Miracle-dz/UniFAR-FTUs huggingface dataset:
Toxoplasma gondii Serointensity and Seropositivity: Heritability and Household-Related Associations in the Old Order Amish

Toxoplasma gondii (T. gondii) is an intracellular parasite infecting one third of the world’s population. Latent T. gondii infection has been associated with mental illness, including schizophrenia and suicidal behavior. T. gondii IgG antibody titers were measured via ELISA. The heritability of T. gondii IgG was estimated using a mixed model that included fixed effects for age and sex and random kinship effect. Of 2017 Old Order Amish participants, 1098 had positive titers (54.4%). The heritability for T. gondii serointensity was estimated to be 0.22 (p = 1.7 × 10−8 and for seropositivity, it was estimated to be 0.28 (p = 1.9 × 10−5). Shared household environmental effects (i.e., household effects) were also determined. Household effects, modeled as a random variable, were assessed as the phenotypic covariance between any two individuals who had the same current address (i.e., contemporaneous household), and nuclear household (i.e., the phenotypic covariance between parents and children only, not other siblings or spouses). Household effects did not account for a significant proportion of variance in either T. gondii serointensity or T. gondii seropositivity. Our results suggest a significant familial aggregation of T. gondii serointensity and seropositivity with significant heritability. The shared household does not contribute significantly to family aggregation with T. gondii, suggesting that there are possible unmeasured non-household shared and non-shared environmental factors that may play a significant role. Furthermore, the small but significant heritability effects justify the exploration of genetic vulnerability to T. gondii exposure, infection, virulence, and neurotropism.
Workplace Violence in Asian Emergency Medical Services: A Pilot Study

Workplace violence among Asian emergency medical services (EMS) has rarely been examined. A cross-sectional, mainly descriptive study using a standardized, paper-based, self-reported questionnaire survey was conducted between August and October 2018 among emergency medical technicians (EMTs) in the Tainan City Fire Bureau, Taiwan. A total of 152 EMT-paramedics responded to the questionnaire survey, constituting an overall response rate of 96.2%. The participants were predominantly male (96.1%), college-educated (4-year bachelor’s degree) (49.3%), and middle-aged (35–44 years old) (63.8%). Among them, 113 (74.3%) and 75 (49.3%) participants had experienced verbal and physical assaults at work, respectively. Only 12 (7.9%) participants were familiar with relevant regulations or codes. The assaults predominantly occurred during evening shifts (16:00–24:00) and at the scene of the emergency. The most predominant violence perpetrators included patients, patients’ families, or patients’ friends. Nearly 10% of participants had experienced verbal assaults from hospital personnel. EMTs who encountered workplace violence rarely completed a paper report, filed for a lawsuit, or sought a psychiatric consultation. Fifty-eight (38.2%) and 16 (10.5%) participants were victims of frequent (at least once every 3 months) verbal and physical forms of violence, respectively; however, no statistically significant association was observed in terms of EMT gender, age, working years, education level, or the number of EMS deployments per month. The prevalence of workplace violence among Asian EMS is considerable and is comparable to that in Western countries. Strategies to prevent workplace violence should be tailored to local practice and effectively implemented.
Computational approaches to therapeutic antibody design: established methods and emerging trends

Abstract Antibodies are proteins that recognize the molecular surfaces of potentially noxious molecules to mount an adaptive immune response or, in the case of autoimmune diseases, molecules that are part of healthy cells and tissues. Due to their binding versatility, antibodies are currently the largest class of biotherapeutics, with five monoclonal antibodies ranked in the top 10 blockbuster drugs. Computational advances in protein modelling and design can have a tangible impact on antibody-based therapeutic development. Antibody-specific computational protocols currently benefit from an increasing volume of data provided by next generation sequencing and application to related drug modalities based on traditional antibodies, such as nanobodies. Here we present a structured overview of available databases, methods and emerging trends in computational antibody analysis and contextualize them towards the engineering of candidate antibody therapeutics.
Using remote sensing to detect whale strandings in remote areas: The case of sei whales mass mortality in Chilean Patagonia

