Miracle-dz/UniFAR-FTUs huggingface dataset:
TNF-α potentiates uric acid-induced interleukin-1β (IL-1β) secretion in human neutrophils

Abstract Objective: Monosodium urate (MSU) has been shown to promote interleukin-1β (IL-1β) secretion in human monocytes, but the priming signals for NOD-like receptor family pyrin domain containing 3 (NLRP3) inflammasome pathway remains elusive. In this study, we investigated the role of Tumor necrosis factor-alpha (TNF-α) on MSU-mediated IL-1β induction in human neutrophils. Methods: Human neutrophils were stimulated with MSU, in the presence or absence of TNF-α priming. The cellular supernatants were analyzed for IL-1β, IL-18, and caspase-1 by enzyme-linked immunosorbent assay (ELISA) methods. Pro-IL-1β mRNA expressions in human neutrophils were analyzed by real-time PCR method. Results: TNF-α stimulation induced pro-IL-1β mRNA expression; however, MSU stimulation did not induce pro-IL-1β mRNA expression in human neutrophils. TNF-α alone or MSU stimulation did not result in efficient IL-1β secretion in human neutrophils, whereas in TNF-α-primed neutrophils, MSU stimulation resulted in a marked IL-1β and IL-18 secretion. TNF-α-primed neutrophils secreted cleaved caspase-1 (p20), in response to MSU stimulation. Conclusion: Our data demonstrate that priming of human neutrophils with TNF-α promotes uric acid-mediated IL-1β secretion in the absence of microbial stimulation. These findings provide insights into the neutrophils-mediated inflammatory processes in gouty arthritis.
Assessment of lower extremity motor adaptation via an extension of the Force Field Adaptation Paradigm

Lower extremity rehabilitation has seen recent increased interest. New tools are available to improve gait retraining in both adults and children. However, it remains difficult to determine optimal ways to plan interventions due to difficulties in continuously monitoring outcomes in patients undergoing rehabilitation. In this paper, we introduce an extension of the Force Field Adaptation Paradigm, used to quantitatively assess upper extremity motor adaptation, to the lower extremity. The algorithm is implemented on the Lokomat lower extremity gait orthosis and utilized to assess short-term motor adaptation. Establishing an understanding of how healthy adults' motor systems adapt to external perturbations will be important to understanding how the adaptive mechanisms involved in gait are altered by disease.
Universal Steganographic Detection in JPEG Image Using the Graph Laplacian Semi-supervised Kernel

Current image steganographic detection algorithms are unable to make full use of the geometry of unlabeled image examples, detection performance is subject to a few labeled examples, which is utilized for training. In this paper, we propose an effective steganographic detection method for JPEG image that rely on the overall dataset. The method is combined with semi-supervised kernel in the presence of unlabeled examples. Semi-supervised kernel method constructs data adjacency graph to obtain Gram matrix, then we obtain the proposed method by incorporating graph Laplacian into kernel-based algorithms, which is effective integration of the cluster assumption and manifold assumption. Our method utilizes the geometry of all examples with manifold regularization to produce smooth decision functions and thus improving the performance universal steganographic detection. Experimental results show the effectiveness of our proposed method.
A data-analytic strategy for protein biomarker discovery: profiling of high-dimensional proteomic data for cancer detection.

