Miracle-dz/UniFAR-FTUs huggingface dataset:
MuD: an interactive web server for the prediction of non-neutral substitutions using protein structural data

The discrimination between functionally neutral amino acid substitutions and non-neutral mutations, affecting protein function, is very important for our understanding of diseases. The rapidly growing amounts of experimental data enable the development of computational tools to facilitate the annotation of these substitutions. Here, we describe a Random Forests-based classifier, named Mutation Detector (MuD) that utilizes structural and sequence-derived features to assess the impact of a given substitution on the protein function. In its automatic mode, MuD is comparable to alternative tools in performance. However, the uniqueness of MuD is that user-reported protein-specific structural and functional information can be added at run-time, thereby enhancing the prediction accuracy further. The MuD server, available at http://mud.tau. ac.il, assigns a reliability score to every prediction, thus offering a useful tool for the prioritization of substitutions in proteins with an available 3D structure.
Planning Capture–Recapture Studies: Straightforward Precision, Bias, and Power Calculations

Abstract Wildlife management and conservation is becoming ever more complex. Concomitantly, managers are in need of simple quantitative approaches and tools that could help them to make better management decisions. We present an approach that consists of generating a single simulated data set of expected data using a reference model, to which various capture–recapture models can be fitted. Using the general-purpose capture–recapture software M-SURGE, we apply this approach to bias, precision, and power calculations. After a quick statistical background refresher, we illustrate this approach with 3 simple examples: 1) the bias induced on survival by capture heterogeneity, 2) the precision of an estimate in the context of a reward-band study, and 3) the power of a test for detecting compensatory mortality. We believe this numerical approach based on expected values can potentially be applied to complex cases, thus making it possible to deal with real situations. We advocate that bias, precision, and power calculations be more routinely performed at the design stage of management or conservation studies. We believe the method we present can become a valuable tool to facilitate wildlife management and conservation.
Economic Burden Associated with Head Louse (Pediculus humanus capitis) Infestation in Iran

Background: The head louse infestation is a public health issue in the world especially, affecting most people who live in camps, school-aged children and their families. Head lice treatment has economic ramifications that often under calculated. The aim of this study was evaluation of economic burden associated with head louse infestation in Iran. Methods: In a cross-sectional study, 500,002 infestations were diagnosed among suspected head lice infested people who referred to health care system in all provinces of Iran during 2017. Direct and indirect costs related to paid by patients and government systems were extracted by referring to accounting documents and interviews with patients and experts and were recorded in researcher-made forms. Microsoft Excel 2010 software was used for economic burden calculation. Results: The incidence rate of head lice infestation in Iran was 500,002/79,926,270 (625.5 per 100,000 populations). Economic burden of head lice in the country was calculated at 5,790,143$. Direct and indirect costs, governmental cost, out of pocket and total costs of head lice were included 3.14$, 2.84$, 5.98$, 5.60$ and 11.58$ per case respectively. Conclusion: The direct and indirect costs associated with treatment of infestations were relatively high. Therefore, the creation of medical facilities such as availability of diagnostic and treatment strategies can be effective in the control of infestation. The adoption of infestation prevention methods, such as health education to people at risk of infestation, reduces the incidence of head lice and imposition of related treatment costs on governmental health care system and head lice cases.
Characterisation of the local Muscovy duck in Nigeria and its potential for egg and meat production

Research results and facts about indigenous Muscovy duck production in Nigeria are reviewed with the aim of assessing its current status and delivering relevant information to stakeholders and other potential beneficiaries. There are large variations in phenotypic and biochemical characteristics of indigenous Muscovy ducks in the country, which could serve as a basis for genetic improvement. These ducks have the potential for a mean live weight of 2.73 and 1.52 kg and dressing percentage of 71.2% and 69.8% for drakes and ducks, respectively. Under scavenging, backyard farming conditions, the ducks can lay between 60 and 80 eggs each per year, and about 100 and 125 eggs per bird per year with an egg weight of about 72g under improved management conditions. The morphological, meat and egg attributes of local Muscovy ducks may be exploited in management decisions geared towards ensuring an increase in productivity, thereby making an important contribution to food security in a developing economy.
MANAGING SUBTERRANEAN TERMITE POPULATIONS