We test the ability of Very High Resolution satellite (VHR) imagery to detect stranded whales using both manual and automated methods. We use the 2015 mass mortality event in the Gulf of Penas locality, central Patagonia, Chile, as an initial case study. This event was the largest known mass mortality of baleen whales, with at least 343 whales, mainly sei whales (Balaenoptera borealis), documented as stranding. However, even with such a large number of whales, due to the remote location of the gulf the strandings went unrecorded for several weeks. Aerial and boat surveys of the area were conducted two to four months after the mortality event. In this study we use 50cm resolution WorldView2 imagery to identify and count strandings from two archival images acquired just after the stranding event and two months before the aerial and ground surveys, and to test manual and automated methods of detecting stranded whales. Our findings show that whales are easily detected manually in the images but due to the heterogeneous colouration of decomposing whales, spectral indices are unsuitable for automatic detection. Our satellite counts suggest that, at the time the satellite images were taken, more whales were stranded than recorded in the aerial survey, possibly due to the non-comprehensive coverage of the aerial survey or movement of the carcases between survey acquisition. With even higher resolution imagery now available, satellite imagery may be a cost effective alternative to aerial surveys for future assessment of the extent of mass whale stranding events, especially in remote and inaccessible areas.
Quantitation of eumelanin and pheomelanin markers in diverse biological samples by HPLC-UV-MS following solid-phase extraction

Eumelanin and pheomelanin are well known and common pigments found in nature. However, their complex polymer structure and high thermostability complicate their direct chemical identification. A widely used analytical method is indirect determination using HPLC with UV detection of both types of melanin by their most abundant oxidation products: pyrrole-2,3-dicarboxylic acid (PDCA), pyrrole-2,3,5-tricarboxylic acid (PTCA), thiazole-4,5-dicarboxylic acid (TDCA), and thiazole-2,4,5-tricarboxylic acid (TTCA). An increasing interest in pigmentation in biological research led us to develop a highly sensitive and selective method to identify and quantify these melanin markers in diverse biological samples with complex matrices. By introducing solid-phase extraction (SPE, reversed-phase) following alkaline oxidation we could significantly decrease background signals while maintaining recoveries greater than 70%. Our HPLC-UV-MS method allows for confident peak identification via exact mass information in corresponding UV signals used for quantitation. In addition to synthetic melanin and Sepia officinalis ink as reference compounds eumelanin markers were detected in brown human hair and a brown bivalve shell (Mytilus edulis). Brown feathers from the common chicken (Gallus g. domesticus) yielded all four eumelanin and pheomelanin markers. The present method can be easily adapted for a wide range of future studies on biological samples with unknown melanin content.
Polymorphisms in vasoactive eicosanoid genes of kidney donors affect biopsy scores and clinical outcomes in renal transplantation

Cytochrome P450 (CYP) enzymes metabolize arachidonic acid to vasoactive eicosanoids such as epoxyeicosatrienoic acids (EETs) and 20-Hydroxyeicosatetraenoic acid (20-HETE), whilst soluble epoxide hydrolase, encoded by the EPHX2 gene, is in charge of EETs degradation. We aimed to analyze the influence of common, functional polymorphisms in four genes of the donor on the renal biopsy scores independently assigned by pathologists. Additionally, we examined whether this score or the presence of these SNPs were independent risk factors of clinical outcomes in the first year after grafting. A cohort of 119 recipients and their corresponding 85 deceased donors were included in the study. Donors were genotyped for the CYP4F2 V433M, CYP2C8*3, CYP2J2*7, EPHX2 3’UTR A>G, EPHX2 K55R and EPHX2 R287Q polymorphisms. The association of the donors’ SNPs with the biopsy scores and clinical outcomes was retrospectively evaluated by multivariate regression analysis. The CYP2C8*3 polymorphism in the donor was significantly associated with higher scores assigned to pretransplant biopsies [OR = 3.35 (1.03–10.93), p = 0.045]. In turn, higher scores were related to an increased risk of acute rejection [OR = 5.28 (1.32–21.13), p = 0.019] and worse glomerular filtration rate (eGFR) (45.68±16.05 vs. 53.04±16.93 ml/min in patients whose grafts had lower scores, p = 0.010) one year after transplant. Patients whose donors carried the CYP4F2 433M variant showed lower eGFR values (48.96±16.89 vs. 55.94±18.62 ml/min in non-carriers, p = 0.038) and higher risk of acute rejection [OR = 6.18 (1.03–37.21), p = 0.047]. The CYP2J2*7 SNP in the donor was associated with elevated risk of delayed graft function [OR = 25.68 (1.52–43.53), p = 0.025]. Our results taken together suggest that donor genetic variability may be used as a predictor of tissue damage in the graft as well as to predict clinical outcomes and graft function in the recipient.
Factors Associated With Fast Recovery of Bell Palsy in Children