With recent advances in mass spectrometry techniques, it is now possible to investigate proteins over a wide range of molecular weights in small biological specimens. This advance has generated data-analytic challenges in proteomics, similar to those created by microarray technologies in genetics, namely, discovery of 'signature' protein profiles specific to each pathologic state (e.g. normal vs. cancer) or differential profiles between experimental conditions (e.g. treated by a drug of interest vs. untreated) from high-dimensional data. We propose a data-analytic strategy for discovering protein biomarkers based on such high-dimensional mass spectrometry data. A real biomarker-discovery project on prostate cancer is taken as a concrete example throughout the paper: the project aims to identify proteins in serum that distinguish cancer, benign hyperplasia, and normal states of prostate using the Surface Enhanced Laser Desorption/Ionization (SELDI) technology, a recently developed mass spectrometry technique. Our data-analytic strategy takes properties of the SELDI mass spectrometer into account: the SELDI output of a specimen contains about 48,000 (x, y) points where x is the protein mass divided by the number of charges introduced by ionization and y is the protein intensity of the corresponding mass per charge value, x, in that specimen. Given high coefficients of variation and other characteristics of protein intensity measures (y values), we reduce the measures of protein intensities to a set of binary variables that indicate peaks in the y-axis direction in the nearest neighborhoods of each mass per charge point in the x-axis direction. We then account for a shifting (measurement error) problem of the x-axis in SELDI output. After this pre-analysis processing of data, we combine the binary predictors to generate classification rules for cancer, benign hyperplasia, and normal states of prostate. Our approach is to apply the boosting algorithm to select binary predictors and construct a summary classifier. We empirically evaluate sensitivity and specificity of the resulting summary classifiers with a test dataset that is independent from the training dataset used to construct the summary classifiers. The proposed method performed nearly perfectly in distinguishing cancer and benign hyperplasia from normal. In the classification of cancer vs. benign hyperplasia, however, an appreciable proportion of the benign specimens were classified incorrectly as cancer. We discuss practical issues associated with our proposed approach to the analysis of SELDI output and its application in cancer biomarker discovery.
Construction of variety competition cyclic balanced designs on square lattice

A class of cyclic balanced designs with ten test-hills is introduced; these designs can be repeated cyclically any number of times up to the requirement of the experimenter and subject to the availability of experimental material. The designs are balanced with respect to first order nearest neighbours and there are 26 isomorphism classes of such designs. The designs are suitable for de Wit replacement series, mixed cropping trials or two component plant breeding trials, etc. ∗ Also at Queen Mary University of London, School of Mathematical Sciences, Mile End Road, London E1 4NS, U.K. 178 M. NAWAZ, M. ZAFAR-YAB AND M. AKHTAR
Acute Responses of Strength and Running Mechanics to Increasing and Decreasing Pain in Patients With Patellofemoral Pain.

CONTEXT Patellofemoral pain (PFP) is typically exacerbated by repetitive activities that load the patellofemoral joint, such as running. Understanding the mediating effects of changes in pain in individuals with PFP might inform injury progression, rehabilitation, or both. OBJECTIVE To investigate the effects of changing pain on muscular strength and running biomechanics in those with PFP. DESIGN Crossover study. SETTING University research laboratory. PATIENTS OR OTHER PARTICIPANTS Seventeen participants (10 men, 7 women) with PFP. INTERVENTION(S) Each participant completed knee pain-reducing and pain-inducing protocols in random order. The pain-reducing protocol consisted of 15 minutes of transcutaneous electric nerve stimulation (TENS) around the patella. The pain-inducing protocol was sets of 20 repeated single-legged squats (RSLS). Participants completed RSLS sets until either their pain was within at least 1 cm of their pain during an exhaustive run or they reached 10 sets. MAIN OUTCOME MEASURE(S) Pain, isometric hip and trunk strength, and running mechanics were assessed before and after the protocols. Dependent variables were pain, normalized strength (abduction, extension, external rotation, lateral trunk flexion), and peak lower extremity kinematics and kinetics in all planes. Pain scores were analyzed using a Friedman test. Strength and mechanical variables were analyzed using repeated-measures analyses of variance. The α level was set at P < . 05. RESULTS Pain was decreased after the TENS (pretest: 3.10 ± 1.95, posttest: 1.89 ± 2.33) and increased after the RSLS (baseline: 3.10 ± 1.95, posttest: 4.38 ± 2.40) protocols (each P < .05). The RSLS protocol resulted in a decrease in hip-extension strength (baseline: 0.355 ± 0.08 kg/kg, posttest: 0.309 ± 0.09 kg/kg; P < .001). Peak plantar-flexion angle was decreased after RSLS (baseline: -13.97° ± 6.41°, posttest: -12.84° ± 6.45°; P = .003). Peak hip-extension (pretest: -2.31 ± 0.46) and hip-abduction (pretest: -2.02 ± 0.35) moments decreased after both the TENS (extension: -2.15 ± 0.48 Nm/kg, P = .015; abduction: -1.91 ± 0.33 Nm/kg, P = .015) and RSLS (extension: -2.18 ± 0.52 Nm/kg, P = .003; abduction: -1.87 ± 0.36 Nm/kg, P = .039) protocols. CONCLUSIONS This study presents a novel and effective method of increasing pain in persons with PFP. Functionally increased pain after RSLS coincides with reduced hip-extensor muscle strength and decreased plantar-flexion angle during running. The TENS treatment decreased pain during running in those with PFP but failed to influence strength. Hip moments were reduced by both protocols, which may demonstrate that acute increases or decreases in pain cause runners to change their mechanics.
Applying the motivation-opportunity-ability (MOA) model to reveal factors that influence inclusive engagement within local community festivals : The case of UtcaZene 2012

