Miracle-dz/UniFAR-FTUs huggingface dataset:
Development of an antibody cocktail for treatment of Sudan virus infection

Significance Ebolaviruses pose a significant threat to the global community, particularly in areas of equatorial and West Africa. While Ebola virus has caused the greatest number of human cases, Sudan virus is responsible for numerous outbreaks with equally lethal consequences. Antibody-based immunotherapies against ebolaviruses have gained prominence in recent years, resulting in the development of several Ebola virus-specific antibody cocktails, yet no Sudan virus-specific cocktails exist. In collaboration with industry partners, we generated a library of human chimeric monoclonal antibodies (mAbs) specific for the glycoprotein of Sudan virus. Through a series of in vitro assays and rodent efficacy studies, we down-selected a lead mAb cocktail that demonstrated protective efficacy in a nonhuman primate model of Sudan virus infection. Antibody-based therapies are a promising treatment option for managing ebolavirus infections. Several Ebola virus (EBOV)-specific and, more recently, pan-ebolavirus antibody cocktails have been described. Here, we report the development and assessment of a Sudan virus (SUDV)-specific antibody cocktail. We produced a panel of SUDV glycoprotein (GP)-specific human chimeric monoclonal antibodies (mAbs) using both plant and mammalian expression systems and completed head-to-head in vitro and in vivo evaluations. Neutralizing activity, competitive binding groups, and epitope specificity of SUDV mAbs were defined before assessing protective efficacy of individual mAbs using a mouse model of SUDV infection. Of the mAbs tested, GP base-binding mAbs were more potent neutralizers and more protective than glycan cap- or mucin-like domain-binding mAbs. No significant difference was observed between plant and mammalian mAbs in any of our in vitro or in vivo evaluations. Based on in vitro and rodent testing, a combination of two SUDV-specific mAbs, one base binding (16F6) and one glycan cap binding (X10H2), was down-selected for assessment in a macaque model of SUDV infection. This cocktail, RIID F6-H2, provided protection from SUDV infection in rhesus macaques when administered at 50 mg/kg on days 4 and 6 postinfection. RIID F6-H2 is an effective postexposure SUDV therapy and provides a potential treatment option for managing human SUDV infection.
Work Conditions, Social Incorporations, and Foodborne Diseases Risk: Reflections About the (Non)Compliance of Food Safety Practices

The number of foodborne diseases has increased in all continents, and efforts must be made to control this urgent and expressive public health problem. This article aims to present and discuss situations related to the compliance and noncompliance of food safety practices (FSPs) in light of Bourdieu's social theory. This qualitative study was conducted in commercial restaurants in two cities in São Paulo, Brazil. Participant observation was used in the restaurants, and notes referring to the kitchen workers and their bosses’ work processes were registered in field journals. Thematic type content analysis was used to determine the meaning cores of field journals. It was found that aspects inherent to convenience and haste at work, deficient infrastructure, lack of employees, negative boss examples, exposure to noise, and body pain experienced by workers can contribute to noncompliance of FSPs and consolidate in the habitus and practical sense some dispositions that can increase the risk of foodborne diseases. This study highlights the necessity of creating environments that address food safety, which means being able to perform a service properly.
PLANiTS: a curated sequence reference dataset for plant ITS DNA metabarcoding

Abstract DNA metabarcoding combines DNA barcoding with high-throughput sequencing to identify different taxa within environmental communities. The ITS has already been proposed and widely used as universal barcode marker for plants, but a comprehensive, updated and accurate reference dataset of plant ITS sequences has not been available so far. Here, we constructed reference datasets of Viridiplantae ITS1, ITS2 and entire ITS sequences including both Chlorophyta and Streptophyta. The sequences were retrieved from NCBI, and the ITS region was extracted. The sequences underwent identity check to remove misidentified records and were clustered at 99% identity to reduce redundancy and computational effort. For this step, we developed a script called ‘better clustering for QIIME’ (bc4q) to ensure that the representative sequences are chosen according to the composition of the cluster at a different taxonomic level. The three datasets obtained with the bc4q script are PLANiTS1 (100 224 sequences), PLANiTS2 (96 771 sequences) and PLANiTS (97 550 sequences), and all are pre-formatted for QIIME, being this the most used bioinformatic pipeline for metabarcoding analysis. Being curated and updated reference databases, PLANiTS1, PLANiTS2 and PLANiTS are proposed as a reliable, pivotal first step for a general standardization of plant DNA metabarcoding studies. The bc4q script is presented as a new tool useful in each research dealing with sequences clustering. Database URL: https://github.com/apallavicini/bc4q; https://github.com/apallavicini/PLANiTS.
Low-dose ketamine improves LPS-induced depression-like behavior in rats by activating cholinergic anti-inflammatory pathways.

