Miracle-dz/UniFAR-FTUs huggingface dataset:
Probing RNA structures and functions by solvent accessibility: an overview from experimental and computational perspectives

Abstract Characterizing RNA structures and functions have mostly been focused on 2D, secondary and 3D, tertiary structures. Recent advances in experimental and computational techniques for probing or predicting RNA solvent accessibility make this 1D representation of tertiary structures an increasingly attractive feature to explore. Here, we provide a survey of these recent developments, which indicate the emergence of solvent accessibility as a simple 1D property, adding to secondary and tertiary structures for investigating complex structure–function relations of RNAs.
Different Exercise Time on 5-HT and Anxiety-like Behavior in the Rat With Vascular Dementia

Background Previous studies have demonstrated that pre-exercise suppresses anxiety-like behavior, but the effects of different exercise times on vascular dementia induced anxiety-like behavior have not been well investigated. Objective The present study aims to investigate the underlying neurochemical mechanism of different pre-vascular-dementia exercise times on 5-HT and anxiety-like behavior in rats with vascular dementia. Methods 32 Sprague-Dawley (SD) rats were randomly divided into 4 groups: sham group (S group, n = 8), vascular dementia group (VD group, n = 8), 1-week physical exercise and vascular dementia group (1WVD group, n = 8), and 4 weeks physical exercise and vascular dementia group (4WVD group, n = 8). 1 week and 4 weeks of voluntary wheel running were used as pre-exercise training. The vascular dementia model was established by bilateral common carotid arteries occlusion (BCCAo) for 1 week. But bilateral common carotid arteries were not ligated in the sham group. The level of hippocampal 5-HT was detected with in vivo microdialysis coupled with high-performance liquid chromatography (MD-HPLC). Elevated plus maze (EPM), open field (OF), and light/dark box test were used to test anxiety-like behavior. Results Compared with the C group, the hippocampal 5-HT was significantly decreased in the VD group after 1 week of ligated operation. The hippocampal 5-HT levels in 1WVD and 4WVD groups were substantially higher than the level in the VD group. The hippocampal 5-HT level has no significant difference among C, 1WVD, and 4WVD. Behavioral data suggested that the rats in the VD group developed obvious anxiety-like behavior after 1 week of ligation surgery. Still, the rats in 1WVD and 4WVD groups did not show significant anxiety-like behavior. Conclusion Both 1 week and 4 weeks of voluntary running wheel exercise can inhibit the anxiety-like behavior in rats with vascular dementia by upregulating 5-HT levels in the hippocampus in the VD model.
Building Nurse Manager Well-being by Reducing Healthcare System Demands

The National Academies of Medicine consensus study committee reported that US healthcare workers experience high levels of burnout resulting from external pressures on the healthcare system and the organization of work. Nurse managers are especially susceptible to burnout. This column provides evidence-based strategies to improve the work environment, reduce the burden of job demands, and promote well-being among nurse managers.
Complete pathologic response (pCR) following neoadjuvant pembrolizumab monotherapy in treatment-naive locally advanced, mismatch repair protein-deficient (dMMR) colonic cancer: a case report and literature review

Alfonso Tan-Garcia , Lai Mun Wang, James Chi-Yong Ngu and Lynne Goh Department of Anatomical Pathology, Singapore General Hospital, Singapore, Singapore; Pathology Section, Department of Laboratory Medicine, Changi General Hospital, Singapore; Pathology Academic Clinical Programme, SingHealth Duke-NUS Academic Medical Centre, Singapore; Department of General Surgery, Changi General Hospital, Singapore, Singapore
A New Method of Bone Stromal Cell Characterization by Flow Cytometry

The bone microenvironment cellular composition plays an essential role in bone health and is disrupted in bone pathologies, such as osteoporosis, osteoarthritis, and cancer. Flow cytometry protocols for hematopoietic stem cell lineages are well defined and well established. Additionally, a consensus for mesenchymal stem cell flow markers has been developed. However, flow cytometry markers for bone‐residing cells—osteoblasts, osteoclasts, and osteocytes—have not been proposed. Here, we describe a novel partial digestion method to separate these cells from the bone matrix and present new markers for enumerating these cells by flow cytometry. We optimized bone digestion and analyzed markers across murine, nonhuman primate, and human bone. The isolation and staining protocols can be used with either cell sorting or flow cytometry. Our method allows for the enumeration and collection of hematopoietic and mesenchymal lineage cells in the bone microenvironment combined with bone‐residing stromal cells. Thus, we have established a multi‐fluorochrome bone marrow cell‐typing methodology. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC.
The Impact of 120 Minutes of Soccer-Specific Exercise on Recovery