The purpose of this study was to identify the clinical characteristics and factors affecting the prognosis of children with Bell palsy. We retrospectively reviewed the medical records of 53 pediatric patients diagnosed with Bell palsy. After a mean follow-up period of 30 days, 30 patients (56%) were completely recovered, 21 patients (40%) were partially recovered, and 2 patients (4%) had not recovered. The patients in the complete recovery group were significantly younger than those in the partial and nonrecovery groups (8.8 ± 4.2 years vs 12.2 ± 3.0 years, P = .003). Patients <8 years old had a higher complete recovery rate than was found in patients >8 years old (80% vs 47%, P = .031). Sex, affected side, and early or late treatment did not influence the recovery rate. These results suggest that younger age may be a good prognostic factor affecting the fast recovery of children with Bell palsy.
Applying the Stress Process Model to Stress–Burnout and Stress–Depression Relationships in Biomedical Doctoral Students: A Cross-Sectional Pilot Study

Although doctoral students in the biomedical sciences have been recognized as a population at particular risk for mental health problems such as burnout and depression, little research has been conducted to identify candidate targets for intervention. To this end, we used the stress process model to evaluate potential mediators of stress–burnout and stress–depression relationships in biomedical doctoral students. A cross-sectional sample (n = 69) completed validated self-report measures of stress; symptoms of burnout and depression; and perceptions of mastery, social support, and advisor support. In linear regression models, we found that academic stressors were most predictive of burnout, whereas family/monetary stressors were most predictive of depression. In mediation models, we found that the relationship between stress and burnout was partially mediated by mastery and advisor support, while the stress–depression relationship was partially mediated by mastery. These findings represent a first step in identifying interventional targets to improve mental health in this at-risk population. Whereas certain stressors are inherent to the doctoral training environment, psychosocial interventions to enhance one’s sense of mastery and/or to improve advisor relationships may mitigate the influence of such stressors on burnout and depression.
The RNA binding protein fragile X mental retardation protein promotes myelin sheath growth

During development, oligodendrocytes in the central nervous system extend a multitude of processes that wrap axons with myelin. The highly polarized oligodendrocytes generate myelin sheaths on many different axons, which are far removed from the cell body. Neurons use RNA binding proteins to transport, stabilize, and locally translate mRNA in distal domains of neurons. Local synthesis of synaptic proteins during neurodevelopment facilitates the rapid structural and functional changes underlying neural plasticity and avoids extensive protein transport. We hypothesize that RNA binding proteins also regulate local mRNA regulation in oligodendrocytes to promote myelin sheath growth. Fragile X mental retardation protein (FMRP), an RNA binding protein that plays essential roles in the growth and maturation of neurons, is also expressed in oligodendrocytes. To determine whether oligodendrocytes require FMRP for myelin sheath development, we examined fmr1−/− mutant zebrafish and drove FMR1 expression specifically in oligodendrocytes. We found oligodendrocytes in fmr1−/− mutants developed myelin sheaths of diminished length, a phenotype that can be autonomously rescued in oligodendrocytes with FMR1 expression. Myelin basic protein (Mbp), an essential myelin protein, was reduced in myelin tracts of fmr1−/− mutants, but loss of FMRP function did not impact the localization of mbpa transcript in myelin. Finally, expression of FMR1‐I304N, a missense allele that abrogates FMRP association with ribosomes, failed to rescue fmr1−/− mutant sheath growth and induced short myelin sheaths in oligodendrocytes of wild‐type larvae. Taken together, these data suggest that FMRP promotes sheath growth through local regulation of translation.
Development and validation of a revised trauma-specific quality of life instrument

