Miracle-dz/UniFAR-FTUs huggingface dataset:
Principal component analysis of blood microRNA datasets facilitates diagnosis of diverse diseases

Early, ideally pre-symptomatic, recognition of common diseases (e.g., heart disease, cancer, diabetes, Alzheimer’s disease) facilitates early treatment or lifestyle modifications, such as diet and exercise. Sensitive, specific identification of diseases using blood samples would facilitate early recognition. We explored the potential of disease identification in high dimensional blood microRNA (miRNA) datasets using a powerful data reduction method: principal component analysis (PCA). Using Qlucore Omics Explorer (QOE), a dynamic, interactive visualization-guided bioinformatics program with a built-in statistical platform, we analyzed publicly available blood miRNA datasets from the Gene Expression Omnibus (GEO) maintained at the National Center for Biotechnology Information at the National Institutes of Health (NIH). The miRNA expression profiles were generated from real time PCR arrays, microarrays or next generation sequencing of biologic materials (e.g., blood, serum or blood components such as platelets). PCA identified the top three principal components that distinguished cohorts of patients with specific diseases (e.g., heart disease, stroke, hypertension, sepsis, diabetes, specific types of cancer, HIV, hemophilia, subtypes of meningitis, multiple sclerosis, amyotrophic lateral sclerosis, Alzheimer’s disease, mild cognitive impairment, aging, and autism), from healthy subjects. Literature searches verified the functional relevance of the discriminating miRNAs. Our goal is to assemble PCA and heatmap analyses of existing and future blood miRNA datasets into a clinical reference database to facilitate the diagnosis of diseases using routine blood draws.
Targeting miR-27a/VE-cadherin interactions rescues cerebral cavernous malformations in mice

Cerebral cavernous malformations (CCMs) are vascular lesions predominantly developing in the central nervous system (CNS), with no effective treatments other than surgery. Loss-of-function mutation in CCM1/krev interaction trapped 1 (KRIT1), CCM2, or CCM3/programmed cell death 10 (PDCD10) causes lesions that are characterized by abnormal vascular integrity. Vascular endothelial cadherin (VE-cadherin), a major regulator of endothelial cell (EC) junctional integrity is strongly disorganized in ECs lining the CCM lesions. We report here that microRNA-27a (miR-27a), a negative regulator of VE-cadherin, is elevated in ECs isolated from mouse brains developing early CCM lesions and in cultured ECs with CCM1 or CCM2 depletion. Furthermore, we show miR-27a acts downstream of kruppel-like factor (KLF)2 and KLF4, two known key transcription factors involved in CCM lesion development. Using CD5-2 (a target site blocker [TSB]) to prevent the miR-27a/VE-cadherin mRNA interaction, we present a potential therapy to increase VE-cadherin expression and thus rescue the abnormal vascular integrity. In CCM1- or CCM2-depleted ECs, CD5-2 reduces monolayer permeability, and in Ccm1 heterozygous mice, it restores dermal vessel barrier function. In a neonatal mouse model of CCM disease, CD5-2 normalizes vasculature and reduces vascular leakage in the lesions, inhibits the development of large lesions, and significantly reduces the size of established lesions in the hindbrain. Furthermore, CD5-2 limits the accumulation of inflammatory cells in the lesion area. Our work has established that VE-cadherin is a potential therapeutic target for normalization of the vasculature and highlights that targeting miR-27a/VE-cadherin interaction by CD5-2 is a potential novel therapy for the devastating disease, CCM.
Factors influencing carbon, nitrogen, and phosphorus content of fish from a Lake Superior coastal wetland

The narrow fish nutrient ranges (C, 42.8-48.4%; N, 9.6-12.7%; P, 1.91-2.74%) in this study suggest that overall mean values are adequate for quantifying movement of C, N, or P as part of fish-mediated nutrient transport. We measured C, N, and P in 20 species of Lake Superior coastal wetland fish to better understand variability in fish elemental content caused by differences in species, habitat, season, life stage, or size. Fish were sampled within Bark Bay slough and at its inlet/outlet to Bark Bay, Lake Superior, from May to November 1995. Elemental content averaged across all fish (n = 192) was 45.1% for C, 11.3% for N, and 2.45% for P. We did find significant differences (p 0.05) among nine tested species. However, less than one third of the analyses were significant for effects of location or date of capture or fish length on fish nutrient content and nutrient ratios. Regressions of N:P ratios against growth rate indices and, separately, fineness ratios were significant, suggesting that growth rate a.
Group size influences foraging effort independent of predation risk: an experimental study on rainbow trout

