Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of Oil Sprinkling in Swine Finishing Barns on Odor Characteristics and Emissions

The effects of soybean oil sprinkling (SOS), misting of essential oils (MEO), and misting of essential oils and water (MEOW) on odor emitted from swine finishing houses were evaluated in tests at a commercial operation. Measurements were taken between 27 August 2002 and 21 July 2003 at two mechanically-ventilated barns that were flushed daily with lagoon wastewater. The tests consisted of four trials over three pig groups (cycles): SOS and SOS+ (with additional spray nozzles) for the first and second cycles, MEO for the second cycle, and MEOW for the third cycle. The barn treated with SOS resulted in 30% less odor than the control barn in one trial, and MEO and MEOW slightly improved hedonic tone of barn air. The mean odor concentration and emission were 519 OU/m and 23.5 OU/s-AU (n=21). Odor increased for 4 to 8 min when pits were flushed with lagoon effluent.
Summertime coastal current reversal opposing offshore forcing and local wind near the middle east coast of Korea: Observation and dynamics

A 6 year long current measurement at a buoy station off the middle east coast of Korea reveals an equatorward reversal of coastal current in summer opposing poleward local wind stress and offshore boundary current. The current reversal extends about 40 km offshore from the coast and is concurrent with warming and freshening of water column. Estimates of the depth‐averaged alongshore momentum balance suggest a major balance between the alongshore pressure gradient and the lateral friction. Sources of the pressure gradient for the summertime current reversal are identified as the alongshore buoyancy gradient driven by the wind curl gradient and the prevalence of warmer and lower salinity water in the north. Alongshore pressure gradient and velocity induced by the wind curl gradient are quantified, which yields the observed seasonal current reversal.
In vitro establishment of Bambusa oldhamii Munro from field-grown matrices and molecular identification of endophytic bactéria

ABSTRACT In plant micropropagation, the establishment stage is difficult, due to the presence of microorganisms in tissues from field-grown matrices, especially for bamboo. This study aimed to establish an efficient asepsis protocol for Bambusa oldhamii explants from field plants, as well as to carry out the molecular identification of a possible endophytic bacterial isolate. The explants were exposed to 70 % alcohol, 1 % sodium hypochlorite (NaOCl), 0.1 % mercuric chloride (HgCl2), thiophanate-methyl (Cercobin®) and chlorhexidine digluconate (2 % Riohex®) in different combinations, and introduced into Murashige and Skoog culture medium (solid or liquid), supplemented or not with 4 mL L-1 of Plant Preservative Mixture (PPMTM), totaling seven treatments. The asepsis and immersion of the explants in the liquid culture medium containing 4 mL L-1 of PPMTM visually inhibited the bacterial and fungal growth, allowed the development of shoots with a mean length of 2.2 cm and posterior subcultures, being the best treatment used for the in vitro establishment of B. oldhamii. The molecular identification of an endophytic bacterium performed by 16S rDNA sequencing allowed to identify the bacterial isolate as Ralstonia sp. , with 100 % of similarity, and the phylogenetic analysis grouped it with Ralstonia pickettii. In addition, the bacterial isolate showed to be sensitive to 4 mL L-1 of PPMTM by the minimum inhibitory concentration test.
SpliceWiz: interactive analysis and visualization of alternative splicing in R

Abstract Alternative splicing (AS) is a crucial mechanism for regulating gene expression and isoform diversity in eukaryotes. However, the analysis and visualization of AS events from RNA sequencing data remains challenging. Most tools require a certain level of computer literacy and the available means of visualizing AS events, such as coverage and sashimi plots, have limitations and can be misleading. To address these issues, we present SpliceWiz, an R package with an interactive Shiny interface that allows easy and efficient AS analysis and visualization at scale. A novel normalization algorithm is implemented to aggregate splicing levels within sample groups, thereby allowing group differences in splicing levels to be accurately visualized. The tool also offers downstream gene ontology enrichment analysis, highlighting ASEs belonging to functional pathways of interest. SpliceWiz is optimized for speed and efficiency and introduces a new file format for coverage data storage that is more efficient than BigWig. Alignment files are processed orders of magnitude faster than other R-based AS analysis tools and on par with command-line tools. Overall, SpliceWiz streamlines AS analysis, enabling reliable identification of functionally relevant AS events for further characterization. SpliceWiz is a Bioconductor package and is also available on GitHub (https://github.com/alexchwong/SpliceWiz).
Nano- and micro-crystalline diamond film structuring with electron beam lithography mask.

