Miracle-dz/UniFAR-FTUs huggingface dataset:
Protein Loop Structure Prediction Using Conformational Space Annealing

We have developed a protein loop structure prediction method by combining a new energy function, which we call EPLM (energy for protein loop modeling), with the conformational space annealing (CSA) global optimization algorithm. The energy function includes stereochemistry, dynamic fragment assembly, distance-scaled finite ideal gas reference (DFIRE), and generalized orientation- and distance-dependent terms. For the conformational search of loop structures, we used the CSA algorithm, which has been quite successful in dealing with various hard global optimization problems. We assessed the performance of EPLM with two widely used loop-decoy sets, Jacobson and RAPPER, and compared the results against the DFIRE potential. The accuracy of model selection from a pool of loop decoys as well as de novo loop modeling starting from randomly generated structures was examined separately. For the selection of a nativelike structure from a decoy set, EPLM was more accurate than DFIRE in the case of the Jacobson set and had similar accuracy in the case of the RAPPER set. In terms of sampling more nativelike loop structures, EPLM outperformed EDFIRE for both decoy sets. This new approach equipped with EPLM and CSA can serve as the state-of-the-art de novo loop modeling method.
Consumption of ultra-processed foods and cancer risk: results from NutriNet-Santé prospective cohort

Abstract Objective To assess the prospective associations between consumption of ultra-processed food and risk of cancer. Design Population based cohort study. Setting and participants 104 980 participants aged at least 18 years (median age 42.8 years) from the French NutriNet-Santé cohort (2009-17). Dietary intakes were collected using repeated 24 hour dietary records, designed to register participants’ usual consumption for 3300 different food items. These were categorised according to their degree of processing by the NOVA classification. Main outcome measures Associations between ultra-processed food intake and risk of overall, breast, prostate, and colorectal cancer assessed by multivariable Cox proportional hazard models adjusted for known risk factors. Results Ultra-processed food intake was associated with higher overall cancer risk (n=2228 cases; hazard ratio for a 10% increment in the proportion of ultra-processed food in the diet 1.12 (95% confidence interval 1.06 to 1.18); P for trend<0.001) and breast cancer risk (n=739 cases; hazard ratio 1.11 (1.02 to 1.22); P for trend=0.02). These results remained statistically significant after adjustment for several markers of the nutritional quality of the diet (lipid, sodium, and carbohydrate intakes and/or a Western pattern derived by principal component analysis). Conclusions In this large prospective study, a 10% increase in the proportion of ultra-processed foods in the diet was associated with a significant increase of greater than 10% in risks of overall and breast cancer. Further studies are needed to better understand the relative effect of the various dimensions of processing (nutritional composition, food additives, contact materials, and neoformed contaminants) in these associations. Study registration Clinicaltrials.gov NCT03335644.
European Society of Cardiology, acute cardiovascular care association, SCAD study group: a position paper on spontaneous coronary artery dissection.

Spontaneous coronary artery dissection (SCAD) has long been recognized as a cause of acute coronary syndromes (ACS). Initially considered very rare and associated primarily with pregnancy and the peripartum period, the use of higher sensitivity Troponin assays and early angiography in ACS, coupled with greater awareness of the condition, has led to increased diagnosis, and it is now understood that SCAD represents a significant cause of ACS in predominantly young to middle-aged women, with most cases occurring outside the context of recent pregnancy.1,2 Although there are no randomized controlled trials in SCAD, knowledge has further advanced in the last 5-years as a result of an international research effort primarily focused on building and studying national SCAD registries.3–19 These studies have demonstrated, not only that SCAD is a distinct pathophysiological entity, but that there are key differences in management and outcomes compared to ACS of atherosclerotic aetiology. This position paper aims to set-out current knowledge on SCAD for the benefit of practicing clinicians caring for patients with this condition. It presents the consensus on contemporary management and areas of controversy and uncertainty, which remain a focus of ongoing research. The information is provided to support clinical care providers but is not intended to replace individualized decision-making by clinicians and other health care professionals.
Overcoming the Neonatal Limitations of Inducing Germinal Centers through Liposome-Based Adjuvants Including C-Type Lectin Agonists Trehalose Dibehenate or Curdlan

