Miracle-dz/UniFAR-FTUs huggingface dataset:
Integrative analysis of genomic and transcriptomic data of normal, tumour, and co‐occurring leukoplakia tissue triads drawn from patients with gingivobuccal oral cancer identifies signatures of tumour initiation and progression

A thickened, white patch — leukoplakia — in the oral cavity is usually benign, but sometimes (in ~9% of individuals) it progresses to malignant tumour. Because the genomic basis of this progression is poorly understood, we undertook this study and collected samples of four tissues — leukoplakia, tumour, adjacent normal, and blood — from each of 28 patients suffering from gingivobuccal oral cancer. We performed multiomics analysis of the 112 collected tissues (four tissues per patient from 28 patients) and integrated information on progressive changes in the mutational and transcriptional profiles of each patient to create this genomic narrative. Additionally, we generated and analysed whole‐exome sequence data from leukoplakia tissues collected from 11 individuals not suffering from oral cancer. Nonsynonymous somatic mutations in the CASP8 gene were identified as the likely events to initiate malignant transformation, since these were frequently shared between tumour and co‐occurring leukoplakia. CASP8 alterations were also shown to enhance expressions of genes that favour lateral spread of mutant cells. During malignant transformation, additional pathogenic mutations are acquired in key genes (TP53, NOTCH1, HRAS) (41% of patients); chromosomal‐instability (arm‐level deletions of 19p and q, focal‐deletion of DNA‐repair pathway genes and NOTCH1, amplification of EGFR) (77%), and increased APOBEC‐activity (23%) are also observed. These additional alterations were present singly (18% of patients) or in combination (68%). Some of these alterations likely impact immune‐dynamics of the evolving transformed tissue; progression to malignancy is associated with immune suppression through infiltration of regulatory T‐cells (56%), depletion of cytotoxic T‐cells (68%), and antigen‐presenting dendritic cells (72%), with a concomitant increase in inflammation (92%). Patients can be grouped into three clusters by the estimated time to development of cancer from precancer by acquiring additional mutations (range: 4–10 years). Our findings provide deep molecular insights into the evolutionary processes and trajectories of oral cancer initiation and progression. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
Suggestions for Incorporating Entrepreneurship Education in the Classical Performance Studio

Abstract:As music institutions strive to embody the nature of entrepreneurship in greater capacities, both a lack of understanding and a lack of pedagogical knowledge serve as detriments to this end. The purpose of this exploratory study is to equip classical brass performance professors, whose goal it is to incorporate entrepreneurship in their studios, with practical suggestions on how to do so. Information from a survey of brass players was combined with literature regarding entrepreneurship education teaching practices, as well as practices from content areas generated from the survey in order to devise a set of suggestions for brass professors. The survey found that most brass players thought entrepreneurship should be taught in the private studio and that hard work, perseverance, and learning from failure were viewed as the most valuable content areas for a career in music. The suggestions are broken down into four themes: attitude; experiential learning; moving outside the studio; and character development. Subthemes are acting as a mentor, assisting in students' pursuit of individual goals, diverging from a didactic teaching approach, learning by doing, learning through failure, reflection, interacting with the community, social engagement, interaction with entrepreneurs, and grit.
Communication practices of parents and unaffected sibling needs in families impacted by a diagnosis of Angelman syndrome

Angelman syndrome (AS) is a rare neurodevelopmental condition affecting approximately 1 in 15,000 individuals. To date, limited research elucidates how parents communicate about AS with unaffected siblings and their needs. This study aimed to understand if, when, and what parents are communicating with unaffected siblings. The study also evaluated unaffected siblings' knowledge of AS and their perceptions of their siblings with AS. Recruitment took place through social media platforms and a multidisciplinary Chromosome 15 clinic. Families were eligible for the study if they had a child diagnosed with AS and at least one unaffected sibling age five years or older. Two novel surveys, one for the parent and one for each of the unaffected siblings, were created based on a detailed literature review and input from AS professionals. Eighty‐two families met the criteria and completed the required surveys. The majority of parents (94%) discussed AS with the unaffected siblings, but despite these discussions 41% of unaffected siblings still had unanswered questions. This study highlights the need for improved communication between parents and the unaffected siblings and emphasizes the importance of educational materials for unaffected siblings.
Anticipating VA/non-VA care coordination demand for Veterans at high risk for hospitalization