Purpose – The purpose of this paper is to debate on community engagement and participation in local community festivals and events by empirically analysing the factors which either inhibit or facilitate engagement. The application of the motivation-opportunity-ability (MOA) model to the analysis of community festivals is an important contribution. Design/methodology/approach – Recognising the complexity associated with community participation in festivals produced a set of four research questions which are addressed via a mixed methodology research design. The model was then tested using four key data collection methods including the interviews and the questionnaires analysed within this paper. Findings – The MOA model can be seen as an appropriate framework with which to analyse community engagement in a local community festival setting, in the case of “The Utcazene-Fesztival”, a Street Music Festival in Veszprem, Hungary. Community participation is often interpreted quite simply as a way of involving lo.
WHOLE SKY IMAGER INSTRUMENT USING NEURAL NETWORKS

The knowledge of the placement and size of clouds in the atmosphere has many applications in Atmospheric Science. In particular, clouds play a major role in the earth’s radiation budget. Given the large amounts of image data and the relative short time this information is relevant requires an automated detection algorithm that runs in real-time on current workstations. We present such an algorithm in this paper. We show that given daytime images, human analysts agree amongst themselves at most 94% on the placement of clouds within the image. The subjectivity of the problem motivates our approach. The algorithm uses a combination of neural networks to compute the probability of a pixel being clear or cloud. Images are first sorted into neighborhoods via a Self-Organizing map based on the image’s gray scale levels. After sorting, each pixel is processed using a Mixture of Experts neural network unique to the neighborhood. The calculation is of the probability that a pixel represents clear or cloudy. A pixel level cloud mask is then constructed by assigning the most likely designation to each pixel. The algorithm reliably identifies a variety of clouds from images. Relative agreements with human analysts are typically greater than 90%. In addition, the pixel level cloud masks show high visual correlations with unprocessed images as well as very good temporal correlations.
Cholinergic Basal Forebrain Structure Influences the Reconfiguration of White Matter Connections to Support Residual Memory in Mild Cognitive Impairment

The fornix and hippocampus are critical to recollection in the healthy human brain. Fornix degeneration is a feature of aging and Alzheimer's disease. In the presence of fornix damage in mild cognitive impairment (MCI), a recognized prodrome of Alzheimer's disease, recall shows greater dependence on other tracts, notably the parahippocampal cingulum (PHC). The current aims were to determine whether this shift is adaptive and to probe its relationship to cholinergic signaling, which is also compromised in Alzheimer's disease. Twenty-five human participants with MCI and 20 matched healthy volunteers underwent diffusion MRI, behavioral assessment, and volumetric measurement of the basal forebrain. In a regression model for recall, there was a significant group × fornix interaction, indicating that the association between recall and fornix structure was weaker in patients. The opposite trend was present for the left PHC. To further investigate this pattern, two regression models were generated to account for recall performance: one based on fornix microstructure and the other on both fornix and left PHC. The realignment to PHC was positively correlated with free recall but not non-memory measures, implying a reconfiguration that is beneficial to residual memory. There was a positive relationship between realignment to PHC and basal forebrain gray matter volume despite this region demonstrating atrophy at a group level, i.e., the cognitive realignment to left PHC was most apparent when cholinergic areas were relatively spared. Therefore, cholinergic systems appear to enable adaptation to injury even as they degenerate, which has implications for functional restoration.
Methods for Identifying Neisseria meningitidis Carriers: A Multi-Center Study in the African Meningitis Belt