Neonates and infants are more vulnerable to infections and show reduced responses to vaccination. Consequently, repeated immunizations are required to induce protection and early life vaccines against major pathogens such as influenza are yet unavailable. Formulating antigens with potent adjuvants, including immunostimulators and delivery systems, is a demonstrated approach to enhance vaccine efficacy. Yet, adjuvants effective in adults may not meet the specific requirements for activating the early life immune system. Here, we assessed the neonatal adjuvanticity of three novel adjuvants including TLR4 (glucopyranosyl lipid adjuvant-squalene emulsion), TLR9 (IC31®), and Mincle (CAF01) agonists, which all induce germinal centers (GCs) and potent antibody responses to influenza hemagglutinin (HA) in adult mice. In neonates, a single dose of HA formulated into each adjuvant induced T follicular helper (TFH) cells. However, only HA/CAF01 elicited significantly higher and sustained antibody responses, engaging neonatal B cells to differentiate into GCs already after a single dose. Although antibody titers remained lower than in adults, HA-specific responses induced by a single neonatal dose of HA/CAF01 were sufficient to confer protection against influenza viral challenge. Postulating that the neonatal adjuvanticity of CAF01 may result from the functionality of the C-type lectin receptor (CLR) Mincle in early life we asked whether other C-type lectin agonists would show a similar neonatal adjuvanticity. Replacing the Mincle agonist trehalose 6,6′-dibehenate by Curdlan, which binds to Dectin-1, enhanced antibody responses through the induction of similar levels of TFH, GCs and bone marrow high-affinity plasma cells. Thus, specific requirements of early life B cells may already be met after a single vaccine dose using CLR-activating agonists, identified here as promising B cell immunostimulators for early life vaccines when included into cationic liposomes.
Respiratory motion correction for free-breathing 3D abdominal MRI using CNN-based image registration: a feasibility study.

OBJECTIVE Free-breathing abdomen imaging requires non-rigid motion registration of unavoidable respiratory motion in three-dimensional undersampled data sets. In this work, we introduce an image registration method based on the convolutional neural network (CNN) to obtain motion-free abdominal images throughout the respiratory cycle. METHODS Abdominal data were acquired from 10 volunteers using a 1.5 T MRI system. The respiratory signal was extracted from the central-space spokes, and the acquired data were reordered in three bins according to the corresponding breathing signal. Retrospective image reconstruction of the three near-motion free respiratory phases was performed using non-Cartesian iterative SENSE reconstruction. Then, we trained a CNN to analyse the spatial transform among the different bins. This network could generate the displacement vector field and be applied to perform registration on unseen image pairs. To demonstrate the feasibility of this registration method, we compared the performance of three different registration approaches for accurate image fusion of three bins: non-motion corrected (NMC), local affine registration method (LREG) and CNN. RESULTS Visualization of coronal images indicated that LREG had caused broken blood vessels, while the vessels of the CNN were sharper and more consecutive. As shown in the sagittal view, compared to NMC and CNN, distorted and blurred liver contours were caused by LREG. At the same time, zoom-in axial images presented that the vessels were delineated more clearly by CNN than LREG. The statistical results of the signal-to-noise ratio, visual score, vessel sharpness and registration time over all volunteers were compared among the NMC, LREG and CNN approaches. The SNR indicated that the CNN acquired the best image quality (207.42 Â± 96.73), which was better than NMC (116.67 Â± 44.70) and LREG (187.93 Â± 96.68). The image visual score agreed with SNR, marking CNN (3.85 Â± 0.12) as the best, followed by LREG (3.43 Â± 0.13) and NMC (2.55 Â± 0.09). A vessel sharpness assessment yielded similar values between the CNN (0.81 Â± 0.03) and LREG (0.80 Â± 0.04), differentiating them from the NMC (0.78 Â± 0.06). When compared with the LREG-based reconstruction, the CNN-based reconstruction reduces the registration time from 1 h to 1 min. CONCLUSION Our preliminary results demonstrate the feasibility of the CNN-based approach, and this scheme outperforms the NMC- and LREG-based methods. Advances in knowledge: This method reduces the registration time from ~1 h to ~1 min, which has promising prospects for clinical use. To the best of our knowledge, this study shows the first convolutional neural network-based registration method to be applied in abdominal images.
Robust trajectory tracking and visual servoing schemes for MEMS manipulation