Foraging effort, swimming activity, vertical position and flight response were recorded in focal juvenile rainbow trout Oncorhynchus mykiss at three group sizes: without company, or in visual and chemical contact with either one or five companion fish at two levels of predation risk: high (simulated aerial predator attack) or low (no attack). The predator attack induced a pronounced flight reaction as well as a reduction in vertical position, feeding and swimming activity. The foraging effort of the focal fish increased with group size independent of the level of predation risk, which suggests that the group-mediated increase in foraging activity is caused by competition rather than by reduction in perceived risk. The flight response to the predator attack, however, was stronger when the focal fish had company, suggesting that individuals may benefit from copying the anti-predator response of other group members. # 2003 The Fisheries Society of the British Isles
Optical Coherence Tomography Angiography in Diabetes and Diabetic Retinopathy

Diabetic retinopathy (DR) is a common complication of diabetes mellitus that disrupts the retinal microvasculature and is a leading cause of vision loss globally. Recently, optical coherence tomography angiography (OCTA) has been developed to image the retinal microvasculature, by generating 3-dimensional images based on the motion contrast of circulating blood cells. OCTA offers numerous benefits over traditional fluorescein angiography in visualizing the retinal vasculature in that it is non-invasive and safer; while its depth-resolved ability makes it possible to visualize the finer capillaries of the retinal capillary plexuses and choriocapillaris. High-quality OCTA images have also enabled the visualization of features associated with DR, including microaneurysms and neovascularization and the quantification of alterations in retinal capillary and choriocapillaris, thereby suggesting a promising role for OCTA as an objective technology for accurate DR classification. Of interest is the potential of OCTA to examine the effect of DR on individual retinal layers, and to detect DR even before it is clinically detectable on fundus examination. We will focus the review on the clinical applicability of OCTA derived quantitative metrics that appear to be clinically relevant to the diagnosis, classification, and management of patients with diabetes or DR. Future studies with longitudinal design of multiethnic multicenter populations, as well as the inclusion of pertinent systemic information that may affect vascular changes, will improve our understanding on the benefit of OCTA biomarkers in the detection and progression of DR.
Effect of Native Bioinoculants on Vegetable Crops Grown on Alkaline Soil Under Field Conditions

ABSTRACT Due to expansive and environment-polluting chemical amendments for reclaiming alkaline salt-affected wastelands that have large share worldwide, it is important to use biological means like native bioinoculants to counteract the alkalinity and increase crop productivity on a sustainable basis. Field experiments were conducted to culture native Arbuscular Mycorrhiza fungi (AMF) on an alkaline soil and to study the efficacy of the native and exotic strains of AMF and Azotobacter in four vegetable crops [Brassica oleracea var. capitata (cabbage), Allium cepa (onion), Solanum melongena (eggplant) and Brassica oleracea var. botrytis (cauliflower)] separately, as well as in combination. The Ricinus communis (castor) was found to be a suitable host for AM culturing on normal soil and Trigonella foenum graecum (fenugreek) on alkaline soil, however, alkalinity affected germination and survival % of R. communis and Zea mays plants significantly. The combined inoculation of native AM fungi and Azotobacter in B. oleracea var. capitata and B. oleracea var. botrytis resulted in maximum fruit yield and plant growth, which was probably through better uptake of nutrients as a result of secretion of phospho-enzyme and other growth-promoting substances and by inhibiting adverse effect of the root exudates of Brassica sp. In the case of Allium cepa, Azotobacter (native strain) and in Solanum melongena, native AM fungi produced results at par with AMF+ Azotobacter. Overall, the native strains of bioinoculants isolated from native (local) alkaline soils were found to be more adaptive and tolerant to alkalinity than exotic ones.
Synthesis of a DNA knot containing both positive and negative nodes

A figure-eight (4 1 ) knot, staining two positive and two negative nodes, has been synthesized by ligating a single-stranded DNA molecule into a closed cycle. The molecule consists of two single-turn double-helical domains connected by four dT 14 or dT 15 linkers. One of the domains contains the sequence (dCpdGp) 6 , which is capable of forming left-handed Z-DNA. Ligation yields a trefoil (3 1 ) knot or a 4 1 knot, depending upon the conditions in solution
An ethogram of White Leghorn-type hens in battery cages.

