Miracle-dz/UniFAR-FTUs huggingface dataset:
ADEPt, a semantically-enriched pipeline for extracting adverse drug events from free-text electronic health records

Adverse drug events (ADEs) are unintended responses to medical treatment. They can greatly affect a patient’s quality of life and present a substantial burden on healthcare. Although Electronic health records (EHRs) document a wealth of information relating to ADEs, they are frequently stored in the unstructured or semi-structured free-text narrative requiring Natural Language Processing (NLP) techniques to mine the relevant information. Here we present a rule-based ADE detection and classification pipeline built and tested on a large Psychiatric corpus comprising 264k patients using the de-identified EHRs of four UK-based psychiatric hospitals. The pipeline uses characteristics specific to Psychiatric EHRs to guide the annotation process, and distinguishes: a) the temporal value associated with the ADE mention (whether it is historical or present), b) the categorical value of the ADE (whether it is assertive, hypothetical, retrospective or a general discussion) and c) the implicit contextual value where the status of the ADE is deduced from surrounding indicators, rather than explicitly stated. We manually created the rulebase in collaboration with clinicians and pharmacists by studying ADE mentions in various types of clinical notes. We evaluated the open-source Adverse Drug Event annotation Pipeline (ADEPt) using 19 ADEs specific to antipsychotics and antidepressants medication. The ADEs chosen vary in severity, regularity and persistence. The average F-measure and accuracy achieved by our tool across all tested ADEs were 0.83 and 0.83 respectively. In addition to annotation power, the ADEPT pipeline presents an improvement to the state of the art context-discerning algorithm, ConText.
Extracting Socioeconomic Patterns from the News: Modelling Text and Outlet Importance Jointly

Information from news articles can be used to study correlations between textual discourse and socioeconomic patterns. This work focuses on the task of understanding how words contained in the news as well as the news outlets themselves may relate to a set of indicators, such as economic sentiment or unemployment rates. The bilinear nature of the applied regression model facilitates learning jointly word and outlet importance, supervised by these indicators. By evaluating the predictive ability of the extracted features, we can also assess their relevance to the target socioeconomic phenomena. Therefore, our approach can be formulated as a potential NLP tool, particularly suitable to the computational social science community, as it can be used to interpret connections between vast amounts of textual content and measurable societydriven factors.
Using Undirected Graphs to Guide Mutli-label Text Classification

Supervised machine learning techniques can be used to identify the topics within a body of text and predict the appropriate tags. Using these techniques may substantially improve the consistency of text annotation and make finding relevant information easier. This requires machine learning algorithms capable of accurately modeling many tags and processing large data sets in reasonable amounts of time.
The Toxoplasma gondii Plastid replication and Repair Enzyme Complex, PREX

SUMMARY A plastid-like organelle, the apicoplast, is essential to the majority of medically and veterinary important apicomplexan protozoa including Toxoplasma gondii and Plasmodium. The apicoplast contains multiple copies of a 35 kb genome, the replication of which is dependent upon nuclear-encoded proteins that are imported into the organelle. In P. falciparum an unusual multi-functional gene, pfprex, was previously identified and inferred to encode a protein with DNA primase, DNA helicase and DNA polymerase activities. Herein, we report the presence of a prex orthologue in T. gondii. The protein is predicted to have a bi-partite apicoplast targeting sequence similar to that demonstrated on the PfPREX polypeptide, capable of delivering marker proteins to the apicoplast. Unlike the P. falciparum gene that is devoid of introns, the T. gondii prex gene carries 19 introns, which are spliced to produce a contiguous mRNA. Bacterial expression of the polymerase domain reveals the protein to be active. Consistent with the reported absence of a plastid in Cryptosporidium species, in silico analysis of their genomes failed to demonstrate an orthologue of prex. These studies indicate that prex is conserved across the plastid-bearing apicomplexans and may play an important role in the replication of the plastid genome.
Systematic VCP-UBXD Adaptor Network Proteomics Identifies a Role for UBXN10 in Regulating Ciliogenesis

