Miracle-dz/UniFAR-FTUs huggingface dataset:
Novel Approaches in Fabrication and Integration of Nanowire for Micro/Nano Systems

Abstract Nanowires have been utilized widely in the generation of high-performance nanosensors. Laser ablation, chemical vapor, thermal evaporation and alternating current electrodeposition are in use in developing nanowires. Nanowires are in a great attention because of their submicron feature and their potentials in the front of nanoelectronics, accelerated field effect transistors, chemical- and bio-sensors, and low power consuming light-emitting devices. With the control of nanowire size and concentration of dopant, the electrical sensitivity and other properties of nanowires can be tuned for the reproducibility. Nanowires comprise of arrays of electrodes that form a nanometer electrical circuit. One of advantages of nanowires is that they can be fabricated in nanometer-size for various applications in different approaches. Several studies have been conducted on nanowires and researchers discovered that nanowires have the potential in the applications with material properties at the nanometer scale. The unique electrical properties of nanowires have made them to be promising for numerous applications. Nowadays, for example, MOS field-effect transistors are largely used as fundamental building elements in electronic circuits. Also, the dimension of MOS transistors is gradually decreasing to the nanoscale based on the prediction made by Moor's law. However, their fabrication is challenging. This review summarized different techniques in the fabrication of nanowires, global nanowire prospect, testing of nanowires to understand the real electrical behavior using higher resolution microscopes, and brief applications in the detection of biomolecules, disease such as corona viral pandemic, heavy metal in water, and applications of nanowires in agriculture.
Development of the cartilaginous connecting apparatuses in the fetal sphenoid, with a focus on the alar process

The human fetal sphenoid is reported to have a cartilaginous connecting apparatus known as the alar process (AP), which connects the ala temporalis (AT) (angle of the greater wing of the sphenoid) to the basisphenoid (anlage of the sphenoid body). However, how the AP develops in humans is unclear. In addition, although the AP is a common structure of the mammalian chondrocranium, little is known about whether it is really a fundamental feature in mammals. This study examined the histological sections of 20 human embryos and fetuses from 6 to 14 weeks of development, of 20 mouse embryos from embryonic days 12–18, and of 4 rats embryos form embryonic days 17 and 20. In addition, we reconsidered the definition of the AP by comparing humans and rats with mice. In humans, the AP was continuous with the basisphenoid but was separated from the AT by a thick perichondrium. Then, the AP–AT connection had a key-and-keyhole structure. Unlike a joint, no cavitation developed in this connection. In mice, there was no boundary between the AT and the basisphenoid, indicating the absence of the AP in the mouse chondrocranium. In rats, the AP was, however, separated from the AT by a thick perichondrium. Therefore, the AP can be defined as follows: the AP is temporally separated from the AT by a thick perichondrium or a key-and-keyhole structure during the fetal period. This is the first study that confirms the absence of the alar process in the mice skull, and its presence in other mammals skull should be further investigated.
From neglect to earlier diagnosis: a qualitative meta-synthesis of psycho-social factors associated with consultation delay in advanced basal cell carcinoma

ABSTRACT Local malignant potential of basal cell carcinoma (BCC) can lead at advanced stages to the destruction of underlying tissues and significant morbidity. The primary risk factor for progression of advanced basal cell carcinoma (aBCC) is the long duration of the tumour, which results from delay in seeking medical care. To assess the implication of psycho-social factors in the delay before the first medical consultation among patients with aBCC, in order to identify potentially targetable factors enabling earlier diagnosis. Three-step qualitative meta-synthesis: (1) systematic review of the literature; (2) structured qualitative analysis of these documents; (3) construction of a logical model. After screening, 81 articles were included. Self-neglect and denial in patients are roundly put forward as the main obstacles to consultation. We found that avoidance behaviour, mistaken interpretation and banalisation of symptoms, and fear of treatment all played a role. The strongest motivation to seek help comes from the realisation that new symptoms may be dangerous; the role of interpersonal surroundings is highlighted as helpful. Patient delay has multifactorial origins in aBCC, especially self-neglect ranging from denial of tumours to conscious refusal of treatment.
Hibernation-Promoting Factor Sequesters Staphylococcus aureus Ribosomes to Antagonize RNase R-Mediated Nucleolytic Degradation

