Miracle-dz/UniFAR-FTUs huggingface dataset:
Early Interleukin-6 and Slope of Monocyte Human Leukocyte Antigen-DR: A Powerful Association to Predict the Development of Sepsis after Major Trauma

Objective Major trauma is characterized by a pro-inflammatory response, followed by an immunosuppression. Recently, in trauma patients, the lack of recovery of monocyte Human Leukocyte Antigen DR (mHLA-DR, a biomarker of ICU-acquired immunosuppression) between days 1–2 and days 3–4 has been demonstrated to be independently associated with sepsis development. The main objective of this study was to determine whether early measurements of IL-6 (interleukin-6) and IL-10 plasma concentrations (as markers of initial severity) could improve, in association with mHLA-DR recovery, the prediction of sepsis occurrence in severe trauma patients. Design Prospective observational study over 24 months in a Trauma ICU at university hospital. Patients Trauma patients with an ISS over 25 and age over 18 were included. Measurements and Main Results mHLA-DR was assessed by flow cytometry, IL-6 and IL-10 concentrations by ELISA. 100 consecutive severely injured patients were monitored (mean ISS 37±10). 37 patients developed sepsis. IL-6 concentrations and slope of mHLA-DR expression between days 1–2 and days 3–4 were significantly different between septic and non-septic patients. IL-10 was not detectable in most patients. After adjustment for usual clinical confounders, when assessed as a pair, multivariate logistic regression analysis revealed that a slope of mHLA-DR expression (days 3–4/days 1–2)≤1.1 and a IL-6 concentration ≥ 67.1 pg/ml remained highly associated with the development of sepsis (adjusted OR 18.4, 95% CI 4.9; 69.4, p = .00002). Conclusions After multivariate regression logistic analysis, when assessed as a pair, a high IL-6 concentration and a persistent mHLA-DR decreased expression were found to be in relation with the development of sepsis with the best predictive value. This study underlines the usefulness of daily monitoring of immune function to identify trauma patients at a high risk of infection.
Membrane Repair Defects in Muscular Dystrophy Are Linked to Altered Interaction between MG53, Caveolin-3, and Dysferlin*◆

Defective membrane repair can contribute to the progression of muscular dystrophy. Although mutations in caveolin-3 (Cav3) and dysferlin are linked to muscular dystrophy in human patients, the molecular mechanism underlying the functional interplay between Cav3 and dysferlin in membrane repair of muscle physiology and disease has not been fully resolved. We recently discovered that mitsugumin 53 (MG53), a muscle-specific TRIM (Tri-partite motif) family protein (TRIM72), contributes to intracellular vesicle trafficking and is an essential component of the membrane repair machinery in striated muscle. Here we show that MG53 interacts with dysferlin and Cav3 to regulate membrane repair in skeletal muscle. MG53 mediates active trafficking of intracellular vesicles to the sarcolemma and is required for movement of dysferlin to sites of cell injury during repair patch formation. Mutations in Cav3 (P104L, R26Q) that cause retention of Cav3 in Golgi apparatus result in aberrant localization of MG53 and dysferlin in a dominant-negative fashion, leading to defective membrane repair. Our data reveal that a molecular complex formed by MG53, dysferlin, and Cav3 is essential for repair of muscle membrane damage and also provide a therapeutic target for treatment of muscular and cardiovascular diseases that are linked to compromised membrane repair.
A Coarse-to-Fine Approach for Layout Analysis of Ancient Manuscripts

Many applications along the manuscript analysis pipeline rely on the accuracy of pre-processing steps. Perfectly detecting the main text area in ancient historical documents is of great importance for these applications. We propose a learning-free approach to detect the main text area in ancient manuscripts. First, we coarsely segment the main text area by using a texture-based filter. Then, we refine the segmentation by formulating the problem as an energy minimization task and achieving the minimum using graph cuts. The energy function is derived from properties of the text components. Spatial coherence of the segmented text regions is explicitly encouraged by the energy function. We evaluate the suggested method on a publicly available dataset of 38 historical document images. Experiments show that the suggested approach outperforms another state-of-the-art page segmentation method in terms of segmentation quality and time performance.
Explorer Bone marrow transplantation modulates tissue macrophage phenotype and enhances cardiac recovery after subsequent acute myocardial infarction