This paper focuses on the automation of manipulation and assembly of microcomponents using visual feedback controls. Trajectory planning and tracking methods are proposed in order to avoid occlusions during microparts manipulation and to increase the success rate of pick-and-place manipulation cycles. The methods proposed are validated using a five degree-of-freedom (DOF) microrobotic cell including a 3 DOF mobile platform, a 2 DOF micromanipulator, a gripping system and a top-view imaging system. Promising results on accuracy and repeatability of microballs manipulation tasks are obtained and presented.
Vaccination with Melanoma Cells Infected with Recombinant Newcastle Disease Virus Suppresses Tumor Metastasis

Newcastle Disease Virus (NDV) is an RNA virus, which infects several tumor cells and shows cellular toxicity towards them. The antitumor activity of NDV has been reported in several tumors. In this study, we evaluated the antitumor effect of a NDV-infected melanoma cell vaccine on lung metastasis based on tumor-specific immune responses in a mouse model. B16 mouse melanoma cells were infected with the GFP-expressing recombinant NDV (rNDV) to prepare the vaccine (rNDV-BV). C57BL/6 mice were then immunized twice with rNDV-BV and intravenously inoculated with B16 cells, and the number of metastasis dots in the lungs was evaluated 21 days later. The mice were divided into three groups: pre-inoculation (mice were vaccinated before inoculation with B16 cells), post-inoculation (mice were vaccinated after inoculation with B16 cells), and control (mice were inoculated with DMEM) groups. To evaluate the immune responses, the mouse splenocytes were monitored for lymphocyte subsets and dendritic cells, and IFN-γ and IL-10gene expression after metastasis was measured. The mice receiving rNDV-BV showed prolonged survival and a lower number of metastasis dots. Furthermore, lung metastasis was significantly decreased upon post-metastasis vaccination with rNDV-BV. In pre-inoculation group, cytokine responses against tumor antigens were also significantly affected: IFN-γ levels were increased, but IL-10 levels were decreased. The vaccination also increased the T cell population along with the number of CD8+ dendritic cells during early metastasis. These results indicated that rNDV-BV induced an IFN-γ response against the tumor antigen and suppressed metastasis in the mouse model. Keywords: Autologous-tumor Vaccine; Newcastle Disease Virus; Melanoma Lung Metastasis Mouse Model; Cell-Mediated Immunity; IFN-γ; Abbreviations: NDV: Newcastle Disease Virus; rNDV: Recombinant Newcastle Disease Virus; rNDV-BV: Recombinant Newcastle Disease Virus to Prepare the Vaccine; B16: B16 Mouse Melanoma Cell; IFN: Interferon; IL: Interleukin.
Using the Inflammacheck Device to Measure the Level of Exhaled Breath Condensate Hydrogen Peroxide in Patients With Asthma and Chronic Obstructive Pulmonary Disease (The EXHALE Pilot Study): Protocol for a Cross-Sectional Feasibility Study