ABSTRACT Purpose: The extra-time (ET) period of soccer is competed during fixture congested schedules with often limited recovery time between matches. The aim of this study was to assess muscle damage recovery following 90- and 120-min (i.e., incorporation of ET) of simulated soccer match-play. Methods: Twelve semiprofessional soccer players completed 90 and 120-min treadmill-based soccer-specific exercise in a counterbalanced order. Creatine kinase (CK), creatinine, urea, aspartate aminotransferase, perceived muscle soreness, pain pressure threshold, reactive strength index, countermovement jump height, and isokinetic strength assessments of eccentric knee flexors at 60, 180 and 270 deg‧s−1 were taken at baseline and immediately-, 24, 48 and 72-hr post-exercise to assess recovery. Results: No significant between-trial interactions except for CK were found. Pairwise comparisons detected a 53% increase in CK at 24-hr (455 ± 29 μ∙L−1) following 120-min of simulated match-play vs. the corresponding post 90-min time-point (299 ± 29 μ∙L−1; p < .01). The 120-min trial caused a 58% higher CK response at 72-hr (244 ± 25 μ∙L−1) vs. post 90-min comparisons (154 ± 29 μ∙L−1; p = .02). No interaction effects were detected for any other recovery variables. Creatine kinase and perceived muscle soreness remained elevated up to 72-hr in both trials (p < .01). Conclusions: These data indicate that 120 min of simulated soccer match-play delays the time-course of CK recovery up to 72-hr post-match. However, 120 min of simulated soccer has no additional impact on functional recovery and perceived muscle soreness vs. 90 min. Recovery should be investigated following 90- and 120-min of actual match-play.Trial registration The study was pre-registered on the Open Science Framework (DOI: 10.17605/OSF.IO/VGU6T Date: 10/06/2019).
Electroconductive and Anisotropic Structural Color Hydrogels for Visual Heart‐on‐a‐Chip Construction

Heart‐on‐a‐chip plays an important role in revealing the biological mechanism and developing new drugs for cardiomyopathy. Tremendous efforts have been devoted to developing heart‐on‐a‐chip systems featuring simplified fabrication, accurate imitation and microphysiological visuality. In this paper, the authors present a novel electroconductive and anisotropic structural color hydrogel by simply polymerizing non‐close‐packed colloidal arrays on super aligned carbon nanotube sheets (SACNTs) for visualized and accurate heart‐on‐a‐chip construction. The generated anisotropic hydrogel consists of a colloidal array‐locked hydrogel layer with brilliant structural color on one surface and a conductive methacrylated gelatin (GelMA)/SACNTs film on the other surface. It is demonstrated that the anisotropic morphology of the SACNTs could effectively induce the alignment of cardiomyocytes, and the conductivity of SACNTs could contribute to the synchronous beating of cardiomyocytes. Such consistent beating rhythm caused the deformation of the hydrogel substrates and dynamic shifts in structural color and reflection spectra of the whole hybrid hydrogels. More attractively, with the integration of such cardiomyocyte‐driven living structural color hydrogels and microfluidics, a visualized heart‐on‐a‐chip system with more consistent beating frequency has been established for dynamic cardiomyocyte sensing and drug screening. The results indicate that the electroconductive and anisotropic structural color hydrogels are potential for various biomedical applications.
A quarter of a century biomechanical rupture risk assessment of abdominal aortic aneurysms. Achievements, clinical relevance, and ongoing developments