Objective Detection of meningococcal carriers is key to understanding the epidemiology of Neisseria meningitidis, yet no gold standard has been established. Here, we directly compare two methods for collecting pharyngeal swabs to identify meningococcal carriers. Methods We conducted cross-sectional surveys of schoolchildren at multiple sites in Africa to compare swabbing the posterior pharynx behind the uvula (U) to swabbing the posterior pharynx behind the uvula plus one tonsil (T). Swabs were cultured immediately and analyzed using molecular methods. Results One thousand and six paired swab samples collected from schoolchildren in four countries were analyzed. Prevalence of meningococcal carriage was 6.9% (95% CI: 5.4-8.6%) based on the results from both swabs, but the observed prevalence was lower based on one swab type alone. Prevalence based on the T swab or the U swab alone was similar (5.2% (95% CI: 3.8-6.7%) versus 4.9% (95% CI: 3.6-6.4%) respectively (p=0.6)). The concordance between the two methods was 96.3% and the kappa was 0.61 (95% CI: 0.50-0.73), indicating good agreement. Conclusions These two commonly used methods for collecting pharyngeal swabs provide consistent estimates of the prevalence of carriage, but both methods misclassified carriers to some degree, leading to underestimates of the prevalence.
Influence of NanoLC Column and Gradient Length as well as MS/MS Frequency and Sample Complexity on Shotgun Protein Identification of Marine Bacteria

Protein identification by shotgun proteomics, i.e., nano-liquid chromatography (nanoLC) peptide separation online coupled to electrospray ionization (ESI) mass spectrometry (MS)/MS, is the most widely used gel-free approach in proteome research. While the mass spectrometer accounts for mass accuracy and MS/MS frequency, the nanoLC setup and gradient time influence the number of peptides available for MS analysis, which ultimately determine the number of proteins identifiable. Here, we report on the influence of (i) analytical column length (15, 25, or 50 cm) coupled to (ii) the applied gradient length (120, 240, 360, 480, or 600 min), as well as (iii) MS/MS frequency on peptide/protein identification by shotgun proteomics of (iv) 2 marine bacteria. Longer gradients increased the number of peptides/proteins identified as well as the reproducibility of identification. Furthermore, longer analytical columns strictly enlarge the covered proteome complement. Notably, the proteome complement identified with a short column and applying a long gradient is also covered when using longer columns with shorter gradients. Coverage of the proteome complement further increases with higher MS/MS frequency. Compilation of peptide lists of replicate analyses (same gradient length) improves protein identification, while compilation of analyses with different gradient lengths yields a similar or even higher number of proteins using comparable or even less total analysis time.
The Leo Triplet: Common origin or late encounter?

The kinematics, structure, and stellar population properties in the centers of two early-type spiral galaxies of the Leo Triplet, NGC 3627 and NGC 3623, are studied by means of integral-field spectroscopy. Unlike our previous targets, NGC 3384/NGC 3368 in the Leo I Group and NGC 5574/NGC 5576 in LGG 379, NGC 3623 and NGC 3627 do not appear to experience a synchronous evolution. The mean ages of their circumnuclear stellar populations are quite different, and the magnesium overabundance of the nucleus in NGC 3627 is evidence for a very brief last star formation event 1 Gyr ago whereas the evolution of the central part of NGC 3623 looks more quiescent. In the center of NGC 3627 we observe noticeable gas radial motions, and the stars and the ionized gas in the center of NGC 3623 demonstrate more or less stable rotation. However, NGC 3623 has a chemically distinct core - a relic of a past star formation burst - which is shaped as a compact, dynamically cold stellar disk with a radius of ∼250−350 pc which has been formed not later than 5 Gyr ago.
Croth: Effective Process Protection and Monitoring with Hardware Virtualization

