Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of Ion Torrent next-generation sequencing for thalassemia diagnosis

Introduction To evaluate a next-generation sequencing (NGS) workflow in the screening and diagnosis of thalassemia. Methods In this prospective study, blood samples were obtained from people undergoing genetic screening for thalassemia at our centre in Guangzhou, China. Genomic DNA was polymerase chain reaction (PCR)-amplified and sequenced using the Ion Torrent system and results compared with traditional genetic analyses. Results Of the 359 subjects, 148 (41%) were confirmed to have thalassemia. Variant detection identified 35 different types including the most common. Identification of the mutational sites by NGS were consistent with those identified by Sanger sequencing and Gap-PCR. The sensitivity and specificities of the Ion Torrent NGS were 100%. In a separate test of 16 samples, results were consistent when repeated ten times. Conclusion Our NGS workflow based on the Ion Torrent sequencer was successful in the detection of large deletions and non-deletional defects in thalassemia with high accuracy and repeatability.
Leaf apoplastic alkalization promotes transcription of the ABA-synthesizing enzyme Vp14 and stomatal closure in Zea mays

Abstract The chloride component of NaCl salinity causes the leaf apoplast to transiently alkalinize. This transition in pH reduces stomatal aperture. However, whether this apoplastic pH (pHapo) transient initiates stomatal closure by interacting with other chloride stress-induced responses or whether the pH transient alone initiates stomatal closure is unknown. To clarify the problem, the transient alkalinization of the leaf apoplast was mimicked in intact maize (Zea mays L.) by infiltrating near-neutral pH buffers into the leaf apoplast. Effects of the pHapo transient could thus be investigated independently from other chloride stress-derived effects. Microscopy-based ratiometric live pHapo imaging was used to monitor pHapoin planta. LC-MS/MS and real-time quantitative reverse transcription–PCR leaf analyses showed that the artificially induced pHapo transient led to an increase in the concentrations of the stomata-regulating plant hormone abscisic acid (ABA) and in transcripts of the key ABA-synthesizing gene ZmVp14 in the leaf. Since stomatal aperture and stomatal conductance decreased according to pHapo, we conclude that the pHapo transient alone initiates stomatal closure. Therefore, the functionality does not depend on interactions with other compounds induced by chloride stress. Overall, our data indicate that the pH of the leaf apoplast links chloride salinity with the control of stomatal aperture via effects exerted on the transcription of ABA.
Socio-Ecological Predictors of Resilience Development Over Time Among Youth With a History of Maltreatment

While there is a growing body of research examining resilient development in adolescents with a history of maltreatment, it remains unclear whether youth resilient functioning changes over time and what factors predict such change. The current study aimed to identify the socio-ecological predictors of the change in resilient functioning over time among adolescents with a history of maltreatment. Multinomial logistic regression analyses were conducted with a sample of 771 adolescents drawn from the National Survey of Child and Adolescent Well-Being (NSCAW-II). Over 18 months, 23.2% of the adolescents remained in the less resilience group, 45.4% stayed in the greater resilience group, 17.4% moved from the greater resilience group to the less resilience group, and 14.0% moved from the less resilience group to the greater resilience group. Younger age, better parent-child relationship quality, and neighborhood safety were associated with stable and continued resilient functioning over time. Conversely, child physical abuse, affiliation with deviant peers, and receipt of behavioral services were negatively associated with continued resilience. Our findings suggest that interventions that support adolescents in building positive relationships with their parents and peers may prevent a loss of resilience over time and ensure continued resilient functioning in child welfare-involved adolescents.
Cognitive deficits among patients surviving aneurysmal subarachnoid hemorrhage. A contemporary systematic review

