Miracle-dz/UniFAR-FTUs huggingface dataset:
Rapture facilitates inexpensive and high-throughput parent-based tagging in salmonids

Accurate methods for tracking individuals are crucial to the success of fisheries and aquaculture management. Management of migratory salmonid populations, which are important for the health of many economies, ecosystems, and indigenous cultures, is particularly dependent on data gathered from tagged fish. However, the physical tagging methods currently used have many challenges including cost, variable marker retention, and information limited to tagged individuals. Genetic tracking methods combat many of the problems associated with physical tags, but have their own challenges including high cost, potentially difficult marker design, and incompatibility of markers across species. Here we show the feasibility of a new genotyping method for parent-based tagging (PBT), where individuals are tracked through the inherent genetic relationships with their parents. We found that Rapture sequencing, a combination of restriction-site associated DNA and capture sequencing, provides sufficient data for parentage assignment. Additionally, the same capture bait set, which targets specific restriction-site associated DNA loci, can be used for both Rainbow Trout Oncorhynchus mykiss and Chinook Salmon Oncorhynchus tshawytscha. We input 248 single nucleotide polymorphisms from 1,121 samples to parentage assignment software and compared parent-offspring relationships of the spawning pairs recorded in a hatchery. Interestingly, our results suggest sperm contamination during hatchery spawning occurred in the production of 14% of offspring, further confirming the need for genetic tagging in accurately tracking individuals. PBT with Rapture successfully assigned progeny to parents with a 98.86% accuracy with sufficient genetic data. Cost for this pilot study was approximately $3 USD per sample. As costs vary based on the number of markers used and individuals sequenced, we expect that when implemented at a large-scale, per sample costs could be further decreased. We conclude that Rapture PBT provides a cost-effective and accurate alternative to the physical coded wire tags, and other genetic-based methods.
Family factors and health‐related quality of life within 6 months of completion of childhood cancer treatment

The transition from active cancer treatment to survivorship represents a period of uncertainty for youth and their families, but factors associated with adaptation during this period are understudied. We evaluated associations among cancer and treatment‐related variables, family factors (family functioning, caregiver health‐related quality of life [HRQL], and caregiver distress), and patient HRQL after treatment completion. We assessed the indirect effects of neurocognitive difficulties on youth HRQL through family factors.
Serum cystatin C concentration can be used to evaluate glomerular filtration rate in small dogs

Serum cystatin C levels (CysC) are used in human medicine to document progressive kidney failure. Although CysC are not thought to be useful for the diagnosis of kidney dysfunction in dogs, there has been no specific consideration of body weight as a confounding issue. The aim of this study was to assess that the utility of CysC for the diagnosis of decreased glomerular filtration rate (GFR) in smaller vs. larger dogs. In clinically healthy dogs, serum creatinine (Cre) and CysC correlate directly with body weight; we found that dogs weighing <20 kg had significantly lower CysC than those weighing ≥20 kg (0.27 ± 0.07 vs. 0.34 ± 0.05 mg/l, respectively, P<0.001). In dogs weighing <20 kg, CysC had superior diagnostic accuracy for the detection of mildly decreased plasma iohexol clearance (PCio) (<1.8 ml/min/kg) compared with Cre (sensitivity 100% vs. 80.9% and specificity 100% vs. 85.7%); this was not true for dogs weighing ≥20 kg. Additionally, using a cut-off PCio of <1.8 ml/min/kg, the area under receiver-operating characteristics curve (AUC) of CysC was significantly higher than that of Cre in dogs weighing <20 kg (P<0.05); this was not true for dogs weighing ≥20 kg (P=0.695). In conclusion, CysC is a useful marker for the detection of a mild decreasing GFR compared with Cre in dogs weighing <20 kg.
[Driving with a positive test result for alcohol in Spain in 2018.]