Abdominal aortic aneurysm (AAA) disease, the local enlargement of the infrarenal aorta, is a serious condition that causes many deaths, especially in men exceeding 65 years of age. Over the past quarter of a century, computational biomechanical models have been developed towards the assessment of AAA risk of rupture, technology that is now on the verge of being integrated within the clinical decision‐making process. The modeling of AAA requires a holistic understanding of the clinical problem, in order to set appropriate modeling assumptions and to draw sound conclusions from the simulation results. In this article we summarize and critically discuss the proposed modeling approaches and report the outcome of clinical validation studies for a number of biomechanics‐based rupture risk indices. Whilst most of the aspects concerning computational mechanics have already been settled, it is the exploration of the failure properties of the AAA wall and the acquisition of robust input data for simulations that has the greatest potential for the further improvement of this technology.
The Volume and Tone of Twitter Posts About Cannabis Use During Pregnancy: Protocol for a Scoping Review

Background Cannabis use has increased in Canada since its legalization in 2018, including among pregnant women who may be motivated to use cannabis to reduce symptoms of nausea and vomiting. However, a growing body of research suggests that cannabis use during pregnancy may harm the developing fetus. As a result, patients increasingly seek medical advice from online sources, but these platforms may also spread anecdotal descriptions or misinformation. Given the possible disconnect between online messaging and evidence-based research about the effects of cannabis use during pregnancy, there is a potential for advice taken from social media to affect the health of mothers and their babies. Objective This study aims to quantify the volume and tone of English language posts related to cannabis use in pregnancy from January 2012 to December 2021. Methods Modeling published frameworks for scoping reviews, we will collect publicly available posts from Twitter that mention cannabis use during pregnancy and use the Twitter Application Programming Interface for Academic Research to extract data from tweets, including public metrics such as the number of likes, retweets, and quotes, as well as health effect mentions, sentiment, location, and users’ interests. These data will be used to quantify how cannabis use during pregnancy is discussed on Twitter and to build a qualitative profile of supportive and opposing posters. Results The CHEO Research Ethics Board reviewed our project and granted an exemption in May 2021. As of December 2021, we have gained approval to use the Twitter Application Programming Interface for Academic Research and have developed a preliminary search strategy that returns over 3 million unique tweets posted between 2012 and 2021. Conclusions Understanding how Twitter is being used to discuss cannabis use during pregnancy will help public health agencies and health care providers assess the messaging patients may be receiving and develop communication strategies to counter misinformation, especially in geographical regions where legalization is recent or imminent. Most importantly, we foresee that our findings will assist expecting families in making informed choices about where they choose to access advice about using cannabis during pregnancy. Trial Registration Open Science Framework 10.17605/OSF.IO/BW8DA; www.osf. io/6fb2e International Registered Report Identifier (IRRID) PRR1-10.2196/34421
Poorer outcomes associated with sarcopenia following emergency laparotomy: a systematic review and meta‐analysis

Despite the negative effect of sarcopenia on postoperative outcomes being well recognized in the elective setting, there remains a paucity of studies describing this phenomenon in the emergency laparotomy (EL) setting. This systematic review and meta‐analysis aimed to compare short‐ and long‐term postoperative outcomes following EL in patients with and without sarcopenia.
Risks for Anaphylaxis With Intravenous Iron Formulations

BACKGROUND The risks for anaphylaxis among intravenous (IV) iron products currently in use have not been assessed. OBJECTIVE To compare risks for anaphylaxis among 5 IV iron products that are used frequently. DESIGN Retrospective cohort study using a target trial emulation framework. SETTING Medicare fee-for-service data with Part D coverage between July 2013 and December 2018. PARTICIPANTS Older adults receiving their first administration of IV iron. MEASUREMENTS The primary outcome was the occurrence of anaphylaxis within 1 day of IV iron administration, ascertained using a validated case definition. Analysis was adjusted for 40 baseline covariates using inverse probability of treatment weighting. The adjusted incidence rates (IRs) for anaphylaxis per 10 000 first administrations and odds ratios (ORs) were computed. RESULTS The adjusted IRs for anaphylaxis per 10 000 first administrations were 9.8 cases (95% CI, 6.2 to 15.3 cases) for iron dextran, 4.0 cases (CI, 2.5 to 6.6 cases) for ferumoxytol, 1.5 cases (CI, 0.3 to 6.6 cases) for ferric gluconate, 1.2 cases (CI, 0.6 to 2.5 cases) for iron sucrose, and 0.8 cases (CI, 0.3 to 2.6 cases) for ferric carboxymaltose. Using iron sucrose as the referent category, the adjusted ORs for anaphylaxis were 8.3 (CI, 3.5 to 19.8) for iron dextran and 3.4 (CI, 1.4 to 8.3) for ferumoxytol. When cohort entry was restricted to the period after withdrawal of high-molecular-weight iron dextran from the U.S. market in 2014, the risk for anaphylaxis associated with low-molecular-weight iron dextran (OR, 8.4 [CI, 2.8 to 24.7]) did not change appreciably. Anaphylactic reactions requiring hospitalizations were observed only among patients using iron dextran or ferumoxytol. LIMITATION Generalizability to non-Medicare populations. CONCLUSION The rates of anaphylaxis were very low with all IV iron products but were 3- to 8-fold greater for iron dextran and ferumoxytol than for iron sucrose. PRIMARY FUNDING SOURCE None.
Chromosome-length genome assembly and linkage map of a critically endangered Australian bird: the helmeted honeyeater