The AAA-ATPase VCP (also known as p97 or CDC48) uses ATP hydrolysis to “segregate” ubiquitinated proteins from their binding partners. VCP acts via UBX-domain containing adaptors that provide target specificity, but targets and functions of UBXD proteins remain poorly understood. Through systematic proteomic analysis of UBXD proteins in human cells, we reveal a network of over 195 interacting proteins, implicating VCP in diverse cellular pathways. We have explored one such complex between an unstudied adaptor UBXN10 and the intraflagellar transport B (IFT-B) complex, which regulates anterograde transport into cilia. UBXN10 localizes to cilia in a VCP-dependent manner and both VCP and UBXN10 are required for ciliogenesis. Pharmacological inhibition of VCP destabilized the IFT-B complex and increased trafficking rates. Depletion of UBXN10 in zebrafish embryos causes defects in left-right asymmetry, which
Comprehensive assessment of the freshwater resources of the world. Sustaining our waters into the 21st century.

This report elaborates on the policy approaches and policy options that would facilitate a long-term sustainable water use building on other background material for the assessment and on the outcome of an international workshop. Various challenges confront water planners managers and users as they enter the 21st century. Among the multiple functions that water fulfills the basic human and ecosystem needs are of paramount importance. Added to this is the indispensable role of water in food production and industrial development and in the numerous activities and processes in the landscape and society. Hence water is recognized as a vital resource for life human and societal development and environmental sustainability. Proper choice of technological and organizational approaches in sustaining freshwater resources requires the involvement of users and sharing of responsibilities and management tasks. It is argued that allocation of finite water resources must be agreed upon through political and socioeconomic negotiations. Due consideration must be given to the various functions that water fulfills in the landscape and in the society. This needs an intensive review of intersectoral coordination and priorities in allocation. In particular the national food-sufficiency versus national food self-reliance issue needs to be addressed in national policies and in international agreements on global food security. Furthermore attention should be given to the qualitative aspects of water to prevent greater impact to the health of humans and ecosystem as well as industrial development.
Influence of the MexAB-OprM Multidrug Efflux System on Quorum Sensing in Pseudomonas aeruginosa

ABSTRACT Pseudomonas aeruginosa nalB mutants which hyperexpress the MexAB-OprM multidrug efflux system produce reduced levels of several extracellular virulence factors known to be regulated by quorum sensing. Such mutants also produce less acylated homoserine lactone autoinducer PAI-1, consistent with an observed reduction inlasI expression. These data suggest that PAI-1 is a substrate for MexAB-OprM, and its resulting exclusion from cells hyperexpressing MexAB-OprM limits PAI-1-dependent activation of lasI and the virulence genes.
Oncoplastic Surgery for Upper/Upper Inner Quadrant Breast Cancer

Tumors located in the upper/upper inner quadrant of the breast warrant more attention. A small lesion relative to the size of breast in this location may be resolved by performing a level I oncoplastic technique. However, a wide excision may significantly reduce the overall quality of the breast shape by distorting the visible breast line. From June 2012 to April 2015, 36 patients with breast cancer located in the upper/upper inner quadrant underwent breast-conservation surgery with matrix rotation mammoplasty. According to the size and location of the tumor relative to the nipple-areola complex, 11 patients underwent matrix rotation with periareolar de-epithelialization (donut group) and the other 25 underwent matrix rotation only (non-donut group). The cosmetic results were self-assessed by questionnaires. The average weights of the excised breast lumps in the donut and non-donut groups were 104.1 and 84.5 g, respectively. During the 3-year follow-up period, local recurrence was observed in one case and was managed with nipple-sparing mastectomy followed by breast reconstruction with prosthetic implants. In total, 31 patients (88.6%) ranked their postoperative result as either acceptable or satisfactory. The treated breasts were also self-evaluated by 27 patients (77.1%) to be nearly identical to or just slightly different from the untreated side. Matrix rotation is an easy breast-preserving technique for treating breast cancer located in the upper/upper inner quadrant of the breast that requires a relatively wide excision. With this technique, a larger breast tumor could be removed without compromising the breast appearance.
Tracing vocal emotion expression through the speech chain : Do listeners perceive what speakers feel ?

