Miracle-dz/UniFAR-FTUs huggingface dataset:
Unstable Phase Response Curves Shown by Spatiotemporal Patterns in the Plant Root Circadian Clock

Phase response curves (PRCs) play important roles in the entrainment of periodic environmental cycles. Measuring the PRC is necessary to elucidate the relationship between environmental cues and the circadian clock. Conversely, the PRCs of plant circadian clocks are unstable due to multiple factors such as biotic/abiotic noise, individual differences, changes in amplitude, growth stage, and organ/tissue specificity. However, evaluating the effect of each factor is important because PRCs are commonly obtained by determining the response of many individuals, which include different amplitude states and organs. The plant root circadian clock spontaneously generates a spatiotemporal pattern called a stripe pattern, whereby all phases of the circadian rhythm exist within an individual root. Therefore, stimulating a plant root expressing this pattern enables phase responses at all phases to be measured using an individual root. In this study, we measured PRCs for thermal stimuli using this spatiotemporal pattern method and found that the PRC changed asymmetrically with positive and negative temperature stimuli. Individual differences were observed for weak but not for strong temperature stimuli. The root PRC changed depending on the amplitude of the circadian rhythm. The PRC in the young root near the hypocotyl was more sensitive than those in older roots or near the tip. Simulation with a phase oscillator model revealed the effect of measurement and internal noises on the PRC. These results indicate that instability in the entrainment of the plant circadian clock involves multiple factors, each having different characteristics. These results may help us understand how plant circadian clocks adapt to unstable environments and how plant circadian clocks with different characteristics, such as organ, age, and amplitude, are integrated within individuals.
Dietary supplementation of alpha-lipoic acid mitigates the negative effects of heat stress in broilers

Heat stress accounts for substantial economic loss in the poultry industry by altering the health and performance of chickens. Alpha-lipoic acid (ALA) is a water and fat-soluble antioxidant which is readily absorbed from the intestine resulting in maximum bioavailability. Moreover, ALA acts as a coenzyme in glucose metabolism and helps generate other antioxidants. Considering these benefits, we hypothesized that dietary supplementation of ALA would help mitigate heat stress in poultry. A total of 72 Day-old broiler chicks were randomly assigned into three treatment groups: no heat stress (NHS), heat stress with basal diet (HS), and heat stress with alpha-lipoic acid (HS+ALA); each treatment group had 6 replicate pens with 4 birds in each pen (n = 24/group). The allocated birds were raised under standard husbandry practices for 3 weeks. After 21 d, birds in the HS and HS+ALA groups were exposed to heat stress (33°C for 8 hours during the day) for 3 weeks, while the NHS group was reared under normal conditions (22–24°C). The HS+ALA group received a basal finisher diet fortified with ALA (500 mg/kg) during the treatment period (22 to 42 d), while other birds were provided with the basal finisher diet. Weekly body weight and feed intake were recorded. The cecum digesta for volatile fatty acids (VFAs) analysis and 16S rRNA sequencing for the gut microbiota analysis; and the ileum tissue samples for histological and gene expression analyses were collected on d 42. Exposure to heat stress decreased (P<0.05) average daily gain (ADG) and final body weight (FBW) in the HS group compared to the NHS group, the supplementation of ALA improved (P<0.05) ADG and FBW in heat-stressed birds. Furthermore, birds in the HS+ALA group had increased (P<0.05) expression of HSP90, PRDX1, GPX3, SOD2, OCLN, and MUC2 genes and higher (P<0.05) concentrations of major VFAs (acetate, propionate, and butyrate). The dietary ALA supplementation also improved the villus height and villus height to crypt depth ratio in the HS+ALA group. The microbial diversity analysis revealed significant abundance (P<0.05) of beneficial bacteria Lactobacillus and Peptostreptococcaceae in the cecum of the ALA group. These results indicate that dietary ALA supplementation effectively mitigates the negative effects of heat stress in broilers by improving the expression of heat-shock, tight-junction, antioxidants, and immune-related genes in the intestine, improving villus structures, increasing concentration of major VFAs, and enriching the beneficial microbiota.
Examining the Associations Between Childhood Trauma, Resilience, and Depression: A Multivariate Meta-Analysis