Abstract Background The helmeted honeyeater (Lichenostomus melanops cassidix) is a Critically Endangered bird endemic to Victoria, Australia. To aid its conservation, the population is the subject of genetic rescue. To understand, monitor, and modulate the effects of genetic rescue on the helmeted honeyeater genome, a chromosome-length genome and a high-density linkage map are required. Results We used a combination of Illumina, Oxford Nanopore, and Hi-C sequencing technologies to assemble a chromosome-length genome of the helmeted honeyeater, comprising 906 scaffolds, with length of 1.1 Gb and scaffold N50 of 63.8 Mb. Annotation comprised 57,181 gene models. Using a pedigree of 257 birds and 53,111 single-nucleotide polymorphisms, we obtained high-density linkage and recombination maps for 25 autosomes and Z chromosome. The total sex-averaged linkage map was 1,347 cM long, with the male map being 6.7% longer than the female map. Recombination maps revealed sexually dimorphic recombination rates (overall higher in males), with average recombination rate of 1.8 cM/Mb. Comparative analyses revealed high synteny of the helmeted honeyeater genome with that of 3 passerine species (e.g., 32 Hi-C scaffolds mapped to 30 zebra finch autosomes and Z chromosome). The genome assembly and linkage map suggest that the helmeted honeyeater exhibits a fission of chromosome 1A into 2 chromosomes relative to zebra finch. PSMC analysis showed a ∼15-fold decline in effective population size to ∼60,000 from mid- to late Pleistocene. Conclusions The annotated chromosome-length genome and high-density linkage map provide rich resources for evolutionary studies and will be fundamental in guiding conservation efforts for the helmeted honeyeater.
Gesture recognition using a depth sensor and machine learning techniques

Advances in depth sensing provide great opportunities for the development of new methods for human computer interactivity. With the launch of the Microsoft Kinect sensor, high-resolution depth and visual sensing has become available for widespread use. As it is suitable for measuring distances to objects at high frame rate, such kind of sensors are increasingly used for 3D acquisitions, and more generally for applications in robotics or computer vision. The aim of this survey is to implement a gesture recognition system using the Kinect version 2 of Microsoft in order to interact with a virtual TV weather studio. The Kinect sensor was used to build up a dataset, which contains motion recordings of 8 different gestures and was build up by two different gesture training machine learning algorithms. Then, the system is evaluated in a user study, which allows a direct comparison and reveals benefits and limits of using such technique. Finally, it is given an overview of the challenges in this field and future work trends.
Competitive metal‐binding stoichiometry between calcium and strontium by cell wall proteins of Neurospora crassa