Abstract U.S. Veterans Affairs (VA) patients’ multi-system use can create challenges for VA clinicians who are responsible for coordinating Veterans’ use of non-VA care, including VA-purchased care (“Community Care”) and Medicare. To examine the relationship between drive distance and time—key eligibility criteria for Community Care—and VA reliance (proportion of care received in VA versus Medicare and Community Care) among Veterans at high risk for hospitalization. We used prepolicy data to anticipate the impact of the 2014 Choice Act and 2018 Maintaining Internal Systems and Strengthening Integrated Outside Networks Act (MISSION Act), which expanded access to Community Care. Cross-sectional analysis using fractional logistic regressions to examine the relationship between a Veteran's reliance on VA for outpatient primary, mental health, and other specialty care and their drive distance/time to a VA facility. Thirteen thousand seven hundred three Veterans over the age of 65 years enrolled in VA and fee-for-service Medicare in federal fiscal year 2014 who were in the top 10th percentile for hospitalization risk. Key explanatory variables were patients’ drive distance to VA > 40 miles (Choice Act criteria) and drive time to VA ≥ 30 minutes for primary and mental health care and ≥60 minutes for specialty care (MISSION Act criteria). Veterans at high risk for hospitalization with drive distance eligibility had increased odds of an outpatient specialty care visit taking place in VA when compared to Veterans who did not meet Choice Act eligibility criteria (odds ratio = 1.10, 95% confidence interval 1.05–1.15). However, drive time eligibility (MISSION Act criteria) was associated with significantly lower odds of an outpatient specialty care visit taking place in VA (odds ratio = 0.69, 95% confidence interval 0.67, 0.71). Neither drive distance nor drive time were associated with reliance for outpatient primary care or mental health care. VA patients who are at high risk for hospitalization may continue to rely on VA for outpatient primary care and mental health care despite access to outside services, but may increase use of outpatient specialty care in the community in the MISSION era, increasing demand for multi-system care coordination.
Enterotoxigenic Escherichia coli: intestinal pathogenesis mechanisms and colonization resistance by gut microbiota

ABSTRACT Enterotoxigenic Escherichia coli (ETEC) is a major cause of diarrhea in children and travelers in developing countries. ETEC is characterized by the ability to produce major virulence factors including colonization factors (CFs) and enterotoxins, that bind to specific receptors on epithelial cells and induce diarrhea. The gut microbiota is a stable and sophisticated ecosystem that performs a range of beneficial functions for the host, including protection against pathogen colonization. Understanding the pathogenic mechanisms of ETEC and the interaction between the gut microbiota and ETEC represents not only a research need but also an opportunity and challenge to develop precautions for ETEC infection. Herein, this review focuses on recent discoveries about ETEC etiology, pathogenesis and clinical manifestation, and discusses the colonization resistances mediated by gut microbiota, as well as preventative strategies against ETEC with an aim to provide novel insights that can reduce the adverse effect on human health.
Self-Supervised Motion Perception for Spatiotemporal Representation Learning

In this study, we propose a novel pretext task and a self-supervised motion perception (SMP) method for spatiotemporal representation learning. The pretext task is defined as video playback rate perception, which utilizes temporal dilated sampling to augment video clips to multiple duplicates of different temporal resolutions. The SMP method is built upon discriminative and generative motion perception models, which capture representations related to motion dynamics and appearance from video clips of multiple temporal resolutions in a collaborative fashion. To enhance the collaboration, we further propose difference and convolution motion attention (MA), which drives the generative model focusing on motion-related appearance, and leverage multiple granularity perception (MG) to extract accurate motion dynamics. Extensive experiments demonstrate SMP’s effectiveness for video motion perception and state-of-the-art performance of self-supervised representation models upon target tasks, including action recognition and video retrieval. Code for SMP is available at github.com/yuanyao366/SMP.
A review on intense pulsed light process as post-treatment for metal oxide thin films and nanostructures for device application

The intense pulsed light (IPL) post-treatment process has attracted great attention in the device fabrication due to its versatility and rapidity particularly for solution process functional structures in devices, flexible/printed electronics, and continuous manufacturing process. The metal oxide materials inherently have multi-functionality and have been widely used in form of thin films or nanostructures in device application such as thin film transistors, light emitting diodes, solar cells, supercapacitors, etc. The IPL treatment enhances the physical and/or chemical properties of the functional metal oxide through photothermal effects. However, most metal oxides are transparent to most range of visible light and require more energy for post-treatment. In this review, we have summarized the IPL post-treatment processes for metal oxide thin films and nanostructures in device applications. The sintering and annealing of metal oxides using IPL improved the device performances by employing additional light absorbing layer or back-reflector. The IPL process becomes an innovative versatile post-treatment process in conjunction with multi-functional metal oxides in near-future device applications.
RELIABILITY AND VALIDITY OF A NEW DIAGNOSTIC DEVICE FOR QUANTIFYING HEMIPARETIC ARM IMPAIRMENTS: AN EXPLORATORY STUDY

