motivation to be physically active in overweight and non-overweight youth in a laboratory setting. METHODS Youth motivation to be physically active as a function of the social context was measured using a computerized relative reinforcing value task to earn points exchangeable for physical and/or sedentary activities. RESULTS The presence of a friend (p<.001) increased youth's; motivation to be physically active. The presence of a peer increased overweight youth's; motivation to be physically active, whereas this was not the case for lean youth (p=.47). Participants biked a greater distance in the presence of a friend than when alone (p<.001). Overweight youth biked a greater distance in the presence of a peer than when alone, while this was not the case for lean youth (p=.23). CONCLUSIONS Friendships may increase youth's motivation to engage in physical activity and promote greater physical activity in non-overweight and overweight youth.
The expression and function of Epstein-Barr virus encoded latent genes

The association of Epstein-Barr virus (EBV) with various malignancies is well established but the pattern of EBV latent gene expression in these different tumours is variable, reflecting distinct aspects of the virus–cell interaction. These different forms of EBV latency are associated with phenotypic variation and highlight the influence of EBV latent proteins on cell growth and survival. The EBV latent proteins have distinct functions associated with the maintenance of EBV infection and the control of various signalling and transcriptional pathways that facilitate the proliferation and survival of infected cells. Understanding the function of these EBV latent proteins will not only provide insight into the mechanisms governing fundamental cell processes but will also identify targets for novel treatment.
Prevalence of temporomandibular dysfunction in a group of scuba divers

Background: Temporomandibular dysfunction (TMD) has been reported to be a common problem in divers, with a prevalence of up to 68%. No evidence for this is available. Objective: To investigate the prevalence of TMD in divers. Method: Sixty three subjects were asked to retrospectively complete a questionnaire on symptoms of TMD after diving in warm and cold water areas and in daily life. Results: The prevalence of TMD was greater in female divers. The prevalence of TMD while diving was about 26%, comparable to that experienced in daily life. Conclusion: Improvements in mouthpiece design and lighter demand valves mean that TMD is now probably exacerbated by diving rather than caused by it.
Seasonal carbon storage and growth in Mediterranean tree seedlings under different water conditions.

In all Mediterranean-type ecosystems, evergreen and deciduous trees differing in wood anatomy, growth pattern and leaf habit coexist, suggesting distinct adaptative responses to environmental constraints. This study examined the effects of summer water stress on carbon (C) storage and growth in seedlings of three coexisting Mediterranean trees that differed in phenology and wood anatomy characteristics: Quercus ilex subsp. ballota (Desf.) Samp. , Quercus faginea Lam. and Pinus halepensis L. Seedlings were subjected to two levels of watering during two consecutive summers and achieved a minimum of -0.5 and -2.5 MPa of predawn water potential in the control and water stress treatment, respectively. Both Quercus species concentrated their growth in the early growing season, demanding higher C in early spring but replenishing C-stores in autumn. These species allocated more biomass to roots, having larger belowground starch and lipid reserves. Quercus species differed in seasonal storage dynamics from P. halepensis. This species allocated most of its C to aboveground growth, which occurred gradually during the growing season, leading to fewer C-reserves. Soluble sugar and starch concentrations sharply declined in August in P. halepensis, probably because reserves support respiration demands as this species closed stomata earlier under water stress. Drought reduced growth of the three species, mainly in Q. faginea and P. halepensis, but not C-reserves, suggesting that growth under water stress conditions is not limited by C-availability.
Self-affirmation and responses to health messages: a meta-analysis on intentions and behavior.

OBJECTIVE The present study aimed to quantify the magnitude of the effect of self-affirmation manipulations on health messages' influence on both intentions and behavior. METHODS A systematic search was conducted for experimental studies comparing participants who self-affirmed prior to reading a threatening health message to those who did not self-affirm. Effect sizes for health intentions and behaviors were aggregated using a random-effects model. RESULTS Data from 16 studies were included. The aggregate effect sizes for intentions and behavior were significant and small in magnitude (d+ = .26, 95% confidence interval [CI] = .04-.48; d+ = .27, 95% CI = .11-.43, respectively). A meta-regression analysis revealed that among studies assessing both outcomes, the size of an effect on intentions did not predict the size of an effect on behavior, β = . 03, 95% CI = -. 30-. 36. Type of health behavior (damaging vs. promoting), timing of the health behavior (proximal vs. distal), type of self-affirmation manipulation (values vs. kindness), and the specificity of the health message (single vs. multiple health issues) did not moderate the effect of self-affirmation on intentions or behavior. CONCLUSIONS Self-affirmation influences health messages' effect on intentions and behavior; however, with the present study finding that intention effect sizes did not predict behavior effect sizes, and with past studies of heath behavior change finding that intentions do not always translate to behavior, little research supports a causal intention-behavior relation among self-affirmation studies. Future research is needed to address which specific health-related responses explain why self-affirmation elicits health behavior change.
Initial Phases of Starvation and Activity of Bacteria at Surfaces

The activity of the hydrophilic Vibrio sp. strain DW1 and the hydrophobic Pseudomonas sp. strain S9, which both undergo starvation-induced responses, was examined at nutrient-enriched and nutrient-deficient interfaces. The initial period of response to a starvation regime (“dwarfing” phase) is a sequence of two processes: fragmentation and continuous size reduction of the fragmented cells. This dwarfing phase is also one of intense metabolic activity as supported by O2 uptake measurements of the endogenous metabolism and the use of inhibitors of the proton flow, the electron transport chain, and membrane-bound ATPase. Hydrophilic bacteria become even smaller at nutrient-deficient surfaces than in the liquid phase upon starvation, and this is reflected in a higher endogenous metabolism exhibited by surface-associated cells compared with those in the liquid phase. On the other hand, hydrophobic bacteria dwarfing at surfaces did not exhibit a greater size reduction and exhibited an endogenous metabolism that was only slightly higher than that of cells in the liquid phase. Bacterial scavenging of surface-localized nutrients is related to the degree of irreversible binding of dwarf and starved bacteria, which in turn may be related to the degree of cell surface hydrophobicity.