Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of Critical Genes and Five Prognostic Biomarkers Associated with Colorectal Cancer

Background Colorectal cancer (CRC) is a common malignant tumor with high incidence and mortality worldwide. The aim of this study was to evaluate the association between differentially expressed genes (DEGs), which may function as biomarkers for CRC prognosis and therapies, and the clinical outcome in patients with CRC. Material/Methods A total of 116 normal mucous tissue and 930 CRC tissue datasets were downloaded from the Gene Expression Omnibus database (GEO) and The Cancer Genome Atlas (TCGA). After screening DEGs based on limma package in R. Gene Ontology (GO) and KEGG enrichment analysis as well as the protein-protein interaction (PPI) networks were performed to predict the function of these DEGs. Meanwhile, Cox proportional hazards regression was used to build a prognostic model of these DEGs. Then, Kaplan-Meier risk analysis was used to test the model in TCGA datasets and validation datasets. Results In the present study, 300 DEGs with 100 upregulated genes and 200 downregulated genes were identified. The PPI networks including 162 DEGs and 256 nodes were constructed and 2 modules with high degree were selected. Moreover, 5 genes (MMP1, ACSL6, SMPD1, PPARGC1A, and HEPACAM2) were identified using the Cox proportional hazards stepwise regression. Kaplan-Meier risk curve in the TCGA and validation cohorts showed that high-risk group had significantly poor overall survival than the low-risk group. Conclusions Our study provided insights into the mechanisms of CRC formation and found 5 prognostic genes, which could potentially inform further studies and clinical therapies.
A Preference for Visual Speed During Smooth Pursuit Eye Movement

Does the preference for visual speed extend to motion perception when the eye moves? Current evidence from psychophysics and neuroscience is limited to small patches of image motion and stationary fixation. Active observers, however, are more likely to use large patches of retinal flow and extraretinal signals accompanying eye movement to judge motion. We therefore investigated whether speed remains a primary dimension during smooth pursuit using a “discrimination-contour” technique. Our results showed that observers struggled most when trying to discriminate pursued stimuli that traveled at the same speed but moved over different distances and durations. This remained the case when retinal flow was added, and when we isolated trials in which extraretinal signals were the only salient cue to motion. Our results suggest that preferential sensitivity for visual speed is quite general, supported by the many different types of motion mechanism used by active observers.
Choosing Between Daily and Event-Driven Pre-exposure Prophylaxis: Results of a Belgian PrEP Demonstration Project

Background: Daily pre-exposure prophylaxis and event-driven pre-exposure prophylaxis (PrEP) are efficacious in reducing HIV transmission among men who have sex with men (MSM). We analyzed baseline data from a PrEP demonstration project “Be-PrEP-ared” in Antwerp, Belgium, to understand preferences for daily PrEP or event-driven PrEP among MSM at high risk of HIV and factors influencing their initial choice. Methods: Cross-sectional data from an open-label prospective cohort study, using mixed methods. Participants who preregistered online were screened for eligibility and tested for sexually transmitted infections (STIs). Eligible participants chose between daily PrEP and event-driven PrEP and reported on behavioral data through an electronic questionnaire. In-depth interviews were conducted with a selected subsample. Bivariate associations were examined between preferred PrEP regimens and sociodemographic factors, sexual behavior, and STIs at screening. Results: In total, 200 participants were enrolled between October 2015 and December 2016. Self-reported levels of sexual risk-taking before enrollment were high. STI screening revealed that 39.5% had at least 1 bacterial STI. At baseline, 76.5% of participants preferred daily PrEP and 23.5% event-driven PrEP. Feeling able to anticipate HIV risk was the most frequent reason for preferring event-driven PrEP. Regimen choice was associated with sexual risk-taking behavior in the past 3 months. Almost all participants (95.7%) considered it likely that they would change their dosing regimen the following year. Conclusion: Event-driven PrEP was preferred by 23.5% of the participants, which better suits their preventive needs. Event-driven PrEP should be included in PrEP provision as a valuable alternative to daily PrEP for MSM at high risk of HIV.
Complex treatment of vascular prostheses infections