Supplemental digital content is available in the text. BACKGROUND The National Academies of Science has called for routine collection of long-term outcomes after injury. One of the main barriers for this is the lack of practical trauma-specific tools to collect such outcomes. The only trauma-specific long-term outcomes measure that applies a biopsychosocial view of patient care, the Trauma Quality-of-Life (T-QoL), has not been adopted because of its length, lack of composite scores, and unknown validity. Our objective was to develop a shorter version of the T-QoL measure that is reliable, valid, specific, and generalizable to all trauma populations. METHODS We used two random samples selected from a prospective registry developed to follow long-term outcomes of adult trauma survivors (Injury Severity Score ≥9) admitted to three level I trauma centers. First, we validated the original T-QoL instrument using the 12-Item Short-Form Health Survey (SF-12) version 2.0 and Breslau post-traumatic stress disorder screening (B-PTSD) tools. Second, we conducted a confirmatory factor analysis to reduce the length of the original T-QoL instrument, and using a different sample, we scored and performed internal consistency and validity assessments of the revised T-QoL (RT-QoL) components. RESULTS All components of the original T-QoL were significantly correlated negatively with the B-PTSD and positively with the SF-12 mental and physical composite scores. After confirmatory factor analysis, a three-component structure using 18 items (six items/component) most appropriately represented the data. Each component in the revised instrument demonstrated a high level of internal consistency (Cronbach's α ≥0.8) and correlated negatively with the B-PTSD and positively with the SF-12, demonstrating concurrent validity. In addition, each of the RT-QoL components was able to distinguish between individuals based on their work status, with those who have returned to work reporting better health. CONCLUSION This more practical RT-QoL measure greatly increases the ability to evaluate long-term outcomes in trauma more efficiently and meaningfully, without sacrificing the validity and psychometric properties of the original instrument. LEVEL OF EVIDENCE Prognostic and epidemiological, level III.
Use of Zebrafish in Drug Discovery Toxicology.

Unpredicted human safety events in clinical trials for new drugs are costly in terms of human health and money. The drug discovery industry attempts to minimize those events with diligent preclinical safety testing. Current standard practices are good at preventing toxic compounds from being tested in the clinic; however, false negative preclinical toxicity results are still a reality. Continual improvement must be pursued in the preclinical realm. Higher quality therapies can be brought forward with more information about potential toxicities and associated mechanisms. The zebrafish model is a bridge between in vitro assays and mammalian in vivo studies. This model is powerful in its breadth of application and tractability for research. In the past two decades our understanding of disease biology and drug toxicity has grown significantly owing to thousands of studies on this tiny vertebrate. This review summarizes challenges and strengths of the model, discusses the 3Rs value that it can deliver, highlights translatable and untranslatable biology, and brings together reports from recent studies with zebrafish focusing on new drug discovery toxicology.
Effects of Pretreatment with Ionic Liquids on Cellulose Hydrolysis under Hydrothermal Conditions