Objective To assess test-retest reliability and validity of a new diagnostic device, the Shoulder Elbow Perturbator, to quantify muscle weakness, abnormal synergy, (muscle activity-related) spasticity, and changes in viscoelastic joint properties of the elbow. Subjects Stroke patients, adults with cerebral palsy and healthy controls. Methods Test-retest reliability was evaluated using intra-class correlations (ICC) and assessment of measurement error. The device’s validity was evaluated by demonstrating differences between patients and healthy controls, and correlations of spasticity and abnormal synergy outcomes using the clinical Modified Tardieu Scale, the Fugl-Meyer Assessment, and the Test of Arm Selective Control. Results Reliability was excellent, with an ICC > 0.75 for synergy and ICCs > 0.90 for all other impairments, with relatively small measurement errors. Validity was confirmed by group differences between patients and healthy controls for muscle weakness, spasticity, and viscoelastic joint properties, but not for abnormal synergy. Correlation analysis with clinical scales confirmed validity for spasticity, while, for synergy, correlations were found in the patients with stroke, but not those with cerebral palsy. Conclusion This new diagnostic device is a reliable and valid instrument to assess multiple upper limb impairments in patients with neurological conditions, supporting its use in clinical practice. Further studies are needed to confirm these findings. LAY ABSTRACT Reliable and valid quantitative measurement of arm impairments due to neurological conditions is important for clinical decision-making. Current clinical measurement tools are subjective and not reliable. The aim of this study was therefore to assess the reliability and validity of a new diagnostic device to quantify multiple arm impairments (muscle weakness, abnormal synergy, spasticity, changes in viscoelastic joint properties) in patients with stroke, adults with cerebral palsy (CP), and healthy controls. Reliability was excellent for all impairments and was analysed by testing the consistency of the results on 2 occasions in the same subject. Validity was confirmed by group differences between patients and healthy controls for all impairments, except for synergy. Also, correlations of the results with clinical measurement tools were found for spasticity and synergy, except for synergy in patients with CP. In conclusion, this new diagnostic device is a reliable and valid instrument to assess multiple impairments of the elbow in patients with neurological conditions. Further studies are needed to confirm these findings.
Aromatase inhibitors and the incidence of Parkinson disease: A population‐based cohort study

Current guidelines recommend the treatment of hormone receptor–positive breast cancer with aromatase inhibitors (AIs) and tamoxifen in the adjuvant setting. Some observational studies have raised concerns that tamoxifen may be associated with an increased risk of Parkinson disease (PD). However, no studies have directly compared the risk of PD between AIs and tamoxifen in women diagnosed with breast cancer.
Integrative treatment of herbal medicine with western medicine on coronary artery lesions in children with Kawasaki disease

Abstract Background: Kawasaki disease (KD) is a major cause of coronary artery lesions (CALs) in children. Approximately 10% to 20% of children treated with intravenous immunoglobulin are intravenous immunoglobulin-resistant. This study evaluated the efficacy and safety of adding herbal medicine to conventional western medicines versus conventional western medicines alone for CALs in children with KD. Methods: This study searched 9 electronic databases until August 31, 2021. The inclusion criteria were the randomized controlled trials (RCTs) that assessed the CALs in children with KD and compared integrative treatment with conventional western treatments. Two authors searched independently for RCTs, including eligible articles that fulfilled the inclusion criteria, extracted data, and assessed the methodological quality using the Cochrane risk of bias tool. Meta-analysis was conducted using Cochrane Collaboration's Review Manager 5.4 software. The effect size was presented as the risk ratio (RR), and the fixed-effect models were used to pool the results. Results: The finally selected 12 studies included a total of 1030 KD patients. According to a meta-analysis, the integrative treatment showed better results than the conventional treatment in the CAL prevalence rate (RR = 2.00; 95% confidence interval [CI], 1.49–2.71; P < .00001), CAL recovery rate (RR = 1.27; 95% CI, 1.05–1.54; P = .02), and total effective rate (RR = 1.17; 95% CI, 1.11–1.23; P < .00001). Only 2 studies referred to the safety of the treatment. The asymmetrical funnel plot of the CAL prevalence rate indicated the possibility of potential publication bias. Conclusions: This review found the integrative treatment to be more effective in reducing the CAL prevalence rate and increasing the CAL recovery rate and total effective rate in KD patients than conventional western treatment. However, additional well-designed RCTs will be needed further to compensate restrictions of insufficient trials on safety, methodological quality, and publication bias.
A platform for optimizing mining complexes with uncertainty