The purpose of this study was to record the ethogram of White Leghorn-type hens in cages and to note changes in behavior over the course of the laying period. Three hundred and eighty-four hens derived from two male parental stocks were randomly assigned as pairs to the cages of two three-tiered, semi-stairstep batteries. Hens within pairs were of the same stock, and the batteries were in the same room. The laying phase comprised 13 28-d periods and on the first 4 d of periods 1, 3, 5, 7, 9 and 11 video recordings were made of eight cages per day. Each cage was observed on 1 d only. The levels of occurrence of a variety of behavioral states were estimated from 60 records of the behavior of each hen obtained over an 8-h interval. Head flicking was the most prevalent of its group of mutually exclusive behavioral states, followed by eating and preening. Cage pecking appeared stereotyped in many hens, but, at a frequency of 5% of observations, was not unusually prevalent. Bobbing was primarily a prelaying beh.
Compiler-directed soft error resilience for lightweight GPU register file protection

This paper presents Penny, a compiler-directed resilience scheme for protecting GPU register files (RF) against soft errors. Penny replaces the conventional error correction code (ECC) based RF protection by using less expensive error detection code (EDC) along with idempotence based recovery. Compared to the ECC protection, Penny can achieve either the same level of RF resilience yet with significantly lower hardware costs or stronger resilience using the same ECC due to its ability to detect multi-bit errors when it is used solely for detection. In particular, to address the lack of store buffers in GPUs, which causes both checkpoint storage overwriting and the high cost of checkpointing stores, Penny provides several compiler optimizations such as storage coloring and checkpoint pruning. Across 25 benchmarks, Penny causes only ≈3% run-time overhead on average.
A Mixture of Algae and Extra Virgin Olive Oils Attenuates the Cardiometabolic Alterations Associated with Aging in Male Wistar Rats

Aging is one of the major risk factors for suffering cardiovascular and metabolic diseases. Due to the increase in life expectancy, there is a strong interest in the search for anti-aging strategies to treat and prevent these aging-induced disorders. Both omega 3 polyunsaturated fatty acids (ω-3 PUFA) and extra virgin olive oil (EVOO) exert numerous metabolic and cardiovascular benefits in the elderly. In addition, EVOO constitutes an interesting ingredient to stabilize ω-3 PUFA and decrease their oxidation process due to its high content in antioxidant compounds. ω-3 PUFA are commonly obtained from fish. However, more ecological and sustainable sources, such as algae oil (AO) can also be used. In this study, we aimed to study the possible beneficial effect of an oil mixture composed by EVOO (75%) and AO (25%) rich in ω-3 PUFA (35% docosahexaenoic acid (DHA) and 20% eicosapentaenoic acid (EPA)) on the cardiometabolic alterations associated with aging. For this purpose; young (three months old) and old (24 months old) male Wistar rats were treated with vehicle or with the oil mixture (2.5 mL/kg) for 21 days. Treatment with the oil mixture prevented the aging-induced increase in the serum levels of saturated fatty acids (SFA) and the aging-induced decrease in the serum concentrations of mono-unsaturated fatty acids (MUFA). Old treated rats showed increased serum concentrations of EPA and DHA and decreased HOMA-IR index and circulating levels of total cholesterol, insulin and IL-6. Treatment with the oil mixture increased the mRNA levels of antioxidant and insulin sensitivity-related enzymes, as well as reduced the gene expression of pro-inflammatory markers in the liver and in cardiac and aortic tissues. In addition, the treatment also prevented the aging-induced endothelial dysfunction and vascular insulin resistance through activation of the PI3K/Akt pathway. Moreover, aortic rings from old rats treated with the oil mixture showed a decreased response to the vasoconstrictor AngII. In conclusion, treatment with a mixture of EVOO and AO improves the lipid profile, insulin sensitivity and vascular function in aged rats and decreases aging-induced inflammation and oxidative stress in the liver, and in the cardiovascular system. Thus, it could be an interesting strategy to deal with cardiometabolic alterations associated with aging.
Cadmium tolerance and toxicity, oxygen radical processes and molecular damage in cadmium‐tolerant and cadmium‐sensitive clones of Holcus lanatus L.