Hydrothermal hydrolysis in hot pressurized liquid water (HPLW) is attractive for biomass conversion into valuable products because it achieves high reaction rates without catalysts and additives. The hydrothermal hydrolysis of high crystalline cellulose requires higher reaction temperature than polysaccharides having low crystallinity. It can be expected to increase the reaction rate or decrease temperature by decreasing the crystallinity. In the present study ashless filter paper as a fibrous pure cellulose sample was pretreated with ionic liquids (ILs) such as imidazolium chloride ILs containing alkyl side chains ranging from two to six carbons, and with an aqueous solution of bis(ethylenediamine ammonium) copper (BEDC). Herein, the pretreatment with ILs was to regenerate filter paper: dissolving in ILs at 373 K for 120 min or in an aqueous BEDC solution at room temperature, precipitating by adding water, washing the solid, and then drying. Subsequently, the pretreated filter paper samples were hydrolyzed at 533 K and 5.0 MPa in HPLW in a small semi-batch reactor, and the effects of the pretreatment with ILs or BEDC on reaction rates and product yields were examined. While the crystallinity indexes with all ILs and BEDC after the pretreatments decreased to 44 to 47 from the original sample of 87, the reaction rates and product yields were significantly affected by the IL species. At 533 K and 5.0 MPa, the dissolution rate with [AMIM][Cl] was nine times as fast as that for untreated sample.
Deep learning based banana plant detection and counting using high-resolution red-green-blue (RGB) images collected from unmanned aerial vehicle (UAV)

The production of banana—one of the highly consumed fruits—is highly affected due to loss of certain number of banana plants in an early phase of vegetation. This affects the ability of farmers to forecast and estimate the production of banana. In this paper, we propose a deep learning (DL) based method to precisely detect and count banana plants on a farm exclusive of other plants, using high resolution RGB aerial images collected from Unmanned Aerial Vehicle (UAV). An attempt to detect the plants on the normal RGB images resulted less than 78.8% recall for our sample images of a commercial banana farm in Thailand. To improve this result, we use three image processing methods—Linear Contrast Stretch, Synthetic Color Transform and Triangular Greenness Index—to enhance the vegetative properties of orthomosaic, generating multiple variants of orthomosaic. Then we separately train a parameter-optimized Convolutional Neural Network (CNN) on manually interpreted banana plant samples seen on each image variants, to produce multiple results of detection on our region of interest. 96.4%, 85.1% and 75.8% of plants were correctly detected on three of our dataset collected from multiple altitude of 40, 50 and 60 meters, of same farm. Further discussion on results obtained from combination of multiple altitude variants are also discussed later in the research, in an attempt to find better altitude combination for data collection from UAV for the detection of banana plants. The results showed that merging the detection results of 40 and 50 meter dataset could detect the plants missed by each other, increasing recall upto 99%.
Cognitive impairment and medication adherence post-stroke: A five-year follow-up of the ASPIRE-S cohort

Background Control of vascular risk factors is essential for secondary stroke prevention. However, adherence to secondary prevention medications is often suboptimal, and may be affected by cognitive impairment. Few studies to date have examined associations between cognitive impairment and medication adherence post-stroke, and none have considered whether adherence to secondary prevention medications might affect subsequent cognitive function. The aim of this study was to explore prospective associations between cognitive impairment and medication non-adherence post-stroke. Methods A five-year follow-up of 108 stroke survivors from the Action on Secondary Prevention Interventions and Rehabilitation in Stroke (ASPIRE-S) prospective observational cohort study. Cognitive function was assessed using the Montreal Cognitive Assessment at 6 months, and a neuropsychological test battery at 5 years. Adherence to antihypertensive, antithrombotic and lipid-lowering medications was assessed using prescription refill data. Results The prevalence of cognitive impairment at five years was 35.6%. The prevalence of non-adherence ranged from 15.1% for lipid-lowering agents to 30.2% for antithrombotics. There were no statistically significant associations between medication non-adherence in the first year post-stroke and cognitive impairment at 5 years, nor between cognitive impairment at 6 months and non-adherence at 5 years. Stroke survivors with cognitive impairment were significantly more likely to report receiving help with taking medications [OR (95% CI): 4.84 (1.17, 20.07)]. Conclusions This is the first study to explore the potential impact of non-adherence to secondary prevention medications on cognitive impairment in stroke survivors. Findings highlight the role of family members and caregivers in assisting stroke survivors with medication administration, particularly in the context of deficits in cognitive function. Involving family members and caregivers may be a legitimate and cost-effective strategy to improve medication adherence in stroke survivors.