Miracle-dz/UniFAR-FTUs huggingface dataset:
An Automated, Single Cell Quantitative Imaging Microscopy Approach to Assess Micronucleus Formation, Genotoxicity and Chromosome Instability

Micronuclei are small, extranuclear bodies that are distinct from the primary cell nucleus. Micronucleus formation is an aberrant event that suggests a history of genotoxic stress or chromosome mis-segregation events. Accordingly, assays evaluating micronucleus formation serve as useful tools within the fields of toxicology and oncology. Here, we describe a novel micronucleus formation assay that utilizes a high-throughput imaging platform and automated image analysis software for accurate detection and rapid quantification of micronuclei at the single cell level. We show that our image analysis parameters are capable of identifying dose-dependent increases in micronucleus formation within three distinct cell lines following treatment with two established genotoxic agents, etoposide or bleomycin. We further show that this assay detects micronuclei induced through silencing of the established chromosome instability gene, SMC1A. Thus, the micronucleus formation assay described here is a versatile and efficient alternative to more laborious cytological approaches, and greatly increases throughput, which will be particularly beneficial for large-scale chemical or genetic screens.
3D Microlithography Using an Integrated System of 5-mm UV-LEDs with a Tilt-Rotational Sample Holder

This paper demonstrates a 3D microlithography system where an array of 5 mm Ultra Violet-Light Emitting Diode (UV-LED) acts as a light source. The unit of the light source is a UV-LED, which comes with a length of about 8.9 mm and a diameter of 5 mm. The whole light source comprises 20 × 20 matrix of such 5 mm UV-LEDs giving a total number of 400 LEDs which makes it a very favorable source with a large area for having a batch production of the desired microstructures. This light source is able to give a level of precision in microfabrication which cannot be obtained using commercial 3D printers. The whole light source performs continuous rotational movement once it is turned on. This can also move up and down in a vertical direction. This multidirectional light source also comprises a multidirectional sample holder. The light source teaming up with the multidirectional sample holder highly facilitates the process of fabrication of a huge range of 3D structures. This article also describes the different levels of characterization of the system and demonstrates several fabricated 3D microstructures including high aspect ratio vertical micro towers, twisted turbine structures, triangles, inclined pillar ‘V’ structures, and hollow horn structures as well.
Pair Distribution Function from Electron Diffraction in Cryogenic Electron Microscopy: Revealing Glassy Water Structure.

In recent years, cryogenic electron microscopy (Cryo-EM) has revolutionized the structure determination of wet samples and especially that of biological macromolecules. The glassy-water medium in which the molecules are embedded is considered an almost in vivo environment for biological samples. The local structure of amorphous ice is known from neutron- and X-ray diffraction studies, techniques appropriate for much larger volumes than those used in cryo-EM. We here present a first study of the pair distribution function g(r) of glassy water under cryo-EM conditions using electron diffraction data. We found g(r) to be in-between that of low-density amorphous ice and that of supercooled water. Under electron exposure, cubic ice regions were found to nucleate in thicker glassy-water samples. Our work enables to obtain quantitative structural information using g(r) from cryo-EM.
The Evaluation and Use of a Food Frequency Questionnaire Among the Population in Trivandrum, South Kerala, India

Dietary record tools such as food frequency questionnaire (FFQ) and food diaries (FD) are the most commonly used choices for assessing dietary intakes in most large-scale epidemiological studies. The authors developed a self-administered 360-item food frequency questionnaire (FFQ) to assess dietary intakes amongst a population-based cohort in South Kerala. In the validation study (n = 460), the data were collected using FFQs that were administered on three different occasions which were then compared to 7-day food records. The intake of foods and nutrients was higher as determined by the FFQ than that assessed using food records. Spearman correlations for macro-nutrients ranged from 0.72 for protein to 0.61 for carbohydrates and for micronutrients, from 0.71 for vitamin B6 to 0.34 for magnesium. The correlation was improved with energy-adjusted nutrient intakes. On average, the exact agreement for the macronutrients ranged from 48.2% to 57.1%, and that for micronutrients ranged from 66.7% to 41.9%, with the median percentage of 49.58%. The authors conclude that the FFQ has an acceptable reproducibility, however, there was a systematic trend towards higher estimates with the FFQ for most nutrients compared to the FD records.
Functional Architecture of Deleterious Genetic Variants in the Genome of a Wrangel Island Mammoth