Abstract Background Subarachnoid hemorrhage (SAH) is associated with high rates of morbidity, including neurological and cognitive deficits that may be difficult to identify and quantify. This review provides an update on the cognitive deficits that may result from spontaneous aneurysmal SAH (aSAH) and identifies factors that may help predict and manage these deficits at discharge and thereafter. Materials and Methods We conducted a systematic review of PubMed and Google Scholar to identify studies published between 2010 and 2019 that assessed cognitive deficits at discharge and during follow-up in patients with aSAH. Full-text articles were assessed for information regarding cognitive testing and factors that may be associated with functional outcomes in this population. Results We reviewed 65 studies published since 2010 that described the cognitive deficits associated with non-traumatic aSAH. Such deficits may impact functional outcomes, quality of life, and return to work and may result in cognitive impairments, such as memory difficulties, speech problems, and psychiatric disorders. Conclusions Patients with aSAH, even those that appear normal at the time of hospital discharge, may harbor cognitive deficits that are difficult to detect, yet can interfere with daily functioning. Further research is needed to provide additional information and to identify stronger correlations to be used in the identification, treatment, and amelioration of long-term cognitive deficits in aSAH patients, including those who are discharged with good clinical outcomes scores.
Individual differences in sensitivity to the early environment as a function of amygdala and hippocampus volumes: An exploratory analysis in 12-year-old boys

Abstract Children differ in their response to environmental exposures, with some being more sensitive to contextual factors than others. According to theory, such variability is the result of individual differences in neurobiological sensitivity to environmental features, with some individuals generally more affected by both negative and/or positive experiences. In this exploratory study we tested whether left and right amygdala and hippocampus volumes (corrected for total brain size) account for individual differences in response to environmental influences in a sample of 62 boys. Cumulative general environmental quality, ranging from low to high, was measured across the first 9 years and child behavior was reported by teachers when boys were 12–13 years old. According to analyses, only the left amygdala volume – not any of the other brain volumes – emerged as an important brain region for sensitivity to positive environmental aspects. Boys with a larger left amygdala benefited significantly more from higher environmental quality than boys with a smaller left amygdala whilst not being more vulnerable to lower quality. Besides providing preliminary evidence for differences in environmental sensitivity due to brain structure, the results also point to the left amygdala as having a specific role regarding the response to environmental influences.
Statistical optimization of hyaluronic acid enriched ultradeformable elastosomes for ocular delivery of voriconazole via Box-Behnken design: in vitro characterization and in vivo evaluation

Abstract Voriconazole (VCZ) is a well-known broad spectrum triazole antifungal, mainly used orally and intravenously. The study aimed to formulate VCZ into ultradeformable elastosomes for the topical treatment of ocular fungal keratitis. Different formulae were prepared using a modified ethanol injection method, employing a 33 Box-Behnken design. They were characterized by measuring their entrapment efficiency (EE%), particle size (PS), polydispersity index (PDI) and zeta potential (ZP). The optimized formula was subjected to further in vitro investigations and in vivo evaluation studies. The prepared vesicles had satisfactory EE%, PS, PDI and ZP values. The numerical optimization process suggested an optimal elastosomal formula (OE) composed of phosphatidyl choline and brij S100 at the weight ratio of 3.62: 1, 0.25%w/v hyaluronic acid and 5% (percentage from phosphatidyl choline/brij mixture) polyvinyl alcohol. It had high EE (72.6%), acceptable PS and PDI (362.4 nm and 0.25, respectively) and highly negative ZP of −41.7 mV. OE exhibited higher elasticity than conventional liposomes, with acceptable stability for three months. Transmission electron microscopy demonstrated the spherical morphology of vesicles with an external transparent coat of Hyaluronic acid. OE was expected to cause no ocular irritation or blurring in vision as reflected by pH and refractive index measurements. The histopathological study revealed the safety of OE for ocular use. The fungal susceptibility testing using Candida albicans demonstrated the superiority of OE to VCZ suspension, with greater and more durable growth inhibition. Therefore, OE can be regarded as a promising formula, achieving both safety and efficacy.
Exploring the ontogenetic development of the inner ear in Aardvarks