About 16% of the world's population has major depressive disorder. Traditional antidepressants have slow effect rates and low response rates. Many studies have shown that low doses of ketamine can produce rapid and effective antidepressant effects. However, its mechanism of action needs further exploration. Lipopolysaccharide (LPS) was used to establish a depression model in rats and PC12 nerve cells were used for in vitro experiments. (2,4)-Dimethoxybenzylidene anabaseine dihydrochloride (GTS-21), a specific agonist of α7 nicotinic acetylcholine receptors (α7nAChRs), was used to compare the rapid antidepressant effect of ketamine. Different doses of α7nAChR antagonist methyllycaconatine (MLA) and α7nAChR-siRNA were used to interfere with the protective effects of ketamine on neuroinflammation in rats and PC12 cells, respectively. MLA intervention downregulated the anti-inflammatory effects of ketamine and decreased the effects of ketamine on behavior, synaptic plasticity, and Nissl bodies in the neuronal cells. Moreover, the dose of MLA was positively correlated with the inhibitory effect in rat hippocampi and the protective effects of GTS-21 were consistent with ketamine. These results demonstrated that low-dose ketamine could produce neuroprotective effects by activating the α7nAChR-mediated cholinergic anti-inflammatory pathway (CAP) in depression, resulting in a rapid antidepressant effect.
Child handwashing in an internally displaced persons camp in Northern Iraq: A qualitative multi-method exploration of motivational drivers and other handwashing determinants

Background Children in humanitarian situations are particularly vulnerable to diseases such as diarrhoea. Handwashing with soap can greatly reduce transmission but handwashing rates are often low and traditional interventions ineffective. To aid future intervention design, this study aims to understand the determinants of child handwashing and the key motivational drivers of children’s behaviour within a specific humanitarian setting. Methods In an internally displaced persons camp in Northern Iraq we conducted a series of 36 friendship-paired interviews with children aged 7–12 years, six semi-structured caregiver interviews, and three semi-structured hygiene promoter interviews. Perceived determinants of child handwashing were explored qualitatively, and motivational drivers were explored quantitatively with children in a rating exercise. Qualitative data were analysed thematically, using an inductive approach, and logistic regression analyses of motive rating data were performed to determine the predicted probabilities of motives being rated as important. Results Access to soap and water was perceived to be high across all participant groups. Children, caregivers and hygiene promoters all perceive the determinants of child handwashing to be associated with familial role, environmental factors pertaining to location and quality of handwashing materials and facilities, and level of exposure to hygiene promotion, and children also attribute their handwashing to social norms. We find that children in this context are motived most by play and nurture. Conclusions Provision of soap and water alone is not sufficient to encourage children to practice handwashing with soap in a humanitarian context. Our findings suggest that equal consideration should be given to the quality and location of handwashing materials and facilities and social norms could be leveraged to promote and enhance child handwashing. Motive-based interventions targeting play or nurture may be a promising approach and are likely most effective when used in conjunction, along with other motivational drivers such as affiliation and love.
Virtual multiplex immunohistochemistry: Application on cell block of effusion and aspiration cytology

With the continuous development of new antibodies, the use of immunohistochemistry (IHC) is becoming more often a requirement. IHC is frequently necessary for establishing cancer diagnosis and making therapeutic decisions. However, cytology specimens such as effusion fluid and fine‐needle aspiration are highly variable in cellularity and contain background inflammatory and mesothelial cells. Compared to biopsy or excision specimens, tissue exhaustion and levels of sections not matching are more commonly encountered. We present a method of integrating whole‐slide cell block image of multiple antibodies by digital image processing and reconstructing a virtual multiplex IHC image for enhanced interpretation.
Annexin A1 drives macrophage skewing to accelerate muscle regeneration through AMPK activation

