Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome structure predicts modular transcriptome responses to genetic and environmental conditions

Understanding the plasticity, robustness, and modularity of transcriptome expression to genetic and environmental conditions is crucial to deciphering how organisms adapt in nature. To test how genome architecture influences transcriptome profiles, we quantified expression responses for distinct temperature-adapted genotypes of the nematode Caenorhabditis briggsae when exposed to chronic temperature stresses throughout development. We found that 56% of the 8795 differentially-expressed genes show genotype-specific changes in expression in response to temperature (genotype-by-environment interactions, GxE). Most genotype-specific responses occur under heat stress, indicating that cold versus heat stress responses involve distinct genomic architectures. The 22 co-expression modules that we identified differ in their enrichment of genes with genetic versus environmental versus interaction effects, as well as their genomic spatial distributions, functional attributes, and rates of molecular evolution at the sequence level. Genes in modules enriched for simple effects of either genotype or temperature alone tend to evolve especially rapidly, consistent with disproportionate influence of adaptation or weaker constraint on these subsets of loci. Chromosome scale heterogeneity in nucleotide polymorphism, however, rather than the scale of individual genes, predominate as the source of genetic differences among expression profiles, and natural selection regimes are largely decoupled between coding sequences and non-coding flanking sequences that contain cis-regulatory elements. These results illustrate how the form of transcriptome modularity and genome structure contribute to predictable profiles of evolutionary change.
Genomics of vancomycin-resistant Enterococcus faecium

Vancomycin-resistant Enterococcus faecium (VREfm) is a globally significant public health threat and was listed on the World Health Organization’s 2017 list of high-priority pathogens for which new treatments are urgently needed. Treatment options for invasive VREfm infections are very limited, and outcomes are often poor. Whole-genome sequencing is providing important new insights into VREfm evolution, drug resistance and hospital adaptation, and is increasingly being used to track VREfm transmission within hospitals to detect outbreaks and inform infection control practices. This mini-review provides an overview of recent data on the use of genomics to understand and respond to the global problem of VREfm.
Non-Intrusive Backplane-Based Testing Platform for Wireless Sensor Networks

Accurate runtime monitoring and testing is critical in the successful field deployment of wireless sensor networks(WSNs). Conventional techniques that demand extra reports from the sensor nodes could easily alter the node and network behaviors.The delay and asynchrony of the extra reports also implies that fine-grained monitoring can hardly be achieved.Sniff-Inside approach is presented in this case,and a non-intrusive backplane-based testing platform for wireless sensor networks is developed.With auxiliary test boards,the testing platform directly captures chip-level signals from wireless sensor nodes and the captured data are transferred through independent network paths to a monitoring server.The remote access client gains access to the test server by subscribing to test data on the server and finishes the analysis and processing of test data.It has been demonstrated that the operations of the monitored WSN can be fully identified through parsing the chip-level data across different nodes.The experimental results show that,through chip-level signal sniffing,the testing platform effectively gathers accurate runtime data with no side effects on the spontaneous behavior of sensor networks.The case study further shows the testing platform facilitates the tests of high-level functionalities,such as signal analysis,protocol verification and accurate evaluation of network performance.
Evaluation of low-cost 3D sound system for immersive virtual reality training systems

Among a PC-based virtual training systems,a 3D sound simulation can improve the capabilities of VR systems dramatically.Unfortunately,realistic 3D sound simulations are expensive and demand a tremendous amount of computational power to calculate re-verberation,occlusion,and obstruction effects.So a cheaper alternative has to be provided,so that a broader range of is applied.The experimental system setup using conventional stereo headsets in combination with a tracked HMD device,and used signal types for loca-lizing simulated sound events in a virtual training environment,for the end,the results is presented with regard to precision,speed.
A Secure Charging System for Electric Vehicles Based on Blockchain