Abstract Infections after vascular reconstructions are very rare; however, when they occur, they are associated with a high risk of morbidity. In order to obtain the best results possible, the treatment needs to be initiated as early as possible, from the very first signs of infection, and it needs to be carried out in centers specializing in vascular surgery. The aim of the present study was to assess the incidence of infections in a single university center. This retrospective analysis over a 2-year period is based on the medical reports of hospitalized patients who were diagnosed with infection following revascularization. From 2013 to 2014, a number of 151 open reconstructive surgical procedures were performed. 15 patients suffered from infection (10%) of the vascular reconstruction. Of these patients, 40% have had an aorto-bifemoral bypass, 53%—a femoro-popliteal bypass, and 7% (n = 1)—an axillo-femoral bypass. According to the Samson classification, the patients were categorized as follows: group 2: 6 cases, group 3: 2 cases, group 4: 4 cases, and group 5: 3 cases. The most frequent bacteria found were methicillin-resistant Staphylococcus aureus (MRSA) (n = 6, 40%), followed by S aureus (n = 5, 33%). The treatment options were: application of antibiotics alone without any invasive treatment in 3 patients, local irrigation and debridement in 6 patients, complete explantation of the prosthesis with a new extra-anatomic bypass in 6 cases, and partial excision of the prosthesis, which was replaced and covered with muscle flap, in 3 cases. The amputation rate in our study was 18%, which corresponds to the rates published in the literature. The treatment of infections in vascular surgery needs to be complex and adapted to each individual patient, because infections being in a permanent dynamic state. The treatment needs to be performed in specialized centers that have large experience in vascular surgery, in order for the patient to have the best chances of survival and protection from amputation.
Earthquake prediction model using support vector regressor and hybrid neural networks

Earthquake prediction has been a challenging research area, where a future occurrence of the devastating catastrophe is predicted. In this work, sixty seismic features are computed through employing seismological concepts, such as Gutenberg-Richter law, seismic rate changes, foreshock frequency, seismic energy release, total recurrence time. Further, Maximum Relevance and Minimum Redundancy (mRMR) criteria is applied to extract the relevant features. A Support Vector Regressor (SVR) and Hybrid Neural Network (HNN) based classification system is built to obtain the earthquake predictions. HNN is a step wise combination of three different Neural Networks, supported by Enhanced Particle Swarm Optimization (EPSO), to offer weight optimization at each layer. The newly computed seismic features in combination with SVR-HNN prediction system is applied on Hindukush, Chile and Southern California regions. The obtained numerical results show improved prediction performance for all the considered regions, compared to previous prediction studies.
Stereosonic vision: Exploring visual-to-auditory sensory substitution mappings in an immersive virtual reality navigation paradigm

Sighted people predominantly use vision to navigate spaces, and sight loss has negative consequences for independent navigation and mobility. The recent proliferation of devices that can extract 3D spatial information from visual scenes opens up the possibility of using such mobility-relevant information to assist blind and visually impaired people by presenting this information through modalities other than vision. In this work, we present two new methods for encoding visual scenes using spatial audio: simulated echolocation and distance-dependent hum volume modulation. We implemented both methods in a virtual reality (VR) environment and tested them using a 3D motion-tracking device. This allowed participants to physically walk through virtual mobility scenarios, generating data on real locomotion behaviour. Blindfolded sighted participants completed two tasks: maze navigation and obstacle avoidance. Results were measured against a visual baseline in which participants performed the same two tasks without blindfolds. Task completion time, speed and number of collisions were used as indicators of successful navigation, with additional metrics exploring detailed dynamics of performance. In both tasks, participants were able to navigate using only audio information after minimal instruction. While participants were 65% slower using audio compared to the visual baseline, they reduced their audio navigation time by an average 21% over just 6 trials. Hum volume modulation proved over 20% faster than simulated echolocation in both mobility scenarios, and participants also showed the greatest improvement with this sonification method. Nevertheless, we do speculate that simulated echolocation remains worth exploring as it provides more spatial detail and could therefore be more useful in more complex environments. The fact that participants were intuitively able to successfully navigate space with two new visual-to-audio mappings for conveying spatial information motivates the further exploration of these and other mappings with the goal of assisting blind and visually impaired individuals with independent mobility.
68Ga-PSMA-11 PET/CT in Primary and Recurrent Prostate Carcinoma: Implications for Radiotherapeutic Management in 121 Patients

The present study analyzed the impact of 68Ga-labeled prostate-specific membrane antigen-HBED-CC (68Ga-PSMA-11) PET/CT on radiotherapeutic management in a large cohort of men with primary or recurrent prostate cancer. Methods: This study investigated 121 men with carcinoma of the prostate who underwent 68Ga-PSMA-11 PET/CT as well as conventional imaging. Fifty patients were treatment-naive, 11 had persistent prostate-specific antigen (PSA) soon after surgery, and 60 presented with recurrent PSA after definitive therapy. Changes in TNM classification of malignant tumor stage (TNM) and radiotherapeutic management after 68Ga-PSMA-11 imaging were compared with results achieved with conventional imaging. Results: In total, a change in TNM stage and radiotherapeutic management was observed for 49 patients (40.5%) and 62 patients (51.2%), respectively. In treatment-naive patients, a change in TNM stage and radiotherapeutic plan occurred in 26.0% and 44.0% of the cohort, respectively. For patients with PSA persistence or recurrence, TNM and radiotherapeutic management changed in 50.7% and 56.3%, respectively. Conclusion: 68Ga-PSMA-11 PET/CT may shortly become an indispensable tool for detecting prostate cancer lesions in treatment-naive patients as well as in men with recurrent disease or persistent PSA and seems to be helpful in personalizing radiotherapeutic management to the individual patients’ distribution of disease.
Maximum gait speed is associated with a wide range of cognitive functions in Japanese older adults with a Clinical Dementia Rating of 0.5