SUMMARY Two clones of the grass Holcus lanatus from a metal-contaminated (Hallen Wood, Avonmouth, UK) and an uncontaminated site (Totley, Sheffield, UK) accumulated cadmium from Cd-amended hydroponic cultures, the Totley material to two-fold higher concentrations than the Hallen Wood. The Totley clone showed impaired growth at relatively low Cd concentrations; the reduction in parallel tolerance indices (TIs) to 50% occurred at an external Cd concentration of 53 μM compared with 94 μM in the Cd-tolerant Hallen Wood material. In both clones Cd was transported to the shoots; in the non-tolerant (Cd-sensitive) Totley tissues the two-fold greater Cd accumulation was accompanied by a two-fold rise in lipid peroxidation, indicative of membrane damage by reactive oxygen species in the shoot, though not in the roots. Evidence for the involvement of activated forms of oxygen was also seen in the highly significant correlations between Cd uptake into the shoot and the activities of superoxide dismutase (r = 0·95) and guaiacol peroxidase (r = 0·96), but confined to the sensitive Totley material. It was concluded that one potentially highly-damaging effect of Cd was to promote the generation of partly-reduced and highly-reactive forms of oxygen in the Cd-sensitive clone and that the site of activated oxygen formation was the shoot rather than the root.
Study protocol of validating a numerical model to assess the blood flow in the circle of Willis

Introduction We developed a zero-dimensional (0D) model to assess the patient-specific haemodynamics in the circle of Willis (CoW). Similar numerical models for simulating the cerebral blood flow (CBF) had only been validated qualitatively in healthy volunteers by magnetic resonance (MR) angiography and transcranial Doppler (TCD). This study aims to validate whether a numerical model can simulate patient-specific blood flow in the CoW under pathological conditions. Methods and analysis This study is a diagnostic accuracy study. We aim to collect data from a previously performed prospective study that involved patients with aneurysmal subarachnoid haemorrhage (aSAH) receiving both TCD and brain Computerd Tomography angiography (CTA) at the same day. The cerebral flow velocities are calculated by the 0D model, based on the vessel diameters measured on the CTA of each patient. In this study, TCD is considered the gold standard for measuring flow velocity in the CoW. The agreement will be analysed using Pearson correlation coefficients. Ethics and dissemination This study protocol has been approved by the Medical Ethics Review Board of the University Medical Center Groningen: METc2019/103. The results will be submitted to an international scientific journal for peer-reviewed publication. Trial registration number NL8114.
GeneRax: A Tool for Species-Tree-Aware Maximum Likelihood-Based Gene Family Tree Inference under Gene Duplication, Transfer, and Loss

Abstract Inferring phylogenetic trees for individual homologous gene families is difficult because alignments are often too short, and thus contain insufficient signal, while substitution models inevitably fail to capture the complexity of the evolutionary processes. To overcome these challenges, species-tree-aware methods also leverage information from a putative species tree. However, only few methods are available that implement a full likelihood framework or account for horizontal gene transfers. Furthermore, these methods often require expensive data preprocessing (e.g., computing bootstrap trees) and rely on approximations and heuristics that limit the degree of tree space exploration. Here, we present GeneRax, the first maximum likelihood species-tree-aware phylogenetic inference software. It simultaneously accounts for substitutions at the sequence level as well as gene level events, such as duplication, transfer, and loss relying on established maximum likelihood optimization algorithms. GeneRax can infer rooted phylogenetic trees for multiple gene families, directly from the per-gene sequence alignments and a rooted, yet undated, species tree. We show that compared with competing tools, on simulated data GeneRax infers trees that are the closest to the true tree in 90% of the simulations in terms of relative Robinson–Foulds distance. On empirical data sets, GeneRax is the fastest among all tested methods when starting from aligned sequences, and it infers trees with the highest likelihood score, based on our model. GeneRax completed tree inferences and reconciliations for 1,099 Cyanobacteria families in 8 min on 512 CPU cores. Thus, its parallelization scheme enables large-scale analyses. GeneRax is available under GNU GPL at https://github.com/BenoitMorel/GeneRax (last accessed June 17, 2020).
Optimal resource allocation in a serotinous non‐resprouting plant species under different fire regimes

