Miracle-dz/UniFAR-FTUs huggingface dataset:
High density genotype storage for plant breeding in the Chado schema of Breedbase

Modern breeding programs routinely use genome-wide information for selecting individuals to advance. The large volumes of genotypic information required present a challenge for data storage and query efficiency. Major use cases require genotyping data to be linked with trait phenotyping data. In contrast to phenotyping data that are often stored in relational database schemas, next-generation genotyping data are traditionally stored in non-relational storage systems due to their extremely large scope. This study presents a novel data model implemented in Breedbase (https://breedbase.org/) for uniting relational phenotyping data and non-relational genotyping data within the open-source PostgreSQL database engine. Breedbase is an open-source, web-database designed to manage all of a breeder’s informatics needs: management of field experiments, phenotypic and genotypic data collection and storage, and statistical analyses. The genotyping data is stored in a PostgreSQL data-type known as binary JavaScript Object Notation (JSONb), where the JSON structures closely follow the Variant Call Format (VCF) data model. The Breedbase genotyping data model can handle different ploidy levels, structural variants, and any genotype encoded in VCF. JSONb is both compressed and indexed, resulting in a space and time efficient system. Furthermore, file caching maximizes data retrieval performance. Integration of all breeding data within the Chado database schema retains referential integrity that may be lost when genotyping and phenotyping data are stored in separate systems. Benchmarking demonstrates that the system is fast enough for computation of a genomic relationship matrix (GRM) and genome wide association study (GWAS) for datasets involving 1,325 diploid Zea mays, 314 triploid Musa acuminata, and 924 diploid Manihot esculenta samples genotyped with 955,690, 142,119, and 287,952 genotype-by-sequencing (GBS) markers, respectively.
A Novel Link between Early Life Allergen Exposure and Neuroimmune Development in Children.

Purpose As COVID-19 unprecedented situation significantly increased the time families spend indoors, the awareness of unhealthy living conditions negatively impacting immune system and early neurodevelopment of children is of crucial importance. Methods We retrospectively reviewed unrelated cases of the children with confirmed multiple indoor allergen sensitization due to prolonged exposure to unhealthy indoor environment with infestation and water damage, who, in addition to multiple health problems related to allergy and asthma, also developed neuroimmune complications and growth delay. Results Documented early in life atypical neurologic and behavioral changes were common in all cases. Clinical analysis did not establish other causative reason aside from prenatal and early life exposure to unhealthy living conditions. Alternaria Alternara and Penicillium/Aspergillus molds were found in all homes and sensitization was confirmed in all cases. Significant similarities in the symptoms recorded in all three families led us to a hypothesis that, likely, a significant level of the immune response to external immunogenic pathological stimulus such as mold spore protein, mycotoxin protein, dust mite protein, decay-related volatile particles (VOC) skewed a balance of the neuroimmune interactions, and further affected neuronal network establishment. As all children exhibited significant spectrum of the systemic inflammatory conditions early in life, coupled with inability to follow normal neurodevelopment, we hypothesize that an overwhelming activation of the aggressive immune mechanisms by the epigenetic factors led to glia activation, cytokine storm and break of tolerance. Conclusions We hypothesize that developing immune system exhibited aggressive responses due to environmental danger signals, subsequently TH-1 or TH-2 switch enables multiple clinical syndromes development with atypical presentation due to the described novel mechanism. An increased due to the COVID-19 lock-down may increase an amount of exposure of vulnerable people to indoor biological particles and volatile organic compounds present in unhealthy buildings. It is of crucial importance to identify and remediate indoor exposure factors that can decrease immune protection, especially against infectious pathogens such as novel coronavirus.
The association of Medicaid expansion and racial/ethnic inequities in access, treatment, and outcomes for patients with acute myocardial infarction