Soil termiticide treatments provide a bamer to exclude soil-borne termites from structures. The vast populations of subterranean termites are generally unaffected by the termiticide application. In the future, monitoring, exclusion (physical or chemical bamers), and population suppression devices (bait- toxicant) will play the major role for the management of subterranean termites.
Osmotic Adjustment Associated with Variation in Bentgrass Tolerance to Drought Stress

Osmotic adjustment (OA) is a major physiological mechanism associated with maintenance of cell turgor in response to dehydration stress. The objectives of this study were to examine changes in capacity for OA in relation to plant tolerance to drought stress for two cool-season turfgrass species, creeping bentgrass (Agrostis stolonifera L.) and velvet bentgrass (A. canina L.), and to determine major solutes contributing to OA in these grass species. Plants of 'L-93' creeping bentgrass and 'Greenwich' velvet bentgrass were grown in a growth chamber in polyvinyl chloride (PVC) tubes (5 cm diameter, 40 cm high) fi lled with a 1:3 (v/v) sterilized mixture of sand and sandy loam soil. The experiment consisted of two soil moisture treatments: 1) well-watered control, irrigated three times per week to main- tain soil moisture near pot capacity; and 2) drought stress, irrigation completely withheld. Velvet bentgrass exhibited higher drought tolerance compared to creeping bentgrass, as manifested by higher visual turfgrass quality (TQ) and leaf relative water content (RWC) under drought stress. Both creeping bentgrass and velvet bentgrass exhibited OA in response to drought stress; however, velvet bentgrass exhibited 50% to 60% higher magnitude of OA, which could be related to the maintenance of higher leaf RWC and TQ for greater drought duration compared to creeping bentgrass. OA for both creeping bentgrass and velvet bentgrass was associated with accumulation of water soluble carbohydrates during the early period of drought and increases in proline content following prolonged period of drought; however, inorganic ion content (Ca 2+ and K + ) did not considerably change under drought stress and did not seem to contribute to OA in these species.
Adaptation of Word-Level Benchmark Datasets for Relation-Level Metaphor Identification

Metaphor processing and understanding has attracted the attention of many researchers recently with an increasing number of computational approaches. A common factor among these approaches is utilising existing benchmark datasets for evaluation and comparisons. The availability, quality and size of the annotated data are among the main difficulties facing the growing research area of metaphor processing. The majority of current approaches pertaining to metaphor processing concentrate on word-level processing due to data availability. On the other hand, approaches that process metaphors on the relation-level ignore the context where the metaphoric expression. This is due to the nature and format of the available data. Word-level annotation is poorly grounded theoretically and is harder to use in downstream tasks such as metaphor interpretation. The conversion from word-level to relation-level annotation is non-trivial. In this work, we attempt to fill this research gap by adapting three benchmark datasets, namely the VU Amsterdam metaphor corpus, the TroFi dataset and the TSV dataset, to suit relation-level metaphor identification. We publish the adapted datasets to facilitate future research in relation-level metaphor processing.
Competitive interaction between strains of Verticillium lecanii on two insect hosts

Summary Differences were observed in the pathogenicities of two strains of Verticillium lecanii (strain numbers 1.72 and 19.79) to the whitefly Trialeurodes uaporariorum and the aphid Macrosiphoniella sanborni. The mean pathogenicity of a mixture of the two strains was intermediate to that of the individual strains, attributable to a competitive interaction during infection. Differences between strains were observed in the production of conidia in vitro and on host insect cadavers. When hosts were infected with the dual-strain suspension, conidia of strain 19.79 only were recovered from T. vaporariorum whereas conidia from both strains were recovered from M. sanborni.
Evaluation of recent patent applications for the diagnosis and treatment of autism and pervasive developmental disorders