Understanding the circuits that promote an efficient resolution of inflammation is crucial to deciphering the molecular and cellular processes required to promote tissue repair. Macrophages play a central role in the regulation of inflammation, resolution, and repair/regeneration. Using a model of skeletal muscle injury and repair, herein we identified annexin A1 (AnxA1) as the extracellular trigger of macrophage skewing toward a pro-reparative phenotype. Brought into the injured tissue initially by migrated neutrophils, and then overexpressed in infiltrating macrophages, AnxA1 activated FPR2/ALX receptors and the downstream AMPK signaling cascade, leading to macrophage skewing, dampening of inflammation, and regeneration of muscle fibers. Mice lacking AnxA1 in all cells or only in myeloid cells displayed a defect in this reparative process. In vitro experiments recapitulated these properties, with AMPK-null macrophages lacking AnxA1-mediated polarization. Collectively, these data identified the AnxA1/FPR2/AMPK axis as an important pathway in skeletal muscle injury regeneration.
DEEPrior: a deep learning tool for the prioritization of gene fusions

Abstract Summary In the last decade, increasing attention has been paid to the study of gene fusions. However, the problem of determining whether a gene fusion is a cancer driver or just a passenger mutation is still an open issue. Here we present DEEPrior, an inherently flexible deep learning tool with two modes (Inference and Retraining). Inference mode predicts the probability of a gene fusion being involved in an oncogenic process, by directly exploiting the amino acid sequence of the fused protein. Retraining mode allows to obtain a custom prediction model including new data provided by the user. Availability and implementation Both DEEPrior and the protein fusions dataset are freely available from GitHub at (https://github.com/bioinformatics-polito/DEEPrior). The tool was designed to operate in Python 3.7, with minimal additional libraries. Supplementary information Supplementary data are available at Bioinformatics online.
Improving Environmental Capacities for Health Promotion in Support Settings for People with Intellectual Disabilities: Inclusive Design of the DIHASID Tool

People with intellectual disabilities (ID) have unhealthier lifestyles than the general population. To sustainably improve their lifestyle and health status, a whole-system approach to creating healthy environments is crucial. To gain insight into how support for physical activity and healthy nutrition can be embedded in a setting, asset mapping can be helpful. Asset mapping involves creating a bottom–up overview of promoting and protective factors for health. However, there is no asset mapping tool available for ID support settings. This study aims to develop an asset mapping tool in collaboration with people with ID to gain insight into assets for healthy nutrition and physical activity in such settings. The tool is based on previous research and development continued in an iterative and inclusive process in order to create a clear, comprehensive, and usable tool. Expert interviews (n = 7), interviews with end-users (n = 7), and pilot testing (n = 16) were conducted to refine the tool. Pilot participants perceived the tool as helpful in pinpointing perceived assets and in prompting ideas on how to create inclusive environments with support for physical activity and healthy nutrition. This overview of assets can be helpful for mobilizing assets and building the health-promoting capacities of ID support settings.
Genipin‐crosslinked decellularized annulus fibrosus hydrogels induces tissue‐specific differentiation of bone mesenchymal stem cells and intervertebral disc regeneration

