Miracle-dz/UniFAR-FTUs huggingface dataset:
The Human CD8+ T Cell Responses Induced by a Live Attenuated Tetravalent Dengue Vaccine Are Directed against Highly Conserved Epitopes

ABSTRACT The incidence of infection with any of the four dengue virus serotypes (DENV1 to -4) has increased dramatically in the last few decades, and the lack of a treatment or vaccine has contributed to significant morbidity and mortality worldwide. A recent comprehensive analysis of the human T cell response against wild-type DENV suggested an human lymphocyte antigen (HLA)-linked protective role for CD8+ T cells. We have collected one-unit blood donations from study participants receiving the monovalent or tetravalent live attenuated DENV vaccine (DLAV), developed by the U.S. National Institutes of Health. Peripheral blood mononuclear cells from these donors were screened in gamma interferon enzyme-linked immunosorbent spot assays with pools of predicted, HLA-matched, class I binding peptides covering the entire DENV proteome. Here, we characterize for the first time CD8+ T cell responses after live attenuated dengue vaccination and show that CD8+ T cell responses in vaccinees were readily detectable and comparable to natural dengue infection. Interestingly, whereas broad responses to structural and nonstructural (NS) proteins were observed after monovalent vaccination, T cell responses following tetravalent vaccination were, dramatically, focused toward the highly conserved NS proteins. Epitopes were highly conserved in a vast variety of field isolates and able to elicit multifunctional T cell responses. Detailed knowledge of the T cell response will contribute to the identification of robust correlates of protection in natural immunity and following vaccination against DENV. IMPORTANCE The development of effective vaccination strategies against dengue virus (DENV) infection and clinically significant disease is a task of high global public health value and significance, while also being a challenge of significant complexity. A recent efficacy trial of the most advanced dengue vaccine candidate, demonstrated only partial protection against all four DENV serotypes, despite three subsequent immunizations and detection of measurable neutralizing antibodies to each serotype in most subjects. These results challenge the hypothesis that seroconversion is the only reliable correlate of protection. Here, we show that CD8+ T cell responses in vaccinees were readily detectable and comparable to natural dengue virus infection. Detailed knowledge of the T cell response may further contribute to the identification of robust correlates of protection in natural immunity and vaccination against DENV.
Health economic benefits of cyanoacrylate skin protectants in the management of superficial skin lesions

Superficial skin damages, including stage II pressure ulcer, skin tears and moisture‐associated skin damages (MASDs) are common and constitute a significant disease burden to the health care system. A cost analysis was conducted by comparing a cyanoacrylate barrier film with routine care in the treatment of superficial skin damages in a chronic care facility. The analysis included 12 patients: four patients with stage II pressure ulcers, six with MASD and two with skin tears. Cost analysis was conducted comparing the cost of care 7 days before and 7 days after the acrylate barrier was used. The total cost took into consideration the time, products and supplies required to manage the skin problem.
Clinical VR applications with the light-exoskeleton for upper-part neurorehabilitation

It is well-known that virtual reality (VR) is a powerful and promising computer-based technology for the motor recovery in stroke patients. The importance of using VR into arm rehabilitation has coined it as clinical VR; where its main sake is to improve the recovery process of post-stroke patients. In this regard, physical therapy and occupational therapy are provided by such technology. As we shall see into this contribution, interesting clinical VR applications have been designed for handling effectively the brain plasticity in chronic stroke patients. To this end, we use the so-called Light¿Exoskeleton which has been presented for arm-robotic therapy such that it serves as the kinesthetic feedback stimulator for assisting the patient during the rehabilitation sessions.
Multi-year changes of mesoscale variations in atmospheric parameters from the data of GNSS satellites