Ribosome hibernation is pivotal for the rapid recovery of translation after quiescence in both bacteria and eukaryotes. Ribosome hibernation factors sterically occlude the entry of mRNA and tRNA and are thought to primarily maintain ribosomes in a translation-repressive state, thereby providing a pool of readily recyclable 70S or 80S complexes upon dissociation of the hibernation factors. ABSTRACT Bacterial and eukaryotic hibernation factors prevent translation by physically blocking the decoding center of ribosomes, a phenomenon called ribosome hibernation that often occurs in response to nutrient deprivation. The human pathogen Staphylococcus aureus lacking the sole hibernation factor HPF undergoes massive ribosome degradation via an unknown pathway. Using genetic and biochemical approaches, we find that inactivating the 3′-to-5′ exonuclease RNase R suppresses ribosome degradation in the Δhpf mutant. In vitro cell-free degradation assays confirm that 30S and 70S ribosomes isolated from the Δhpf mutant are extremely susceptible to RNase R, in stark contrast to nucleolytic resistance of the HPF-bound 70S and 100S complexes isolated from the wild type. In the absence of HPF, specific S. aureus 16S rRNA helices are sensitive to nucleolytic cleavage. These RNase hot spots are distinct from that found in the Escherichia coli ribosomes. S. aureus RNase R is associated with ribosomes, but unlike the E. coli counterpart, it is not regulated by general stressors and acetylation. The results not only highlight key differences between the evolutionarily conserved RNase R homologs but also provide direct evidence that HPF preserves ribosome integrity beyond its role in translational avoidance, thereby poising the hibernating ribosomes for rapid resumption of translation. IMPORTANCE Ribosome hibernation is pivotal for the rapid recovery of translation after quiescence in both bacteria and eukaryotes. Ribosome hibernation factors sterically occlude the entry of mRNA and tRNA and are thought to primarily maintain ribosomes in a translation-repressive state, thereby providing a pool of readily recyclable 70S or 80S complexes upon dissociation of the hibernation factors. Ribosomes in Staphylococcus aureus cells lacking the sole hibernation factor HPF are extremely unstable. Here, we show that HPF binding inhibits ribosome degradation by the evolutionarily conserved exoribonuclease RNase R. The data not only uncover a direct protective role of HPF in ribosome stability but also reinforce the versatility of RNase R in RNA processing, decay, and ribosome quality control.
The effectiveness of eye tracking in the diagnosis of cognitive disorders: A systematic review and meta-analysis

Background Eye tracking (ET) is a viable marker for the recognition of cognitive disorders. We assessed the accuracy and clinical value of ET for the diagnosis of cognitive disorders in patients. Methods We searched the Medline, Embase, Web of Science, Cochrane Library, and Pubmed databases from inception to March 2, 2021, as well as the reference lists of identified primary studies. We included articles written in English that investigated ET for cognitive disorder patients—Mild cognitive impairment (MCI), Alzheimer’s disease (AD), Amyotrophic lateral sclerosis (ALS), and dementia. Two independent researchers extracted the data and the characteristics of each study; We calculated pooled sensitivities and specificities. A hierarchical summary of receiver performance characteristics (HSROC) model was used to test the diagnostic accuracy of ET for cognitive impairment (CI). Findings 11 studies met the inclusion criteria and were included in qualitative comprehensive analysis. Meta-analysis was performed on 9 trials using Neuropsychological Cognitive Testing (NCT) as the reference standard. The comprehensive sensitivity and specificity of ET for detecting cognitive disorders were 0.75 (95% CI 0.72–0.79) and 0.73 (95% CI 0.70 to 0.76), respectively. The combined positive likelihood ratio (LR+) was 2.74 (95%CI 2.32–3.24) and the negative likelihood ratio (LR−) was 0.27 (95%CI 0.18–0.42). Conclusions This review showed that ET technology could be used to detect the decline in CI, clinical use of ET techniques in combination with other tools to assess CI can be encouraged.
Understanding and predicting COVID-19 clinical trial completion vs. cessation