Smart grids incorporating internet-of-things are emerging solutions to provide a reliable, sustainable and efficient electricity supply, and electric vehicle drivers can access efficient charging services in the smart grid. However, traditional electric vehicle charging systems are vulnerable to distributed denial of service and privileged insider attacks when the central charging server is attacked. The blockchain-based charging systems have been proposed to resolve these problems. In 2018, Huang et al. proposed the electric vehicle charging system using lightning network and smart contract. However, their system has an inefficient charging mechanism and does not guarantee security of key. We propose a secure charging system for electric vehicles based on blockchain to resolve these security flaws. Our charging system ensures the security of key, secure mutual authentication, anonymity, and perfect forward secrecy, and also provides efficient charging. We demonstrate that our proposed system provides secure mutual authentication using Burrows–Abadi–Needham logic and prevents replay and man-in-the-middle attacks using automated validation of internet security protocols and applications simulation tool. Furthermore, we compare computation and communication costs with previous schemes. Therefore, the proposed charging system efficiently applies to practical charging systems for electric vehicles.
Pediatric traumatic brain injury and antisocial behavior: are they linked? A systematic review

ABSTRACT Purpose: Despite growing evidence supporting a link between pediatric traumatic brain injury (TBI) and antisocial behavior, little work has rigorously evaluated this. This review aimed to explore systematically previous literature on the association between TBI before the age of 19 and severe behavioral problems such as violence, aggression and assault. Methods: All articles published from 1990 to 2018 were searched using four major databases, alongside manual searching and cross-referencing. Results: Sixteen articles met the eligibility criteria. Overall, they supported an association between pediatric TBI and antisocial behavior. Factors were identified that might influence this link, such as, for example, TBI severity and substance use. Conclusions: The review identified several issues in the current literature, highlighting key areas for improvement. It is imperative that more attention is paid to gathering detailed information regarding the temporal sequencing of events and TBI severity; evaluating the contribution of biopsychosocial variables co-occurring with TBI and antisocial behavior; disentangling which outcomes are specific to TBI versus any injury. The review has implications for the health and justice systems; regardless of whether TBI is the cause versus a contributing factor to antisocial behavior, increased awareness of their association could lead to more comprehensive assessments, tailored interventions and effective sentencing.
Phialomyces macrosporus: Chemical Constituents, Antimicrobial Activity and Complete NMR Assignments for the 7,7′‐Biphyscion

Five known secondary metabolites, chrysophanol (1), 7,7′‐biphyscion (2), secalonic acid D (3), mannitol (4) and trehalose (5) were isolated for the first time from the extracts of the fungus Phialomyces macrosporus. Their structures were elucidated by NMR methods (1D and 2D NMR analysis), optical activity and ESI‐MS. Complete 1H and 13C assignments were performed for compound 2. The antimicrobial activity was evaluated by serial microdilution assay for compounds 2 and 3 and results showed that compound 3 exhibited a significant growth inhibition at concentrations of 15.6 mg/ml (S. aureus and S. choleraesius) and 0.97 mg/mL (B. subtilis), comparable to the positive control.
Epithelial IDO1 Modulates AHR and Notch Signaling to Increase Differentiation of Secretory Cells and Alter Mucus-Associated Microbiota.

