Miracle-dz/UniFAR-FTUs huggingface dataset:
SLC45A2: A Melanoma Antigen with High Tumor Selectivity and Reduced Potential for Autoimmune Toxicity

T cell–based immunotherapy against melanoma-associated antigens can result in on-target/off-tumor cytotoxicity. SLC45A2, a protein overexpressed in melanoma compared with normal melanocytes, was identified as a T-cell target that may be less prone to inducing autoimmune side effects. Cytotoxic T lymphocyte (CTL)–based immunotherapies have had remarkable success at generating objective clinical responses in patients with advanced metastatic melanoma. Although the melanocyte differentiation antigens (MDA) MART-1, PMEL, and tyrosinase were among the first melanoma tumor-associated antigens identified and targeted with immunotherapy, expression within normal melanocytes of the eye and inner ear can elicit serious autoimmune side effects, thus limiting their clinical potential as CTL targets. Using a tandem mass spectrometry (MS) approach to analyze the immunopeptidomes of 55 melanoma patient–derived cell lines, we identified a number of shared HLA class I–bound peptides derived from the melanocyte-specific transporter protein SLC45A2. Antigen-specific CTLs generated against HLA-A*0201- and HLA-A*2402–restricted SLC45A2 peptides effectively killed a majority of HLA-matched cutaneous, uveal, and mucosal melanoma cell lines tested (18/25). CTLs specific for SLC45A2 showed significantly reduced recognition of HLA-matched primary melanocytes that were, conversely, robustly killed by MART1- and PMEL-specific T cells. Transcriptome analysis revealed that SLC45A2 mRNA expression in normal melanocytes was less than 2% that of other MDAs, therefore providing a more favorable melanoma-to-melanocyte expression ratio. Expression of SLC45A2 and CTL sensitivity could be further upregulated in BRAF(V600E)-mutant melanoma cells upon treatment with BRAF or MEK inhibitors, similarly to other MDAs. Taken together, our study demonstrates the feasibility of using tandem MS as a means of discovering shared immunogenic tumor-associated epitopes and identifies SLC45A2 as a promising immunotherapeutic target for melanoma with high tumor selectivity and reduced potential for autoimmune toxicity. Cancer Immunol Res; 5(8); 618–29. ©2017 AACR.
Delay analysis of wormhole based heterogeneous NoC

We introduce a novel evaluation methodology to analyze the delay of a wormhole routing based NoC with variable link capacities and a variable number of virtual channels per link. This methodology can be utilized to analyze different heterogeneous NoC architectures and traffic scenarios for which no analysis framework has been developed before. In particular, it can replace computationally-extensive simulations at the inner-loop of the link capacities and virtual channels allocation steps of the NoC topology optimization process. Our analysis introduces a set of implicit equations which can be efficiently solved iteratively. We demonstrate the accuracy of our approximation by comparing the analysis results to a simulation model for several use-cases and synthetic examples. In addition, we compare the analysis with simulation results for a chip-multi-processor (CMP) using SPLASH-2 and PARSEC traces for both homogeneous and heterogeneous NoC configurations.
Design of sampling set for bandlimited graph signal estimation

It is of particular interest to reconstruct or estimate bandlimited graph signals, which are smoothly varying signals defined over graphs, from partial noisy measurements. However, choosing an optimal subset of nodes to sample is NP-hard. We formularize the problem as the experimental design of a linear regression model if we allow multiple measurements on a single node. By relaxing it to a convex optimization problem, we get the proportion of sample for each node given the budget of total sample size. Then, we use a probabilistic quantization to get the number of each node to be sampled. Moreover, we analyze how the sample size influences whether our object function is well-defined by perturbation analysis. Finally, we demonstrate the performance of the proposed approach through various numerical experiments.
MusiteDeep: a deep‐learning framework for general and kinase‐specific phosphorylation site prediction