Multiyear global climatology of mesoscale variations of atmospheric parameters at altitudes 2 - 35 km from radio occultation experiments with low-orbit satellites receiving GNSS signals is considered. Numerical filtering of vertical radio refraction profiles gives information about standard deviations of variations with vertical scales less than 8 km. Global distributions of the standard deviations are subjects for significant inter-annual changes in the tropo-stratosphere. Seasonal changes of radio refraction and temperature standard deviations obtained with Microlab 1, CHAMP and COSMIC satellites are analyzed and compared. At low latitudes, quasi-biennial oscillations exist. The causes of mesoscale variability may be convection, acoustic-gravity waves and turbulence in the atmosphere.
Non-linear Feedback Neural Network for Solution of Quadratic Programming Problems

quadratic programming problems. The objective is tominimize a quadratic cost function subject to linearconstraints. The proposed circuit employs nonlinearfeedback, in the form of unipolar comparators, to introducetranscendental terms in the energy function ensuring fastconvergence to the solution. The proof of validity of the energy function is also provided. The hardware complexity of the proposed circuit comparesfavorably with other proposed circuits for the same task. PSPICE simulation results arepresented for a chosen optimization problem and are foundto agree with the algebraic solution.
Real 3D digital method for large-scale cultural heritage sites

Digital preservation of cultural heritage sites has become a global problem. The paper proposes a real 3D digital method for culture heritage sites using 3D laser scanners and CCD cameras. Firstly, we preprocess the laser scans for noise removal and hole filling. Next step is using an improved ICP algorithm we present step-by-step registration to align all range scans into a common coordinate system. And then, we proposed a filtering of 3D data compression and use a volumetric-based algorithm for the construction of a coherent 3D mesh that encloses all range scans. Finally, through texture mapping, we obtain real 3D and real texture models. The example of the construction of the 3D model of buildings and grottos are presented.
Association between class III obesity and overall survival in previously untreated younger patients with acute myeloid leukemia enrolled on SWOG S1203

Abstract There has been ongoing debate on the association between obesity and outcomes in acute myeloid leukemia (AML). Currently there are few studies that have stratified outcomes by class I obesity, class II obesity, and class III obesity; and a more nuanced understanding is becoming increasingly important with the rising prevalence of obesity. We examined the association between body mass index (BMI) and outcomes in previously untreated AML in younger patients (age ≤60) enrolled in SWOG S1203 (n=729). Class III obesity was associated with an increased rate of early death (p=0.004) and worse overall survival (OS) in multivariate analysis (hazard ratio (HR) 2.48, 95% confidence interval (CI) 1.62-3.80 versus normal weight). Class III obesity was also associated with worse OS after allogeneic hematopoietic cell transplant (HR 2.37, 95% CI 1.24-4.54 versus normal weight). These findings highlight the unique risk of class III obesity in AML, and the importance of further investigation to better characterize this patient population.
Adaptive MANET Routing for Low Overhead

In wireless mission-critical systems, systems may be resource-constrained including limited bandwidth, so minimising protocol overhead, whilst maintaining performance, is important. Proactive MANET routing protocols tend to provide smaller route discovery latency than on-demand protocols because they maintain route information to all the nodes in the network at all time. However, such protocols may impose excessive soft-state routing control overhead which is generated by disseminating periodic update messages. In order to mitigate the side effects of the soft-state control over-heads, we propose two adaptive proactive routing algorithms, namely DT_MIAD and DT_ODPU. By tuning the value of refresh intervals dynamically and automatically, refresh updates are triggered based on traffic conditions and node mobility. We show through simulations that the proposed adaptive routing algorithms can outperform a traditional proactive routing protocol (OLSR).
Perception methods for continuous humanoid locomotion over uneven terrain

Mobile robots can safely operate in environments that pose risks to human health, such as disaster zones and planetary exploration. Robots in these environments may encounter uneven terrain like debris fields, staircases, and rock ledges that are impossible to traverse with wheels or tracks but are surmountable by legged humanoid platforms through careful selection of footholds. The DARPA Robotics Challenge demonstrated that today's field robots are capable of uneven terrain traversal but they moved slowly and only for short durations. The stretches of walking are separated by longer stationary periods consumed by LIDAR data acquisition and human operator decision making. With the goal of improving autonomy, speed, and reliability, this thesis research investigates new algorithms for continuous locomotion over uneven terrain through online terrain perception and continuous footstep re-planning. A new algorithm for planar segmentation of terrain features is presented, along with a novel approach that integrates stereo depth fusion for terrain perception and online footstep re-planning using mixed-integer quadratic optimization. The approach is implemented within a novel software framework called Director, and results are validated on hardware using the Atlas humanoid robot with autonomous laboratory experiments and semi-autonomous field experiments at the DARPA Robotics Challenge Finals.
Birt–Hogg–Dubé Syndrome