Serotiny, the retention of mature seeds in closed fruits within the canopy for over a year, is a common trait in fire‐prone environments. When competition with adult plants prevents seedling establishment between fire events and in the absence of post‐release soil seed dormancy, strong serotiny, i.e. the retention of all seeds until the next fire, appears as the best strategy. Despite the low levels of inter‐fire seed recruitment for several species in both Australian and South African fire‐prone environments, considerable variation in the duration of fruit retention is nevertheless observed among species. Our aim is to predict optimal age‐specific reproductive schedules in a perennial, serotinous species, when cone maintenance is costly. We focus on species where adults are killed by fire, without a soil seed‐bank. We explicitly consider a trade‐off between growth (which determines plant survival), seed production and seed maintenance. In our model recruitment relies upon fire events. We use dynamic programming to determine, for given fire regimes, the optimal pattern of resource allocation. We further study the effect of changes in fire regime on the viability of populations adapted to some historical fire regime. We find that, whenever maximal plant survival probability is low, the optimal strategy consists in reducing resource allocation to seed maintenance while increasing resource allocation to annual seed production. This illustrates a trade‐off between current and future reproduction. A low rather than a strong level of serotiny should evolve whenever the variance of fire intervals is large and the mean fire interval is low. Low levels of serotiny could constitute a bet‐hedging strategy with decreasing predictability of the arrival of fire. Once adapted to some historical fire regime, serotinous populations are highly sensitive to a change in mean fire frequency and to an increase in the variance of fire intervals. Populations adapted to a historically high level of variance in fire return are more robust to changes in fire regime. Synthesis: Life‐history trade‐offs and low predictability of fire intervals may favour low rather than strong levels of serotiny even when recruitment essentially occurs just after fire events.
Health-Affecting Compounds in Brassicaceae

ABSTRACT: Brassicaceae vegetables are considered to be a staple food in many areas all over the world. Brassica species are not only known for their high fat and protein contents for human and animal consumption, but Brassicaceae vegetables are recognized as a rich source of nutrients such as vitamins (carotenoids, tocopherol, ascorbic acid, folic acid), minerals (Cu, Zn, P, Mg, among others), carbohydrates (sucrose and glucose), amino acids (for example, L-alanine, L-aspartic acid, L-glutamic acid, L-glutamine, L-histidine, L-methionine, L-phenylalanine, L-threonine, L-tryptophan, and L-valine), and different groups of phytochemicals such as indole phytoalexins (brassinin, spirobrassinin, brassilexin, camalexin, 1-methoxyspirobrassinin, 1-methoxyspirobrassinol, and methoxyspirobrassinol methyl ether), phenolics (such as feruloyl and isoferuloylcholine, hydroxybenzoic, neochlorogenic, chlorogenic, caffeic, p-coumaric, ferulic, and sinapic acids, anthocyanins, quercetin, and kaempferol), and glucosinolates (mainly glucoiberin, glucoraphanin, glucoalyssin, gluconapin, glucobrassicanapin, glucobrassicin, gluconasturtiin, and neoglucobrassicin). All of these phytochemicals contribute to the reported antioxidant, anticarcinogenic, and cardiovascular protective activities of Brassica vegetables. However, not all members of this family are equal from a nutritional viewpoint, since significant qualitative variations in the phytochemical profiles of Brassica species and varieties suggest differences in the health-promoting properties among these vegetables. In this article, Brassica phytochemicals with their nutritional value and health-promoting activities are discussed to give an overview of the literature for Brassica as a staple crop.