BACKGROUND & AIMS Inflammation, injury, and infection upregulate expression of the tryptophan metabolizing enzyme indoleamine 2,3-dioxygenase 1 (IDO1) in the intestinal epithelium. We studied the effects of cell-specific IDO1 expression in the epithelium at baseline and during intestinal inflammation in mice. METHODS We generated transgenic mice that overexpress fluorescence-tagged IDO1 in the intestinal epithelium under control of the villin promoter (IDO1-TG). We generated intestinal epithelial spheroids from mice with full-length Ido1 (controls), disruption of Ido1 (KO mice), and IDO1-TG and analyzed them for stem cell and differentiation markers by real-time PCR, immunoblotting, and immunofluorescence. Some mice were gavaged with enteropathogenic Escherichia coli (E2348/69) to induce infectious ileitis, and ileum contents were quantified by PCR. Separate sets of mice were given dextran sodium sulfate or 2,4,6-trinitrobenzenesulfonic acid to induce colitis; intestinal tissues were analyzed by histology. We utilized published datasets GSE75214 and GDS2642 of RNA expression data from ilea of healthy individuals undergoing screening colonoscopies (controls) and patients with Crohn's disease. RESULTS Histologic analysis of small intestine tissues from IDO1-TG mice revealed increases in secretory cells. Enteroids derived from IDO1-TG intestine had increased markers of stem, goblet, Paneth, enteroendocrine, and tuft cells, compared with control enteroids, with a concomitant decrease in markers of absorptive cells. IDO1 interacted non-enzymatically with the aryl hydrocarbon receptor (AHR) to inhibit activation of Notch1. Intestinal mucus layers from IDO1-TG mice were 2-fold thicker than mucus layers from control mice, with increased proportions of Akkermansia muciniphila and Mucispirillum schaedleri. Compared to controls, IDO1-TG mice demonstrated an 85% reduction in ileal bacteria (P=0.03) when challenged with enteropathogenic Escherichia coli, and were protected from immune infiltration, crypt drop-out, and ulcers following administration of dextran sodium sulfate or 2,4,6-trinitrobenzenesulfonic acid. In ilea of Crohn's disease patients, increased expression of IDO1 correlated with increased levels of MUC2, LYZ1 and AHR but reduced levels of SLC2A5. CONCLUSIONS In mice, expression of IDO1 in the intestinal epithelial promotes secretory cell differentiation and mucus production; levels of IDO1 are positively correlated with secretory cell markers in ilea of healthy individuals and Crohn's disease patients. We propose that IDO1 contributes to intestinal homeostasis.
Pancreatic Cancer Cachexia: The Role of Nutritional Interventions

Pancreatic cancer is a cancer with one of the highest mortality rates and many pancreatic cancer patients present with cachexia at diagnosis. The definition of cancer cachexia is not consistently applied in the clinic or across studies. In general, it is “defined as a multifactorial syndrome characterised by an ongoing loss of skeletal muscle mass with or without loss of fat mass that cannot be fully reversed by conventional nutritional support and leads to progressive functional impairment. ” Many regard cancer cachexia as being resistant to dietary interventions. Cachexia is associated with a negative impact on survival and quality of life. In this article, we outline some of the mechanisms of pancreatic cancer cachexia and discuss nutritional interventions to support the management of pancreatic cancer cachexia. Cachexia is driven by a combination of reduced appetite leading to reduced calorie intake, increased metabolism, and systemic inflammation driven by a combination of host cytokines and tumour derived factors. The ketogenic diet showed promising results, but these are yet to be confirmed in human clinical trials over the long-term. L-carnitine supplementation showed improved quality of life and an increase in lean body mass. As a first step towards preventing and managing pancreatic cancer cachexia, nutritional support should be provided through counselling and the provision of oral nutritional supplements to prevent and minimise loss of lean body mass.
Genetic association testing using the GENESIS R/Bioconductor package

SUMMARY The Genomic Data Storage (GDS) format provides efficient storage and retrieval of genotypes measured by microarrays and sequencing. We developed GENESIS to perform various single- and aggregate-variant association tests using genotype data stored in GDS format. GENESIS implements highly flexible mixed models, allowing for different link functions, multiple variance components, and phenotypic heteroskedasticity. GENESIS integrates cohesively with other R/Bioconductor packages to build a complete genomic analysis workflow entirely within the R environment. AVAILABILITY AND IMPLEMENTATION https://bioconductor.org/packages/GENESIS; vignettes included. SUPPLEMENTARY INFORMATION Supplementary tables and figures are available at Bioinformatics online.
Escalonamento e controle de admissão cross-layer para redes IEEE 802.16