Abstract Woolly mammoths were among the most abundant cold-adapted species during the Pleistocene. Their once-large populations went extinct in two waves, an end-Pleistocene extinction of continental populations followed by the mid-Holocene extinction of relict populations on St. Paul Island ∼5,600 years ago and Wrangel Island ∼4,000 years ago. Wrangel Island mammoths experienced an episode of rapid demographic decline coincident with their isolation, leading to a small population, reduced genetic diversity, and the fixation of putatively deleterious alleles, but the functional consequences of these processes are unclear. Here, we show that a Wrangel Island mammoth genome had many putative deleterious mutations that are predicted to cause diverse behavioral and developmental defects. Resurrection and functional characterization of several genes from the Wrangel Island mammoth carrying putatively deleterious substitutions identified both loss and gain of function mutations in genes associated with developmental defects (HYLS1), oligozoospermia and reduced male fertility (NKD1), diabetes (NEUROG3), and the ability to detect floral scents (OR5A1). These data suggest that at least one Wrangel Island mammoth may have suffered adverse consequences from reduced population size and isolation.
Machine Learning and Multidrug-Resistant Gram-Negative Bacteria: An Interesting Combination for Current and Future Research

The dissemination of multidrug-resistant Gram-negative bacteria (MDR-GNB) is associated with increased morbidity and mortality in several countries. Machine learning (ML) is a branch of artificial intelligence that consists of conferring on computers the ability to learn from data. In this narrative review, we discuss three existing examples of the application of ML algorithms for assessing three different types of risk: (i) the risk of developing a MDR-GNB infection, (ii) the risk of MDR-GNB etiology in patients with an already clinically evident infection, and (iii) the risk of anticipating the emergence of MDR in GNB through the misuse of antibiotics. In the next few years, we expect to witness an increasingly large number of research studies perfecting the application of ML techniques in the field of MDR-GNB infections. Very importantly, this cannot be separated from the availability of a continuously refined and updated ethical framework allowing an appropriate use of the large datasets of medical data needed to build efficient ML-based support systems that could be shared through appropriate standard infrastructures.
De Novo Transcriptomic Resources in the Brain of Vespa velutina for Invasion Control

The invasion of Vespa velutina presents a great threat to the agriculture economy, the ecological environment, and human health. An effective strategy for this hornet control is urgently required, but the limited genome information of Vespa velutina restricts the application of molecular-genomic tools for targeted hornet management. Therefore, we conducted large-scale transcriptome profiling of the hornet brain to obtain functional target genes and molecular markers. Using an Illumina HiSeq platform, more than 41 million clean reads were obtained and de novo assembled into 182,087 meaningful unigenes. A total of 56,400 unigenes were annotated against publicly available protein sequence databases and a set of reliable Simple Sequence Repeats (SSRs) and Single Nucleotide Polymorphisms (SNP) markers were developed. The homologous genes encoding crucial behavior regulation factors, odorant binding proteins (OBPs), and vitellogenin, were also identified from highly expressed transcripts. This study provides abundant molecular targets and markers for invasive hornet control and further promotes the genetic and molecular study of Vespa velutina.
Vitamin-D3 (α-1, 25(OH) 2D3) Protects Retinal Pigment Epithelium From Hyperoxic Insults