Birt-Hogg-Dubé syndrome is characterized by multiple noncancerous (benign) skin tumors, particularly on the face, neck, and upper chest. These growths typically first appear in a person's twenties or thirties and become larger and more numerous over time. Affected individuals also have an increased chance of developing cysts in the lungs and an abnormal accumulation of air in the chest cavity (pneumothorax) that may result in the collapse of a lung. Additionally, Birt-Hogg-Dubé syndrome is associated with an elevated risk of developing cancerous or noncancerous kidney tumors. Other types of cancer have also been reported in affected individuals, but it is unclear whether these tumors are actually a feature of Birt-Hogg-Dubé syndrome.
Caleydo: connecting pathways and gene expression

Summary: Understanding the relationships between pathways and the altered expression of their components in disease conditions can be addressed in a visual data analysis process. Caleydo uses novel visualization techniques to support life science experts in their analysis of gene expression data in the context of pathways and functions of individual genes. Pathways and gene expression visualizations are placed in a 3D scene where selected entities (i.e. genes) are visually connected. This allows Caleydo to seamlessly integrate interactive gene expression visualization with cross-database pathway exploration. Availability: The Caleydo visualization framework is freely available on www.caleydo. org for non-commercial use. It runs on Windows and Linux and requires a 3D capable graphics card. Contact: caleydo@icg.tugraz. at; streit@icg.tugraz. at Supplementary information: Supplementary data are available at Bioinformatics online.
Application of CMOS metal barriers to copper plated silicon solar cells

In this paper, alternative front-side metallization schemes for c-Si solar cells are investigated. These are based on the sputtering of different metal barriers followed by copper electroplating. Different emitters have been evaluated. The influence of the plating process and the impact of different barrier materials on contact resistance, plating properties and device reliability are also investigated. Using this approach, large area silicon solar cells with conversion efficiencies up to 19.4% are obtained on Cz material. First results on the application of these deposition techniques in a low-cost industrial compatible process flow show a conversion efficiency of 18.5%. The influence of the plating process and the impact of different barrier materials (Ti, Ti/TiN, Ta and TaN) on the device reliability are studied. The effectiveness of the silicon nitride antireflecting layer and the metal barrier layer to the diffusion of copper is looked upon and the impact on solar cell performance of different aging processes is assessed.
A Class-Information-Based Penalized Matrix Decomposition for Identifying Plants Core Genes Responding to Abiotic Stresses

In terms of making genes expression data more interpretable and comprehensible, there exists a significant superiority on sparse methods. Many sparse methods, such as penalized matrix decomposition (PMD) and sparse principal component analysis (SPCA), have been applied to extract plants core genes. Supervised algorithms, especially the support vector machine-recursive feature elimination (SVM-RFE) method, always have good performance in gene selection. In this paper, we draw into class information via the total scatter matrix and put forward a class-information-based penalized matrix decomposition (CIPMD) method to improve the gene identification performance of PMD-based method. Firstly, the total scatter matrix is obtained based on different samples of the gene expression data. Secondly, a new data matrix is constructed by decomposing the total scatter matrix. Thirdly, the new data matrix is decomposed by PMD to obtain the sparse eigensamples. Finally, the core genes are identified according to the nonzero entries in eigensamples. The results on simulation data show that CIPMD method can reach higher identification accuracies than the conventional gene identification methods. Moreover, the results on real gene expression data demonstrate that CIPMD method can identify more core genes closely related to the abiotic stresses than the other methods.
Neuronal and Glial Apoptosis after Traumatic Spinal Cord Injury