As of March 30 2021, over 5,193 COVID-19 clinical trials have been registered through Clinicaltrial.gov. Among them, 191 trials were terminated, suspended, or withdrawn (indicating the cessation of the study). On the other hand, 909 trials have been completed (indicating the completion of the study). In this study, we propose to study underlying factors of COVID-19 trial completion vs. cessation, and design predictive models to accurately predict whether a COVID-19 trial may complete or cease in the future. We collect 4,441 COVID-19 trials from ClinicalTrial.gov to build a testbed, and design four types of features to characterize clinical trial administration, eligibility, study information, criteria, drug types, study keywords, as well as embedding features commonly used in the state-of-the-art machine learning. Our study shows that drug features and study keywords are most informative features, but all four types of features are essential for accurate trial prediction. By using predictive models, our approach achieves more than 0.87 AUC (Area Under the Curve) score and 0.81 balanced accuracy to correctly predict COVID-19 clinical trial completion vs. cessation. Our research shows that computational methods can deliver effective features to understand difference between completed vs. ceased COVID-19 trials. In addition, such models can also predict COVID-19 trial status with satisfactory accuracy, and help stakeholders better plan trials and minimize costs.
A novel reversed-phase liquid chromatographic method for the simultaneous determination of potential impurities of bisoprolol fumarate and hydrochlorothiazide in a fixed dosage form

ABSTRACT In the present study 12 impurities of bisoprolol fumarate (BISO) and hydrochlorothiazide (HCTZ) were separated simultaneously in a single HPLC method. Out of these 12 impurities, five are potential degradants, which are validated as per The International Council for Harmonisation of Technical Requirements for Pharmaceuticals for Human Use (ICH) guidelines. As the two active drug substances BISO and HCTZ have different solubilities and polarities, the most critical parameters in resolving the components from each other are pH, temperature, and solvents. The method is precise (RSD < 1.0%), accurate, linear (r2 > 0.999), robust, and stability indicating in the range of limit of quantification (LOQ) to 150%. The HPLC method is then migrated to ultra-performance liquid chromatography (UPLC) to further reduce the run time and solvent consumption, and increase the sample throughput.
Characterization of a member of the CEACAM protein family as a novel marker of proton pump-rich ionocytes on the zebrafish epidermis

In humans, several members of the CEACAM receptor family have been shown to interact with intestinal pathogens in an inflammatory context. While CEACAMs have long been thought to be only present in mammals, recent studies have identified ceacam genes in other vertebrates, including teleosts. The function of these related genes remains however largely unknown. To gain insight into the function of CEACAM proteins in fish, we undertook the study of a putative member of the family, CEACAMz1, identified in Danio rerio. Sequence analysis of the ceacamz1 gene product predicted a GPI-anchored extracellular protein containing eleven immunoglobulin domains but revealed no evident orthology with human CEACAMs. Using a combination of RT-PCR analyses and in situ hybridization experiments, as well as a fluorescent reporter line, we showed that CEACAMz1 is first expressed in discrete cells on the ventral skin of zebrafish larvae and later on in the developing gills. This distribution remains constant until juvenile stage is reached, at which point CEACAMz1 is almost exclusively expressed in gills. We further observed that at late larval stages, CEACAMz1-expressing cells mostly localize on the afferent side of the branchial filaments and possibly in the inter-lamellar space. Using immunolabelling and 3D-reconstructions, we showed that CEACAMz1 is expressed in cells from the uppermost layer of skin epidermis. These cells are embedded within the keratinocytes pavement and we unambiguously identified them as proton-pump rich ionocytes (HR cells). As the expression of ceacamz1 is turned on concomitantly to that of other known markers of HR cells, we propose that ceacamz1 may serve as a novel marker of mature HR cells from the zebrafish epidermis.
Weakly supervised learning of RNA modifications from low-resolution epitranscriptome data