Motivation: Computational methods for phosphorylation site prediction play important roles in protein function studies and experimental design. Most existing methods are based on feature extraction, which may result in incomplete or biased features. Deep learning as the cutting‐edge machine learning method has the ability to automatically discover complex representations of phosphorylation patterns from the raw sequences, and hence it provides a powerful tool for improvement of phosphorylation site prediction. Results: We present MusiteDeep, the first deep‐learning framework for predicting general and kinase‐specific phosphorylation sites. MusiteDeep takes raw sequence data as input and uses convolutional neural networks with a novel two‐dimensional attention mechanism. It achieves over a 50% relative improvement in the area under the precision‐recall curve in general phosphorylation site prediction and obtains competitive results in kinase‐specific prediction compared to other well‐known tools on the benchmark data. Availability and implementation: MusiteDeep is provided as an open‐source tool available at https://github.com/duolinwang/MusiteDeep. Contact: xudong@missouri.edu Supplementary information: Supplementary data are available at Bioinformatics online.
Mechanical pulp fines: Effect of particle size and shape

The effect of different types of particles on the properties of the whole-fines fraction and on the paper properties was studied. The purpose of the investigation was to classify the fines particles into two different categories : fibrils and flakes. The fibril fraction consists of fibrillar material, i.e., ribbons, fibrils, and thin lamellae particles. The flake fraction consists of flake-like material, i.e., fiber wall fragments, thick lamellae, and ray cells. An advanced image analysis method was used to characterize the properties of fibrils and flakes. The results demonstrate that the fibril and flake fractions have distinctly different characteristics and effects on sheet properties. The fibrils are strongly responsible for the strength properties, while the flakes improve light scattering. Generally, the smaller the particle size, the higher the sheet density and strength. It is proposed that the amount of fibrillar material is an important basic property of mechanical pulp fines. Application : this study demonstrates how the papermaking properties of mechanical pulp fines are determined. The results can be used to control fines quality and ultimately pulp and paper quality.
Real-Time Obstacles Detection and Status Classification for Collision Warning in a Vehicle Active Safety System

This paper presents real-time obstacles detection and their status classification method for collision warning in the vehicle active safety system. Specifically, stereo cameras and millimeter wave (mmw)-radar are fused to help the driving ego-vehicle to find “Danger” or “Potential Danger” in a timely way through combining with the vehicle kinematic model. The proposed method makes full use of the unique advantages of stereo cameras and mmw-radar to sense the environment through several modules. Cameras are mainly used to detect the near or lateral dynamic objects and to obtain the obstacles region of interest (ROI) considering its rich information and high sensitivity to the lateral displacement, while far or longitudinal relative dynamic objects are detected by mmw-radar according to its observational ability to make up for the disadvantage of cameras. In detail, a cameras detector utilizes ”error vectors” rather than the optical flow to obtain dynamic classes through two times clustering. Mmw-radar mainly detects relative dynamic objects, whose absolute speed can be computed according to the ego-vehicle’s state. Then, the detected objects of these two detectors are integrated in an obstacles ROI map, which is obtained through an UV-disparity obstacles detection algorithm to get the final dynamic and relative dynamic objects. Finally, they are classified by comparing them with a dangerous area that is acquired according to the vehicle kinematic model in a special vehicle coordinate system, which is fixed to the ground temporarily. This method is tested on our mobile platforms and the results prove that it can work effectively even though the ego-vehicle drives quickly.
Elastic compensation of linear shape memory alloy actuators using compliant mechanisms

This article presents a modular architecture for shape memory alloy actuators elastically compensated by thin beams loaded axially beyond their buckling limit. Starting from the exact equations for the elastic curve of the beams, an approximate procedure is developed for the engineering design of the entire compensating system. The theory of the compensator is validated successfully against a finite element model and experimental results. The experimental characterization of a complete prototype actuator shows that the forces generated by the compensated actuator are constant for both instroke and outstroke over the full range of displacements. The actuator concept proposed lends itself to modular assembly to multiply either the stroke covered (series combination) or the force generated (parallel combination).
A Just Noticeable Distortion Based Rate Control Algorithm for Multiview Video Coding