Citation for published version: Protti, A, Mongue-Din, H, Mylonas, K, Sirker, A, Sag, CM, Swim, MM, Maier, L, Sawyer, G, Dong, X, Botnar, R, Salisbury, J, Gray, G & Shah, AM 2015, 'Bone marrow transplantation modulates tissue macrophage phenotype and enhances cardiac recovery after subsequent acute myocardial infarction' Journal of Molecular and Cellular Cardiology. DOI: 10.1016/j.yjmcc. 2015.12. 007
Concise gene signature for point‐of‐care classification of tuberculosis

There is an urgent need for new tools to combat the ongoing tuberculosis (TB) pandemic. Gene expression profiles based on blood signatures have proved useful in identifying genes that enable classification of TB patients, but have thus far been complex. Using real‐time PCR analysis, we evaluated the expression profiles from a large panel of genes in TB patients and healthy individuals in an Indian cohort. Classification models were built and validated for their capacity to discriminate samples from TB patients and controls within this cohort and on external independent gene expression datasets. A combination of only four genes distinguished TB patients from healthy individuals in both cross‐validations and on separate validation datasets with very high accuracy. An external validation on two distinct cohorts using a real‐time PCR setting confirmed the predictive power of this 4‐gene tool reaching sensitivity scores of 88% with a specificity of around 75%. Moreover, this gene signature demonstrated good classification power in HIV+ populations and also between TB and several other pulmonary diseases. Here we present proof of concept that our 4‐gene signature and the top classifier genes from our models provide excellent candidates for the development of molecular point‐of‐care TB diagnosis in endemic areas.
Routing in Wireless Sensor Networks: An approach using Stackelberg games

Due to the limited transmit power and other constraints, the transmission of data between two nodes in a Wireless Sensor Network (WSN) may have to be accomplished with the help of one or multiple relay nodes. Game theory has been proven very useful for accurately modeling the underlying strategic interactions between the sensor nodes and for providing the relays with incentives to forward the other nodes' data. In the present paper, we study a class of such games played at the network layer among a set of relay nodes and the source-destination pair. We formulate the source routing problem using a Stackelberg game framework. The Stackelberg equilibrium strategies derived from our game define the expected performance of the network under different traffic conditions, and motivate an efficient routing protocol design for this type of wireless networks. Different network configurations are studied to illustrate the effectiveness of our game theoretic approach.
Stream Processing in the Cloud

Stock exchanges, sensor networks and other publish/subscribe systems need to deal with highvolume streams of real-time data. Especially financial data has to be processed with low latency in order to cater for high-frequency trading algorithms. In order to deal with the large amounts of incoming data, the stream processing task has to be distributed. Traditionally, distributed stream processing systems balanced their load over a static number of nodes using operator placement or pipelining. In this report we propose a novel way of doing stream processing by exploiting scalable cluster architectures as provided by IaaS/cloud solutions such as Amazon’s EC2. We show how to implement a cloud-centric stream processor based on the MapReduce framework. We will then design a load balancing algorithm which allows a local stream processor to request additional resources from the cloud when its capacity to handle the input stream becomes insufficient .
Taxonomy of Pseudomonas piscicida (Bein) Buck, Meyers, and Leifson

Hansen, A. J. (University of Idaho, Moscow), O. B. Weeks, and R. R. Colwell. Taxonomy of Pseudomonas piscicida (Bein) Buck, Meyers, and Leifson. J. Bacteriol. 89:752–761. 1965. —Twenty strains of marine bacteria showing the properties of pigmentation and icthyotoxicity were studied for selected physiological features. A quantitative taxonomic analysis with an electronic computer was performed. Eighteen species of Pseudomonas were included in the computer analysis as reference strains. The marine collection formed a homogeneous cluster, 80% similarity, and showed a 67 to 70% similarity to certain of the Pseudomonas species: P. atlantica, P. geniculata, P. synxantha, and P. taetrolens. The marine strains are treated as a phenon describing the species P. piscicida. The species was characterized by the hypothetical Median Organism concept; P. piscicida 14 corresponded most closely to the Median Organism.
Adherence of Platelets to CandidaSpecies In Vivo