Biomaterial‐based therapy that can restore annulus fibrosus (AF) function in early stage and promote endogenous repair of AF tissues is a promising approach for AF tissue repair. In this study, we established a genipin‐crosslinked decellularized AF hydrogels (g‐DAF‐G) that are injectable and could manifest better in situ formability than noncrosslinked decellularized AF hydrogel, while preserving the capacity of directing differentiation of human bone mesenchymal stem cells (hBMSCs) towards AF cells. Hematoxylin and eosin staining, 4',6‐diamidino‐2‐phenylindole staining, and so forth showed that the majority of cellular components were removed, whereas extracellular matrix and microstructure were largely preserved. The storage modulus increased from 465.5 ± 9.4 Pa to 3.29 ± 0.24 MPa after 0.02% genipin crosslinking of decellularized AF hydrogels (DAF‐G) to form g‐DAF‐G. AF‐specific genes (COL1A1, COL5A1, TNMD, IBSP, FBLN1) were significantly higher in DAF‐G and g‐DAF‐G groups than that in control group after 21 days of culturing. g‐DAF‐G significantly restored nucleus pulposus water content and preserved intervertebral structure in vivo. Summarily, we produced a novel AF regeneration biomaterial, g‐DAF‐G, which exhibited well biocompatibility, great bioactivity, and much higher mechanical strength than DAF‐G. This study will provide an easy and fast therapeutic alternative to repair AF injuries or tears.
Patterns of Substance Use among Patients in Addiction Rehabilitation in Jordan.

Abstract Background: This study aimed to identify pattern of substance use among patients at two public addiction rehabilitation centers in Amman. It provided a description of substance use career and assessment of addiction severity, quality of life and quality of sleep among participants. Methods: A quantitative cross-sectional study using a structured data collection form consisting of 4 parts: 1. General data including the demographic characteristics, medical history and career of drug abuse. 2. Severity of addiction using the severity of dependence scale (SDS). 3. Quality of life measured by the EQ-5D and 4. Quality of sleep measured by the insomnia severity index (ISI) scale. Results: A total of 93 patients from 2 treatment settings were recruited over 5 months. The total number of actively used substances was 196, with an average of 2 substances per patient. Alcohol and synthetic cannabinoids were the two most commonly used substances (39.8% and 38.7% respectively) followed by benzodiazepines (33.4%). A notable drop in heroin use was observed (5.4%, 5 out of 23 opioid user) compared to the years 2007-2009. The mean SDS score among patients was 11.43 (SD ± 3.48) indicating high dependence. Sleep problems were reported by 45% of patients. Data showed a significant role of community pharmacies in supplying drugs of abuse for users. Conclusion: Pattern of substance use changed significantly in Jordan with synthetic cannabinoids being of the top substances used and heroin use dropping. Actions should be taken to reframe the legalization of dispensing certain drugs by pharmacists without a prescription.
The Use of Antioxidants in the Treatment of Migraine

Despite numerous studies concerning the pathophysiology of migraine, the exact molecular mechanism of disturbances underlying migraine is still unknown. Furthermore, oxidative stress is considered to play a significant role in migraine pathogenesis. The notion of oxidative stress in migraine patients has been discussed for several decades. Over the past few years, among the substances that could potentially be used for migraine treatment, particular attention has been paid to the so-called nutraceutics, including antioxidants. Antioxidants supplied with food prevent oxidative stress by inhibiting initiation, propagation, and the oxidative chain reaction itself. Additionally, the agents used so far in the prevention of migraine indeed show some anti-oxidative action. The antioxidants discussed in the present paper are increasingly more often used by migraine patients not only due to mild or even a lack of side effects but also because of their effectiveness (decreased frequency of migraine episodes or shortening of an episode duration). The present review provides a summary of the studies on nutraceuticals with antioxidative properties.
Assessment of Genetic Relationships between Streptocarpus x hybridus V. Parents and F1 Progenies Using SRAP Markers and FT-IR Spectroscopy

The genetic relationship among three Streptocarpus parents and twelve F1 hybrids was assessed using sequence-related amplified polymorphism (SRAP) molecular markers and Fourier-transform infrared (FT-IR) spectroscopy. Both methods were able to discriminate F1 hybrids and parents as revealed by cluster analysis. For hybrid identification, the type III SRAP marker was the most effective due to the presence of male-specific bands in the hybrids. Different behaviors in the biochemical variability of DNA samples have been observed by FT-IR spectral analysis, which might be attributed to the inherent nature of the genomic DNA from parents and their F1 progenies. Mantel test was also carried out to compare morphological, SRAP, and FT-IR results based on genetic distances. The highest correlation coefficient was found between morphological and SRAP marker distances (R = 0.607; p ≤ 0.022). A lower correlation was observed between the morphological and FT-IR distance matrix (R = 0.231; p ≤0.008). Moreover, a positive correlation was found between the distances generated with SRAP and FT-IR analyses (R = 0.026) but was not statistically significant. These findings show that both SRAP and FT-IR techniques combined with morphological descriptions can be used effectively for nonconventional breeding programs for Streptocarpus to obtain new and valuable varieties.
Epidemiological Features of NAFLD From 1999 to 2018 in China