To quantify human visual system characteristics to carry out rate controlling efficiently, this paper presents a new macroblock (MB) layer rate control algorithm for multi-view video coding (MVC) by improving quadratic rate-quantitative (R-Q) model based on the just noticeable distortion (JND) model. Firstly, the pixel-JND value of color image in multi-view video is stroked according to the related research in order to be used in the MB layer rate control. The proposed algorithm includes view layer, GOP layer, frame layer and MB layer, respectively. In the MB layer, the JND of the MB and mean absolute difference (MAD) in the quadratic R-Q model are firstly analyzed, the MAD is re-defined as perceptual MAD according to the JND with a pixel adjustment factor, and then QP of MB is computed through the re-defined quadratic R-Q model. Finally, a frequently-used image quality metric, peak signal-to-noise ratio (PSNR), is similarly re-defined as perceptual PSNR according to the JND. Experimental results show that the proposed algorithm can obtain higher image quality while precisely controls the bitrates. Moreover, the proposed algorithm not only can achieve better subjective quality, but also save the bitrates about 14.47% ~ 32.13%.
Myonectin Predicts the Development of Type 2 Diabetes

Context Myonectin has been identified as a myokine, expressed predominantly in skeletal muscle. However, its clinical implications are largely unknown. Objective The aim of this study is to investigate the relationship between myonectin (C1q tumor necrosis factor-α-related protein isoform 15) and type 2 diabetes mellitus (T2DM) in cross-sectional and interventional studies. Design In a separate study, oral glucose tolerance tests, a 45-minute bout of exercise, lipid infusions, and euglycemic-hyperinsulinemic clamps (EHCs) were performed to investigate the association of myonectin with homeostasis model assessment of insulin resistance (HOMA-IR) and T2DM. Circulating myonectin was measured by enzyme-linked immunosorbent assay. Patients One hundred four newly diagnosed T2DM (nT2DM), 109 impaired glucose tolerance (IGT), and 128 healthy individuals were recruited for this study. Results nT2DM and IGT subjects had higher circulating myonectin concentrations than normal subjects (82.3 ± 47.6 and 68.9 ± 46.6 vs. 45.2 ± 23.5 µg/L, P < 0.05 or P < 0.01). It was also found that in nT2DM individuals, circulating myonectin was higher than in IGT subjects. Plasma myonectin correlated positively with waist/hip ratio, percentage of body fat, triglyceride, fasting blood glucose, 2-hour blood glucose after glucose overload, fasting insulin, hemoglobin A1c, and HOMA-IR and negatively with the insulin sensitivity index in all of the study population. Multivariate logistic regression analysis revealed that circulating myonectin levels were significantly correlated with IGT and T2DM. A 45-minute bout of exercise did not change circulating myonectin levels in healthy, young individuals. Circulating myonectin levels were not significantly altered in response to an oral glucose challenge or EHC. In addition, acute elevated free fatty acid levels induced by lipid infusion had no effects on circulating myonectin. Conclusions These data suggest that myonectin may be a useful marker in predicting the development of prediabetes and diabetes.
Hierarchical Structure Controls Nanomechanical Properties of Vimentin Intermediate Filaments