This review covers patent literature for new targets, biomarkers and potential drugs for the treatment of autism and related pervasive developmental disorders, for patent applications published between 2000 and mid-year 2005. Recent studies into the underlying genetic aetiology of autism has resulted in a number of potential targets for drug development. Less research is being carried out in the clinical examination of agents specifically designed to treat autism. Nonetheless, promising leads in target and drug discovery have been discovered over the course of the time period examined.
High and low functioning team-based pre-licensure interprofessional learning: an observational evaluation

ABSTRACT Interprofessional education (IPE) is embedded in many health professional training programs, often with a focus on collaborative teamwork. Most studies into whether IPE delivers the desired collaborative teamwork capabilities has tended to rely on short term, self-assessed changes in learners’ attitudes, knowledge and skills. This study adopted overt ethnographic observation to understand how a convenience sample of students behave in groups during interprofessional team-based clinical placements. Interprofessional student teams were observed by two independent observers on eight occasions (a total of 720 hours) across three sites. Thematic analysis of the observational data indicates that student teams fell into two categories: higher and lower functioning. Higher functioning teams were observed using humor to build rapport, reduce tension and express humility, and evidenced a greater emphasis on shared client goals. In contrast, lower functioning teams were more formal, with no evidence of humor and less interaction. The higher functioning teams, therefore, not only demonstrated greater interprofessional collaboration they also appeared to have higher levels of psychological safety. Participants in the higher functioning teams also demonstrated mutual trust and confidence and took more risks, often speaking up to provide suggestions, share knowledge and skills, and seek or offer feedback. The results suggest that further explicit training in, and assessment of, psychological safety in IPE needs to be undertaken.
Evaporating droplets on oil-wetted surfaces: Suppression of the coffee-stain effect

Significance Evaporating suspension droplets in general leave ring-like stains. For many applications requiring homogeneous deposition, the stains imply a major problem. This in particular holds for inkjet printing, surface patterning, self-assembly, and 3D printing technologies. Here we offer a robust method to suppress the coffee-stain effect by letting particle-laden droplets evaporate on oil-wetted surfaces. Through tuning the surface energy of the droplets by adding surfactants, we can manipulate the contact line behavior, the flow structure, and the wetting state of the thin film surrounding the droplet and accomplish a controlled particle deposition. Our findings may open perspectives for uniform coatings in the abovementioned applications, but are also relevant for other complex liquid droplet evaporation, e.g., for disease transmission or in agriculture. The evaporation of suspension droplets is the underlying mechanism in many surface-coating and surface-patterning applications. However, the uniformity of the final deposit suffers from the coffee-stain effect caused by contact line pinning. Here, we show that control over particle deposition can be achieved through droplet evaporation on oil-wetted hydrophilic surfaces. We demonstrate by flow visualization, theory, and numerics that the final deposit of the particles is governed by the coupling of the flow field in the evaporating droplet, the movement of its contact line, and the wetting state of the thin film surrounding the droplet. We show that the dynamics of the contact line can be tuned through the addition of a surfactant, thereby controlling the surface energies, which then leads to control over the final particle deposit. We also obtain an analytical expression for the radial velocity profile which reflects the hindering of the evaporation at the rim of the droplet by the nonvolatile oil meniscus, preventing flow toward the contact line, thus suppressing the coffee-stain effect. Finally, we confirm our physical interpretation by numerical simulations that are in qualitative agreement with the experiment.
PARTICIPATORY PLANT BREEDING IS BETTER DESCRIBED AS HIGHLY CLIENT-ORIENTED PLANT BREEDING. II. OPTIONAL FARMER COLLABORATION IN THE SEGREGATING GENERATIONS