Cell wall proteins from Neurospora crassa were isolated and evaluated to demonstrate their metal ability to bind Ca2+/Sr2+ by loading the solubilized protein fraction on to immobilized metal affinity chromatography (IMAC) column pre‐equilibrated with Ca2+/Sr2+. The sodium dodecyl sulfate–polyacrylamide gel electrophoresis analysis IMAC eluent, revealed ∼18 proteins with a similarity in the proteome pattern of Ca2+/Sr2+ fractions. Diethyl aminoethyl chromatography showed five proteins in common in binding to Ca2+ and Sr2+, were subjected to N‐terminal sequencing. The sequence analysis was studied for the determination of metal‐binding site prediction by CHED software indicating that all five were found to have a high affinity toward Ca2+. From these five, two were randomly selected and denoted as CWP‐A (possess five Ca binding sites of six metal‐binding sites) and CWP‐B (possess six binding sites of eight metal‐binding sites). They were selected for further characterization studies to determine their Ca2+ bound Sr2+ binding properties. Surprisingly, these proteins were able to bind Sr2+ ions (29 μmol) with equal affinity as to Ca2+ ions (42 μmol) by means of direct binding, and/or by displacing calcium as observed in metal‐dependent proteolytic protection, fluorescence‐based metal exchange assays, and molecular simulation studies. From the results, we demonstrate for the first time, that there is a stoichiometry between Ca2+ (an essential macro elemental metal ion) and Sr2+ ions (a nonessential element for which no reported metabolic activity is reported) for the metal‐binding sites on cell wall proteins. This stoichiometry could be due to similar atomic dimensions and metal‐protein structure stabilizing properties of Sr2+ compared to Ca2+.
Nap effects on preschool children’s learning of letter‐sound mappings

Abstract This study explored whether a daytime nap aids children's acquisition of letter‐sound knowledge, which is a fundamental component for learning to read. Thirty‐two preschool children in Sydney, Australia (M age = 4 years;3 months) were taught letter‐sound mappings in two sessions: one followed by a nap and the other by a wakeful period. Learning was assessed by explicit letter‐sound mappings (“Which sound does this letter make? ”) and knowledge generalization tasks (“Here's Tav and Cav, which one is /kav/? ”). Results from the knowledge generalization task showed better performance after a nap than after wake. However, no nap benefit was found for explicit letter‐sound knowledge. This study provides initial evidence that naps could be beneficial for preschool children's learning of letter‐sound mappings.
Få meget ud af lidt: langtidseffekt af workshop til universitetsstuderende i naturvidenskabelig formidling i uformelle læringsmiljøer

Denne artikel rapporterer et evalueringsprojekt der havde til hensigt at forbedre formidlingenaf naturvidenskab i det uformelle laeringsmiljo “Natur i Teltet” i Aarhus. Forfatterne forberedte pabaggrund af en evaluering af arrangementet en tredages workshop for de studerende der formidledei teltet. Temaerne var blandt andet Barriaults teori om uformel laering, sporgeteknik og de besogendes(skoleelever og andres) forskellige niveauer. De studerende blev fulgt i to ar for at vurdere langtidseffektenaf workshoppen. Vi konkluderer at selv en forholdsvis lille indsats formaede at flytte pa destuderendes viden om god formidling i uformelle laeringsmiljoer.This paper reports an evaluation project whose purpose was to improve the dissemination of knowledgeof science in the out-of-school time informal learning programme “Nature in the tent” inAarhus. Based on a programme evaluation, the authors prepared a three day workshop for theuniversity students who disseminate. The themes were Barriault’s theory of informal learning,questioning tech niques, the various levels of the visitors (school pupils and others) etc. The studentswere followed for two years. We concluded that the short workshop made it possible to change thestudents’ knowledge about dissemination in an out-of-school time context.
The Role of Beetroot Extract in Overcoming Chemoresistance of Neoadjuvant Adriamycin Cyclophosphamide Regimen by Targeting Immune Response in Tumor Microenvironment: A Preclinical Study in Mammary Adenocarcinoma Rats

Objective: This study aims to determine the role of beetroot extract in overcoming the chemoresistance of Neoadjuvant Adriamycin Cyclophosphamide (NAC) regimens with a target immune response in the tumour microenvironment at the pre-clinical stage. Methods: This study was conducted on rats with 7,12-Dimethyl Benz (α) Anthracene (DMBA) induced mammary adenocarcinoma. Adriamycin Cyclophosphamide was given in 4 cycles, whereas beetroot extract was administered three times each cycle. Observations of CD8 T cells and Myeloid Derivative Suppressive Cells (MDSC) expression levels and pathological responses were carried out on tumour tissue taken at the end of the observation. Results: Supplementation of beetroot extract to NAC could significantly increase CD8 T cells and decrease MDSC in the tumour microenvironment. The addition of beetroot extract gave a better pathological response. Conclusion: Beetroot extract enhances the immune response in the tumor microenvironment so that it has the potential to overcome chemoresistance in NAC.