OBJECTIVE The association between alcohol and traffic collision injuries is well established. Our objective was to analyze the frequency of driving with a positive result in on-road tests for alcohol with considering different concentrations of alcohol in exhaled air, as well as driving while positive only for alcohol or for alcohol and drugs. METHODS In 2018, a cross-sectional study was carried out in a representative sample of motor vehicle drivers on Spanish public roads, excluding cyclists and drivers of vehicles weighing more than 3,500 kg. 2,881 drivers were included in this study. Data was analysed with the statistics program SPSS 24.0. RESULTS 10.9% (95% CI, 9.8-12.1) of the drivers were positive cases for any substance: In 3.9% (3.2-4.6) alcohol alone (i.e., without any other substance), and in 0.8% (0.6-1.3) alcohol plus another substance, were observed. 2.1% (1.6-2.7) of the drivers had a level of alcohol in expired air higher than the legal allowed limit for drivers (>0.25 mg/L, that excluding novice and profesional drivers). 0.4% (0.2-0.7) of the drivers had an alcohol concentration in expired air >0.60 mg/L. Driving with the presence of alcohol and drugs is observed in two out of ten positive cases for alcohol. CONCLUSIONS Driving while positive for alcohol is common among Spanish drivers, and drivers positive for alcohol and drugs should not be ignored.
Toxoplasma gondii destroys Her2/Neu-expressing mammary cancer cells in vitro using a continuous feed medium approach.

INTRODUCTION Toxoplasma gondii is an opportunistic protozoan and can be grown using several human cell lines. Breast cancer is the second leading cause of cancer death in women. Her2/Neu-expressing mammary cancer cell lines called TUBO can be grown in vitro. In recent years, protozoan parasites have become popular means of use in cancer therapy research. In this study, we analyzed whether T. gondii tachyzoites can destroy TUBO cells using a novel continuous feed medium approach. METHODOLOGY Two sets of flasks (each containing four groups) containing TUBO cells were inoculated with T. gondii Ankara strain tachyzoites. First set containing 5×106 TUBO cells were inoculated with TUBO-tachyzoite ratios of 1:2, 1:1, 2:1, and 4:1 and second set containing 1×106 TUBO cells were inoculated with TUBO-tachyzoite ratios of 10:1, 100:1, 1000:1, and 2000:1. Thereafter, culture supernatants were harvested at various days until TUBO cells were destroyed and tachyzoites were counted. RESULTS In the first and second sets of flasks, TUBO cells were destroyed between days 8 to 12 and 12 to 25, respectively. In addition, the amount of tachyzoites increased 7- 43 and 595 to 112500 times in the first and second set of flasks, respectively. CONCLUSIONS These results show that T. gondii tachyzoites successfully destroy Her2/Neu-expressing mammary cancer cells using a continuous feed medium approach. Although this idea may be too premature for the moment, the approach defined herein may support future researchers investigating the relationship between cancer and parasites which can make important progress toward saving cancer patient lives.
Factors Affecting the Household Succession in Agricultural Occupation in Nakhon Ratchasima Province, Thailand

This research aims to determine the factors affecting the succession of youths from farming households in agricultural occupations within Nakhon Ratchasima Province, Thailand. Primary information was collected from 400 farm households using a structured questionnaire. Binary logistic regression analysis shows that five variables significantly influence the decision of the new generation on succession in agricultural occupation: Their experience in agricultural work, attitude towards agriculture as an occupation, the number of agricultural labor within a household, marital status, and if they faced problems with the agricultural resources in the past. The results also imply the need for agriculture-related agencies and other relevant sectors to focus on the promotion of agricultural occupation succession by educating, creating awareness, and attitude shifting for the new generation, to make them realize both the significance and benefits gained from taking up agriculture as an occupation. Moreover, publicizing the Young Smart Farmers Program—youths who are successful in agriculture—would also help promote youths’ succession in agricultural occupation in households.
Integrated analysis of transcriptomic and metabolomic data demonstrates the significant role of pyruvate carboxylase in the progression of ovarian cancer