Abstract Motivation Increasing evidence suggests that post-transcriptional ribonucleic acid (RNA) modifications regulate essential biomolecular functions and are related to the pathogenesis of various diseases. Precise identification of RNA modification sites is essential for understanding the regulatory mechanisms of RNAs. To date, many computational approaches for predicting RNA modifications have been developed, most of which were based on strong supervision enabled by base-resolution epitranscriptome data. However, high-resolution data may not be available. Results We propose WeakRM, the first weakly supervised learning framework for predicting RNA modifications from low-resolution epitranscriptome datasets, such as those generated from acRIP-seq and hMeRIP-seq. Evaluations on three independent datasets (corresponding to three different RNA modification types and their respective sequencing technologies) demonstrated the effectiveness of our approach in predicting RNA modifications from low-resolution data. WeakRM outperformed state-of-the-art multi-instance learning methods for genomic sequences, such as WSCNN, which was originally designed for transcription factor binding site prediction. Additionally, our approach captured motifs that are consistent with existing knowledge, and visualization of the predicted modification-containing regions unveiled the potentials of detecting RNA modifications with improved resolution. Availability implementation The source code for the WeakRM algorithm, along with the datasets used, are freely accessible at: https://github.com/daiyun02211/WeakRM Supplementary information Supplementary data are available at Bioinformatics online.
Cyclic Voltammetry of the EC′ Mechanism at Hemispherical Particles and Their Arrays: The Split Wave

The EC′ (catalytic) mechanism, (1) A + e– ⇌ B; (2) B + X → K2 A + P, in which the reduction of ‘X’ to ‘P’ is mediated by the A/B redox couple, is studied at a regularly distributed array of hemispherical particles on a planar surface using simulated cyclic voltammetry. It is assumed that the supporting surface itself is not electroactive and therefore the electron transfer in process (1) occurs exclusively on the surface of the particles. Two-dimensional finite difference simulations are performed for a range of scan rates, particle surface coverages, and second-order rate constants, K2. Additionally, for the case of an isolated particle, the effect of the concentration of reactant species ‘X’ is also examined. Particular attention is paid to the ‘split-wave’ phenomenon, where two peaks are observed in the forward scan of a cyclic voltammogram, which tends to occur when the values of [A] and [X] are similar and the second-order rate constant, K2, is relatively high. The conditions under which two peaks ar.
Validity and reliability of the Swedish version of the Self-Efficacy for Managing Chronic Disease scale for individuals with systemic sclerosis

Objective To investigate aspects of validity and reliability of the Swedish version of the Self-Efficacy for Managing Chronic Disease (SEMCD-Swe) scale in systemic sclerosis (SSc). Method A forward–backward translation procedure was used. Content validity was assessed through interviews with 11 people with SSc and 10 healthcare professionals. Construct validity, internal consistency, test–retest reliability, and floor and ceiling effects were evaluated in 104 SSc patients. Results The content validity of the SEMCD-Swe was interpreted as satisfactory, but some adjustments were made to increase the understanding. Confirmatory factor analysis supported a single-factor structure. Moderate to strong correlations between the SEMCD-Swe and Scleroderma Health Assessment Questionnaire; Multidimensional Assessment of Fatigue; Patient Health Questionnaire-8 (rs = −0.4 to −0.7), and RAND-36 subscales (rs = 0.5 to 0.7) were found. Weak correlations were found between SEMCD-Swe and modified Rodnan skin score; and disease severity of peripheral vascular and lung (rs = −0.1 to −0.2) and kidney (rs = 0.1) systems (Medsger severity scale). Cronbach’s alpha was sufficient (0.85) and corrected item-to-total correlations were good (≥ 0.50). The intraclass correlation coefficient for the total score was sufficient (0.82). No floor or ceiling effects were found. Conclusion Support for construct validity was indicated, as the SEMCD-Swe in SSc show a single-factor structure and is more strongly associated with pain, fatigue, depressive symptoms, interferences with daily activities, disability, and quality of life than with disease severity. Our results also indicate support for content validity and reliability. However, the responsiveness of the SEMCD-Swe needs to be tested.
Metaball skinning of synthetic astroglial morphologies into realistic mesh models for in silico simulations and visual analytics