Topic of review: Childhood trauma has been associated with increased depression; however, resilience has been found to reduce this association. Method of review: Present analyses were based on multivariate meta-analytical techniques, an extension of univariate meta-analysis. All computations were performed using the metafor package and the metaRmat package from R. Bivariate associations (r) between trauma, resilience, and depression were utilized as the pooled effect sizes. Criteria for inclusion: Following Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, articles were coded based on the following inclusion criteria: (a) sample participants had a history of childhood trauma; (b) studies included one of the four instruments of trait resilience; (c) studies included measures of individual outcomes of depression; (d) studies were published in peer-reviewed journals, dissertations, book chapters since 2009, or provided by leading scholars who had yet to publish their data; (e) all manuscripts were written in English; and (f) studies included the Pearson Product Moment Correlation Coefficient (r) for the effect size. Criteria for review: We systematically coded for the following items for each study: year of publication, type of report, peer-reviewed, funding, sampling strategy, sample size, gender, mean age, country of study, measure of resilience, measure depression, and measure of childhood trauma. Major findings: The pooled correlations indicate that trauma, resilience, and depression are significantly associated. There were no significant differences in symptoms of depression for high versus low reports of resilience for individuals with a history of trauma. Year of publication was a significant moderator for the associations between trauma, resilience, and depression. Resilience significantly mediated the association between trauma and depression.
Heterogeneity and Cancer-Related Features in Lymphangioleiomyomatosis Cells and Tissue

Lymphangioleiomyomatosis (LAM) is a rare, low-grade metastasizing disease characterized by cystic lung destruction. LAM can exhibit extensive heterogeneity at the molecular, cellular, and tissue levels. However, the molecular similarities and differences among LAM cells and tissue, and their connection to cancer features are not fully understood. By integrating complementary gene and protein LAM signatures, and single-cell and bulk tissue transcriptome profiles, we show sources of disease heterogeneity, and how they correspond to cancer molecular portraits. Subsets of LAM diseased cells differ with respect to gene expression profiles related to hormones, metabolism, proliferation, and stemness. Phenotypic diseased cell differences are identified by evaluating lumican (LUM) proteoglycan and YB1 transcription factor expression in LAM lung lesions. The RUNX1 and IRF1 transcription factors are predicted to regulate LAM cell signatures, and both regulators are expressed in LAM lung lesions, with differences between spindle-like and epithelioid LAM cells. The cancer single-cell transcriptome profiles most similar to those of LAM cells include a breast cancer mesenchymal cell model and lines derived from pleural mesotheliomas. Heterogeneity is also found in LAM lung tissue, where it is mainly determined by immune system factors. Variable expression of the multifunctional innate immunity protein LCN2 is linked to disease heterogeneity. This protein is found to be more abundant in blood plasma from LAM patients than from healthy women. Implications: This study identifies LAM molecular and cellular features, master regulators, cancer similarities, and potential causes of disease heterogeneity.
Feasible Synthesis of TiO2 Deposited on Kaolin for Photocatalytic Applications

The aim of the present study was to synthesize a photocatalyst on the basis of TiO2 with kaolin as the support material. Properties such as layered structure and a suitable particle size of kaolin could be beneficial in the production of a high-quality and relatively cheap photocatalyst on an industrial scale. Homogeneous hydrolysis with urea as a precipitation agent and kaolin as support material was used to obtain a kaolin surface covered with TiO2. Samples were characterized by means of X-ray powder diffraction, infrared and Raman spectroscopy, high-resolution transmission electron microscopy, Brunauer-Emmett-Teller surface area, and Barrett-Joyner-Halenda porosity determination. Photocatalytic activity was assessed by a Reactive Black 5 azo dye discoloration in a water suspension and by acetone decomposition on a thin layer of sample in a gas phase. The characterization confirmed that the well crystallized TiO2 was distributed effectively over the whole surface of a kaolin substrate, and photocatalytic tests revealed that the active surface layer of titania particles on kaolin performed well, suggesting that kaolin acts as a suitable support.
Sex‐specific and caste‐specific brain adaptations related to spatial orientation in Cataglyphis ants