Purpose Oxidative stress affects the retinal pigment epithelium (RPE) leading to development of vascular eye diseases. Cholecalciferol (VIT-D) is a known modulator of oxidative stress and angiogenesis. This in vitro study was carried out to evaluate the protective role of VIT-D on RPE cells incubated under hyperoxic conditions. Methods Cadaver primary RPE (PRPE) cells were cultured in hyperoxia (40% O2) with or without VIT-D (α-1, 25(OH) 2D3). The functional and physiological effects of PRPE cells with VIT-D treatment were analyzed using molecular and biochemical tools. Results Vascular signaling modulators, such as vascular endothelial growth factor (VEGF) and Notch, were reduced in hyperoxic conditions but significantly upregulated in the presence of VIT-D. Additionally, PRPE conditioned medium with VIT-D induced the tubulogenesis in primary human umbilical vein endothelial cells (HUVEC) cells. VIT-D supplementation restored phagocytosis and transmembrane potential in PRPE cells cultured under hyperoxia. Conclusions VIT-D protects RPE cells and promotes angiogenesis under hyperoxic insult. These findings may give impetus to the potential of VIT-D as a therapeutic agent in hyperoxia induced retinal vascular diseases.
Imipramine Ameliorates Depressive Symptoms by Blocking Differential Alteration of Dendritic Spine Structure in Amygdala and Prefrontal Cortex of Chronic Stress-Induced Mice

Previous studies have shown disrupted synaptic plasticity and neural activity in depression. Such alteration is strongly associated with disrupted synaptic structures. Chronic stress has been known to induce changes in dendritic structure in the basolateral amygdala (BLA) and medial prefrontal cortex (mPFC), but antidepressant effect on structure of these brain areas has been unclear. Here, the effects of imipramine on dendritic spine density and morphology in BLA and mPFC subregions of stressed mice were examined. Chronic restraint stress caused depressive-like behaviors such as enhanced social avoidance and despair level coincident with differential changes in dendritic spine structure. Chronic stress enhanced dendritic spine density in the lateral nucleus of BLA with no significant change in the basal nucleus of BLA, and altered the proportion of stubby or mushroom spines in both subregions. Conversely, in the apical and basal mPFC, chronic stress caused a significant reduction in spine density. The proportion of stubby or mushroom spines in these subregions overall reduced while the proportion of thin spines increased after repeated stress. Interestingly, most of these structural alterations by chronic stress were reversed by imipramine. In addition, structural changes caused by stress and blocking the changes by imipramine were corelated well with altered activation and expression of synaptic plasticity-promoting molecules such as phospho-CREB, phospho-CAMKII, and PSD-95. Collectively, our data suggest that imipramine modulates stress-induced changes in synaptic structure and synaptic plasticity-promoting molecules in a coordinated manner although structural and molecular alterations induced by stress are distinct in the BLA and mPFC.
Cannabis use among U.S. adolescents in the era of marijuana legalization: a review of changing use patterns, comorbidity, and health correlates

Abstract Decriminalization, medicalization, and legalization of cannabis use by a majority of U.S. states over the past 25 years have dramatically shifted societal perceptions and use patterns among Americans. How marijuana policy changes have affected population-wide health of U.S. youth and what the downstream public health implications of marijuana legalization are topics of significant debate. Cannabis remains the most commonly used federally illicit psychoactive drug by U.S. adolescents and is the main drug for which U.S. youth present for substance use treatment. Converging evidence indicates that adolescent-onset cannabis exposure is associated with short- and possibly long-term impairments in cognition, worse academic/vocational outcomes, and increased prevalence of psychotic, mood, and addictive disorders. Odds of negative developmental outcomes are increased in youth with early-onset, persistent, high frequency, and high-potency Δ-9-THC cannabis use, suggesting dose-dependent relationships. Cannabis use disorders are treatable conditions with clear childhood antecedents that respond to targeted prevention and early intervention strategies. This review indicates that marijuana policy changes have had mixed effects on U.S. adolescent health including potential benefits from decriminalization and negative health outcomes evidenced by increases in cannabis-related motor vehicle accidents, emergency department visits, and hospitalizations. Federal and state legislatures should apply a public health framework and consider the possible downstream effects of marijuana policy change on paediatric health.
Understanding the relative contribution of technical and tactical performance to match outcome in Australian Football