The aardvark is the last living Tubulidentata, an order of afrotherian mammals. Afrotheria is supported strongly by molecular analyses, yet sparingly by morphological characters. Moreover, the biology of the aardvark remains incompletely known. The inner ear, and its ontogeny in particular, has not been studied in details yet, though it bears key ecomorphological characters and phylogenetical signal. The aim of this study is to decipher and discuss the ontogenetic development of the different areas of the inner ear of Orycteropus afer. We focused in particular on their relative size and morphological rates of development. Specimens were scanned with 3D imaging techniques. 3D and 2D geometric morphometrics coupled with qualitative descriptions of the petrosal ossification allowed us to evidence several stages through development. Based on our sample, the cochlea is the first structure of the inner ear to reach adult size, but it is the last one to acquire its adult morphology close to parturition. In contrast, after a delayed growth spurt, the semicircular canals reach their mature morphology before the cochlea, concomitantly with the increase of petrosal ossification. The ontogeny of the aardvark inner ear shows similarities with that of other species, but the apex of the cochlea presents some autapomorphies.
Obesity, dyslipidemia, and high blood pressure are associated with cardiovascular risk, determined using high-sensitivity C-reactive protein concentration, in young adults

Objective Few studies have investigated the relationships between high-sensitivity C-reactive protein (hs-CRP) concentration and conventional cardiometabolic markers in young adults. The aim of this study was to characterize the cardiometabolic profile of young adults who are at high cardiovascular risk, according to hs-CRP concentration. Methods A cross-sectional study was conducted in 300 young adults (18 to 30 years old) from southern Mexico (n = 150 normal-weight and n = 150 obese). Their circulating lipid and glucose concentrations were measured using colorimetric enzymatic assays, and their hs-CRP, ApoA, and ApoB concentrations were measured using turbidimetric assays. Results The most prevalent abnormalities in the participants with high cardiovascular risk, determined using an hs-CRP >28.57 nmol/L, were high waist circumference (85.7%), obesity (83.9%), high low-density lipoprotein-cholesterol (64.3%), low high-density lipoprotein-cholesterol (50%), Apo B in the highest tertile (39.3%), hypertriglyceridemia (35.7%), and high blood pressure (30.4%). In addition, there were strong associations between hs-CRP >28.57 nmol/L and obesity (odds ratio [OR] = 13.9), high waist circumference (OR = 8.0), hypertriglyceridemia (OR = 4.0), high blood pressure (OR = 3.4), hypercholesterolemia (OR = 2.8), and Apo B in the highest tertile (OR = 2.4). Conclusion The principal cardiometabolic alterations associated with high cardiovascular risk, determined using hs-CRP, are obesity, dyslipidemia, and high blood pressure in young adults.
In silico analysis of kiss2, expression studies and protein–protein interaction with gonadotropin-releasing hormone 2 (GnRH2) and luteinizing hormone beta (LHβ) in Heteropneustes fossilis

Abstract Kisspeptins, encoded by the kiss genes, are neuropeptides that regulate the onset of puberty, maturation of gonads, and fertility in higher vertebrates including fishes. The gene ontology suggests that kisspeptin plays an important role not only in reproduction but also in cell signaling, immune response and metabolic processes, and to decipher protein–protein interactions, computational approach has been favored. The present investigation focuses on the detailed structural analysis and molecular docking of kiss2 gene using in silico tools. A putative kiss2 protein of 113 amino acids was encoded by an open reading frame of 342 bp kiss2 gene. The protein is of 13.12 kDa with isoelectric point of 9.45. The secondary structure of the protein indicates more than 50% random coils, followed by 34% of alpha helix and 13% extended strand. The protein was found to be extracellular and secretory in nature. Since, protein–protein interactions play a very crucial role in every cellular process and due to unavailability of crystal structure of our protein of interest in fishes computational approach has been employed. The 3D PDB modeling and the molecular docking of kiss2, Gonadotropin-releasing hormone 2 (GnRH2) and luteinizing hormone beta (LHβ) proteins in fishes have been demonstrated applying protein-docking approach. Molecular interactions of kiss2 protein were the highest with kisspeptin receptor 2 and lowest for the neuropeptide FF-amide peptide precursor protein. Expression of kiss2 transcripts, mainly in the brain and ovary of H. fossilis, supports its hypothalamic–pituitary–gonadal axis signaling and reproductive function. Further, changes in expression patterns of kiss2 mRNA during different developmental stages, indicate its potential role in embryonic development also. The present study conclusively reveals interaction of kiss2 with other neuropeptides. Prediction of binding structures and identification of key residues in protein–protein interaction illustrate direct interaction among these proteins, playing a cardinal role in neuroendocrine regulation of reproduction in catfish. Communicated by Ramaswamy H. Sarma
De novo small deletion affecting transcription start site of short isoform of AUTS2 gene in a patient with syndromic neurodevelopmental defects