Cataglyphis desert ants are charismatic central place foragers. After long‐ranging foraging trips, individual workers navigate back to their nest relying mostly on visual cues. The reproductive caste faces other orientation challenges, i.e. mate finding and colony foundation. Here we compare brain structures involved in spatial orientation of Cataglyphis nodus males, gynes, and foragers by quantifying relative neuropil volumes associated with two visual pathways, and numbers and volumes of antennal lobe (AL) olfactory glomeruli. Furthermore, we determined absolute numbers of synaptic complexes in visual and olfactory regions of the mushroom bodies (MB) and a major relay station of the sky‐compass pathway to the central complex (CX). Both female castes possess enlarged brain centers for sensory integration, learning, and memory, reflected in voluminous MBs containing about twice the numbers of synaptic complexes compared with males. Overall, male brains are smaller compared with both female castes, but the relative volumes of the optic lobes and CX are enlarged indicating the importance of visual guidance during innate behaviors. Male ALs contain greatly enlarged glomeruli, presumably involved in sex‐pheromone detection. Adaptations at both the neuropil and synaptic levels clearly reflect differences in sex‐specific and caste‐specific demands for sensory processing and behavioral plasticity underlying spatial orientation.
microRNA-26a shuttled by extracellular vesicles secreted from adipose-derived mesenchymal stem cells reduce neuronal damage through KLF9-mediated regulation of TRAF2/KLF2 axis

ABSTRACT Extracellular vesicles (EVs) are nano-sized vesicles secreted actively by numeorus cells and have fundamental roles in intercellular communication through shuttling functional RNAs. This study sets out to elucidate the role of microRNA-26a (miR-26a) shuttled by EVs derived from adipose-derived mesenchymal stem cells (ASCs) in neuronal damage. After extraction and identification of ASC-derived EVs (ASC-EVs), mouse cortical neuronal cells were selected to establish an in vivo cerebral ischemia/reperfusion mouse model and an in vitro oxygen glucose deprivation/reperfusion (OGD/RP) cell model. The downstream genes of miR-26a were analyzed. The gain- and loss-of function of miR-26a and KLF9 was performed in mouse and cell models. Neuronal cells were subjected to co-culture with ASC-EVs and biological behaviors were detected by flow cytometry, Motic Images Plus, TTC, TUNEL staining, qRT-PCR and western blot analysis. ASC-EVs protected neuronal cells against neuronal damage following cerebral ischemia/reperfusion, which was related to transfer of miR-26a into neuronal cells. In neuronal cells, miR-26a targeted KLF9. KLF9 could suppress the expression of TRAF2 and KLF2 to facilitate neuronal damage. In vitro and in vivo results showed that miR-26a delivered by ASC-EVs inhibited neuronal damage. In summary, ASC-EVs-derived miR-26a can arrest neuronal damage by disrupting the KLF9-meidated suppression on TRAF2/KLF2 axis.
Highly sensitive fusion detection using plasma cell‐free RNA in non‐small‐cell lung cancers

ALK, ROS1, and RET kinase fusions are important predictive biomarkers of tyrosine kinase inhibitors (TKIs) in non‐small‐cell lung cancer (NSCLC). Analysis of cell‐free DNA (cfDNA) provides a noninvasive method to identify gene changes in tumor cells. The present study sought to use cfRNA and cfDNA for identifying fusion genes. A reliable protocol was established to detect fusion genes using cfRNA and assessed the analytical validity and clinical usefulness in 30 samples from 20 cases of fusion‐positive NSCLC. The results of cfRNA‐based assays were compared with tissue biopsy and cfDNA‐based liquid biopsy (Guardant360 plasma next‐generation sequencing [NGS] assay). The overall sensitivity of the cfRNA‐based assay was 26.7% (8/30) and that of cfDNA‐based assay was 16.7% (3/18). When analysis was limited to the samples collected at chemo‐naïve or progressive disease status and available for both assays, the sensitivity of the cfRNA‐based assay was 77.8% (7/9) and that of cfDNA‐based assay was 33.3% (3/9). Fusion gene identification in cfRNA was correlated with treatment response. These results suggest that the proposed cfRNA assay is a useful diagnostic test for patients with insufficient tissues to facilitate effective administration of first‐line treatment and is a useful tool to monitor the progression of NSCLC for consideration of second‐line treatments.
The role of acetic acid in orthopaedic surgery