Many public-sector breeding programmes do not use explicit techniques to orient their programmes close to their clients' needs. Participatory techniques can be used to achieve high client orientation but these techniques do not have to involve farmers making selections during the segregating generations. This particularly applies when a sound initial market survey has been made or the learning from a participatory varietal selection (PVS) programme provides feedback to scientists. However, some published results on selection by farmers in the segregating generations (collaborative selection) indicate that it can produce appropriate varieties more effectively than less collaborative research. There is also evidence, from the few cases reported in the literature, that it is cost-effective. Alternative, less collaborative, approaches are also effective. Consultative forms of farmer participation, i.e. where farmers evaluate material grown by scientists, to aid selection in the segregating generations are more widely applicable because they demand fewer resources than collaborative methods. For more time-consuming tasks, such as in the selection of aromatic rice in segregating material, the most appropriate from of participation is contractual i.e., farmers are paid for their work. Mainly using examples from our research in Nepal, we present the particular circumstances in which the involvement of farmers in selection in the segregating generations is desirable or essential. These include: the occurrence of market failure (where the usual mechanisms of supply and demand have failed so there is no incentive to breed new varieties) and supply can only be met by actively involving farmers in the breeding process; when there are cost advantages to involving farmers – this is determined by the particular resources available to the institute undertaking the plant breeding research; when grain quality is both important and determined by a complex set of factors that are difficult to measure in the laboratory; when the objective is to learn in more detail about farmers' selection criteria to better orient the breeding programme to client needs; and when the goal is to empower farmers.
Endoscopic Treatment for Gastrointestinal Stromal Tumors in the Upper Gastrointestinal Tract

383 Gastrointestinal stromal tumors (GISTs) are the most common malignant subepithelial tumors (SETs) of the gastrointestinal tract. They originate from the intestinal cells of Cajal. Currently, the diagnosis of GISTs is based on immunohistochemical staining for c-kit protein and CD34, which are expressed in >80% of GISTs. GISTs must be differentiated from other SETs because of the malignancy potential of GISTs. According to the current guidelines, surgery is recommended for gastric GISTs of >2 cm in size, and endoscopic surveillance is recommended for GISTs of <2 cm in size. However, even if the size of a GIST is small and the probability of malignancy is low, up to 3.7% of small GISTs (<2 cm) are reported to have a high risk or an unexpected increase in size. Furthermore, the regular surveillance strategy involves some risks, including delayed diagnosis of the malignancy of the disease, complications arising from repetitive endoscopy, and poor patient compliance. In addition, patients must bear the financial burden or emotional stress of follow-up. For patients who are reluctant to undergo surgery, endoscopic resection may be a better option than surgery. Endoscopic resection techniques have many advantages to surgery, such as shorter operative time, lower cost, less intraoperative bleeding, and improved quality of life. In addition, they show favorable outcomes. In this issue of Clinical Endoscopy, Marcella et al. introduced endoscopic submucosal dissection (ESD), endoscopic full-thickness resection (EFTR), and submucosal tunneling endoscopic resection (STER) as endoscopic methods for removing GISTs, with favorable outcomes. Endoscopic treatment (ET) attained a 100% en bloc resection rate, 77.4% complete resection rate, and 8.3% complication rate. Eight patients in the ESD group showed apparent adverse events such as intraoperative perforation (n=7) and massive bleeding (n=1). Most patients were managed with endoscopic repair. Only one patient underwent emergency laparoscopic surgery for a large tumor that was tightly adhered to the third layer. Endoscopic resection of GISTs is superior in some aspects such as having good accessibility to the cardia or esophagogastric junction, which are technically difficult to approach using the laparoscopic method. Moreover, surgery is sometimes challenging when localizing an intracavitary tumor. However, it is preferred for the resection of larger tumors and achieves a sufficient negative resection margin. In this issue of Clinical Endoscopy, Marcella et al. indicated that ET is a feasible and favorable alternative option for surgery for GISTs even if they are large (3 cases, >5 cm included). However, the resection of large GISTs using ET remains controversial, and no consensus has been reached. Minimal complication risk with optimal endoscopic choice is important, and the treatment may be decided on the basis of the surgeon’s preference and experience and patient/tumor characteristics. COMMENTARY
Association between the ACE I/D polymorphism and muscle injuries in Italian and Japanese elite football players

