Miracle-dz/UniFAR-FTUs huggingface dataset:
Expression and Functional Characterization of the First Bacteriophage-Encoded Chaperonin

ABSTRACT Chaperonins promote protein folding in vivo and are ubiquitously found in bacteria, archaea, and eukaryotes. The first viral chaperonin GroEL ortholog, gene product 146 (gp146), whose gene was earlier identified in the genome of bacteriophage EL, has been shown to be synthesized during phage propagation in Pseudomonas aeruginosa cells. The recombinant gp146 has been expressed in Escherichia coli and characterized by different physicochemical methods for the first time. Using serum against the recombinant protein, gp146's native substrate, the phage endolysin gp188, has been immunoprecipitated from the lysate of EL-infected bacteria and identified by mass spectrometry. In vitro experiments have shown that gp146 has a protective effect against endolysin thermal inactivation and aggregation, providing evidence of its chaperonin function. The phage chaperonin has been found to have the architecture and some properties similar to those of GroEL but not to require cochaperonin for its functional activity.
Parameters Tuning Approach for Proportion Integration Differentiation Controller of Magnetorheological Fluids Brake Based on Improved Fruit Fly Optimization Algorithm

In order to improve the response performance of a proportion integration differentiation (PID) controller for magnetorheological fluids (MRF) brake and to reduce the braking fluctuation rate, an improved fruit fly optimization algorithm for PID controller parameters tuning of MRF brake is proposed. A data acquisition system for MRF brake is designed and the transfer function of MRF brake is identified. Moreover, an improved fruit fly optimization algorithm (IFOA) through integration of PID control strategy and cloud model algorithm is proposed to design a PID controller for MRF brake. Finally, the simulation and experiment are carried out. The results show that IFOA, with a faster response output and no overshoot, is superior to the conventional PID and fruit fly optimization algorithm (FOA) PID controller.
C-Reactive Protein for the Enhanced Evaluation of the Systemic Inflammatory Response Syndrome (SIRS)

Introduction: An elevation in the CRP may provide an early indication of developing SIRS with progression to sepsis that is more sensitive than the standard clinical criteria of fever (or hypothermia), tachypnea, tachycardia, and leukocytosis with neutrophilia (or neutropenia). The problem of false positive rate for SIRS resides mainly in the common occurance of tachypnea and tachycardia in presenting patients, and in the confounding presence of neutrophilia without reference to good measures of a left shift. The objective of this study was to investigate how using CRP as a marker to confirm the presence of early sepsis might reduce the false positive rate inherent in the defining SIRS criteria. Materials and Methods: One hundred sixty eight patients with leukocytosis greater than 12,000 associated with a high absolute neutrophil count were studied. Those that met the inclusion criteria were analyzed for CRP response. Results: A linear correlation between CRP elevation and the defining criteria for SIRS was found except there was no correlation with absolute neutrophil count.
High cancer risk and increased mortality in patients with Peutz–Jeghers syndrome

Background Peutz–Jeghers syndrome (PJS) is associated with an increased cancer risk. As the determination of optimal surveillance strategies is hampered by wide ranges in cancer risk estimates and lack of data on cancer-related mortality, we assessed cancer risks and mortality in a large cohort of patients with PJS. Methods Dutch PJS patients were included in this cohort study. Patients were followed prospectively between January 1995 and July 2009, and clinical data from the period before 1995 were collected retrospectively. Data were obtained by interview and chart review. Cumulative cancer risks were calculated by Kaplan–Meier analysis and relative cancer and mortality risks by Poisson regression analysis. Results We included 133 PJS patients (48% males) from 54 families, contributing 5004 person-years of follow-up. 49 cancers were diagnosed in 42 patients (32%), including 25 gastrointestinal (GI) cancers. The median age at first cancer diagnosis was 45 years. The cumulative cancer risk was 20% at age 40 (GI cancer 12%), increasing to 76% at age 70 (GI cancer 51%). Cumulative cancer risks were higher for females than for males (p=0.005). The relative cancer risk was higher in PJS patients than in the general population (HR 8.96; 95% CI 6.46 to 12.42), and higher among female (HR 20.40; 95% CI 13.43 to 30.99) than among male patients (HR 4.76; 95% CI 2.82 to 8.04). 42 patients had died at a median age of 45 years, including 28 cancer-related deaths (67%). Mortality was increased in our cohort compared to the general population (HR 3.50; 95% CI 2.57 to 4.75). Conclusions PJS patients carry high cancer risks, leading to increased mortality. The malignancies occur particularly in the GI tract and develop at young age. These results justify surveillance in order to detect malignancies in an early phase to improve outcome.
Dynamic Scheduling for Semiconductor Production Line Based on Composite Rule