Direct Current Plasma Enhanced Chemical Vapor Deposition (CVD) was employed to create polycrystalline diamond films from CH4/H2 gaseous mixture at 98 mbar pressure and various substrate temperatures between 720°C and 960 °C. The Si chips with patterns of periodic masked and open seeded zones were used as substrates. The mask free seeded areas evolved into polycrystalline diamond films after CVD process. The diamond crystallites of the films featured single crystal ordering individually with distinct cubic (100) or octahedral (111) facets on the film surfaces. Notably, specific growth conditions were determined for obtaining diamond films composed of the crystallites of nanometre and micrometre scale. These conditions are differing from those observed for non-pattern-prepared Si substrates. The nano-crystalline diamonds (NCDs) emerged within the 4.5A to 5A current range, with growth conditions involving 3% CH4/H2 mixture at 98 mbar. The micro-crystalline diamonds (MCDs) predominantly characterized by well-developed rectangular (100) crystal faces on the film surface were successfully grown with current settings of 5.5 A to 6A, under 3% CH4/H2 mixture at 98 mbar. Furthermore, MCDs characterized by entirely crystalline (111) diamond faces forming CVD film surface were attained within a growth parameter range of 4.5 A to 5.8A, employing 3% CH4/H2 mixture for certain samples, or alternatively, utilizing 5A with a 1.5% CH4/H2 mixture for others. Upon thorough evaluation, it was established that SiO2, TiO2, and Cr masks are well-suited materials for the planar patterning of both nano- and micro-crystalline diamond films, and the bottom-up approach can pave the way for the production of diamond planar structures through Chemical Vapor Deposition (CVD), facilitated by electron beam lithography (EBL).
Bio-Inspired Small Target Motion Detection With Spatio-Temporal Feedback in Natural Scenes

Small moving objects at far distance always occupy only one or a few pixels in image and exhibit extremely limited visual features, which bring great challenges to motion detection. Highly evolved visual systems endow flying insects with remarkable ability to pursue tiny mates and prey, providing a good template to develop image processing method for small target motion detection. The insects’ excellent sensitivity to small moving objects is believed to come from a class of specific neurons called small target motion detectors (STMDs). However, existing STMD-based methods often experience performance degradation when coping with complex natural scenes. In this paper, we propose a bio-inspired visual system with spatio-temporal feedback mechanism (called Spatio-Temporal Feedback STMD) to suppress false positive background movement while enhancing system responses to small targets. Specifically, the proposed visual system is composed of two complementary subnetworks and a feedback loop. The first subnetwork is designed to extract spatial and temporal movement patterns of cluttered background by neuronal ensemble coding. The second subnetwork is developed to capture small target motion information where its output and signal from the first subnetwork are integrated together via the feedback loop to filter out background false positives in a recurrent manner. Experimental results demonstrate that the proposed spatio-temporal feedback visual system is more competitive than existing methods in discriminating small moving targets from complex natural environments.
Impact of Liver Cirrhosis on Early and Midterm Results After Transcatheter Aortic Valve Replacement: A Retrospective, Observational Study

ABSTRACT Background: Liver cirrhosis (LC) is a risk factor for open cardiac surgery; however, its impact on transcatheter aortic valve replacement (TAVR) remains unclear. This study aimed to validate the outcomes of TAVR for severe aortic valve stenosis (sAS) in patients with LC. Methods: Propensity score matching was performed using logistic regression, following which 22 patients with LC and 66 without LC, who underwent TAVR for sAS, were recruited. Early and midterm mortality and morbidity were compared between the LC and non-LC groups. Results: No significant difference was observed in perioperative results, including intraoperative bleeding and transfusion, 30-day mortality, and major morbidity, between the groups. Three-year-survival rate after TAVR was significantly lower (37.8%) in the LC group than in the non-LC group (85.9%) (p < 0.001). Cox regression analysis revealed that serum albumin level was the sole independent risk factor for overall survival in patients with LC. Two-year survival rate in patients with LC having preoperative serum albumin level ≥3.0 g/dL was significantly lower than that in those having preoperative serum albumin level <3.0 g/dL (29.2% vs. 84.8%, p = 0.002). Conclusions: LC, belonging to Child–Pugh classes A and B, does not impact the early outcomes after TAVR. Preoperative hypoalbuminemia may affect the mid-term survival after TAVR in patients with LC.
Yoga therapy on elderly patients with fear of fall: an open-label randomised controlled trial (YOFEAR trial)