This study examines whether vocal cues can be used to reliably infer speaker happiness. Two-hundred speakers were asked to perform a simple referential communication task and to rate their current emotional state. A range of vocal cues was traced through the speech chain using path analysis. The results indicate that reported happiness of the speakers and perceived happiness of the listeners were not related. The only vocal cue that mediated between reported and perceived happiness was F1, and, for the female speakers, pitch range. The findings suggest that listeners tend to over-interpret vocal cues as most of them are not likely to be related to speakers’ internal states.
Body-Related Self-Conscious Emotions Relate to Physical Activity Motivation and Behavior in Men

The aim of this study was to examine the associations between the body-related self-conscious emotions of shame, guilt, and pride and physical activity motivation and behavior among adult males. Specifically, motivation regulations (external, introjected, indentified, intrinsic) were examined as possible mediators between each of the body-related self-conscious emotions and physical activity behavior. A cross-sectional study was conducted with adult men (N = 152; Mage = 23.72, SD = 10.92 years). Participants completed a questionnaire assessing body-related shame, guilt, authentic pride, hubristic pride, motivational regulations, and leisure-time physical activity. In separate multiple mediation models, body-related shame was positively associated with external and introjected regulations and negatively correlated with intrinsic regulation. Guilt was positively linked to external, introjected, and identified regulations. Authentic pride was negatively related to external regulation and positively correlated with both identified and intrinsic regulations and directly associated with physical activity behavior. Hubristic pride was positively associated with intrinsic regulation. Overall, there were both direct and indirect effects via motivation regulations between body-related self-conscious emotions and physical activity (R2 shame = .15, guilt = .16, authentic pride = .18, hubristic pride = .16). These findings highlight the importance of targeting and understanding self-conscious emotions contextualized to the body and links to motivation and positive health behavior among men.
Gait measurements in the transverse plane using a wearable system: An experimental study of test-retest reliability

3D gait analysis comprises the study of kinematics in the sagittal, coronal, and transverse planes. The transverse plane measurements are usually less used and generally show the lowest reliability. Nevertheless, the knee and ankle joint center trajectories, in the transverse plane, provide new parameters that may be important in clinical gait analysis. The aim of this study is to analyze the test-retest variability of these parameters. Gait measurements were performed using H-Gait, a wearable system based on magnetic and inertial sensors. A normal weight and an overweight subject were recruited and were asked to walk at their preferred speed for 6 trials. For both of them, the angle between the right and left knee and ankle joint center trajectories were analyzed. Overall, results showed a standard deviation across trials always lower than 2°. This small standard deviation was found also in the overweight subject, for whom it is usually challenging to obtain reliable gait measurements. In addition, a greater knee angle between the right and left joint center trajectories was found in the overweight subject compared to the normal weight. The promising results of this study suggest that the new parameters introduced might be suitable to assess gait of subjects with different anthropometric characteristics.
Salmonid Chromosome Evolution as Revealed by a Novel Method for Comparing RADseq Linkage Maps