Various factors and constraints should be considered when developing a manufacturing 13 production schedule, and such a schedule is often based on rules. This paper develops a composite 14 dispatching rule based on heuristic rules that comprehensively consider various factors in a 15 semiconductor production line. The composite rule is obtained by exploring various states of a 16 semiconductor production line (machine status, queue size, etc.), where such indicators as 17 makespan and equipment efficiency are used to judge performance. A model of the response 18 surface, as a function of key variables, is then developed to find the optimized parameters of a 19 composite rule for various production states. Further, dynamic scheduling of semiconductor 20 manufacturing is studied based on support vector regression (SVR). This approach dynamically 21 obtains a composite dispatching rule (i.e. parameters of the composite dispatching rule) that can be 22 used to optimize production performance according to real-time production line state. Following 23 optimization, the proposed dynamic scheduling approach is tested in a real semiconductor 24 production line to validate the effectiveness of the proposed composite rule set. 25
The Functional Role of Calcineurin in Hypertrophy, Regeneration, and Disorders of Skeletal Muscle

Skeletal muscle uses calcium as a second messenger to respond and adapt to environmental stimuli. Elevations in intracellular calcium levels activate calcineurin, a serine/threonine phosphatase, resulting in the expression of a set of genes involved in the maintenance, growth, and remodeling of skeletal muscle. In this review, we discuss the effects of calcineurin activity on hypertrophy, regeneration, and disorders of skeletal muscle. Calcineurin is a potent regulator of muscle remodeling, enhancing the differentiation through upregulation of myogenin or MEF2A and downregulation of the Id1 family and myostatin. Foxo may also be a downstream candidate for a calcineurin signaling molecule during muscle regeneration. The strategy of controlling the amount of calcineurin may be effective for the treatment of muscular disorders such as DMD, UCMD, and LGMD. Activation of calcineurin produces muscular hypertrophy of the slow-twitch soleus muscle but not fast-twitch muscles.
An Improved JPS Algorithm in Symmetric Graph

Path planning is one of the most studied problems in the field of robotics, unmanned aerial vehicles (uavs), vehicle navigation and fields like these. The majority algorithms of path planning produce possible paths of grid graph, and then apply in problems such as classical graph route searching. Astar algorithm, Hierarchical Path-Finding A-star (HPA*) and Jump Point Search (JPS) algorithms are studied in this paper to compare the maze searching capacity and different search maps' efficiency. We also propose an improved JPS algorithm in symmetric grid graph. In this paper, we compare their search time and efficiency. Conducted experiment shows that by adopting the same benchmarks our algorithm not only tackles the congestion problem, but also solves the problem more efficiently. Experiments validated the improved JPS algorithm and results show it outperforms the other algorithms.
Stylization of Lighting Effects for Images

We propose a new model to stylize lighting effects in 2D images. Our stylizations are based on well-known artistic styles ranging from Chiaroscuro to comics. Lighting has always been used in graphical art to give realism to an illustration or to enhance visual contrasts between objects in a scene. This allows creating a global atmosphere. Giving an input image, our model automatically generates a lighting map of the image which may be modified by the user to determine different types of shadows or light effects like highlights. Following graphical arts styles, we propose six stylizations. Our model is flexible and specifically designed to help users and even amateur users, to semi-automatically stylize the different kinds of light effects in an image.
Evaluation of human papillomavirus antibodies and risk of subsequent head and neck cancer.