ABSTRACT The aim of this study was to assess if tactical and technical performance indicators (PIs) could be used in combination to model match outcomes in Australian Football (AF). A database of 101 technical PIs and 14 tactical PIs from every match in the 2009–2016 Australian Football League (AFL) seasons was merged. Two outcome measures Win-loss and Score margin were used as dependent variables. The top 45 ranked technical and tactical PIs from a feature selection process were used to model match outcome using decision tree and Generalised Linear Models (GLMs). Of the top 45 selected features, this included seven tactical PIs. The Win-loss-based Decision tree model achieved a classification accuracy of 89.0% and GLM 93.2%. A Score margin-based GLM achieved a root mean squared error (RMSE) of 6.9 points. A combined approach to the classification of match outcomes provided no improvement in model accuracy compared with previous literature. However, this study has established the relative importance of technical and tactical measures of performance in relation to successful team performance in AF.
Blueberry Juice Antioxidants Protect Osteogenic Activity against Oxidative Stress and Improve Long-Term Activation of the Mineralization Process in Human Osteoblast-Like SaOS-2 Cells: Involvement of SIRT1

Diets rich in fruits and vegetables with many antioxidants can be very important in the prevention and treatment of osteoporosis. Studies show that oxidative stress, often due to lack of antioxidants, is involved in alteration of bone remodeling and reduction in bone density. This study demonstrates in human osteoblast-like SaOS-2 cells that blueberry juice (BJ), containing 7.5 or 15 μg∙mL−1 total soluble polyphenols (TSP), is able to prevent the inhibition of osteogenic differentiation and the mineralization process due to oxidative stress induced by glutathione depletion. This situation mimics a metabolic condition of oxidative stress that may occur during estrogen deficiency. The effect of BJ phytochemicals occurs through redox- and non-redox-regulated mechanisms. BJ protects from oxidative damage factors related to bone remodeling and bone formation, such as alkaline phosphatase and Runt-related transcription factor 2. It upregulates these factors by activation of sirtuin type 1 deacetylase expression, a possible molecular target for anti-osteoporotic drugs. Quantitative analysis of TSP in BJ shows high levels of anthocyanins with high antioxidant capacity and bioavailability. These novel data may be important to elucidate the molecular and cellular beneficial effects of blueberry polyphenols on bone regeneration, and they suggest their use as a dietary supplement for osteoporosis prevention and therapies.
Molecular Pathway of Influenza Pan-neuraminidase Inhibitor Resistance in an Immunocompromised Patient

Background Neuraminidase (NA) inhibitors (NAIs), including oseltamivir and zanamivir, play an important therapeutic role against influenza infections in immunocompromised patients. In such settings, however, NAI therapy may lead to the emergence of resistance involving mutations within the influenza surface genes. The aim of this study was to investigate the evolution of NA and haemagglutinin (HA) genes of influenza A(H1N1) pdm09 virus in an immunocompromised patient receiving oseltamivir then zanamivir therapies. Methods Nasopharyngeal swab (NPS) samples were collected between 27 January 2018 and 11 April 2018 from a haematopoietic stem cell transplant recipient. These include 10 samples collected either pre-therapy, during oseltamivir and zanamivir treatment as well as after therapy. The A(H1N1)pdm09 HA/NA genes were sequenced. The H275Y NA substitution was quantified by droplet digital RT-PCR assay. A(H1N1)pdm09 recombinant viruses containing HA mutations were tested by HA elution experiments to investigate in vitro binding properties. Results Oseltamivir rapidly induced the H275Y NA mutation which constituted 98.33% of the viral population after 15 days of oseltamivir treatment. The related HA gene contained S135A and P183S substitutions within the receptor-binding site. After a switch to zanamivir, 275H/Y and 119E/G/D mixed populations were detected. In the last samples, the double H275Y-E119G NA variant dominated with S135A and P183S HA substitutions. Conclusions This report confirms that oseltamivir can rapidly induce the emergence of the H275Y substitution in A(H1N1)pdm09 viruses and subsequent switch to zanamivir can lead to additional substitutions at codon E119 resulting in multi-drug resistance. Such data additionally suggest a potential compensatory role for HA substitutions near the receptor binding site.
A-Kinase Anchoring Proteins Diminish TGF-β1/Cigarette Smoke-Induced Epithelial-To-Mesenchymal Transition