Acetic acid has become more commonly used in orthopaedic surgery. The purposed roles include biofilm eradication and surgical debridement, postoperative scar reduction and managing soft tissue injuries. Current research is scarce and does not provide conclusive evidence behind acetic acid’s efficacy in orthopaedic procedures such as biofilm eradication or acetic acid iontophoresis in soft tissue injuries. Current literature on acetic acid’s effects on biofilm eradication is composed of in-vitro studies, which do not demonstrate the potential clinical efficacy of acetic acid. Acetic acid iontophoresis is a novel technique which is now more commonly accepted for soft tissues injuries. Our literature search identified calcifying tendonitis of the shoulder, rotator cuff tendinopathy, heel pain syndrome, plantar fasciitis, achilles tendonitis, calcifying tendonitis of the ankle, myositis ossificans and cervical spondylosis as documented clinical uses. In this narrative review, we present the current uses of acetic acid and acetic acid iontophoresis, while evaluating the evidence revolving around its efficacy, benefits and risks.
Fast and Accurate Craniomaxillofacial Landmark Detection via 3D Faster R-CNN

Automatic craniomaxillofacial (CMF) landmark localization from cone-beam computed tomography (CBCT) images is challenging, considering that 1) the number of landmarks in the images may change due to varying deformities and traumatic defects, and 2) the CBCT images used in clinical practice are typically large. In this paper, we propose a two-stage, coarse-to-fine deep learning method to tackle these challenges with both speed and accuracy in mind. Specifically, we first use a 3D faster R-CNN to roughly locate landmarks in down-sampled CBCT images that have varying numbers of landmarks. By converting the landmark point detection problem to a generic object detection problem, our 3D faster R-CNN is formulated to detect virtual, fixed-size objects in small boxes with centers indicating the approximate locations of the landmarks. Based on the rough landmark locations, we then crop 3D patches from the high-resolution images and send them to a multi-scale UNet for the regression of heatmaps, from which the refined landmark locations are finally derived. We evaluated the proposed approach by detecting up to 18 landmarks on a real clinical dataset of CMF CBCT images with various conditions. Experiments show that our approach achieves state-of-the-art accuracy of 0.89 ± 0.64mm in an average time of 26.2 seconds per volume.
Developing, validating and implementing performance metrics to evaluate the health and safety performance of sustainable building projects

Objectives. This research aims to develop, validate and implement health and safety performance metrics to evaluate the health and safety performance of sustainable building projects throughout their design and construction in Manitoba. Methods. Thirty-four metrics were developed following a detailed literature review and validated by expert judgement based on analytic soundness, practicality and predictability. Only 25 metrics satisfied these criteria, of which five were implemented via data collected on seven sustainable buildings and seven non-sustainable buildings. Results. The results showed that sustainable building projects had 12.7% higher recordable injuries rates than non-sustainable projects, although the difference was statistically insignificant. Findings from this research showed that for sustainable and non-sustainable building, PM 19 ‘The percentage of workers with unsafe behaviour based on conducted safety observations’ had a statistically significant and strong negative correlation with PM 8 ‘The percentage of workers who attended safety meetings’ and with PM 21 ‘The percentage of the total workdays in which safety meetings were held’. Conclusion. The findings of this research can be used by general contractors and safety practitioners looking to enact evidence-based guidance to manage safety proactively on site and improve health and safety performance of their sustainable building projects.
Halothane sensitivity as a field test for stress-susceptibility in the pig