O padrao IEEE 802.16, tambem conhecido como WiMAX (Worldwide Interoperability for Microwave Access) e seu adendo, o IEEE 802.16-2005, apresentam uma solucao de baixo custo para o acesso a Internet. A tecnologia e capaz de prover altas taxas de transferencias de dados para amplas areas geograficas, alto nivel de escalabilidade e baixo custo de instalacao e manutencao. Alem disso, a tecnologia inclui uma arquitetura para provisao de Qualidade de Servico (QoS) para aplicacoes de tempo real e aplicacoes que demandam altas taxas de transferencias. Para garantir os requisitos de QoS, o padrao define um mecanismo de sinalizacao entre a estacao base (BS) e a estacao cliente (SS), cinco classes de servico, um mecanismo de escalonamento e um mecanismo de controle de admissao de novas conexoes. Entretanto, as politicas que devem ser utilizadas na implementacao dos mecanismos de escalonamento e controle de admissao nao foram especificadas no padrao. O mecanismo de escalonamento e responsavel principalmente por garantir os requisitos de banda minima das conexoes, enquanto que o controle de admissao restringe o numero de conexoes para evitar a sobrecarga do enlace sem fio. Esta dissertacao propoe dois mecanismos de escalonamento e um mecanismo de controle de admissao para redes baseadas no padrao IEEE 802.16. Os mecanismos propostos sao totalmente compativeis com o padrao IEEE 802.16 e sao capazes de atender os requisitos de QoS das cinco classes de servico. Devido a alta variabilidade do sinal do canal sem fio, os mecanismos de escalonamento para redes cabeadas nao sao adequados para dispositivos sem fio. Dessa forma, as duas politicas de escalonamento e o mecanismo de controle de admissao propostos utilizam informacoes sobre a qualidade do sinal, atraves de uma abordagem cross-layer, para promover um uso eficiente do enlace sem fio. As tres solucoes foram avaliadas atraves de experimentos de simulacao utilizando um modulo para simulacao de redes IEEE 802.16. Abstract
Performance of primary care in different healthcare facilities: a cross-sectional study of patients’ experiences in Southern Malawi

Objective In most African countries, primary care is delivered through a district health system. Many factors, including staffing levels, staff experience, availability of equipment and facility management, affect the quality of primary care between and within countries. The purpose of this study was to assess the quality of primary care in different types of public health facilities in Southern Malawi. Study design This was a cross-sectional quantitative study. Setting The study was conducted in 12 public primary care facilities in Neno, Blantyre and Thyolo districts in July 2018. Participants Patients aged ≥18 years, excluding the severely ill, were selected to participate in the study. Primary outcomes We used the Malawian primary care assessment tool to conduct face-to-face interviews. Analysis of variance at 0.05 significance level was performed to compare primary care dimension means and total primary care scores. Linear regression models at 95% CI were used to assess associations between primary care dimension scores, patients’ characteristics and healthcare setting. Results The final number of respondents was 962 representing 96.1% response rate. Patients in Neno hospitals scored 3.77 points higher than those in Thyolo health centres, and 2.87 higher than those in Blantyre health centres in total primary care performance. Primary care performance in health centres and in hospital clinics was similar in Neno (20.9 vs 19.0, p=0.608) while in Thyolo, it was higher at the hospital than at the health centres (19.9 vs 15.2, p<0.001). Urban and rural facilities showed a similar pattern of performance. Conclusion These results showed considerable variation in experiences among primary care users in the public health facilities in Malawi. Factors such as funding, policy and clinic-level interventions influence patients’ reports of primary care performance. These factors should be further examined in longitudinal and experimental settings.
Economic burden of managing oral cancer patients in Sri Lanka: a cross-sectional hospital -based costing study