With the development of network malicious code, the existing security holes in present systems facilitate data loss. Though protection methods and software are updated day by day, some recent rootkits, that can still invisibly access kernel, make new challenges for the system security. The focal point on system security is how to protect a chosen process on the infected operating system. Process protection and monitoring are becoming more and more important for emerging networks and systems. In this paper, we present a new technique, Croth, which is based on hardware virtualization technology. It introduces a novel mechanism, Cape, that is located in Virtual Machine Monitor (VMM). The main work of Cape is to emulate most of the operations originally done by operating system. This primitive offers an additional dimension of protection beyond the hierarchical protection domains, implemented by traditional operating systems and processor architectures. The design and implementation of hiding sensitive data is also presented in this paper. Our design has been fully implemented and used to protect a wide range of legacy process without any modification on Windows operating system. Our experimental result shows that the operating system could not get accurate data while the chosen process is controlled by Croth. It has provided a little performance overhead, however, performance is still acceptable.
Coordination of peptidoglycan synthesis and outer membrane constriction during Escherichia coli cell division

To maintain cellular structure and integrity during division, Gram-negative bacteria must carefully coordinate constriction of a tripartite cell envelope of inner membrane, peptidoglycan (PG), and outer membrane (OM). It has remained enigmatic how this is accomplished. Here, we show that envelope machines facilitating septal PG synthesis (PBP1B-LpoB complex) and OM constriction (Tol system) are physically and functionally coordinated via YbgF, renamed CpoB (Coordinator of PG synthesis and OM constriction, associated with PBP1B). CpoB localizes to the septum concurrent with PBP1B-LpoB and Tol at the onset of constriction, interacts with both complexes, and regulates PBP1B activity in response to Tol energy state. This coordination links PG synthesis with OM invagination and imparts a unique mode of bifunctional PG synthase regulation by selectively modulating PBP1B cross-linking activity. Coordination of the PBP1B and Tol machines by CpoB contributes to effective PBP1B function in vivo and maintenance of cell envelope integrity during division. DOI: http://dx.doi. org/10.7554/eLife.07118. 001
Performance of the VAX-11/780 translation buffer: simulation and measurement

A virtual-address translation buffer (TB) is a hardware cache of recently used virtual-to-physical address mappings. The authors present the results of a set of measurements and simulations of translation buffer performance in the VAX-11/780. Two different hardware monitors were attached to VAX-11/780 computers, and translation buffer behavior was measured. Measurements were made under normal time-sharing use and while running reproducible synthetic time-sharing work loads. Reported measurements include the miss ratios of data and instruction references, the rate of TB invalidations due to context switches, and the amount of time taken to service TB misses. Additional hardware measurements were made with half the TB disabled. Trace-driven simulations of several programs were also run; the traces captured system activity as well as user-mode execution. Several variants of the 11/780 TB structure were simulated.
Analysis of bittorrent-like protocols for on-demand stored media streaming

This paper develops analytic models that characterize the behavior of on-demand stored media content delivery using BitTorrent-like protocols. The models capture the effects of different piece selection policies, including Rarest-First and two variants of In-Order. Our models provide insight into transient and steady-state system behavior, and help explain the sluggishness of the system with strict In-Order streaming. We use the models to compare different retrieval policies across a wide range of system parameters, including peer arrival rate, upload/download bandwidth, and seed residence time. We also provide quantitative results on the startup delays and retrieval times for streaming media delivery. Our results provide insights into the optimal design of peer-to-peer networks for on-demand media streaming.