The aim of this study was to explore prognosis-related biomarkers and underlying mechanisms during ovarian carcinoma progression and development. mRNA expression profiles and GSE49997 dataset were downloaded. Survival analyses were performed for genes with high expression levels. Expression level of candidate genes was explored in four ovarian cancer cells lines. Pyruvate carboxylase (PC) was found to be one of significantly differentially expressed gene (DEG). The role of PC knockdown was analyzed in SKOV cells using cell proliferation, flow cytometric, and Transwell migration and invasion assays. DEGs and metabolites in PC-shRNA (shPC)-treated samples vs. control groups were identified. PC was a prognosis-related gene and related to metabolic pathway. Knockdown of PC regulated cell proliferation, cell cycle progression, and migration and invasion of SKOV-3 cells. Transcriptome sequencing analyses showed STAT1 and TP53 gained higher degrees in PPI network. A total of 44 metabolites were identified. These DEGs and metabolites in PC samples were related with neuroactive ligands receptor interaction, glycine, serine and threonine metabolism, and ABC transporter pathways. PC may affect the tumor biology of ovarian cancer through the dysregulation of glycine, serine, and threonine metabolism, and ABC transporter pathways, as well as STAT1 and TP53 expression.
Estimation of US Children’s Educational Attainment and Years of Life Lost Associated With Primary School Closures During the Coronavirus Disease 2019 Pandemic

Key Points Question Based on the current understanding of the associations between school disruption and decreased educational attainment and between decreased educational attainment and lower life expectancy, is it possible to estimate the association between school closure during the coronavirus disease 2019 pandemic and decreased life expectancy of publicly educated primary school–aged children in the United States? Findings This decision analytical model found that missed instruction during 2020 could be associated with an estimated 5.53 million years of life lost. This loss in life expectancy was likely to be greater than would have been observed if leaving primary schools open had led to an expansion of the first wave of the pandemic. Meaning These findings suggest that the decision to close US public primary schools in the early months of 2020 may be associated with a decrease in life expectancy for US children.
Metabolic indices in schizophrenia: Association of negative symptoms with higher HDL cholesterol in female patients

Abstract Objectives Negative symptoms of schizophrenia can be related to metabolic abnormalities. The study aimed to assess negative symptoms using the Positive and Negative Syndrome Scale (PANSS) and the Brief Negative Symptoms Scale (BNSS), and their relationship with body mass index (BMI) and lipid indices, in male and female schizophrenic patients. Methods Fifty chronic schizophrenia patients (29 males, 21 females) were included. They have mild to moderate severity of the illness (total PANSS score <80), and received unchanged pharmacological treatment in the last three weeks. Psychopathology symptoms were assessed using the PANSS and BNSS. The measurements of BMI and serum lipids were done in all patients. Results In female patients, a significant positive correlation between the intensity of negative symptoms measured by the PANSS and BNSS scales and the concentration of high-density lipoprotein (HDL) cholesterol, and a trend for negative correlation with BMI was observed. Such correlations were not found in male patients. Conclusions Assessing the negative symptoms of schizophrenia, and investigating the relationship of these symptoms with metabolic indices, we showed distinctive features in male and female schizophrenia patients. The positive correlation between negative symptoms and HDL cholesterol in female patients needs to be confirmed in further studies.
Identification of potential lipid biomarkers for active pulmonary tuberculosis using ultra-high-performance liquid chromatography-tandem mass spectrometry