Background Asthma and Chronic Obstructive Pulmonary Disease (COPD) are common conditions that affect over 5 million people in the United Kingdom. These groups of patients suffer significantly from breathlessness and recurrent exacerbations that can be difficult to diagnose and go untreated. A common feature of COPD and asthma is airway inflammation that increases before and during exacerbations. Current methods of assessing airway inflammation can be invasive, difficult to perform, and are often inaccurate. In contrast, measurement of exhaled breath condensate (EBC) hydrogen peroxide (H2O2) is performed during normal tidal breathing and is known to reflect the level of global inflammation in the airways. There is a need for novel tools to diagnose asthma and COPD earlier and to detect increased airway inflammation that precedes an exacerbation. Objective The aim of this study was to explore the use of a new handheld device (called Inflammacheck) in measuring H2O2 levels in EBC. We will study whether it can measure EBC H2O2 levels consistently and whether it can be used to differentiate asthma and COPD from healthy controls. Methods We will perform a cross-sectional, feasibility, pilot study of EBC H2O2 levels, as measured by Inflammacheck, and other markers of disease severity and symptom control in patients with asthma and COPD and volunteers with no history of lung disease. Participants will be asked to provide an exhaled breath sample for measurement of their EBC H2O2 using Inflammacheck. The result will be correlated with disease stage, spirometry, fractional exhaled nitric oxide (FeNO), and symptom control scores. Results This study’s recruitment is ongoing; it is anticipated that the results will be available in 2018. Conclusions The EXhaled Hydrogen peroxide As a marker of Lung diseasE (EXHALE) pilot study will provide an evaluation of a new method of measuring EBC H2O2. It will assess the device’s consistency and ability to distinguish airway inflammation in asthma and COPD compared with healthy controls.
Membrane Topology and Heme Binding of the Histidine Kinases HrrS and ChrS in Corynebacterium glutamicum

The HrrSA and the ChrSA two-component systems play a central role in the coordination of heme homeostasis in the Gram-positive soil bacterium Corynebacterium glutamicum and the prominent pathogen Corynebacterium diphtheriae, both members of the Corynebacteriaceae. In this study, we have performed a comparative analysis of the membrane topology and heme-binding characteristics of the histidine kinases HrrS and ChrS of C. glutamicum. While the cytoplasmic catalytic domains are highly conserved between HrrS and ChrS, the N-terminal sensing parts share only minor sequence similarity. PhoA and LacZ fusions of the N-terminal sensor domains of HrrS and ChrS revealed that both proteins are embedded into the cytoplasmic membrane via six α-helices. Although the overall membrane topology appeared to be conserved, target gene profiling indicated a higher sensitivity of the ChrS system to low heme levels (< 1 μM). In vitro, solubilized and purified full-length proteins bound heme in a 1:1 stoichiometry per monomer. Alanine-scanning of conserved amino acid residues in the N-terminal sensor domain revealed three aromatic residues (Y112, F115, and F118), which apparently contribute to heme binding of HrrS. Exchange of either one or all three residues resulted in an almost abolished heme binding of HrrS in vitro. In contrast, ChrS mutants only displayed a red shift of the soret band from 406 to 418 nm suggesting an altered set of ligands in the triple mutant. In line with target gene profiling, these in vitro studies suggest distinct differences in the heme-protein interface of HrrS and ChrS. Since the membrane topology mapping displayed no extensive loop regions and alanine-scanning revealed potential heme-binding residues in α-helix number four, we propose an intramembrane sensing mechanism for both proteins. Overall, we present a first comparative analysis of the ChrS and HrrS kinases functioning as transient heme sensors in the Corynebacteriaceae.
Parameter identification and automatic control loop tuning for PMAC servo motor drives

High performance servo motor drives generally consisted of current, velocity, and position control loops. Tuning these controllers to achieve satisfactory and consistent dynamic responses is important. In this paper, a parameter identification and auto-tuning scheme for PMAC servo motor drives is presented. Motor electrical parameters such as resistance and inductances are identified first for current control loop tuning. Then, torque constant and mechanical parameters are identified for velocity and position loop tuning. The experimental results verified that the proposed scheme can estimate parameters with good accuracy. Furthermore, depending on the setting of the tuning process, the auto-tune process can be completed within 1.9 seconds. The control system tuned by the proposed scheme can achieve good dynamic performance.
IgA and IgG against Mycobacterium tuberculosis Rv2031 discriminate between pulmonary tuberculosis patients, Mycobacterium tuberculosis-infected and non-infected individuals