ABSTRACT The in vivo interactions of platelets with Candidaspecies yeast cells were investigated in a murine model. Mice were injected intravenously via the lateral caudal vein, and blood drawn by periorbital puncture was collected in phosphate-buffered saline–formaldehyde to avoid in vitro platelet activation. The study of the clearance of blastoconidia of Candida albicans andCandida glabrata showed that these cells disappeared quickly from the bloodstream. Microscopic observation of blood samples, stained by Calcofluor white or May Grunwald Giemsa, demonstrated the rapid attachment of platelets to fungal elements of all theCandida spp. tested. The attachment of murine platelets toC. albicans cells, observed by scanning electron microscopy, revealed morphological changes. The platelets lost their discoid shape, generated pseudopodia, and flattened against the yeast cells. The reversibility of platelet binding to C. albicansby chelating agents suggests a cation-dependent link. In contrast, the fixation of C. glabrata and Candida tropicaliswas not modified by chelating agents. The mechanisms involved in the in vivo adherence of platelets to Candida cells may therefore differ according to the species of Candida.
Purification and characterization of extremely thermostable beta-mannanase, beta-mannosidase, and alpha-galactosidase from the hyperthermophilic eubacterium Thermotoga neapolitana 5068

Thermostable and thermoactive beta-mannanase (1,4-beta-D-mannan mannanohydrolase [EC 3.2.1.78]), beta-mannosidase (beta-D-mannopyranoside hydrolase [EC 3.2.1.25]) and alpha-galactosidase (alpha-D-galactoside galactohydrolase [EC 3.2.1.22]) were purified to homogeneity from cell extracts and extracellular culture supernatants of the hyperthermophilic eubacterium Thermotoga neapolitana 5068 grown on guar gum-based media. The beta-mannanase was an extracellular monomeric enzyme with a molecular mass of 65 kDa. The optimal temperature for activity was 90 to 92 degrees C, with half-lives (t1/2) of 34 h at 85 degrees C, 13 h at 90 degrees C, and 35 min at 100 degrees C. The beta-mannosidase and alpha-galactosidase were found primarily in cell extracts. The beta-mannosidase was a homodimer consisting of approximately 100-kDa molecular mass subunits. The optimal temperature for activity was 87 degrees C, with t1/2 of 18 h at 85 degrees C, 42 min at 90 degrees C, and 2 min at 98 degrees C. The alpha-galactosidase was a 61-kDa monomeric enzyme with a temperature optimum of 100 to 103 degrees C and t1/2 of 9 h at 85 degrees C, 2 h at 90 degrees C, and 3 min at 100 degrees C. These enzymes represent the most thermostable and thermoactive versions of these types yet reported and probably act synergistically to hydrolyze extracellular galactomannans to monosaccharides by T. neapolitana for nutritional purposes. The significance of such substrates in geothermal environments remains to be seen.
Hybrid FEB Face Recognition Algorithm

In this paper a new algorithm has been proposed for face recognition which is an important area of object recognition and has received substantial attention in recent years from researchers in biometrics, pattern recognition, computer vision and image processing communities. This new algorithm is a hybrid approach for recognizing a person based on Feature based, Eigen based and Unified Bayesian algorithms and hence called Hybrid FEB. This algorithm has been tested on IITK Face database and IET Jaunpur database and average accuracy is found to be 93.37%. Key-Words: Face recognition, Detection, Color space, Features, PCA, Unified Bayesian, Image processing.
CleanURL: A Privacy Aware Link Shortener

When URLs containing application parameters are posted in public settings privacy can be compromised if the those arguments contain personal or tracking data. To this end we describe a privacy aware link shortening service that attempts to strip sensitive and non-essential parameters based on difference algorithms and human feedback. Our implementation, CleanURL, allows users to validate our automated logic and provides them with intuition about how these otherwise opaque arguments function. Finally, we apply CleanURL over a large Twitter URL corpus to measure the prevalence of such privacy leaks and further motivate our tool.
The discontinuous nature of neurofilament transport accommodates both establishment and repair of the axonal neurofilament array