Introduction Fear of fall is experienced by the elderly irrespective of the presence or absence of history of fall. Falls contribute to injuries that culminate in hospitalisation that incur unwarranted medical expenses. Yoga is unique to Indian cultural practices, with a potential to enhance proprioception. It increases self-body awareness, ultimately improving the balancing capacity of older adults. Thus, the objective of this study is to compare the effect of yoga therapy in the study and control groups at 12 weeks from the baseline. Methods and analysis This study is designed as an open-label, randomised controlled trial (1:1) with a sample size of 62 elderly patients more than or equal to 60 years of age. Participation of either sex, male or female with a fear of fall will be considered. Two randomised groups of 31 participants each will receive standard therapy for their primary diseases as per the local, national or international guidelines. However, participants in the intervention arm will receive additional structured yoga therapy sessions. The primary objective of this study is to assess and compare the change in fear of fall score of participants in each group using Falls Efficacy Scale (FES) and Berg Balance Scale (BBS) at 12 weeks versus baseline. The secondary endpoint will assess the change in the quality of life of participants at 3 months compared with the baseline. Data will be gathered, entered into Microsoft Excel and further analysed by R software (V.4.3.0). Changes in FES-Intervention and BBS of two groups will be compared either by Student’s t-test for parametric data or Mann-Whitney U test for non-parametric data. Statistical significance will be considered if p<0.05 at 95% confidence level. Ethics and dissemination Ethical approval for this study protocol (version 1.0, 22 April 2022) was obtained from the institute ethics committee (AIIMS/IEC/22/195). Trial registration number CTRI/2022/06/043287.
Relation between Double Layer Structure, Capacitance, and Surface Tension in Electrowetting of Graphene and Aqueous Electrolytes

Deciphering the mechanisms of charge storage on carbon-based materials is pivotal for the development of next-generation electrochemical energy storage systems. Graphene, the building block of graphitic electrodes, is an ideal model for probing such processes on a fundamental level. Herein, we investigate the thermodynamics of the graphene/aqueous electrolyte interface by utilizing a multiscale quantum mechanics–classical molecular dynamics (QM/MD) approach to provide insights into the effect of alkali metal ion (Li+) concentration on the interfacial tension (γSL) of the charged graphene/electrolyte interface. We demonstrate that the dependence of γSL on the applied surface charge exhibits an asymmetric behavior relative to the neutral surface. At the positively charged graphene sheet, the electrowetting response is amplified by electrolyte concentration, resulting in a strongly hydrophilic surface. On the contrary, at negative potential bias, γSL shows a weaker response to the charging of the electrode. Changes in γSL greatly affect the total areal capacitance predicted by the Young–Lippmann equation but have a negligible impact on the simulated total areal capacitance, indicating that the EDL structure is not directly correlated with the wettability of the surface and different interfacial mechanisms drive the two phenomena. The proposed model is validated experimentally by studying the electrowetting response of highly oriented pyrolytic graphite over a wide range of electrolyte concentrations. Our work presents the first combined theoretical and experimental study on electrowetting using carbon surfaces, introducing new conceptual routes for the investigation of wetting phenomena under potential bias.
A meta‐analysis examining the impact of intrawound treatment on reducing deep surgical site infections during instrumented spine surgery