Disruption of the autism susceptibility candidate 2 (AUTS2) gene through genomic rearrangements, copy number variations (CNVs), and intragenic deletions and mutations, has been recurrently involved in syndromic forms of developmental delay and intellectual disability, known as AUTS2 syndrome. The AUTS2 gene plays an important role in regulation of neuronal migration, and when altered, associates with a variable phenotype from severely to mildly affected patients. The more severe phenotypes significantly correlate with the presence of defects affecting the C‐terminus part of the gene. This article reports a new patient with a syndromic neurodevelopmental disorder, who presents a deletion of 30 nucleotides in the exon 9 of the AUTS2 gene. Importantly, this deletion includes the transcription start site for the AUTS2 short transcript isoform, which has an important role in brain development. Gene expression analysis of AUTS2 full‐length and short isoforms revealed that the deletion found in this patient causes a remarkable reduction in the expression level, not only of the short isoform, but also of the full AUTS2 transcripts. This report adds more evidence for the role of mutated AUTS2 short transcripts in the development of a severe phenotype in the AUTS2 syndrome.
The impact of empowerment and technology on safety behavior: evidence from mining companies

Major technological advances that are being introduced in the global mining industry have an impact on work and employee attitudes toward safety. The objective of this study was to analyze the impact of empowerment and technology on safety behavior. The research design was cross-sectional, and the sample was composed of 403 employees in mining companies. To measure safety behavior we used Neal, Griffin and Hart scales, and psychological empowerment was measured using the Spreitzer scale. The results indicated high levels of empowerment on safety behavior and medium levels of technology’s promotion and prevention factors in the employees surveyed. Also, the study revealed that the meaning dimension of empowerment and the promotion technology factor positively affect safety behavior. A further contribution of the study is in the design of a scale to measure the impact of technology on safety behavior, as there are no known scales for this.
Antibacterial effects of the lectin from pomegranate sarcotesta (PgTeL) against Listeria monocytogenes

To investigate the effects of the lectin from Punica granatum sarcotesta (PgTeL) on growth, viability, cell structure, biofilm formation and chitinase activity of Listeria monocytogenes. In addition, the effect of PgTeL on the adhesion and invasion of human cells (HeLa) was determined.
The SARS-CoV-2 Cytopathic Effect Is Blocked by Lysosome Alkalizing Small Molecules

Understanding the SARS-CoV-2 virus’ pathways of infection, virus–host–protein interactions, and mechanisms of virus-induced cytopathic effects will greatly aid in the discovery and design of new therapeutics to treat COVID-19. Chloroquine and hydroxychloroquine, extensively explored as clinical agents for COVID-19, have multiple cellular effects including alkalizing lysosomes and blocking autophagy as well as exhibiting dose-limiting toxicities in patients. Therefore, we evaluated additional lysosomotropic compounds to identify an alternative lysosome-based drug repurposing opportunity. We found that six of these compounds blocked the cytopathic effect of SARS-CoV-2 in Vero E6 cells with half-maximal effective concentration (EC50) values ranging from 2.0 to 13 μM and selectivity indices (SIs; SI = CC50/EC50) ranging from 1.5- to >10-fold. The compounds (1) blocked lysosome functioning and autophagy, (2) prevented pseudotyped particle entry, (3) increased lysosomal pH, and (4) reduced (ROC-325) viral titers in the EpiAirway 3D tissue model. Consistent with these findings, the siRNA knockdown of ATP6V0D1 blocked the HCoV-NL63 cytopathic effect in LLC-MK2 cells. Moreover, an analysis of SARS-CoV-2 infected Vero E6 cell lysate revealed significant dysregulation of autophagy and lysosomal function, suggesting a contribution of the lysosome to the life cycle of SARS-CoV-2. Our findings suggest the lysosome as a potential host cell target to combat SARS-CoV-2 infections and inhibitors of lysosomal function could become an important component of drug combination therapies aimed at improving treatment and outcomes for COVID-19.
Beyond Openness to Experience and Conscientiousness: Testing links between lower-level personality traits and American political orientation.