Neurofilaments (NFs) provide structural support to axons. Timely and regional deposition of NFs is essential during axonogenesis, since progressive stabilization of proximal axons is essential to support continued pathfinding of distal axonal regions. NFs undergo short bursts of microtubule‐mediated axonal transport interspersed by prolonged pauses. We demonstrate herein that it is this unique “on‐off” method of axonal transport, coupled with the ability of NFs to form cation‐dependent, phosphomediated lateral associations that allow neurons to mediate the orderly transition from exploratory process to stabilized axon following synaptogenesis. We further demonstrate how this transport method provides for NF maintenance following maturation and encompasses the potential for regeneration. © 2012 Wiley Periodicals, Inc.
MONOSPECIFICITY OF BONE MARROW-DERIVED LYMPHOCYTES

The clonal selection hypothesis suggests that during ontogeny individual antibodyforming cell precursors (AFCP), 1 now known to be bone marrow-derived (B) lymphocytes (1), become committed to respond to a limited number of antigens, and express this commitment by displaying immunogiobuiin (Ig) receptors on their surface with the same specifcity as the antibody that the cell or clone will eventually secrete (2). There is now abundant evidence supporting this hypothesis. Antibody-secreting cells have been shown in general to secrete Ig of a single class, light chain type, allotype, idiotype, and specificity (3). B lymphocytes have been demonstrated to have Ig on their surface (4), and there is much indirect evidence that it serves as receptor for antigen (5). The ability of anti-idiotype antibody treatment of normal spleen cells to specifically inhibit the subsequent production of antibody expressing the idiotype (6) argues strongly that the Ig receptors on AFCP are of the same specificity as the secreted antibody. In addition, AFCP from immune and nonimmune animals have been selectively inactivated by treatment with highly radioactive antigen (7, 8) or selectively removed from cell suspensions by passage over antigen-coated beads (9). Although, taken together, all of this evidence indicates that antibody-secreting cells are monospecific and that AFCP have Ig receptors of restricted specificity, they do not establish whether AFCP are monospecific (having receptors with identical combining sites) or oligospecific (having various receptors with different combining sites) (10). The experiments reported here provide direct evidence for monospecificity of normal and primed B lymphocytes.
Research on a Graph-Based Algorithm

Mining association rules is an important field in data mining. The article discussed a graph-based association mining algorithm, which directly generate frequent candidate itemsets through constructing directed graphs to form association rules. But this algorithm occupy a great deal of time for checking the candidate itemsets, so an improved algorithm proposed. The improved algorithm utilize the method of judging the nodes' io-value to cut the redundant nodes of candidate itemsets. The experimental results shows that, with smaller minimum support value,the improved algorithm effectively improve the discovery efficiency of the frequent itemsets.
SARCOPLASMIC RETICULUM AND T TUBULES IN DIFFERENTIATING RAT SKELETAL MUSCLE

An electron microscope study has been made of the distribution of membrane couplings between the sarcoplasmic reticulum (SR) and either the plasmalemma or the T tubules in fetal and neonatal rat intercostal muscle. Within primitive muscle cells at 12 days of gestation, the SR forms both simple and specialized membrane junctions with the plasmalemma; caveolae are very few, and T tubules are not detected. Undifferentiated cells neighbor muscle cells. Occasionally these cells contain subsurface couplings between the endoplasmic reticulum and plasmalemmae. Possible relationships between these couplings and the peripheral couplings of muscle cells are discussed. By 15–18 days of gestation, caveolae and beaded T tubules, comparable to those of cultured muscle, develop; T tubules lie along-side myofibrils and are rarely transverse. SR couples both to T tubules and to plasmalemmae during this period. T tubules with lineal profiles appear after further development and their orientation transverse to A–I junctions becomes increasingly evident. Membrane couplings between SR and T tubules also increase in number, whereas the incidence of peripheral coupling declines rapidly Evidence suggests that peripheral couplings are swept into myotubes as caveolae proliferate and T tubules form. SR thus appears to initially couple with the plasmalemma and then to await T tubular growth. This contrasts with the developmental pattern described in cultured chick muscle in which peripheral couplings are not reported and T tubules with diads and triads occur at very primitive stages of muscle differentiation.
Mobile Communities - Extending Online Communities into the Real World