Epithelial-to-mesenchymal transition (EMT) plays a role in chronic obstructive pulmonary diseases (COPD). Cyclic adenosine monophosphate (cAMP) can inhibit transforming growth factor-β1 (TGF-β1) mediated EMT. Although compartmentalization via A-kinase anchoring proteins (AKAPs) is central to cAMP signaling, functional studies regarding their therapeutic value in the lung EMT process are lacking. The human bronchial epithelial cell line (BEAS-2B) and primary human airway epithelial (pHAE) cells were exposed to TGF-β1. Epithelial (E-cadherin, ZO-1) and mesenchymal markers (collagen Ӏ, α-SMA, fibronectin) were analyzed (mRNA, protein). ELISA measured TGF-β1 release. TGF-β1-sensitive AKAPs Ezrin, AKAP95 and Yotiao were silenced while using siRNA. Cell migration was analyzed by wound healing assay, xCELLigence, Incucyte. Prior to TGF-β1, dibutyryl-cAMP (dbcAMP), fenoterol, rolipram, cilostamide, and forskolin were used to elevate intracellular cAMP. TGF-β1 induced morphological changes, decreased E-cadherin, but increased collagen Ӏ and cell migration, a process that was reversed by the inhibitor of δ/epsilon casein kinase I, PF-670462. TGF-β1 altered (mRNA, protein) expression of Ezrin, AKAP95, and Yotiao. St-Ht31, the AKAP antagonist, decreased E-cadherin (mRNA, protein), but counteracted TGF-β1-induced collagen Ӏ upregulation. Cigarette smoke (CS) increased TGF-β1 release, activated TGF signaling, augmented cell migration, and reduced E-cadherin expression, a process that was blocked by TGF-β1 neutralizing antibody. The silencing of Ezrin, AKAP95, and Yotiao diminished TGF-β1-induced collagen Ӏ expression, as well as TGF-β1-induced cell migration. Fenoterol, rolipram, and cilostamide, in AKAP silenced cells, pointed to distinct cAMP compartments. We conclude that Ezrin, AKAP95, and Yotiao promote TGF-β1-mediated EMT, linked to a TGF-β1 release by CS. AKAP members might define the ability of fenoterol, rolipram, and cilostamide to modulate the EMT process, and they might represent potential relevant targets in the treatment of COPD.
Patient experience of preheated and room temperature skin disinfection prior to cardiac device implantation: A randomised controlled trial

Background: Clinically, patients often comment on the coolness of the skin disinfectant. However, scarce evidence is available regarding patients’ experience during intraoperative skin disinfection. Aims: The aim of this study was to describe and compare intraoperative patient experiences with preheated and room temperature skin disinfectant. Method: This randomised controlled trial included 220 patients undergoing cardiac device implantation. Patients allocated to preheated (36°C) or room temperature (20°C) chlorhexidine in 70% ethanol verbally answered an open-ended question regarding their experience with the skin disinfection. Results were assessed using a qualitative approach with comparative quantification. Results: The analysis resulted in nine categories describing the patients’ experiences with preheated and room temperature skin disinfection. Most of the patients described the skin disinfection process as a negative experience, which consisted of six categories: cold, smell, change in temperature, unpleasant, wet and painful. In addition, two neutral categories of response (nothing in particular and neither pleasant nor unpleasant) and one positive response (pleasant) emerged through the analysis. Preheated skin disinfection yielded significantly fewer negative experiences in the category cold (85% vs. 15%, P<0.0001) and significantly more positive experiences (66% vs. 34%, P<0.002). Neutral categories (neither pleasant nor unpleasant 65% vs. 35%, P=0.01, nothing in particular 74% vs. 26%, P<0.001) dominated after preheated skin disinfection. Conclusion: The use of preheated skin disinfection promotes a positive patient experience with skin disinfection. Trial registration: ClinicalTrials.gov registration number NCT02260479 (https://clinicaltrials.gov/ct2/results? cond=preheated+skin+disinfection).