With dramatic changes in lifestyles over the last 20 years, nonalcoholic fatty liver disease (NAFLD) has become the most prevalent liver disorder in China but has not received sufficient attention. NAFLD‐related advanced liver disease and its mortality along with its overall disease burden are expected to increase substantially. There is thus an imperative need to clarify the epidemiological features of NAFLD to guide a holistic approach to management. We summarize eight epidemiological features of NAFLD in China over the past two decades using systematic review and meta‐analysis methodology. Our data reveal a rapid growth in the NAFLD population, especially among younger individuals. Importantly, there is a strong ethnic difference in body mass index (BMI) and genetic risk of NAFLD compared with the US population. The etiology of advanced liver disease and its complications (e.g., hepatocellular carcinoma) has been altered because of a Westernized lifestyle and the implementation of effective vaccination strategies against viral hepatitis. Regional epidemiological patterns of NAFLD indicate that economics, environment, and lifestyle are critical factors in disease progression. The analysis also indicates that a large number of patients remain undiagnosed and untreated because of the inadequacy of diagnostic tools and the absence of effective pharmacologic therapies. Given the burden of NAFLD, future policy and research efforts need to address knowledge gaps to mitigate the risk burden.
Absolute and Relative Strength, Power and Physiological Characteristics of Indian Junior National-Level Judokas

The physical qualities that underpin successful junior judokas requires continuing investigation. We investigated the physical and physiological characteristics of junior national level judokas. We tested 25 (15 male, 10 female) Indian judokas for absolute and relative strength (back-squat and bench-press one-repetition maximum (1RM) as well as isometric handgrip), aerobic (RAMP test) and lower-body anaerobic power (Wingate 6-s sprint and countermovement jump), change-of-direction (5-0-5 test) and speed (30 m sprint). Athletes were grouped according to national-level competition placing (gold-medal winners (GM; n = 8), all medal winners (MW; n = 13), non-medallists (NM; n = 12), and NM plus silver and bronze; all others (AO; n = 17)). Stepwise discriminant function analysis determined characteristics likely to predict successful performance. Independent t-tests and effect size (Hedge’s g) analyses were performed between groups. GM demonstrated greater lower-body absolute (20.0%; g = 0.87, p = 0.046) and relative 1RM strength (21.0%; g = 0.87, p = 0.047), and greater lower-body absolute (25.4%; g=1.32, p=0.004) and relative (27.3%; g = 1.27, p = 0.005) anaerobic power compared to AO. Furthermore, anaerobic power can correctly predict 76.5% and 62.5% of AO and GM athletes, respectively. No differences were observed between MW and NM groups. The results suggest the importance of lower-body strength and power for junior national-level judokas and provides information for professionals working with these athletes.
Experimental Malaria Infection Affects Songbirds’ Nocturnal Migratory Activity

Migratory animals encounter multiple parasite communities, raising concerns that migration may aid transport of infectious disease. How migration affects disease spread depends fundamentally on how disease affects migration, specifically whether infection alters individuals’ migratory physiology and behavior. We inoculated white-throated sparrows (Zonotrichia albicollis) with avian malaria parasites (Plasmodium sp.), monitored parasite loads for 5 wk as the birds reached spring migratory condition, and compared nocturnal migratory restlessness (Zugunruhe), body composition (fat, lean, and whole-body mass), and hematocrit among experimentally infected birds, sham-inoculated birds, and birds that were exposed to parasites but resisted infection. Migratory restlessness increased over time in the study, but the rate of change varied between sham (control) birds, infected birds, and birds that resisted infection. We were unable to detect any effects of malaria exposure on body condition. Our findings suggest that encountering parasites affects migratory activity, regardless of whether infection occurs or is resisted.