Communities offer a context for people to meet, communicate and collaborate. Tools to support communities usually provide a communication and coordination medium and functionalities to find communication partners. Thereby, they strengthen existing communities or enable completely new (virtual) communities. In this paper we briefly present some ideas towards the extension of community support to mobile environments from the ongoing project COSMOS. 1 The objectives of COSMOS are the development of new technologies and concepts for this support. We discuss ideas for mobile community support services and lay out a plan for future work.
An introduction to low dose electron tomography-from specimen preparation to data collection

Electron tomography is a technique that uses a Transmission Electron Microscope (TEM) to determine a three-dimensional (3D) structure from any given asymmetric object [1]. This process can be simply broken down into 3 steps. First, a series of two dimension projection images of the specimen are recorded and systematically tilted to different angles in the microscope. Second, these individual images are aligned to a common origin. Finally, the projections are then backprojected to create a 3D representation of the sample [2]. Modern commercial instruments now provide a computerized interface, which has been exploited to develop software for automated data collection of the tilt series. As a result, electron tomography is growing in popularity. Before attempting to collect data for tomography it is important to note that the resolution of the data will depend on specimen preparation, imaging conditions and image processing. In this review we attempt to address two of the important issues in electron tomography namely biological specimen preparation and imaging conditions. The reader is directed to Frank 2006 [3] for a comprehensive overview of the current data processing methods.
A novel human IL2RB mutation results in T and NK cell–driven immune dysregulation

A novel homozygous mutation in human IL2RB results in decreased IL-2Rβ protein expression and dysregulated IL-2/15 signaling. This hypomorphic mutation leads to decreased regulatory T cell frequency and an abnormal NK cell compartment, with clinical manifestations of autoimmunity and susceptibility to CMV.
Natural History of Skeletal Muscle Mass Changes in Chronic Kidney Disease Stage 4 and 5 Patients: An Observational Study

Cross-sectional studies in dialysis demonstrate muscle wasting associated with loss of function, increased morbidity and mortality. The relative drivers are poorly understood. There is a paucity of data regarding interval change in muscle in pre-dialysis and dialysis-dependant patients. This study aimed to examine muscle and fat mass change and elucidate associations with muscle wasting in advanced CKD. 134 patients were studied (60 HD, 28 PD, 46 CKD 4–5) and followed up for two years. Groups were similar in age, sex and diabetes prevalence. Soft tissue cross-sectional area (CSA) was measured annually on 3 occasions by a standardised multi-slice CT thigh. Potential determinants of muscle and fat CSA were assessed. Functional ability was assessed by sit-to-stand testing. 88 patients completed follow-up (40 HD, 16 PD, 32 CKD). There was a significant difference in percentage change in muscle CSA (MCSA) over year 1, dependant on treatment modality (χ2 = 6.46; p = 0.039). Muscle loss was most pronounced in pre-dialysis patients. Muscle loss during year 1 was partially reversed in year 2 in 39%. Incident dialysis patients significantly lost MCSA during the year which they commenced dialysis, but not the subsequent year. Baseline MCSA, change in MCSA during year 1 and dialysis modality predicted year 2 change in MCSA (adjusted R2 = 0.77, p<0.001). There was no correlation between muscle or fat CSA change and any other factors. MCSA correlated with functional testing, although MCSA change correlated poorly with change in functional ability. These data demonstrate marked variability in MCSA over 2 years. Loss of MCSA in both pre-dialysis and established dialysis patients is reversible. Factors previously cross-sectionally shown to correlate with MCSA did not correlate with wasting progression. The higher rate of muscle loss in undialysed CKD patients, and its reversal after dialysis commencement, suggests that conventional indicators may not result in optimal timing of dialysis initiation.