PURPOSE Human papillomavirus type 16 (HPV16) infection is causing an increasing number of oropharyngeal cancers in the United States and Europe. The aim of our study was to investigate whether HPV antibodies are associated with head and neck cancer risk when measured in prediagnostic sera. METHODS We identified 638 participants with incident head and neck cancers (patients; 180 oral cancers, 135 oropharynx cancers, and 247 hypopharynx/larynx cancers) and 300 patients with esophageal cancers as well as 1,599 comparable controls from within the European Prospective Investigation Into Cancer and Nutrition cohort. Prediagnostic plasma samples from patients (collected, on average, 6 years before diagnosis) and control participants were analyzed for antibodies against multiple proteins of HPV16 as well as HPV6, HPV11, HPV18, HPV31, HPV33, HPV45, and HPV52. Odds ratios (ORs) of cancer and 95% CIs were calculated, adjusting for potential confounders. All-cause mortality was evaluated among patients using Cox proportional hazards regression. RESULTS HPV16 E6 seropositivity was present in prediagnostic samples for 34.8% of patients with oropharyngeal cancer and 0.6% of controls (OR, 274; 95% CI, 110 to 681) but was not associated with other cancer sites. The increased risk of oropharyngeal cancer among HPV16 E6 seropositive participants was independent of time between blood collection and diagnosis and was observed more than 10 years before diagnosis. The all-cause mortality ratio among patients with oropharyngeal cancer was 0.30 (95% CI, 0.13 to 0.67), for patients who were HPV16 E6 seropositive compared with seronegative. CONCLUSION HPV16 E6 seropositivity was present more than 10 years before diagnosis of oropharyngeal cancers.
OPRM1 A118G genotype fails to predict the effectiveness of naltrexone treatment for alcohol dependence

Given the evidence from retrospective studies indicating that alcohol-dependent patients with homozygous or heterozygous A118G variant of the &mgr;-opioid receptor, OPRM1, gene have significantly better outcomes when treated with naltrexone; this study examined this prospectively in 100 alcohol-dependent participants prescribed naltrexone for 12 weeks and offered six sessions of cognitive-behavioral therapy or intervention. Comparisons were made among OPRM1 genotypic groups on several outcome measures. Naltrexone treatment produced significant decreases in self-reported and objective indicators of alcohol use and craving from baseline (P<0.0001 and 0.017, respectively), particularly during the first 2 months of treatment, with 68% completing the study. However, there was no evidence of a significant association between OPRM1 A118G genotype and treatment success on any of the outcome measures. Therefore, while naltrexone was an effective treatment for alcohol dependence, the OPRM1 A118G genotype was not a predictor of success.
Extended latent class models for collaborative recommendation

With the advent of the World Wide Web, providing just-in-time personalized product recommendations to customers now becomes possible. Collaborative recommender systems utilize correlation between customer preference ratings to identify "like-minded" customers and predict their product preference. One factor determining the success of the recommender systems is the prediction accuracy, which in many cases is limited by lacking adequate ratings (the sparsity problem). Recently, the use of latent class model (LCM) has been proposed to alleviate this problem. In this paper, we first study how the LCM can be extended to handle customers and products outside the training set. In addition, we propose the use of a pair of LCMs (called dual latent class model-DLCM), instead of a single LCM, to model customers' likes and dislikes separately for enhancing the prediction accuracy. Experimental results based on the EachMovie dataset show that DLCM outperforms both LCM and the conventional correlation-based method when the available ratings are sparse.
Stochastic models for generic images