ABSTRACT ACE I/D polymorphism has been recently associated with the susceptibility to inflammation and muscle damage after exercise. The aim of this study was to understand the association between the ACE I/D polymorphism and muscle injuries in a large cohort of elite football players from two different countries. Seven hundred and ten male elite football players from Italy (n = 341) and Japan (n = 369) were recruited for the study. Genomic DNA was extracted from either the buccal epithelium or saliva using a standard protocol. Structural-mechanical injuries and functional muscle disorders were recorded from 2009 to 2018. A meta-analysis was performed using Review Manager 5.3. 5. In the Japanese cohort, the ACE I/D polymorphism was significantly associated with muscle injury using the D-dominant model (OR: 0.48, 95% CI: 0.24–0.97, P = 0.040). The meta-analysis showed that in the pooled model (Italian and Japanese populations), the frequencies of the DD+ID genotypes were significantly lower in the injured groups than in non-injured groups (OR: 0.61, 95% CI: 0.38–0.98, P = 0.04) with a low degree of heterogeneity (I2 = 0%). Our findings suggest that the ACE I/D polymorphism could influence the susceptibility to developing muscle injuries among football players.
DeepMet: A Reading Comprehension Paradigm for Token-level Metaphor Detection

Machine metaphor understanding is one of the major topics in NLP. Most of the recent attempts consider it as classification or sequence tagging task. However, few types of research introduce the rich linguistic information into the field of computational metaphor by leveraging powerful pre-training language models. We focus a novel reading comprehension paradigm for solving the token-level metaphor detection task which provides an innovative type of solution for this task. We propose an end-to-end deep metaphor detection model named DeepMet based on this paradigm. The proposed approach encodes the global text context (whole sentence), local text context (sentence fragments), and question (query word) information as well as incorporating two types of part-of-speech (POS) features by making use of the advanced pre-training language model. The experimental results by using several metaphor datasets show that our model achieves competitive results in the second shared task on metaphor detection.
Modulating Innate Immune Response to Combat Viral Infections-Use HCV as an Example

Volume 5(3): xvii-xviii (2013) xvii J Antivir Antiretrovir ISSN:1948-5964 JAA, an open access journal Innate immunity is host’s first line of defense against invading microbial pathogens, limiting pathogen spread. Two major players contribute to the innate immune response: type I interferon (IFN) and Natural killer (NK) cells. Type I IFN (α/β) functions as innate cytokine elicited in response to viral/bacterial infections. There are two distinct pathways that sense viral infection and initialize the induction of type I IFN. One is Toll-like receptors (TLR) mediated [1] and the other is retinoic acid-inducible gene I (RIG-I)/melanoma differentiation–associated gene 5 (MDA5) mediated [2]. These receptors recognize pathogen associated molecular patterns (PAMPs) which are conservatively present in the genome of viruses/bacteria, leading to the production of type I IFN. After binding to the receptors, IFN α/β activates Janus activated kinase (JAK)/signal transducer and activator of transcription (STAT) signaling to induce the expression of a few hundred interferon stimulated genes (ISGs) which are involved inimmuno regulation and host defense [3]. NK cell is another contributor to innate immune system activated by viral proteins via activating NK receptors (e.g. natural cytotoxicity receptor, NCR) [4]. Activated NK cells can not only mediate cytotoxicity through granuleexocytosis pathway or classical caspase-dependent apoptosis in target cells, but also produce some cytokines, for example, the IFN-γ [5], to activate a number of important signal pathways involved in direct antiviral function and/or immune modulation.