Over the past several years, there has been substantial progress in developing new stochastic mine planning optimization models and computationally efficient solvers that are capable of managing risk throughout the entire mineral value chain. Recent models have focused on modelling the economic value of the products sold to customers, rather than attempting to evaluate the economic value of the individual mining blocks. This modelling shift permits the integration of many aspects that could not be previously considered, such as the ability to incorporate non-linear geometallurgical interactions in the processing streams. These advanced models have consistently shown the ability to generate a higher net present value than traditional deterministic optimization methods, which is a direct result of risk management. Despite these developments and consistent value-added results, existing commercial mine planning optimization tools have been reluctant to incorporate these new concepts in their platforms. This paper provides an overview of the ongoing development of COSMO Suite, a platform designed to aid in the dissemination of new stochastic mine planning optimization algorithms, techniques and models to the mining industry. COSMO Suite provides a graphical user interface to create advanced multi-mine and multi-process models for mineral value chains, create tailored optimization models and perform risk analyses on existing mine designs. This software is driven by COSMO Suite Library, a C++ application programming interface that compartmentalizes the process of modelling the mineral value chain, the optimization objectives and constraints, and the solvers, which allows for the rapid development, testing, benchmarking and deployment of new stochastic optimization models and algorithms. As a result, users can benefit from the accelerated knowledge transfer from an academic setting to industrial use.
Practices and issues of moulting programs for laying hens: a review

ABSTRACT 1. Moulting is a natural physiological process in birds when they shed their old feathers and replace them with new ones, and it is followed by reproductive quiescence resulting in reduced egg production. Different birds undergo moulting at different points in their life. Some birds have seasonal moulting while some moult at the end of their breeding cycle. This review will mainly focus on moulting practices associated with commercial layer birds because, in all other bird types, this is not managed. 2. Commercial farms commonly analyse the cost–benefit ratio to decide the time and method to adopt for moulting. Commercial layer farms adopt different practices to force birds out of moult and restart the production cycle. Animal welfare groups consider this as stressful and against animal welfare, raising questions about the ethics of this practice. 3. Many studies have been conducted using complete or partial feed withdrawal and non-feed withdrawal programs to measure their effectiveness in maintaining animal welfare, economy, and post-moult performance in mind. 4. Animal welfare should not be compromised during moulting. The United States Egg Producers and other such groups from the United Kingdom and Europe have decided to sell eggs produced only through a non-feed withdrawal moulting programs.
Enhanced Recovery After Surgery (ERAS) protocols for spine surgery – review of literature

Enhanced Recovery After Surgery (ERAS) is a multidisciplinary approach that uses a combination of evidence-based methods to improve patient care. Different ERAS protocols are used in various surgical fields but for spine surgery there is no widely used standard ERAS protocol. We compiled and examined the multiple available publications on ERAS protocols for spine surgery. Some general commonalities exist between ERAS protocols; however, a great deal of variety is observed in the granularity of important details such as differing drug choices or specific dosing. To assess and relate the different available ERAS protocols, we conducted a comprehensive narrative literature review focused on comparing commonalities and differences among the following aspects of ERAS protocols: mechanisms of action, post-surgery pain levels, opioid consumption, utilization of muscle relaxants, use of anti-inflammation drugs, and ambulation after surgery. Our goal in this project was to simplify the search process for institutions who review the literature. In this review, certain ERAS elements such as early ambulation, blood loss, pain management, and patient positioning are further explored in more depth.
Systematic identification of the interventional mechanism of Qingfei Xiaoyan Wan (QFXYW) in treatment of the cytokine storm in acute lung injury using transcriptomics-based system pharmacological analyses

Abstract Context Acute lung injury (ALI) is a complex, severe inflammation disease with high mortality, and there is no specific and effective treatment for ALI. Qingfei Xiaoyan Wan (QFXYW) has been widely used to treat lung-related diseases for centuries. Objective This study evaluates the potential effects and elucidates the therapeutic mechanism of QFXYW against LPS induced ALI in mice. Materials and methods BALB/c Mice in each group were first orally administered medicines (0.9% saline solution for the control group, 0.5 mg/kg Dexamethasone, or 1.3, 2.6, 5.2 g/kg QFXYW), after 4 h, the groups were injected LPS (1.0 mg/kg) to induce ALI, then the same medicines were administered repeatedly. The transcriptomics-based system pharmacological analyses were applied to screen the hub genes, RT-PCR, ELISA, and protein array assay was applied to verify the predicted hub genes and key pathways. Results QFXYW significantly decreased the number of leukocytes from (6.34 ± 0.51) × 105/mL to (4.01 ± 0.11) × 105/mL, accompanied by the neutrophil from (1.41 ± 0.19) × 105/mL to (0.77 ± 0.10) × 105/mL in bronchoalveolar lavage fluid (BALF). Based on Degree of node connection (Degree) and BottleNeck (BN), important parameters of network topology, the protein-protein interaction (PPI) network screened hub genes, including IL-6, TNF-α, CCL2, TLR2, CXCL1, and MMP-9. The results of RT-PCR, ELISA, and protein chip assay revealed that QFXYW could effectively inhibit ALI via multiple key targets and the cytokine-cytokine signalling pathway. Conclusions This study showed that QFXYW decreased the number of leukocytes and neutrophils by attenuating inflammatory response, which provides an important basis for the use of QFXYW in the treatment of ALI.