The idea of using statistical inference for analyzing and understanding images has been used for at least 20 years, going back, for instance, to the work of Grenander [Gr] and Cooper [Co]. To apply these techniques, one needs, of course, a probabilistic model for some class of images or some class of structures present in images. Many models of this type have been introduced. There are stochastic models for image textures [GGGD], [ZMW], for contours in images [Mu], [GCK], for the decomposition of an image into regions [G-G], [M-S], for disparity maps, for grammatical parsing of shapes [Fu], for template matching, for speci c tasks such as face recognition [HGYGM]. The common framework for all these studies is to describe some class of images I(x; y) by means of a set of auxiliary variables fx g representing the salient structures in the images, e.g. edges, texture statistics, inferred depth values or relations, illumination features, medial axes or shape features, locations of key points such as eyes in a face, labels (as in character recognition), etc. Then i) a prior probability model for the `hidden' variables p(fx g) and ii) an imagingmodel p(Ijfx g) for I, given the hidden variables, are de ned. Finally, an image is analyzed using Bayes's rule p(fx gjI) / p(Ijfx g)p(fx g)
PATHOLOGY AND PROPOSED PATHOPHYSIOLOGY OF DICLOFENAC POISONING IN FREE-LIVING AND EXPERIMENTALLY EXPOSED ORIENTAL WHITE-BACKED VULTURES (GYPS BENGALENSIS)

Oriental white-backed vultures (Gyps bengalensis; OWBVs) died of renal failure when they ingested diclofenac, a nonsteroidal anti-inflammatory drug (NSAID), in tissues of domestic livestock. Acute necrosis of proximal convoluted tubules in these vultures was severe. Glomeruli, distal convoluted tubules, and collecting tubules were relatively spared in the vultures that had early lesions. In most vultures, however, lesions became extensive with large urate aggregates obscuring renal architecture. Inflammation was minimal. Extensive urate precipitation on the surface and within organ parenchyma (visceral gout) was consistently found in vultures with renal failure. Very little is known about the physiologic effect of NSAIDs in birds. Research in mammals has shown that diclofenac inhibits formation of prostaglandins. We propose that the mechanism by which diclofenac induces renal failure in the OWBV is through the inhibition of the modulating effect of prostaglandin on angiotensin II-mediated adrenergic stimulation. Renal portal valves open in response to adrenergic stimulation, redirecting portal blood to the caudal vena cava and bypassing the kidney. If diclofenac removes a modulating effect of prostaglandins on the renal portal valves, indiscriminant activation of these valves would redirect the primary nutrient blood supply away from the renal cortex. Resulting ischemic necrosis of the cortical proximal convoluted tubules would be consistent with our histologic findings in these OWBVs.
Computerized Lung Acoustic Monitoring Can Help to Differentiate between Various Chest Radiographic Densities in Critically Ill Patients

Background: Complementary bedside lung monitoring modalities are often sought in order to assist in the differentiation between several lung opacities in the intensive care unit (ICU). Objectives: To evaluate the use of computerized lung acoustic monitoring as a complementary approach in the differentiation between various chest radiographic densities in critically ill patients. Methods: Lung vibration intensity was assessed in 82 intensive care patients using vibration response imaging. Patients were classified according to their primary findings on chest radiography (CXR): consolidation (n = 35), congestion (n = 10), pleural effusion (n = 15), atelectasis/hypoinflation (n = 10) and normal findings (n = 12). Sixty patients were mechanically ventilated and 22 patients were spontaneously breathing. Results: Significantly elevated vibration intensity was detected in patients with consolidation, as opposed to pleural effusion, atelectasis and normal CXR (p < 0.01, Mann-Whitney U test). Vibration intensity was also increased for congestion, but this increase was not significant. The positive predictive value of CXR lung opacity in combination with increased vibration intensity to detect consolidations and/or congestions was 95% (20/21). Furthermore, vibration intensity was significantly higher in mechanically ventilated patients compared to spontaneously breathing patients (p = 0.001, Mann-Whitney U test). Differences related to gender, age and body position were not significant. Conclusions: Computerized lung acoustic monitoring at the bedside was found to be a useful, readily available, noninvasive, adjunctive tool in the differentiation between various CXR densities in critically ill patients.
Structural properties of MoS2 layers grown by CVD technique