Physical and cognitive functions are mutually associated. However, it is unknown which markers of physical functions or body composition are most strongly associated with cognition. Here, we explored the association between body composition/physical performance and comprehensive neuropsychological assessments in an effort to identify reliable markers of cognition among factors in body composition/physical performance, including both usual and maximum gait speeds.
Biological Activities and Safety of Citrus spp. Essential Oils

Citrus fruits have been a commercially important crop for thousands of years. In addition, Citrus essential oils are valuable in the perfume, food, and beverage industries, and have also enjoyed use as aromatherapy and medicinal agents. This review summarizes the important biological activities and safety considerations of the essential oils of sweet orange (Citrus sinensis), bitter orange (Citrus aurantium), neroli (Citrus aurantium), orange petitgrain (Citrus aurantium), mandarin (Citrus reticulata), lemon (Citrus limon), lime (Citrus aurantifolia), grapefruit (Citrus × paradisi), bergamot (Citrus bergamia), Yuzu (Citrus junos), and kumquat (Citrus japonica).
A partially linear proportional hazards model for current status data

For analyzing current status data, a flexible partially linear proportional hazards model is proposed. Modeling flexibility is attained through using monotone splines to approximate the baseline cumulative hazard function, as well as B‐splines to accommodate nonlinear covariate effects. To facilitate model fitting, a computationally efficient and easy to implement expectation‐maximization algorithm is developed through a two‐stage data augmentation process involving carefully structured latent Poisson random variables. Asymptotic normality and the efficiency of the spline estimator of the regression coefficients are established, and the spline estimators of the nonparametric components are shown to possess the optimal rate of convergence under suitable regularity conditions. The finite‐sample performance of the proposed approach is evaluated through Monte Carlo simulation and it is further illustrated using uterine fibroid data arising from a prospective cohort study on early pregnancy.
Integrated Urban Sensing: A Geo-sensor Network for Public Health Monitoring and Beyond

Pervasive environmental monitoring implies a wide range of technical, but also socio-political challenges, and this applies especially to the sensitive context of the city. In this paper, we elucidate issues for bringing out pervasive urban sensor networks and associated concerns relating to fine-grained information provision. We present the Common Scents project, which is based on the Live Geography approach, and show how it can overcome these challenges. As opposed to hitherto sensing networks, which are mostly built up in monolithic and closed systems, the Common Scents approach aims to establish an open, standards based and modular infrastructure. This ensures interoperability, portability and flexibility, which are crucial prerequisites for pervasive urban sensing. The implementation – a real-time data integration and analysis system for air quality assessment – has been realised on top of the CitySense sensor network in the City of Cambridge, MA US together with the city’s Public Health Department responding to concrete needs of the city and its inhabitants. The second pilot using mobile sensors mounted on bicycles has been deployed in Copenhagen, Denmark. Preliminary results show highly fine-grained variability of pollutant dispersion in urban environments.
An automated high-resolution in vivo screen in zebrafish to identify chemical regulators of myelination

Myelinating oligodendrocytes are essential for central nervous system (CNS) formation and function. Their disruption is implicated in numerous neurodevelopmental, neuropsychiatric and neurodegenerative disorders. However, recent studies have indicated that oligodendrocytes may be tractable for treatment of disease. In recent years, zebrafish have become well established for the study of myelinating oligodendrocyte biology and drug discovery in vivo. Here, by automating the delivery of zebrafish larvae to a spinning disk confocal microscope, we were able to automate high-resolution imaging of myelinating oligodendrocytes in vivo. From there, we developed an image analysis pipeline that facilitated a screen of compounds with epigenetic and post-translational targets for their effects on regulating myelinating oligodendrocyte number. This screen identified novel compounds that strongly promote myelinating oligodendrocyte formation in vivo. Our imaging platform and analysis pipeline is flexible and can be employed for high-resolution imaging-based screens of broad interest using zebrafish.
The transient receptor potential channel TRPA 1 : from gene to pathophysiology