Cell death was examined by studying the spinal cords of rats subjected to traumatic insults of mild to moderate severity. Within minutes after mild weight drop impact (a 10 gm weight falling 6.25 mm), neurons in the immediate impact area showed a loss of cytoplasmic Nissl substances. Over the next 7 d, this lesion area expanded and cavitated. Terminal deoxynucleotidyl transferase (TdT)-mediated deoxyuridine triphosphate–biotin nick end labeling (TUNEL)-positive neurons were noted primarily restricted to the gross lesion area 4–24 hr after injury, with a maximum presence at 8 hr after injury. TUNEL-positive glia were present at all stages studied between 4 hr and 14 d, with a maximum presence within the lesion area 24 hr after injury. However 7 d after injury, a second wave of TUNEL-positive glial cells was noted in the white matter peripheral to the lesion and extending at least several millimeters away from the lesion center. The suggestion of apoptosis was supported by electron microscopy, as well as by nuclear staining with Hoechst 33342 dye, and by examination of DNA prepared from the lesion site. Furthermore, repeated intraperitoneal injections of cycloheximide, beginning immediately after a 12.5 mm weight drop insult, produced a substantial reduction in histological evidence of cord damage and in motor dysfunction assessed 4 weeks later. Present data support the hypothesis that apoptosis dependent on active protein synthesis contributes to the neuronal and glial cell death, as well as to the neurological dysfunction, induced by mild-to-moderate severity traumatic insults to the rat spinal cord.
The Role of Liver Fructose-1,6-Bisphosphatase in Regulating Appetite and Adiposity

Liver fructose-1,6-bisphosphatase (FBPase) is a regulatory enzyme in gluconeogenesis that is elevated by obesity and dietary fat intake. Whether FBPase functions only to regulate glucose or has other metabolic consequences is not clear; therefore, the aim of this study was to determine the importance of liver FBPase in body weight regulation. To this end we performed comprehensive physiologic and biochemical assessments of energy balance in liver-specific transgenic FBPase mice and negative control littermates of both sexes. In addition, hepatic branch vagotomies and pharmacologic inhibition studies were performed to confirm the role of FBPase. Compared with negative littermates, liver-specific FBPase transgenic mice had 50% less adiposity and ate 15% less food but did not have altered energy expenditure. The reduced food consumption was associated with increased circulating leptin and cholecystokinin, elevated fatty acid oxidation, and 3-β-hydroxybutyrate ketone levels, and reduced appetite-stimulating neuropeptides, neuropeptide Y and Agouti-related peptide. Hepatic branch vagotomy and direct pharmacologic inhibition of FBPase in transgenic mice both returned food intake and body weight to the negative littermates. This is the first study to identify liver FBPase as a previously unknown regulator of appetite and adiposity and describes a novel process by which the liver participates in body weight regulation.
H-Factors in Dense Graphs

The following asymptotic result is proved. For every? >0, and for every positive integerh, there exists ann0=n0(? , h) such that for every graphHwithhvertices and for everynn0, any graphGwithhnvertices and with minimum degreed? ((? (H)? 1)/? (H)+? )hncontainsnvertex disjoint copies ofH. This result is asymptotically tight and its proof supplies a polynomial time algorithm for the corresponding algorithmic problem.
Therapeutic Seal Robot as Biofeedback Medical Device: Qualitative and Quantitative Evaluations of Robot Therapy in Dementia Care