Abstract Different layers of Transition Metal Dichalcogenide (TMDC) based compound MoS2 have been grown on SiO2/Si substrate by using the CVD technique. Raman spectra analysis of the samples showed that monolayer, bilayer and few layers of MoS2 are grown when the duration of growth is varied. From the photoluminescence studies direct band gap of the samples are determined - band gap of the monolayer is highest and with the increase of number of layers there is a decrease in the value of the bandgap. The observed change in the band structure of MoS2 with layer thickness is explained due to the quantum confinement effect. Microstructural studies are done using Scanning Electron Microscopy, distribution of triangular shape grains over the surface of the film is observed. Density, thickness and population of these grains are changed when the duration of growth is changed.
Low complexity resolution progressive image coding algorithm: progres (progressive resolution decompression)

A very fast, low complexity algorithm for resolution scalable and random access decoding is presented. The algorithm avoids the multiple passes of bit-plane coding for speed improvement. The decrease in dynamic ranges of wavelet coefficients magnitudes is efficiently coded. The hierarchical dynamic range coding naturally enables a resolution scalable representation of a wavelet transformed image.
Special Topic: Mechanism of Bacterial Pathogenesis Insights into Bacterial Protein Glycosylation in Human Microbiota

The study of human microbiota is an emerging research topic. The past efforts have mainly centered on studying the composition and genomic landscape of bacterial species within the targeted communities. The interaction between bacteria and hosts is the pivotal event in the initiation and progression of infectious diseases. There is a great need to identify and characterize the molecules that mediate the bacteria-host interaction. Bacterial surface exposed proteins play an important role in the bacteria host interaction. Numerous surface proteins are glycosylated, and the glycosylation is crucial for their function in mediating the bacterial interaction with hosts. Here we present an overview of surface glycoproteins from bacteria that inhabit three major mucosal environments across human body: oral, gut and skin. We describe the important enzymes involved in the process of protein glycosylation, and discuss how the process impacts the bacteria-host interaction. Emerging molecular details underlying glycosylation of bacterial surface proteins may lead to new opportunities for designing anti-infective small molecules, and developing novel vaccines in order to treat or prevent bacterial infection.
Statistical Analysis of Two Experimental Studies

Software inspection is well-known as an eeective defect nding process. One avenue of inspection research concerns tool support, with the aim of further increasing its eeciency and eeectiveness. This has resulted in the production of a number of prototype tools. In general, however, these tools are poorly evaluated and the performance gain which these tools may provide has not been quantiied. This paper describes an incremental, cyclic approach to the development and evaluation of a tool to support software inspection. A version of the tool was developed then evaluated against traditional, paper-based inspection. The results were then used to guide development of the next version. This paper describes two of these cycles and the results of the corresponding evaluations. The approach was found to be a useful one, and is applicable to the development of many other tools, processes or procedures.
A Fast and Accurate Two-Stage Algorithm for 1-bit Compressive Sensing

Compressive sensing (CS) shows that a sparse or compressible signal can be exactly recovered from its linear measurements at a rate significantly lower than the Nyquist rate. As an extreme case, 1-bit compressive sensing (1-bit CS) states that an original sparse signal can be recovered from the 1-bit measurements. In this paper, we intrduce a Fast and Accurate Two-Stage (FATS) algorithm for 1-bit compressive sensing. Simulations show that FATS not only significantly increases the signal reconstruction speed but also improves the reconstruction accuracy. key words: compressive sensing, 1-bit compressive sensing, FATS
Drift-free attitude estimation for accelerated rigid bodies

We study the attitude estimation problem for an accelerated rigid body using gyros and accelerometers. The application in mind is that of a walking robot and particular attention is paid to the large and abrupt changes in accelerations that can be expected in such an environment. We propose a state estimation algorithm that fuses data from rate gyros and accelerometers to give long-term drift free attitude estimates. The algorithm does not use any local parameterization of the rigid body kinematics and can thus be used for a rigid body performing any kind of rotations. The algorithm is a combination of two non-standard, but in a sense linear, Kalman filters between which a trigger based switching takes place. The kinematics representation used makes it possible to construct a linear algorithm that can be shown to give convergent estimates for this nonlinear problem. The state estimator is evaluated in simulations demonstrating how the estimates are long term stable even in the presence of gyrodrift.