Abstract The purpose of the meta‐analysis was to evaluate and compare the effect of intrawound management on decreasing deep surgical site infections (SSIs) in instrumented spinal surgery (SS). The results of this meta‐analysis were analysed, and the odds ratio (OR) and mean difference (MD) with 95% confidence intervals (CIs) were calculated using dichotomous or contentious random or fixed effect models. For the current meta‐analysis, 29 examinations spanning from 2006 to 2022 were included, encompassing 11 181 people who had instrumented SS. Intrawound management had a significantly lower deep SSI when using vancomycin (OR, 0.34; 95% CI, 0.25–0.44, p < 0.001) and povidone‐iodine as intrawound management (OR, 0.24; 95% CI, 0.13–0.42, p < 0.001) compared to control in instrumented SS subjects. The data that was looked at showed that using vancomycin and povidone‐iodine as intrawound management had a much lower deep SSI than using a control group of instrumented SS subjects. However, given that some studies included a small number of subjects, attention should be given to their values.
Investigating cell death responses associated with histotripsy ablation of canine osteosarcoma

Abstract Background Osteosarcoma (OS) is the most frequently occurring primary bone tumor in dogs and people and innovative treatment options are profoundly needed. Histotripsy is an emerging tumor ablation modality, and it is essential for the clinical translation of histotripsy to gain knowledge about the outcome of nonablated tumor cells that could remain postablation. The objective of this study was to characterize the cell death genetic signature and proliferation response of canine OS cells post a near complete histotripsy ablation (96% ± 1.5) and to evaluate genetic cell death signatures associated with histotripsy ablation and OS in vivo. Methods In the current study, we ablated three canine OS cell lines with a histotripsy dose that resulted in near complete ablation to allow for a viable tumor cell population for downstream analyses. To assess the in vivo cell death genetic signature, we characterized cell death genetic signature in histotripsy-ablated canine OS tumors collected 24-h postablation. Results Differential gene expression changes observed in the 4% viable D17 and D418 cells, and histotripsy-ablated OS tumor samples, but not in Abrams cells, were associated with immunogenic cell death (ICD). The 4% viable OS cells demonstrated significantly reduced proliferation, compared to control OS cells, in vitro. Conclusion Histotripsy ablation of OS cell lines leads to direct and potentially indirect cell death as evident by, reduced proliferation in remaining viable OS cells and cell death genetic signatures suggestive of ICD both in vitro and in vivo.
Why does youth unemployment lead to scarring of depressive symptoms in adulthood? The importance of early adulthood drinking.

AIM The aim of the paper is to analyse if alcohol consumption could explain the scarring effect of youth unemployment on later depressive symptoms. METHODS The analyses are based on the 24-year follow-up of school leavers in a municipality in Northern Sweden (the Northern Swedish Cohort). Four-way decomposition analyses were performed to analyse if alcohol use at age 30 years could mediate and/or moderate the effect of youth unemployment (ages 18/21 years) on depressive symptoms in later adulthood (age 43 years). RESULTS Excessive alcohol use at early adulthood (age 30 years) mediates 18% of the scarring effect of youth unemployment on depressive symptoms in later adulthood. The scarring effect was seen among both those with and without excessive alcohol use. CONCLUSIONS Youth unemployment leads to poor mental health later in life and part of these relations are explained by excessive alcohol consumption in early adulthood. Policy interventions should target the prevention of youth unemployment for reaching a lower alcohol consumption and better mental health.
Novel Drug Screening Assay for Acanthamoeba castellanii and the Anti-Amoebic Effect of Carbonic Anhydrase Inhibitors

Acanthamoeba castellanii is an amoeba that inhabits soil and water in every part of the world. Acanthamoeba infection of the eye causes keratitis and can lead to a loss of vision. Current treatment options are only moderately effective, have multiple harmful side effects, and are tedious. In our study, we developed a novel drug screening method to define the inhibitory properties of potential new drugs against A. castellanii in vitro. We found that the clinically used carbonic anhydrase inhibitors, acetazolamide, ethoxzolamide, and dorzolamide, have promising antiamoebic properties.
APPLIED GENETICS AND MOLECULAR BIOTECHNOLOGY