As part of a major project to investigate protective and diagnostic immune markers against tuberculosis (TB), we measured antibody isotype responses to Mycobacterium tuberculosis (Mtb) antigens (LAM, Rv2031, and HBHA) in cohorts of 149 pulmonary tuberculosis patients (PTBP), 148 household contacts (HHCs), and 68 community controls (CCs) in an endemic setting. ELISA was used to measure levels of IgA, IgG, and IgM from sera of cohorts at baseline, and at 6 and 12 months from entry. The results show that there were significant differences in IgA, IgG, and IgM responses to the different antigens and in the three cohorts. At baseline, the level of IgM against RV2031 and LAM did not vary between cohorts, but the levels of IgA and IgG against Rv2031 were significantly higher in PTB patients than HHCs and CCs, followed by HHCs, and the lowest in CCs. In patients, there was a significant variation in antibody responses before and after chemotherapy. The levels of IgA and IgG against HBHA, and IgA against Rv2031 decreased significantly and remained low, while IgA and IgG against LAM increased significantly and remained high following chemotherapy. However, the levels of IgM against Rv2031 and LAM increased at 6 months but decreased again at 12 months. IgM against HBHA did not show any significant variation before and after chemotherapy. Similarly, there were also significant variations in antibody responses in HHCs over time. Our results show that there are significant variations in IgA, IgG and IgM responses to the different antigens and in the three cohorts, implying that not all antibody isotype responses are markers of clinical TB. In addition, the current and previous studies consistently show that IgA and IgG against Rv2031 discriminate between clinical disease, Mtb-infected and non-infected individuals.
Research on Accumulation of Zinc (Zn) and Cadmium (Cd) in Sunflower Oil

Bulgaristan kokenli hibrit Albena, U-41 ve U-70 aycicegi cesitleri kullanilmistir. Calisma, agir metallerle kirlenmis ve kirlenmemis iki farkli bolgede yapilmistir. Agir metallerle kirlenmis bolgelerde aycicegi yagindaki kadmiyum birikimi bakimindan onemli farkliliklar belirlenmistir
Methodology for the IPM motor magnetic model computation based on finite element analysis

This paper describes a methodology for the computation of the magnetic models of interior permanent magnet synchronous motors based on finite element analysis. The anisotropic rotor magnetic structure imposes to account for the saturation and cross-coupling effects in the machine model; the temperature effect on the permanent magnets is considered too. The proposed magnetic model can be used in numerical dynamic simulations aimed to identify the most suitable control strategy to fully exploit the machine performance without the necessity of other finite element simulations except those for the magnetic model identification. The feasibility of the presented methodology has been proved with a case of study modeling a six-phase IPM machine; the obtained numerical results are presented and discussed in detail.
Motion Signals With Velocity Jumps: Velocity Estimation Employing Only Quantized Position Data

This letter addresses the problem of causal velocity estimation of motion signals exhibiting sudden velocity changes. It is explicitly assumed that only sampled quantized position data are available, and that no dynamic system model is at hand, to allow for an effective solution with minimal a priori information. Our solution consists of a finite-response filter with adaptive window length and a velocity jump detection algorithm. A velocity jump is detected when the difference between sampled position data and predicted position is larger than a parametric threshold. The specific value for the threshold is obtained via an analytical formula that depends on sampling time, maximum allowed variation in acceleration (away from velocity jumps), and encoder resolution. The developed method is first demonstrated on simulated quantized data corresponding to a bouncing motion and its performance compared to that of other existing non-model-based methods. Its effectiveness is furthermore illustrated by means of trajectory tracking results on an experimental setup experiencing impacts.
Optimization of Real-Time Software Implementing Multi-Rate Synchronous Finite State Machines

Model-based design using Synchronous Reactive (SR) models is becoming widespread for control software development in industry. However, software synthesis is challenging for multi-rate SR models consisting of blocks modeled with finite state machines, due to the complexity of validating the system’s real-time schedulability. The existing approach uses the simplified periodic task model to allow an efficient schedulability analysis, which leads to pessimistic and suboptimal solutions. Instead, in this paper, we adopt a more accurate but more complex schedulability analysis. We develop several optimization techniques to improve the algorithm’s efficiency. Experimental results on synthetic systems and an industrial case study show that the proposed optimization framework preserves the solution optimality but is much faster (e.g., 1000× for systems with 15 blocks) than the branch-and-bound algorithm, and it generates better control software than the existing approach.