Introduction After having an acute myocardial infarction (AMI), racial and ethnic minorities have less access to care, decreased rates of invasive treatments such as percutaneous coronary intervention (PCI), and worse outcomes compared with white patients. The objective of this study was to determine whether the Affordable Care Act’s expansion of Medicaid eligibility was associated with changes in racial disparities in access, treatments, and outcomes after AMI. Methods Quasi-experimental, difference-in-differences-in-differences analysis of non-Hispanic white and minority patients with acute myocardial infarction in California and Florida from 2010–2015, using linear regression models to estimate the difference-in-differences. This population-based sample included all Medicaid and uninsured patients ages 18–64 hospitalized with acute myocardial infarction in California, which expanded Medicaid through the Affordable Care Act beginning as early as July 2011 in certain counties, and Florida, which did not expand Medicaid. The main outcomes included rates of admission to hospitals capable of performing PCI, rates of transfer for patients who first presented to hospitals that did not perform PCI, rates of PCI during hospitalization and rates of early (within 48 hours of admission) PCI, rates of readmission to the hospital within 30 days, and rates of in-hospital mortality. Results A total of 55,991 hospital admissions met inclusion criteria, 32,540 of which were in California and 23,451 were in Florida. Among patients with AMI who initially presented to a non-PCI hospital, the likelihood of being transferred increased by 12 percentage points (95% CI 2 to 21) for minority patients relative to white patients after the Medicaid expansion. The likelihood of undergoing PCI increased by 3 percentage points (95% CI 0 to 5) for minority patients relative to white patients after the Medicaid expansion. We did not find an association between the Medicaid expansion and racial disparities in overall likelihood of admission to a PCI hospital, hospital readmissions, or in-hospital mortality. Conclusions The Medicaid expansion was associated with a decrease in racial disparities in transfers and rates of PCI after AMI. We did not find an association between the Medicaid expansion and admission to a PCI hospital, readmissions, and in-hospital mortality. Additional factors outside of insurance coverage likely continue to contribute to disparities in outcomes after AMI. These findings are crucial for policy makers seeking to reduce racial disparities in access, treatment and outcomes in AMI.
Virtual Reality to Reduce Procedural Pain During IV Insertion in the Pediatric Emergency Department

Supplemental Digital Content is available in the text. Objective: The objective of this study was to evaluate the feasibility of using virtual reality (VR) for distraction during intravenous (IV) insertion in the pediatric emergency department (ED) and of conducting a full-scale randomized controlled trial. Materials and Methods: Children aged 8 to 17 years old attending a tertiary care pediatric ED were randomized to interactive VR or an attention control (video on a tablet) for distraction during their IV insertion. Feasibility was determined by recruitment rates, acceptability of the intervention, response rates to outcome measures, and safety or technical problems. Satisfaction questionnaires and pain, fear, and distress scores were completed by the child, caregiver, nurse, and research assistant. Immersion in the intervention was rated by the child. Heart rate was measured. Results: Children were recruited between February 2018 and May 2019. A total of 116 children were screened and 72.3% of eligible children were enrolled. Overall, 60 children were randomized to either VR (n=32) or attention control (n=28). Children, caregivers, and nurses were highly satisfied with both distraction methods. There were no significant safety, technical, or equipment issues. There was minimal disruption to clinical workflow in both groups due to study protocols. There was a clinically significant reduction in pain in the VR group. There was no significant difference in fear or distress. Children reported higher immersion in the VR environment. Heart rate increase from baseline was higher in the VR group. Discussion: Our data support the feasibility of using VR for distraction during IV insertion and of conducting a full-scale randomized controlled trial. Identifying eligible patients and minimizing the number of outcome measures will be important considerations for future research.
Metabolomic differences of seminal plasma between boars with high and low average conception rates after artificial insemination.