The ability of biosurfactant obtained from the probiotic bacterium Lactococcus lactis 53 to inhibit adhesion of four bacterial and two yeast strains isolated from explanted voice prostheses to silicone rubber with and without an adsorbed biosurfactant layer was investi- gated in a parallel-plate flow chamber. The microbial cell surfaces and the silicone rubber with and without an adsorbed biosurfactant layer were characterized using contact-angle measurements. Water contact angles indi- cated that the silicone-rubber surface with adsorbed biosurfactant was more hydrophilic (48°) than bare silicone rubber (109°). The results showed that the biosurfactant was effective in decreasing the initial deposition rates of Staphylococcus epidermidis GB 9/6 from 2,100 to 220 microorganisms cm �2 s �1 , Streptococ- cus salivarius GB 24/9 from 1,560 to 137 microorganisms cm �2 s �1 , and Staphylococcus aureus GB 2/1 from 1,255 to 135 microorganisms cm �2 s �1 , allowing for a 90% reduction of the deposition rates. The deposition rates of Rothia dentocariosa GBJ 52/2B, Candida albicans GBJ 13/4A, and Candida tropicalis GB 9/9 were far less reduced in the presence of the biosurfactant as compared with the other strains. This study constitutes a step ahead in developing strategies to prevent microbial colonization of silicone-rubber voice prostheses.
Production of CRISPR‐Cas9 Transgenic Cell Lines for Knocksideways Studies

Protein activity is generally functionally integrated and spatially restricted to key locations within the cell. Knocksideways experiments allow researchers to rapidly move proteins to alternate or ectopic regions of the cell and assess the resultant cellular response. Briefly, individual proteins to be tested using this approach must be modified with moieties that dimerize under treatment with rapamycin to promote the experimental spatial relocalizations. CRISPR technology enables researchers to engineer modified protein directly in cells while preserving proper protein levels because the engineered protein will be expressed from endogenous promoters. Here we provide straightforward instructions to engineer tagged, rapamycin‐relocalizable proteins in cells. The protocol is described in the context of our work with the microtubule depolymerizer MCAK/Kif2C, but it is easily adaptable to other genes and alternate tags such as degrons, optogenetic constructs, and other experimentally useful modifications. Off‐target effects are minimized by testing for the most efficient target site using a split‐GFP construct. This protocol involves no proprietary kits, only plasmids available from repositories (such as addgene.org). Validation, relocalization, and some example novel discoveries obtained working with endogenous protein levels are described. A graduate student with access to a fluorescence microscope should be able to prepare engineered cells with spatially controllable endogenous protein using this protocol. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC.
Are JAKis more effective among elderly patients with RA, smokers and those with higher cardiovascular risk? A comparative effectiveness study of b/tsDMARDs in Sweden

Objectives To investigate whether the relative effectiveness of janus kinase inhibitors (JAKis) versus tumour necrosis factor inhibitors (TNFi) or other biological disease-modifying antirheumatic drugs in rheumatoid arthritis differ by the presence or absence of risk factors for cardiovascular (CV) disease, age, sex and smoking. Methods Through Swedish registers, we identified 13 493 individuals with 3166 JAKi, 5575 non-TNFi and 11 286 TNFi treatment initiations 2016–2022. All lines of therapy were included, with the majority in second line or higher. Treatment response was defined as the proportion reaching European Alliance of Associations for Rheumatology (EULAR) good response and Clinical Disease Activity Index (CDAI) remission, respectively, within 6 months. Crude percentage point differences in these proportions (JAKis, and non-TNFis, vs TNFis) overall and by risk factors were observed, and adjusted for confounders using linear regression models. Predicted probabilities of response and remission were estimated from adjusted Poisson models, and presented across CV risk and age. Results Overall, adjusted percentage point differences indicated higher response (+5.0%, 95% CI 2.2% to 7.9%) and remission (+5.8%, 95% CI 3.2% to 8.5%) with JAKis versus TNFis. The adjusted percentage point differences for response in those above 65, at elevated CV risk, and smokers were +5.9% (95% CI 2.7% to 9.0%), +8.3% (95% CI 5.3% to 11.4%) and +6.0% (95% CI 3.3% to 8.7%), respectively. The corresponding estimates for remission were +8.0% (95% CI 5.3% to 10.8%), +5.6% (95% CI 3.0% to 8.2%) and +7.6% (95% CI 5.5% to 9.7%). Conclusions As used in clinical practice, response and remission at 6 months with JAKis are higher than with TNFi. Among patients with risk factors of concern, effectiveness is similar or numerically further increased. For individualised benefit-to-risk ratios to guide treatment choice, safety and effectiveness in specific patient segments should be considered.