Whole genome duplication (WGD) can provide material for evolutionary innovation. Assembly of large, outbred eukaryotic genomes can be difficult, but structural rearrangements within such taxa can be investigated using linkage maps. RAD sequencing provides unprecedented ability to generate high-density linkage maps for non-model species, but can result in low numbers of homologous markers between species due to phylogenetic distance or differences in library preparation. Family Salmonidae is ideal for studying the effects of WGD as the ancestral salmonid underwent WGD relatively recently, around 65 million years ago, then rediploidized and diversified. Extensive synteny between orthologous chromosomes occurs in extant salmonids, but each species has both conserved and unique chromosome arm fusions and fissions. Here we generate a high-density linkage map (3826 markers) for the Salvelinus genera (Brook Charr S. fontinalis), and then identify orthologous chromosome arms among the other available salmonid high-density linkage maps, including six species of Oncorhynchus, and one species for each of Salmo and Coregonus, as well as the sister group for the salmonids, Esox lucius for homeolog designation. To this end, we developed MapComp, a program that identifies identical and proximal markers between linkage maps using a reference genome of a related species as an intermediate. This approach increases the number of comparable markers between linkage maps by 5-fold, enabling a characterization of the most likely history of retained chromosomal rearrangements post-WGD, and identifying several conserved chromosomal inversions. Analyses of RADseq-based linkage maps from other taxa will also benefit from MapComp, available at: https://github.com/enormandeau/mapcomp/
Comparison between the Au and MgO pressure calibration standards at high temperature

We compare the MgO pressure scales previously developed using molecular dynamics simulations based on empirical and non‐empirical interatomic potentials, to check the accuracy of the reported pressure scales at high temperatures. We find excellent agreement between the two independent pressure scales over wide temperature and pressure ranges, with simulated pressure discrepancies between the two for specified relative volumes being within 0.5 GPa in the temperature and pressure ranges up to 2000 K and 30 GPa. Based on recent simultaneous pressure measurements using both the MgO and Au scales with a multi‐anvil apparatus at 1873 K, we then compare the resulting pressures based on the MgO scale with those based on the Anderson's Au scale, which is recently widely used to estimate pressures in high temperature and high pressure experiments. We find the Andrerson's Au scale underestimates pressures by 1.4 ± 0.3 GPa relative to the MgO scale at 1873 K.
BIOCHEMICAL AND PHYSIOLOGICAL CHANGES INDUCED BY WATER STRESS IN HOT PEPPER (Capsicum annum L.) GENOTYPES

In the agricultural ecosystems, environmental stresses impede plants from expressing full genetic potential. Water stress is one of the major constraints of agriculture production in the world. Ever-changing environmental conditions and lowered ground water levels remained as a significant cause for increased water stress conditions. As chilli is highly prone to water stress owing to their shallow roots, present investigation was carried out to identify drought tolerant genotypes in hot pepper. To distinguish different physiological and biochemical characteristics, twenty six hot pepper genotypes were subjected to mild (80% Field Capacity), moderate (60% Field Capacity) and severe water stress (40% Field Capacity) for one week in the green house. From the present investigation, a significant accumulation of proline and malondialdehyde levels and decrease in the chlorophyll content and relative water content was observed among 26 genotypes. A significant negative correlation was observed between relative water content and Ion Leakage. Furthermore, genotypes showed different responses to drought stress. Principal Component Analysis revealed differential interrelationships among different traits under control and stress conditions. From present investigation five genotypes viz., SHP4884-1-1, LCA353-1-1, BSS355-1-1, CA960-1-1 and LCA334-1-1 were considered to be drought tolerant while four genotypes viz., G4-1-1, S2-1-1, Preethi-1-1 and NCH5-1-1 were considered as drought susceptible. Identified drought tolerant genotypes may be used as parents in the breeding programme.
Dealing with Coronary Artery Disease in Early Encountering: A Qualitative Study