Seminal plasma is a complex biological fluid containing many metabolites including amino acids, fructose, carbohydrates, lipids etc. Metabolites play important roles in multiple biological processes, but details and significance of the seminal plasma metabolome related to boar fertility are unknown. The aim of the present study was to compare the comprehensive metabolome of seminal plasma from boars with different conception rate after artificial insemination and to identify the potential biomarkers. Semen samples were collected from boars which divided into two groups according to the conception rates in the offspring. Seminal plasma metabolites were isolated, purified, and then subjected to Ultra-high Performance Liquid Chromatography-Quadrupole Time-of-Flight Mass Spectrometry (UHPLC-qTOF-MS) procession. A total of 576 (Positive ion mode) and 377 (Negative ion mode) metabolites were identified in seminal plasma. Metabolites were identified and categorized according to their major chemical classes, including carboxylic acids and derivatives, organooxygen compounds, amino acids, peptides, and alogues, fatty amides, fatty acyls, benzene and substituted derivatives, purine nucleotides, pyrimidine nucleotides, glycosyl compounds, fatty acids, and conjugates. The results showed that 4-Aminobenzoate, Pro-Asn, Ile-Tyr, Homoveratric acid, and D-Biotin were higher in semen of boar with higher conception rate (HG) versus lower conception rate (LG) (P < 0.05), whereas L-Serine, Butoxyacetic acid, S-Methyl-5'-thioadenosine, Capsaicin, and 1-O-(cis-9-Octadecenyl)-2-O-acetyl-sn-glycero-3-phosphocholine (PAF) were lower in HG than in LG (P < 0.05). These metabolites may be considered as candidate biomarkers for different fertility in boars.
Late arm and shoulder problems after axillary therapeutic lymph node dissection in patients with melanoma

Abstract Introduction Lymphedema is exempted, only a few studies have dealt with the late adverse effects in melanoma patients who have undergone axillary therapeutic lymph node dissection (ATLND) for the clinical nodal disease. We evaluated the data on late arm/shoulder problems (ASPs) reported by the patients and daily life impairment after ATLND and identified the risk factors. Material and methods Between 2008 and 2014, 82 patients underwent full en bloc Level I-III ATLND. After a median of 56 months (range 34–104), 76 patients (compliance: 93%) rated their ASPs and daily life dysfunction in a questionnaire, leading to the calculation of individual a Symptom/Problem Summary Score and a Function Summary Score. Multivariate analyses identified risk factors. Results Two groups of patients were identified. Group 1: no or mild ASPs, n = 56 (74%). Group 2: at least one moderate, severe and very severe ASP, n = 20 (26%). Overall, lymphedema, numbness and restricted arm movements represented the most frequent ASPs. Based on the distribution of the summary scores, about 60% of the patients reported no or only mild symptoms/problems and no or mild dysfunction. More than mild impairment of daily life was reported by five patients. On multivariate analyses, increasing tumor size and decreasing age were identified as risk factors. Conclusion Our sample shows that ATLND in melanoma patients with the clinically detectable disease can be performed without a major risk of late ASPs and impaired daily life. Increasing tumor size and decreasing age at the surgery are risk factors for developing ASP-related dysfunction.
[Osteogenic effect of collagen/bioglass composites carrying noggin siRNA].

OBJECTIVE To investigate osteogenic effect of collagen/bioglass composites loaded with a small interfering RNA (siRNA) targeting noggin. METHODS The collagen/bioglass composites loaded with the negative control siRNA or noggin siRNA were prepared by freeze-drying method. CCK8 test was used to evaluate the proliferation of MC3T3 cells exposed to the aqueous extracts of collagen/bioglass composites and the siRNA-loaded collagen/bioglass composites. ALP activity assay, quantitative real-time PCR and Alizarin Red staining were used to assess the effect of the 3 composites on mineralization in MC3T3 cells. RESULTS MC3T3 cells cultured for 3 and 5 days in the presence of the extracts of the 3 composites all showed significantly more active proliferation than the blank control cells (P < 0.05). Compared with the cells seeded on the scaffold without siRNA, MC3T3 cells seeded on collagen/bioglass scaffold loaded with noggin siRNA showed a significantly higher ALP activity at 14 days after seeding (P < 0.05) with significantly increased expression of ALP, Runx2 and BSP mRNAs (P < 0.05). Alizarin Red staining showed that the cells seeded on the noggin siRNA-loading collagen/bioglass scaffold contained significantly more mineralized nodules than the other cells (P < 0.05). CONCLUSIONS The collagen/bioglass composites loaded with noggin siRNA have a good biocompatibility, and the collagen/bioglass composites and noggin siRNA show a synergistic effect in promoting osteogenesis.
Hepatic Thermal Injury Promotes Colorectal Cancer Engraftment in C57/black 6 Mice.