Abstract Motivation Astrocytes, the most abundant glial cells in the mammalian brain, have an instrumental role in developing neuronal circuits. They contribute to the physical structuring of the brain, modulating synaptic activity and maintaining the blood–brain barrier in addition to other significant aspects that impact brain function. Biophysically, detailed astrocytic models are key to unraveling their functional mechanisms via molecular simulations at microscopic scales. Detailed, and complete, biological reconstructions of astrocytic cells are sparse. Nonetheless, data-driven digital reconstruction of astroglial morphologies that are statistically identical to biological counterparts are becoming available. We use those synthetic morphologies to generate astrocytic meshes with realistic geometries, making it possible to perform these simulations. Results We present an unconditionally robust method capable of reconstructing high fidelity polygonal meshes of astroglial cells from algorithmically-synthesized morphologies. Our method uses implicit surfaces, or metaballs, to skin the different structural components of astrocytes and then blend them in a seamless fashion. We also provide an end-to-end pipeline to produce optimized two- and three-dimensional meshes for visual analytics and simulations, respectively. The performance of our pipeline has been assessed with a group of 5000 astroglial morphologies and the geometric metrics of the resulting meshes are evaluated. The usability of the meshes is then demonstrated with different use cases. Availability and implementation Our metaball skinning algorithm is implemented in Blender 2.82 relying on its Python API (Application Programming Interface). To make it accessible to computational biologists and neuroscientists, the implementation has been integrated into NeuroMorphoVis, an open source and domain specific package that is primarily designed for neuronal morphology visualization and meshing. Supplementary information Supplementary data are available at Bioinformatics online.
Wild garlic extract reduces lipid peroxidation in terbuthylazine-treated human erythrocytes

Abstract Background: Among other negative effects, herbicides induce oxidative stress, leading to lipid peroxidation and protein oxidation. Therefore, there is a growing need to identify natural compounds with sufficient antioxidant capacity and mitigate the negative effects of herbicides without side effects. Objective: Our study aimed to examine the protective effect of the phenolic extract of wild garlic (WG) leaves on terbuthylazine-treated erythrocytes. Material and methods: In human erythrocytes treated with the herbicide terbuthylazine (4.5 mg/L) alone and a combination of terbuthylazine and WG extract, we measured malondialdehyde (MDA) and haemoglobin (Hb) concentrations and the antioxidant activities of CuZn superoxide dismutase (SOD1; EC 1.15.1.1) and catalase (CAT; EC 1.11.1.6) in vitro. Results: In comparison with terbuthylazine, WG extract reduced the concentrations of MDA and Hb from 59.69 to 43.45 nmol/gHb (27%, p < 0.001) and 165.08 to 128.64 g/L (22%, p < 0.05), respectively. Catalase activity was induced for samples treated with both WG extract and terbuthylazine compared with terbuthylazine alone (p < 0.05). Conclusions: The results demonstrated that WG may reduce the toxicity of terbuthylazine, and the erythrocyte membrane may be the primary site of phenolic action. Therefore, the lipid peroxidation intensity could be a biomarker of oxidative damage caused by terbuthylazine and the protective effect of WG.
Users’ experience of community-based power assisted exercise: a transition from NHS to third sector services

ABSTRACT Purpose Seated Power Assisted Exercise (PAE) equipment is an accessible exercise mode for people with limited mobility following stroke and is available at a small number of community-based venues. The purpose of this qualitative study was to understand the lived experience of using PAE amongst PwS in a community venue and identify recommendations for the development and advancement of PAE equipment. Method Semi-structured interviews were conducted with 8 participants (PwS) attending a community stroke venue where PAE equipment was available. Transcribed data were analysed using interpretative phenomenological analysis. Results Three overarching themes emerged from the analysis; 1) Don’t tell me I’ve plateaued; 2) PAE facilitates the transition into long-term recovery; 3) Reframing the experience of stroke. Participants associated the uptake of PAE alongside venue membership as a turning point in their adjustment to life following stroke. In addition, recommendations for future development of the equipment were identified. Conclusion These findings indicate that membership of a stroke venue alongside engagement with PAE facilitated transition from early stroke rehabilitation into longer term recovery. The results of this study have informed the need for future product design and highlighted PAE is an effective mode for continued rehabilitation in third-sector services.