Intermediate filaments (IFs), in addition to microtubules and microfilaments, are one of the three major components of the cytoskeleton in eukaryotic cells, playing a vital role in mechanotransduction and in providing mechanical stability to cells. Despite the importance of IF mechanics for cell biology and cell mechanics, the structural basis for their mechanical properties remains unknown. Specifically, our understanding of fundamental filament properties, such as the basis for their great extensibility, stiffening properties, and their exceptional mechanical resilience remains limited. This has prevented us from answering fundamental structure-function relationship questions related to the biomechanical role of intermediate filaments, which is crucial to link structure and function in the protein material's biological context. Here we utilize an atomistic-level model of the human vimentin dimer and tetramer to study their response to mechanical tensile stress, and describe a detailed analysis of the mechanical properties and associated deformation mechanisms. We observe a transition from alpha-helices to beta-sheets with subsequent interdimer sliding under mechanical deformation, which has been inferred previously from experimental results. By upscaling our results we report, for the first time, a quantitative comparison to experimental results of IF nanomechanics, showing good agreement. Through the identification of links between structures and deformation mechanisms at distinct hierarchical levels, we show that the multi-scale structure of IFs is crucial for their characteristic mechanical properties, in particular their ability to undergo severe deformation of ≈300% strain without breaking, facilitated by a cascaded activation of a distinct deformation mechanisms operating at different levels. This process enables IFs to combine disparate properties such as mechanosensitivity, strength and deformability. Our results enable a new paradigm in studying biological and mechanical properties of IFs from an atomistic perspective, and lay the foundation to understanding how properties of individual protein molecules can have profound effects at larger length-scales.
Efficacy and safety of Elevate® system on apical and anterior compartment prolapse repair with personal technique modification

ABSTRACT Aim: To evaluate the effectiveness and safety of Anterior Elevate® mesh kit system (AES) in woman with symptomatic stage 3 or 4 anterior and/or apical pelvic organ prolapse (POP). Materials and Methods: This retrospective, monocentric, single surgeon study enrolled between May 2010 and January 2013 fifty-six woman experiencing symptomatic anterior vaginal prolapse with or without apical descent (POP-Q stage 3 or 4). All women received a AES and 7 (12.5%) received a concomitant transvaginal hysterectomy. Primary endpoint was anatomic correction of prolapse; success was defined as POP-Q stage ≤ 1 or asymptomatic stage 2. Secondary endpoints were quality-of-life (QOL) results and patients' safety outcomes, which were assessed by 3 validated self-reporting questionnaires at baseline and annually: ICIQ-UI short form, ICIQ-VS and P-QOL. All patients completed 2-years and 28 women 3-years of follow-up. Surgical approach was modified in women with uterus, moving the two-propylene strips anteriorly around the cervix itself crossing one another, so the left will take place in the right side and the right on the opposite. This modification was made in order to better support the uterus. Results: Vaginal mesh exposure was present in 3 (5,3%) patients. Very good anatomical outcomes were seen, with one (1,8%) failure at 6-months, 4 (7,1%) at 1-year, 6 at 2-years (10,7%). Statistically significant improvements were seen in the ICIQ-VS and P-QOL questionnaires throughout follow-up. Conclusion: Our data suggest that AES is a minimally-invasive transvaginal procedure to repair anterior and apical POP, with good evidence related to mid-term safety and efficacy.
Secure and Efficient Regression Analysis Using a Hybrid Cryptographic Framework: Development and Evaluation

Background Machine learning is an effective data-driven tool that is being widely used to extract valuable patterns and insights from data. Specifically, predictive machine learning models are very important in health care for clinical data analysis. The machine learning algorithms that generate predictive models often require pooling data from different sources to discover statistical patterns or correlations among different attributes of the input data. The primary challenge is to fulfill one major objective: preserving the privacy of individuals while discovering knowledge from data. Objective Our objective was to develop a hybrid cryptographic framework for performing regression analysis over distributed data in a secure and efficient way. Methods Existing secure computation schemes are not suitable for processing the large-scale data that are used in cutting-edge machine learning applications. We designed, developed, and evaluated a hybrid cryptographic framework, which can securely perform regression analysis, a fundamental machine learning algorithm using somewhat homomorphic encryption and a newly introduced secure hardware component of Intel Software Guard Extensions (Intel SGX) to ensure both privacy and efficiency at the same time. Results Experimental results demonstrate that our proposed method provides a better trade-off in terms of security and efficiency than solely secure hardware-based methods. Besides, there is no approximation error. Computed model parameters are exactly similar to plaintext results. Conclusions To the best of our knowledge, this kind of secure computation model using a hybrid cryptographic framework, which leverages both somewhat homomorphic encryption and Intel SGX, is not proposed or evaluated to this date. Our proposed framework ensures data security and computational efficiency at the same time.
Mindfulness training for parents of children with special needs: Guidance for nurses in mental health practice