BACKGROUND Treatment of liver metastases (primarily colorectal cancer) is limited by high recurrence rates and tumor progression. Surgical approaches to management of these metastases typically utilize heat energy: including electrocautery; argon beam coagulation; thermal ablation of surgical margins for hemostasis; and preemptive thermal ablation to prevent bleeding or effect tumor destruction. Based on high rates of local recurrence, these studies assess whether local effects of hepatic thermal injury (HTI) might contribute to poor outcomes by promoting a hepatic microenvironment favorable for tumor engraftment or progression due to induction of pro-cancer cytokines and deleterious immune infiltrates at the site of thermal injury. Approach and Results:To test this hypothesis, an immunocompetent mouse model was developed wherein HTI was combined with concomitant intrasplenic injection of cells from a well characterized MC38 colon carcinoma cell line. In this model, HTI resulted in a significant increase in engraftment and progression of MC38 tumors at the site of thermal injury. Further, there were local increases in expression of mRNA for Hif1a, Arg1, and Vegfaand activation changes in recruited macrophages at the HTI site but not in untreated liver tissue. Inhibition of HIF1α following HTI significantly reduced discreet hepatic tumor development (p=0.03). CONCLUSIONS Taken together, these findings demonstrate that HTI creates a favorable local environment that is associated with pro-tumorigenic activation of macrophages and circulating tumors implanting. Discrete targeting of HIF1α and/or its up and downstream pathways and/or inhibiting macrophages offer potential strategies for improving the outcome of surgical management of hepatic metastases where HTI is utilized.
Effects of Virgin Coconut Oil on Aluminium Chloride-Induced Alzheimer-Like Dementia in the Prefrontal Cortex

Aims: The aim of this investigation is to study the effect of virgin coconut oil on the prefrontal cortex upon aluminium chloride-induced Alzheimerlikes dementia. Study Design and Methodology: Twenty-eight (28) adult male Wistar rats were used and were randomly assigned into four groups: Group A: Considered to be the control group which took water and food daily. Group B: Virgin coconut oil treated group, were administered virgin coconut oil orally with 1700 mg/kg BW for 42 days. Group C: Aluminium chloride treated group, were administered Aluminium chloride orally with 200 mg/kg BW for 42 days. Group D: Aluminium chloride + virgin coconut oil treated group, the Wistar rats were administered Original Research Article Olanrewaju et al.; JAMPS, 18(1): 1-12, 2018; Article no.JAMPS. 35221 2 Aluminium chloride orally with 200 mg/BW for 21 days and then virgin coconut oil orally with 1700 mg/BW for the next 21 days. The neurobehavioural investigation was done after the experiment to evaluate learning and memory using Barnes Maze. Animals were sacrificed by cervical dislocation. The whole brain was carefully excised from the skull. Prefrontal cortex was removed and fixed in 10% formal saline for histological analysis which includes H&E stain for general histoarchitecture and Cresyl fast violet for Nissl substance. Place and Duration of Study: The study was done in Babcock University and approved by the Babcock University Ethics commission (BUHREC) with the BUHREC number 672/16. The experiment took the total of 45 days. Results: Neurobehavioral study revealed a significant high latency in the animals treated with Aluminium chloride when compared with control and other treated groups. H &E technique, as well as Cresyl fast violet, did not show any observable altered morphological presentation in the control and VCO treated groups. Also, a cellular density between the control and virgin coconut oil group appears normal across the cortical layers with appreciable spines and neuronal projections. The Aluminium chloride treated group induced degenerative changes in the cortex and was characterized by fragmented pyramidal and granule cell layer with observable pyknotic cells. Also, there was a comparatively increased cell density in the cortical layers of the VCO and Aluminium chloride + VCO treated groups. Conclusion: Findings from this study support the view that, virgin coconut oil has ameliorative effects which neutralize the adverse effect of Aluminum chloride and tried to restore the integrity of the prefrontal cortex.
Vessel-on-a-chip models for studying microvascular physiology, transport, and function in vitro.