Recently developed robotics technologies are used not only in factories, but also in our daily living environment. Human-interactive robots, used to improve the quality of life, are becoming increasingly common. Their purposes and functions vary depending on their use, such as assistance, therapy, guide, entertainment, and education. Robot therapy, which uses robots as a substitution for animals in “animal therapy,” is a new robot application in the fields of welfare and patient care. The seal robot PARO began development for robot therapy in 1993. PARO was commercialized in Japan in 2005, and in Europe and the United States in 2009, and it has been used in hospitals and care facilities in approximately 30 countries. Recent research has revealed that robot therapy has a similar effect on patients as animal therapy. In 2009, the U.S. Food and Drug Administration (FDA) certified PARO as a “biofeedback medical device. ” While PARO can be used in various kinds of therapy similar to that where real animals are used, this study focuses on its use with elderly dementia patients because explicit differences can be easily observed before and after interacting with PARO. First, this paper explains the purposes and functions of PARO. Second, because there are several observational studies on the therapeutic effects of the elderly with dementia interacting with PARO, some typical cases and interesting special cases are introduced. These cases include recovery from depression, reduction of agitation, and recovery from speech disorders. Finally, this paper discusses why PARO has the potential to change moods and behaviors of the elderly with dementia as a nonpharmacological approach.
Jitter-free co-processing on a prototype exascale storage stack

In the petascale era, the storage stack used by the extreme scale high performance computing community is fairly homogeneous across sites. On the compute edge of the stack, file system clients or IO forwarding services direct IO over an interconnect network to a relatively small set of IO nodes. These nodes forward the requests over a secondary storage network to a spindle-based parallel file system. Unfortunately, this architecture will become unviable in the exascale era. As the density growth of disks continues to outpace increases in their rotational speeds, disks are becoming increasingly cost-effective for capacity but decreasingly so for bandwidth. Fortunately, new storage media such as solid state devices are filling this gap; although not cost-effective for capacity, they are so for performance. This suggests that the storage stack at exascale will incorporate solid state storage between the compute nodes and the parallel file systems. There are three natural places into which to position this new storage layer: within the compute nodes, the IO nodes, or the parallel file system. In this paper, we argue that the IO nodes are the appropriate location for HPC workloads and show results from a prototype system that we have built accordingly. Running a pipeline of computational simulation and visualization, we show that our prototype system reduces total time to completion by up to 30%.
Testing, diagnosis and repair methods for NBTI-induced SRAM faults

NBTI is a major SRAM aging mechanism, leading to reduced read and hold static noise margins, and increased soft error rate. The existing techniques including guard banding, on-chip sensor-based detection, and recovery. In this paper, we propose a group of testing, diagnosis, and repair methods for NBTI-induced memory faults. We observe that NBTI leads to SRAM read errors rather than write errors. We propose to identify NBTI-induced memory read errors based on the existing ECC circuitry, differentiate them with soft errors by correction and double checking, and keep them idle for recovery. We further propose an predictive test method for NBTI-induced memory faults by adaptive body biasing. We achieve an adaptive body biasing formula to simulate the NBTI effect. Our experimental results validate the proposed methods and show that they cost little silicon area and power consumption.
Large Kr‐free subgraphs in Ks‐free graphs and some other Ramsey‐type problems

In this paper we present three Ramsey‐type results, which we derive from a simple and yet powerful lemma, proved using probabilistic arguments. Let 3 ≤ r < s be fixed integers and let G be a graph on n vertices not containing a complete graph Ks on s vertices. More than 40 years ago Erdős and Rogers posed the problem of estimating the maximum size of a subset of G without a copy of the complete graph Kr. Our first result provides a new lower bound for this problem, which improves previous results of various researchers. It also allows us to solve some special cases of a closely related question posed by Erdős. For two graphs G and H, the Ramsey number R(G, H) is the minimum integer N such that any red‐blue coloring of the edges of the complete graph KN, contains either a red copy of G or a blue copy of H. The book with n pages is the graph Bn consisting of n triangles sharing one edge. Here we study the book‐complete graph Ramsey numbers and show that R(Bn, Kn) ≤ O(n3/log3/2n), improving the bound of Li and Rousseau. Finally, motivated by a question of Erdős, Hajnal, Simonovits, Sós, and Szemerédi, we obtain for all 0 < δ < 2/3 an estimate on the number of edges in a K4‐free graph of order n which has no independent set of size n1‐δ. © 2004 Wiley Periodicals, Inc. Random Struct. Alg. , 2005