Early diagnosis of active pulmonary tuberculosis (TB) is the key to controlling the disease. Host lipids are nutrient sources for the metabolism of Mycobacterium tuberculosis. In this research work, we used ultra-high-performance liquid chromatography-tandem mass spectrometry to screen plasma lipids in TB patients, lung cancer patients, community-acquired pneumonia patients, and normal healthy controls. Principal component analysis, orthogonal partial least squares discriminant analysis, and K-means clustering algorithm analysis were used to identify lipids with differential abundance. A total of 22 differential lipids were filtered out among all subjects. The plasma phospholipid levels were decreased, while the cholesterol ester levels were increased in patients with TB. We speculate that the infection of M. tuberculosis may regulate the lipid metabolism of TB patients and may promote host-assisted bacterial degradation of phospholipids and accumulation of cholesterol esters. This may be related to the formation of lung cavities with caseous necrosis. The results of receiver operating characteristic curve analysis revealed four lipids such as phosphatidylcholine (PC, 12:0/22:2), PC (16:0/18:2), cholesteryl ester (20:3), and sphingomyelin (d18:0/18:1) as potential biomarkers for early diagnosis of TB. The diagnostic model was fitted by using logistic regression analysis and combining the above four lipids with a sensitivity of 92.9%, a specificity of 82.4%, and the area under the curve (AUC) value of 0.934 (95% CI 0.873 – 0.971). The machine learning method (10-fold cross-validation) demonstrated that the model had good accuracy (0.908 AUC, 85.3% sensitivity, and 85.9% specificity). The lipids identified in this study may serve as novel biomarkers in TB diagnosis. Our research may pave the foundation for understanding the pathogenesis of TB.
An FSCV Deep Neural Network: Development, Pruning, and Acceleration on an FPGA

Fast-scan cyclic voltammetry (FSCV) is an electrochemical technique for measuring rapid changes in the extracellular concentration of neurotransmitters within the brain. Due to its fast scan rate and large output-data size, the current analysis of the FSCV data is often conducted on a computer external to the FSCV device. Moreover, the analysis is semi-automated and requires a good understanding of the characteristics of the underlying chemistry to interpret, making it unsuitable for real-time implementation on low-resource FSCV devices. This paper presents a hardware-software co-design approach for the analysis of FSCV data. Firstly, a deep neural network (DNN) is developed to predict the concentration of a dopamine solution and identify the data recording electrode. Secondly, the DNN is pruned to decrease its computation complexity, and a custom overlay is developed to implement the pruned DNN on a low-resource FPGA-based platform. The pruned DNN attains a recognition accuracy of 97.2% with a compression ratio of 3.18. When the DNN overlay is implemented on a PYNQ-Z2 platform, it achieves the execution time of 13 ms and power consumption of 1.479 W on the entire PYNQ-Z2 board. This study demonstrates the possibility of operating the DNN for FSCV data analysis on portable FPGA-based platforms.
Protective effects of honey and bee venom against lipopolysaccharide and carbon tetrachloride-induced hepatoxicity and lipid peroxidation in rats.

In the present study, the protective effects of honey and bee venom (BV) either independently or in combination against lipopolysaccharide (LPS) and carbon tetrachloride (CCl4)-induced hepatoxicity, lipid peroxidation, and hematological alterations in male albino rats were investigated. In addition, histopathological alterations of hepatic tissues induced by LPS/CCL4 were recorded. Sixty-four of male albino rats of average weight 120-150 g were included in this study. Rats were divided into eight equal groups of eight. The obtained results demonstrated that treatment with LPS/CCl4 caused an increase in the levels of alpha-fetoprotein, which was accompanied by changes in the hepatic function biomarkers that characterized by the increased levels of transaminases (AST, ALT). The results showed oxidative stress as assigned by the increase in lipid peroxide. Meantime detraction in the antioxidants, including glutathione peroxidase was observed. Interruptions in biochemical parameters accompanied by disturbances in hematological parameters and liver histopathology were resulted due to exposure to LPS/CCl4. This study showed the use of honey and BV provided a protective effect on hepatotoxicity induced by LPS/CCl4. This might have been occurred through the reduction of hepatic transaminases and the "Alpha-fetoprotein" in serum and the equilibration of the antioxidation system, thereby, inhibiting the reactive oxygen species accumulation. Honey and BV administration reestablish disturbed hematological parameters and liver histopathology persuaded by LPS/CCl4. More interesting, we demonstrated that using a combination of the honey and BV showed promising enhancement in their protective effects over the use of just one of the two reagents.
Adverse Events in Intensive Care and Continuing Care Units During Bed-Bath Procedures: The Prospective Observational NURSIng during critical carE (NURSIE) Study