To understand how the microvasculature grows and remodels, researchers require reproducible systems that emulate the function of living tissue. Innovative contributions toward fulfilling this important need have been made by engineered microvessels assembled in vitro using microfabrication techniques. Microfabricated vessels, commonly referred to as "vessels on a chip," are from a class of cell culture technologies that uniquely integrate microscale flow phenomena, tissue-level biomolecular transport, cell-cell interactions, and proper 3-D extracellular matrix environments under well-defined culture conditions. Here, we discuss the enabling attributes of microfabricated vessels that make these models more physiological compared to established cell culture techniques, and the potential of these models for advancing microvascular research. This review highlights the key features of microvascular transport and physiology, critically discusses the strengths and limitations of different microfabrication strategies for studying the microvasculature, and provides a perspective on current challenges and future opportunities for vessel on a chip models.
Coral calcification responses to the North Atlantic Oscillation and coral bleaching in Bermuda

The North Atlantic Oscillation (NAO) has been hypothesized to drive interannual variability in Bermudan coral extension rates and reef-scale calcification through the provisioning of nutritional pulses associated with negative NAO winters. However, the direct influence of the NAO on Bermudan coral calcification rates remains to be determined and may vary between species and reef sites owing to implicit differences in coral life history strategies and environmental gradients across the Bermuda reef platform. In this study, we investigated the connection between negative NAO winters and Bermudan Diploria labyrinthiformis, Pseudodiploria strigosa, and Orbicella franksi coral calcification rates across rim reef, lagoon, and nearshore reef sites. Linear mixed effects modeling detected an inverse correlation between D. labyrinthiformis calcification rates and the winter NAO index, with higher rates associated with increasingly negative NAO winters. Conversely, there were no detectable correlations between P. strigosa or O. franksi calcification rates and the winter NAO index suggesting that coral calcification responses associated with negative NAO winters could be species-specific. The correlation between coral calcification rates and winter NAO index was significantly more negative at the outer rim of the reef (Hog Reef) compared to a nearshore reef site (Whalebone Bay), possibly indicating differential influence of the NAO as a function of the distance from the reef edge. Furthermore, a negative calcification anomaly was observed in 100% of D. labyrinthiformis cores in association with the 1988 coral bleaching event with a subsequent positive calcification anomaly in 1989 indicating a post-bleaching recovery in calcification rates. These results highlight the importance of assessing variable interannual coral calcification responses between species and across inshore-offshore gradients to interannual atmospheric modes such as the NAO, thermal stress events, and potential interactions between ocean warming and availability of coral nutrition to improve projections for future coral calcification rates under climate change.
Reoxygenation induces reactive oxygen species production and ferroptosis in renal tubular epithelial cells by activating aryl hydrocarbon receptor

During the reperfusion phase of ischemia-reperfusion injury, reactive oxygen species (ROS) production aggravates the course of many diseases, including acute kidney injury. Among the various enzymes implicated in ROS production are the enzymes of the cytochromes P450 superfamily (CYPs). Since arylhydrocarbon receptor (AhR) controls the expression of certain CYPs, the involvement of this pathway was evaluated in reperfusion injury. Because AhR may interact with the nuclear factor erythroid 2-related factor 2 (Nrf2) and the hypoxia-inducible factor-1α (HIF-1α), whether such an interaction takes place and affects reperfusion injury was also assessed. Proximal renal proximal tubular epithelial cells were subjected to anoxia and subsequent reoxygenation. At the onset of reoxygenation, the AhR inhibitor CH223191, the HIF-1α activator roxadustat, or the ferroptosis inhibitor α-tocopherol were used. The activity of AhR, Nrf2, HIF-1α, and their transcriptional targets were assessed with western blotting. ROS production, lipid peroxidation and cell death were measured with colorimetric assays or cell imaging. Reoxygenation induced ROS production, lipid peroxidation and cell ferroptosis, whereas CH223191 prevented all. Roxadustat did not affect the above parameters. Reoxygenation activated AhR and increased CYP1A1, while CH223191 prevented both. Reoxygenation with or without CH223191 did not alter Nrf2 or HIF-1α activity. Thus, AhR is activated during reoxygenation and induces ROS production, lipid peroxidation and ferroptotic cell death. These detrimental effects may be mediated by AhR-induced CYP overexpression, while the Nrf2 or the HIF-1α pathways remain unaffected. Accordingly, the AhR pathway may represent a promising therapeutic target for the prevention of reperfusion injury.