PROBLEM Parents of children with special needs encounter specific challenges in carrying out their caregiving roles. They experience difficulty accepting their children due to unrealistically high expectations. Mindfulness training (MT) may increase parental psychological well-being and acceptance. OBJECTIVE The purpose of this article is to examine the evidence-base for the effectiveness of MT in enhancing psychological well-being for parents of children with special needs as a foundation for guidance for nurses in mental health practice. METHODS A literature review of relevant research studies was undertaken using specific inclusion criteria. The literature was derived from three databases that identified 56 articles narrowed to 5, which met inclusion criteria. FINDINGS The studies indicated that cultivating a more mindful way of parenting is associated with reduced stress, anxiety, and depression. Parents experienced increased mindful awareness and improved psychological well-being, and they were more accepting of their children. Their children also had fewer behavior problems and enhanced positive interaction with their parents. Because mindfulness interventions fall within the scope of independent nursing practice, nurses can play a significant role in applying mindfulness to promote psychological well-being in parents who have children with special needs.
Effects of Detergent-Based Protocols on Decellularization of Corneas With Sclerocorneal Limbus. Evaluation of Regional Differences.

PURPOSE In this work, we decellularized whole porcine corneas including the sclerocorneal limbus (SCL) and we evaluated regional differences in order to identify an efficient method to decellularize whole corneas for future clinical use. METHODS We analyzed the efficiency of four decellularization protocols based on benzalkonium chloride (BAK), Igepal, sodium dodecyl sulfate (SDS), and Triton X-100 detergents on whole porcine corneas. RESULTS Results showed that the decellularization efficiency of most protocols was low, with the specific protocol resulting in more efficient levels of decellularization being 0.1% SDS for 48 hours, especially in the medium and posterior cornea regions. A significant correlation was found between the decellularization efficiency and the concentration of agent used (P = 0.0174; r = 0.1540), but not for the incubation time (P > 0.05). The analysis of cornea components preservation demonstrated that all protocols were able to preserve the integrity of the Bowman's layer and Descemet's membrane. Although the collagen structure was partially altered, the global decellularization groups showing highest preservation of the ECM collagen contents and orientation were Igepal and SDS, with differences among the three regions of the cornea. All global groups showed high levels of proteoglycan and glycoprotein preservation after decellularization, with the best results were found in the SDS group followed by the Igepal group. CONCLUSIONS These results suggest that very powerful protocols are necessary for whole-cornea decellularization. For the generation of lamelar corneas for clinical use, decellularization regional differences should be taken into account. TRANSLATIONAL RELEVANCE Decellularized whole corneas may be potential therapeutic agents for lamelar keratoplasty.
Capacity‐oriented approaches to developing childhood obesity interventions: a systematic review

Capacity‐oriented approaches to health interventions seek to empower the target population or community to manage the health issue themselves using resources they can control. Positive deviance, resilience and asset‐based approaches are three such methods of developing and implementing health interventions. This study aimed to review the efficacy of interventions explicitly applying these methods in addressing childhood obesity using adiposity as the primary outcome, measured by standardized body mass index. The search strategy was developed and implemented across four electronic databases. Of the 181 records identified and screened, 11 studies were identified as using a capacity‐oriented approach overall. Asset‐based approaches (n = 8 studies) consisted of 47 880 participants, positive deviance (n = 2 studies) consisted of 781 participants, and resilience‐based interventions (n = 1 study) consisted of 35 participants. The asset‐based approaches were mixed, with three of the eight studies showing a significant reduction in adiposity, while the other five did not find a difference. The positive deviance and resilience‐based studies showed signs of efficacy in reducing adiposity. There was significant design heterogeneity across studies, and varied interpretations and definitions of the approaches were used. Further work should attempt to achieve some consensus on the use of these approaches to facilitate comparison and advance the science of capacity‐oriented interventions for childhood obesity.