The possible use of a pig's reaction to the anaesthetic halothane as a field test for Porcine Stress Syndrome in genetic improvement pro-grammes was investigated. A standard 3-min halothane test gave incidences of positive reaction of 20% in a composite Pietrain/Hampshire line, 5% in Norwegian Landrace, 1% in Hampshires and zero in Durocs, Large Whites and N. American Yorkshires. In the Pietrain/Hampshire population, two generations oftwo-way selection on the test gave a divergence in incidence of positive reaction of 85%, and the frequencies of affected progeny supported the hypothesis of monogenic recessive inheritance. From second tests made 20 days after the first, the probability of misclassifying a pig's reaction on one test was 5 ± 1%. Positive reactors had significantly shorter and leaner carcasses, fewer pigs born alive, poorer meat quality, higher mortality and greater plasma creatine phosphokinase activity than negative reactors.
Consumption of penicillins in the community, European Union/European Economic Area, 1997–2017

Abstract Objectives Data on consumption of penicillins in the community were collected from 30 EU/European Economic Area (EEA) countries over two decades. This article reviews temporal trends, seasonal variation, presence of change-points and changes in the composition of the main subgroups of penicillins. Methods For the period 1997–2017, data on consumption of penicillins, i.e. β-lactam antibacterials, penicillins (ATC group J01C), in the community aggregated at the level of the active substance, were collected using the WHO ATC/DDD methodology (ATC/DDD index 2019). Consumption was expressed in DDD per 1000 inhabitants per day and in packages per 1000 inhabitants per day. Consumption of penicillins was analysed based on ATC-4 subgroups, and presented as trends, seasonal variation, presence of change-points and compositional changes. Results In 2017, consumption of penicillins in the community expressed in DDD per 1000 inhabitants per day varied by a factor of 4.9 between countries with the highest (Spain) and the lowest (the Netherlands) consumption. An increase in consumption of penicillins, which was not statistically significant, was observed between 1997 and 2003 and up to 2010. A decrease, which was not statistically significant, was observed from 2010 onwards. Proportional consumption of combinations of penicillins, including β-lactamase inhibitors (J01CR) increased during 1997–2017, which coincided with a decrease in the proportional consumption of extended-spectrum penicillins (J01CA) and narrow-spectrum penicillins (J01CE). Conclusions Considerable variation in the patterns of consumption of penicillins was observed between EU/EEA countries. The consumption of penicillins in the EU/EEA community did not change significantly over time, while the proportional consumption of combinations of penicillins increased.
Treatment options for massive rotator cuff tears: a narrative review

The treatment of massive rotator cuff tears poses a challenge to orthopedic surgeons. The prevalence of massive rotator cuff tears is 40% of all rotator cuff tears. Compared with smaller tears, massive rotator cuff tears are often complicated by structural failure and poor outcomes and present a higher rate of recurrent tearing after surgical repair. Several management options are available but the selection of the most appropriate treatment for each patient can be challenging. To achieve the best outcomes, the orthopedic surgeon should have a good understanding of the indications, the pathomechanics and the clinical outcomes of the various treatment modalities. Treatment options include non-operative management, arthroscopic debridement with a biceps tenotomy or tenodesis, complete or partial repair, patch augmentation, superior capsular reconstruction, muscle/tendon transfer and reverse total shoulder arthroplasty. The purpose of this article is to review treatment options and clinical outcomes for the management of massive rotator cuff tears. (www.actabiomedica.it)
Domain-Specific Active and Sedentary Behaviors in Relation to Workers’ Presenteeism and Absenteeism

Objectives: To examine the associations between domain-specific sedentary and active behaviors and workers’ presenteeism and absenteeism in a sample of company employees. Methods: This study recruited participants (n = 2466) from a nationwide online survey database (Japan, 2019). Participants completed a questionnaire that captured data on relative and absolute presenteeism and absenteeism and domain-specific physical activity and sedentary behaviors. Results: Daily minutes of work-related physical activity were negatively associated with relative absenteeism. Daily minutes of leisure-related physical activity were positively associated with absolute presenteeism (ie, better productivity). Daily minutes of total physical activity were negatively and positively associated with relative absenteeism and absolute presenteeism (ie, better productivity). There was also a positive association between car sitting time and absolute absenteeism. Conclusions: A change in work culture and practices that support active behaviors at work and outside of work may improve employee's productivity indices.