Background: The prevalence of cardiovascular diseases is rising in industrial and developing countries. Coronary Artery Disease (CAD) is the most common cardiovascular disease. Thus, understanding the signs and risk factors of CAD from the patients’ perspective and their ways of dealing with this disease is of vital importance. Objectives: This qualitative study aimed to explore the Iranian patients’ viewpoints about CAD and how they dealt with it in their first encounter. Patients and Methods: This study was a qualitative content analysis conducted on 18 patients with CAD. The data were collected through semi-structured interviews. Initially, purposeful sampling was performed followed by maximum variety. Sampling continued until data saturation. Then, all the interviews were recorded and transcribed verbatim. After all, the data were analyzed by constant comparative analysis using MAXQUDA2010 software. Results: The themes manifested in this study included “invasion of disease” with subthemes of “warning signs” and “risk factors” and “confrontation strategies” with subthemes of “seeking for information”, “follow-up”, and “control measures”. Conclusions: The results of this study described the patients’ perceptions of CAD and how they dealt with this disorder in early encountering. Based on the results, physicians and nurses should focus on empowerment of patients by facilitating this process as well as by educating them with regards to dealing with CAD.
Induction and Repression of Collagenase-1 by Keratinocytes Is Controlled by Distinct Components of Different Extracellular Matrix Compartments*

In all forms of cutaneous wounds, collagenase-1 (matrix metalloproteinase-1 (MMP-1)) is invariably expressed by basal keratinocytes migrating over the dermal matrix. We report that native type I collagen mediates induction of MMP-1 by primary human keratinocytes. Collagen-mediated induction of MMP-1 was rapid, being detected 2 h after plating, and was transcriptionally regulated. As demonstrated by in situ hybridization, only migrating keratinocytes expressed MMP-1, suggesting that contact with collagen is not sufficient to induce MMP-1 expression in keratinocytes; the cells must also be migrating. Upon denaturation, type I collagen lost its ability to induce MMP-1 expression but still supported cell adhesion. Other dermal or wound matrix proteins, such as type III collagen, fibrin, and fibronectin, and a mixture of basement membrane proteins did not induce MMP-1 production. In the presence of collagen, laminin-1 inhibited induction of MMP-1 but laminin-5 did not. Taken together, these observations suggest that as basal keratinocytes migrate from the basal lamina onto the dermal matrix contact with native type I collagen induces MMP-1 expression. In addition, our findings suggest that re-establishment of the basement membrane and, in particular, contact with laminin-1 provides a potent signal to down-regulate MMP-1 production as the epithelium is repaired.
Guidelines for the Isolation, Molecular Detection, and Characterization of Bartonella Species.

Bartonellae are fastidious, facultative, intracellular vector-borne bacteria distributed among mammalian reservoirs worldwide. The pathogenic potential of many Bartonella spp. has increased the interest in these bacteria and advanced their research. Isolation of Bartonella spp. is laborious using classical bacteriological methods and requires specific conditions and prolonged incubation periods. In contrast, molecular methods for detection of Bartonella DNA are considered as more practical and sensitive than the former. Among the molecular methods, the use of real-time PCR assays for primary screening of Bartonella spp. , followed by several molecular confirmatory assays, using either conventional or real-time PCR, is recommended. Although primary isolation of Bartonella is a laborious task, we encourage its application to all PCR-positive samples as this is the most reliable proof for the presence of live bacteria. Moreover, a successful trial will enable a broader molecular characterization and speciation of isolated colonies. The present guideline gathers and summarizes recommendations, including advantages and limitations of isolation and molecular detection of Bartonella from mammalian and arthropod samples.
Lane Detection (Part I): Mono-Vision Based Method

In this report, we introduce a mono-vision based lane detection method (pure mono-vision without the aide of any other sensor). The lane detection method consists of the sub-parts of lane mark segment extraction, lane model fitting, and lane tracking. The lane mark segment extractor is based on some criteria that are only related to the inherent physical properties of the lane marks. The lane model is parameterized in the world (the ground plane) reference instead of in the image reference. The lane tracking is carried out in the framework of the particle filter, including the evolution and the update of the lane state; a mechanism that executes on-line estimation of the vehicle pitch angle is naturally incorporated in the lane tracking process. Read-data tests are given to demonstrate the performance of the mono-vision based lane detection method.