INTRODUCTION Research has consistently revealed positive correlations between political liberalism and Openness to Experience, and between conservatism and Conscientiousness. Most of this research has made use of domain-level models of the Big Five personality traits. Recent work suggests, however, that each Big Five trait domain can be divided into distinct aspects or facets, which offer more nuanced characterizations of each trait. METHODS Across four studies (Ns ranging from 1,123 to 116,406), the present research examined the degree to which distinct lower-level traits would be associated with meaningful differences in political orientation. United States residents completed two different hierarchical Big Five personality measures (the Big Five Aspect Scales and the Big Five Inventory-2), as well as a range of measures of political orientation. RESULTS Across both personality measures, liberal political orientation showed distinct positive associations with the lower-level traits Openness/Aesthetic Sensitivity, Intellect/Intellectual Curiosity, Compassion, and Withdrawal/Depression, as well as distinct negative associations with Orderliness/Organization, Politeness, and Assertiveness. DISCUSSION By examining individual differences at a higher level of granularity, these data provide insight into specific motivations that predispose individuals toward different ends of the political spectrum.
PROTONIZABLE WATER MODEL FOR QUANTUM DYNAMICAL SIMULATIONS

A new functional form for describing proton transfer and hydrogen bond potential energy functions in condensed phase simulations is presented. Rather than fitting a potential energy function to ab initio or experimental potential energy profiles, monopole-dipole interactions are used as proton-protolyte pair potential, and Lennard-Jones functions with variable σand -parameters are used to represent protolyte-proton-protolyte three body interactions. The number of parameters increases linearly with the number of protonizable molecule or molecular fragment types, and only eight parameters are needed per protonizable molecule or molecular fragment type. A parameter set for protonizable SPC/E water is presented, and the results of molecular dynamics (MD) and mixed quantum dynamics (QD)/MD simulations are discussed.
Predicting Secukinumab Fast-Responder Profile in Psoriatic Patients: Advanced Application of Artificial-Neural-Networks (ANNs).

BACKGROUND Drug resistance to biologics in psoriasis therapy can occur – it may be acquired during a treatment or else present itself from the beginning. To date, no biomarkers are known that may reliably guide clinicians in predicting responsiveness to biologics. Biologics may pose a substantial economic burden. Secukinumab efficiently targets IL-17 in the treatment of psoriasis. OBJECTIVE To assess the “fast responder” patient profile, predicting it from the preliminary complete blood count (CBC) and clinical examination. MATERIALS AND METHODS From November 2016 to May 2017 we performed a multicenter prospective open label pilot study in three Italian reference centers enrolling bio-naive plaque psoriasis patients, undergoing the initiation phase secukinumab treatment (300mg subcutaneous at week 0,1,2,3,4). We define fast responders as patients having achieved at least PASI 75 at the end of secukinumab induction phase. Clinical and CBC data at week 0 and at week 4 were analyzed with linear statistics, principal component analysis, and artificial neural networks (ANNs), also known as deep learning. Two different ANNs were employed: Auto Contractive Map (Auto-CM), an unsupervised ANNs, to study how this variables cluster and a supervised ANNs, Training with Input Selection and Testing (TWIST), to build the predictive model. RESULTS We enrolled 23 plaque psoriasis patients: 19 patients were responders and 4 were non-responders. 30 attributes were examined by Auto-CM, creating a semantic map for three main profiles: responders, non-responders and an intermediate profile. The algorithm yielded 5 of the 30 attributes to describe the 3 profiles. This allowed us to set up the predictive model. It displayed after training testing protocol an overall accuracy of 91.88% (90% for responders and 93,75% for non-responders). CONCLUSIONS The present study is possibly the first approach employing ANNs to predict drug efficacy in dermatology; a wider use of ANNs may be conducive to useful both theoretical and clinical insight. J Drugs Dermatol. 2020;19(12) doi:10.36849/JDD.2020. 5006.