Supplemental Digital Content is available in the text. OBJECTIVES: Standard nursing interventions, especially bed-baths, in ICUs can lead to complications or adverse events defined as a physiologic change that can be life-threatening or that prolongs hospitalization. However, the frequency and type of these adverse events are rarely reported in the literature. The primary objective of our study was to describe the proportion of patients experiencing at least one serious adverse event during bed-bath. The secondary objectives were to determine the incidence of each type of serious adverse event and identify risk factors for these serious adverse events. DESIGN: Prospective multicenter observational study. SETTING: Twenty-four ICUs in France, Belgium, and Luxembourg. PATIENTS: The patients included in this study had been admitted to an ICU for less than 72 hours and required at least one of the following treatments: invasive ventilation, vasopressors, noninvasive ventilation, high-flow oxygen therapy. Serious adverse events were defined as cardiac arrest, accidental extubation, desaturation and/or mucus plugging/inhalation, hypotension and/or arrhythmia and/or agitation requiring therapeutic intervention, acute pain, accidental disconnection or dysfunction of equipment, and patient fall requiring additional assistance. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: The study included 253 patients from May 1, 2018, to July 31, 2018 in 24 ICUs, representing 1,529 nursing procedures. The mean Simplified Acute Physiology Score II was 54 ± 19. Nursing care was administered by an average of 2 ± 1 caregivers and lasted between 11 and 20 minutes. Of the 253 patients included, 142 (56%) experienced at least one serious adverse event. Of the 1,529 nursing procedures, 295 (19%) were complicated by at least one serious adverse event. In multivariate analysis, the factors associated with serious adverse event were as follows: presence of a specific protocol (p = 0.011); tracheostomy (p = 0.032); administration of opioids (p = 0.007); presence of a physician (p = 0.0004); duration of nursing care between 6 and 10 minutes (p = 0.003), duration of nursing care between 11 and 20 minutes (p = 0.005), duration of nursing care greater than 40 minutes (p = 0.04) with a reference duration of nursing care between 20 and 40 minutes. CONCLUSIONS: Serious adverse events were observed in one-half of patients and concerned one-fifth of nurses, confirming the need for caution. Further studies are needed to test systematic serious adverse event prevention strategies.
Prognostic role of microRNA 182 and microRNA 18a in locally advanced triple negative breast cancer

Background The study assessed the epigenetic regulation and the role of microRNA (miR) expression in locally advanced triple negative breast cancers (TNBC) and comparison with the clinico-pathological variables and survival. Methods Fifty patients of locally advanced TNBC during the period 2011–2013 were included. Expression level of test microRNA (miR-182 and miR-18a) was determined using Taqman quantitative Real time polymerase chain reaction (qRT-PCR) from formalin fixed paraffin embedded biopsy blocks. Clinical and demographic information and survival data was retrieved from the Hospital medical records. Results An improved clinical complete response (cCR) was observed in patients with age ≥ 45 years (80%), premenopausal status (70%), tumor size < 6 cms (80%), nodal status N0-N1 (95%) and grade II-III tumor (80%). A statistically significant correlation was observed on comparison of cCR with menopausal status (p-value 0.020), T category (p-value 0.018) and the clinical nodal status (p-value 0.003). pCR also correlated with clinical nodal status (p-value 0.008). Epigenetically, miR-18a under expression (< 8.84) was most commonly associated with tumor size < 6 cms (76.7%), clinical nodal status N0-N1 (90%), cCR (60%) and pCR (53.3%). A similar trend was observed with miR-182. Statistical significance was observed with T category (p-values 0.003 and 0.004), clinical nodal status (p-values 0.001 and 0.001), clinical response (p-values 0.002 and 0.002) and pathological response (p-values 0.007 and 0.006) with respect to miR-18a and miR-182, respectively. Also, the menopausal status significantly correlated with the miR-182 expression (p-value 0.009). miR-182 overexpression (≥ 6.32) was not observed in any of the postmenopausal patients. A univariate cox proportional hazard regression model also showed statistical interactions (p-values <0.004). Conclusion miR-182 and miR-18a overexpression correlates with worse clinical and pathological tumor characteristics in locally advanced TNBC and hence could be used to predict the outcomes and prognosis in these patients.