Objective Cancer of the oral cavity is the leading malignancy among males in Sri Lanka, and sixth among women. This study aimed to estimate costs of managing patients with oral cancer (OCA) in Sri Lanka for a 12 month period from diagnosis. Design Hospital based costing study. Settings Four selected cancer treatment centres in Sri Lanka. Participants Sixty-nine OCA patients: 60 were males and 12 had recurrent tumours. Outcome Societal perspectives (healthcare, household and indirect costs) were itemised. Costs to the healthcare system included surgery, Intensive Care Unit (ICU) care, chemotherapy and radiotherapy. Capital costs including apportioned value of land, buildings, equipment and furniture. Household costs consisted of out of pocket expenditure for healthcare and indirect costs of lost income. Costs were estimated from the stage of presentation for treatment to 1 year of follow-up. Results Mean cost of managing a single stage II OCA patient for 1 year was Sri Lankan rupees (SLR) 58 979 (US$394, at the midyear exchange rate in 2016) to the health system. Mean household cost was SLR 77 649 (US$518). The annual cost of managing a stage III or IV patient was SLR 303 620 (US$2027), with household costs of SLR 71 932 (US$480). Conclusions Owing to the high incidence of OCA in Sri Lanka, the economic costs associated with these diseases are enormous, resulting in negative impacts on both the healthcare system and individual families, seriously impacting the country’s economy. Policy-makers should take note of this burden and increase steps for prevention and control of this devastating disease.
A Trust Game Method Basing on Probability Model in Networks

随着可信计算的飞速发展,网络可信受到越来越多研究者的关注,信任模型的研究是其中主要研究内容之一. 本文提出一种网络环境下基于概率密度的信任博弈模型,将信任模型的研究和网络环境相结合,把整个信任系统分为证据收集、基于概率密度的信任度量以及服务博弈三部分. 证据收集模块利用数据挖掘和关联规则匹配进行信任证据的判断与评估. 信任度量模块将信任细分为信任度和确定度,并按照熵原理使用概率密度函数来表现. 虽然信任度.
Telemedicine in specialised palliative care: Healthcare professionals' and their perspectives on video consultations—A qualitative study

AIMS AND OBJECTIVES To explore the advantages and disadvantages of using video consultations, as experienced by specialised palliative care healthcare professionals, who are involved in palliative care at home. BACKGROUND One challenge in the work of specialised palliative care teams is the substantial resources used in terms of time and transport to and from the patient's home. Video consultations may be a solution for real-time specialised palliative home care. DESIGNS Hermeneutic, postphenomenology. METHODS An explorative qualitative study utilising data from field notes of an autobiographical diary, participant observations and semi-structured interviews with healthcare professionals. The COREQ guideline was used for reporting the study. See Appendix S1. The data collection took place in patients' homes and at the Department of Oncology, Odense University Hospital, Denmark. RESULTS Eight participants (n = 8); five community nurses; and three specialised palliative care team members-a head physician, a physiotherapist and a nurse-participated in the study. The healthcare professionals' knowledge was based on n = 82 video consultations with 11 patients. The range of video consultations was 3-18 per patient. The use of tablets in video consultations facilitated direct palliative care and led the community nurses and the specialised palliative care team nurse to co-operate. Potential barriers against using video consultations are the discussions about personal, and private issues regarding the illness, while family members are present. CONCLUSIONS Video consultations in specialised palliative home care are feasible, and the technology can facilitate multidisciplinary participation and co-operation among healthcare professionals. The continuous use of video consultations over time may increase the quality of specialised palliative home care. RELEVANCE TO CLINICAL PRACTICE The use of video consultations can provide direct specialised palliative care over distance involving healthcare professionals, patients and their relatives.
Patients with suspected benign tumors and glial fibrillary acidic protein autoantibody: an analysis of five cases

Abstract Aim: To investigate the clinical features of five glial fibrillary acidic protein (GFAP) antibody positive patients with suspected benign tumors and explore its underlying pathogenesis. Materials and methods: Overall, 1018 serum and cerebrospinal fluid (CSF) samples were tested by indirect immunofluorescence assay and data from five patients with suspected tumors and positive for GFAP autoantibody in the CSF were analyzed retrospectively. Results: The positive rate of GFAP antibody in the serum and CSF was 3.93% by indirect immunofluorescence assay. Tumors were diagnosed before or after neurologic onset in 5 of 40 patients (12.5%) and no deterioration of the tumors was found during the long-term follow-up. Of the five patients, one patient suffered a thyroid nodule, one patient had a small nodule in the left lung, two patients suffered meningiomas, and one patient had a suspicious eosinophilic granuloma. Conclusion: GFAP autoimmunity may be a paraneoplastic immune response with a low frequency of tumor in Chinese patients with GFAP astrocytopathy.