The Transient Receptor Potential Ankyrin 1 channel (TRPA1), is a member of the large TRP family of ion channels, and functions as a Ca permeable non-selective cation channel in many different cell processes, ranging from sensory to homeostatic tasks. TRPA1 is highly conserved across the animal kingdom. The only mammalian TRPA subfamily member, TRPA1, is widely expressed in neuronal (e.g. sensory dorsal root and trigeminal ganglia neurons)and in non-neuronal cells (e.g. epithelial cells, hair cells). It exhibits 14–19 amino-(N-)terminal ankyrin repeats, an unusual structural feature. The TRPA1 channel is activated by noxious cold (<17 °C) as well as by a plethora of chemical compounds that includes not only electrophilic compounds and oxidants that can modify, in an alkylative or oxidative fashion, nucleophilic cysteine residues in the channel’s N-terminus, but also compounds that do not covalently bind to the channel proteins (e.g. menthol, nifedipin). Based on localization and functional properties, TRPA1 is considered a key player in acute and chronic (neuropathic) pain and inflammation. Moreover, its role in the (patho)physiology of nearly all organ systems is anticipated, and will be discussed along with the potential of TRPA1 as a drug target for the management of various pathological conditions.
Genetic polymorphisms of organic cation transporter 1 (OCT1) and responses to metformin therapy in individuals with type 2 diabetes

Background: Metformin is one of the most commonly used drugs for the treatment of type 2 diabetes mellitus (T2DM). Despite its widespread use, there are considerable interindividual variations in metformin response, with about 35% of patients failing to achieve initial glycemic control. These variabilities that reflect phenotypic differences in drug disposition and action may indeed be due to polymorphisms in genes that regulate pharmacokinetics and pharmacodynamics of metformin. Moreover, interethnic differences in drug responses in some cases correspond to substantial differences in the frequencies of the associated pharmacogenomics risk allele. Aim: This study aims to highlight and summarize the overall effects of organic cation transporter 1(OCT1) polymorphisms on therapeutic responses to metformin and to evaluate the potential role of such polymorphisms in interethnic differences in metformin therapy. Methods: We conducted a systematic review according to the Preferred Reporting Items for Systematic Review and Meta-Analysis (PRISMA) guidelines. We searched for PubMed/MEDLINE, Embase, and CINAHL, relevant studies reporting the effects of OCT1 polymorphisms on metformin therapy in T2DM individuals. Data were extracted on study design, population characteristics, relevant polymorphisms, measure of genetic association, and outcomes. The presence of gastrointestinal side effects, glycated hemoglobin A1 (HbA1c) levels, fasting plasma glucose (FPG), and postprandial plasma glucose (PPG) concentrations after treatment with metformin were chosen as measures of the metformin responses. This systematic review protocol was registered with the International Prospective Register of Systematic Reviews (PROSPERO). Results: According to the data extracted, a total of 34 OCT1 polymorphisms were identified in 10 ethnic groups. Significant differences in the frequencies of common alleles were observed among these groups. Met408Val (rs628031) variant was the most extensively explored with metformin responses. Although some genotypes and alleles have been associated with deleterious effects on metformin response, others indeed, exhibited positive effects. Conclusion: Genetic effects of OCT1 polymorphisms on metformin responses were population specific. Further investigations in other populations are required to set ethnicity-specific reference for metformin responses and to obtain a solid basis to design personalized therapeutic approaches for T2DM treatment.
Toward adaptive radiotherapy for lung patients: feasibility study on deforming planning CT to CBCT to assess the impact of anatomical changes on dosimetry

Changes in lung architecture during a course of radiotherapy can alter the planned dose distribution to the extent that it becomes clinically unacceptable. This study aims to validate a quantitative method of determining whether a replan is required during the course of conformal radiotherapy. The proposed method uses deformable image registration (DIR) to flexibly map planning CT (pCT) data to the anatomy of online CBCT images. The resulting deformed CT (dCT) images are used as a basis for assessing the effect of anatomical change on dose distributions. The study used retrospective data from a sample of seven replanned lung patients. The settings of an in-house, open-source DIR algorithm were first optimised for CT-to-CBCT registrations of the anatomy of the thorax. Using these optimised parameters, each patient’s pCT was deformed to the CBCT acquired immediately before the replan. Registration accuracy was rigorously validated both geometrically and dosimetrically to confirm that the dCTs could reliably be used to inform replan decisions. A retrospective evaluation of the changes in dose delivered over time was then carried out for a single patient to demonstrate the clinical application of the proposed method. The geometric analysis showed good agreement between deformed structures and those same structures manually outlined on the CBCT images. Results were consistently better than those achieved with rigid-only registration. In the dosimetric analysis, dose distributions derived from the dCTs were found to match closely to the ‘gold standard’ replan CT (rCT) distributions across dose volume histogram and absolute dose difference measures. The retrospective analysis of serial CBCTs of a single patient produced reliable quantitative assessment of the dose delivery. Had the proposed method been available at the time of treatment, it would have enabled a more objective replan decision. DIR is a valuable clinical tool for dose recalculation in adaptive radiotherapy protocols for lung cancer patients.