Miracle-dz/UniFAR-FTUs huggingface dataset:
Canine Antibodies against Salivary Recombinant Proteins of Phlebotomus perniciosus: A Longitudinal Study in an Endemic Focus of Canine Leishmaniasis

Background Phlebotomine sand flies are vectors of Leishmania parasites. During blood feeding, sand flies deposit into the host skin immunogenic salivary proteins which elicit specific antibody responses. These anti-saliva antibodies enable an estimate of the host exposure to sand flies and, in leishmaniasis endemic areas, also the risk for Leishmania infections. However, the use of whole salivary gland homogenates as antigen has several limitations, and therefore, recombinant salivary proteins have been tested to replace them in antibody detection assays. In this study, we have used for the first time sand fly salivary recombinant proteins in a longitudinal field study on dogs. Methodology/Principal Findings Sera from dogs naturally exposed to P. perniciosus bites over two consecutive transmission seasons in a site endemic for canine leishmaniasis (CanL) were tested at different time points by ELISA for the antibodies recognizing whole saliva, single salivary 43 kDa yellow-related recombinant protein (rSP03B), and a combination of two salivary recombinant proteins, 43 kDa yellow-related protein and 35.5 kDa apyrase (rSP01). Dogs were also tested for Leishmania infantum positivity by serology, culture, and PCR and the infection status was evaluated prospectively. We found a significant association between active CanL infection and the amount of anti-P. perniciosus saliva antibodies. Importantly, we detected a high correlation between IgG antibodies recognizing rSP03B protein and the whole salivary antigen. The kinetics of antibody response showed for both a whole saliva and rSP03B a similar pattern that was clearly related to the seasonal abundance of P. perniciosus. Conclusions These results suggest that P. perniciosus rSP03B protein is a valid alternative to whole saliva and could be used in large-scale serological studies. This novel method could be a practical and economically-sound tool to detect the host exposure to sand fly bites in CanL endemic areas.
Endocrine markers during a job intervention

Abstract An intervention consisting of a thorough examination of the psychological worksite problems and a follow-up with feedback and recommendations was made in four different office worksites. One of the sites («active» group) was more organizational change-oriented than the others («passive» group). The course was followed before, three times during the 3 months of the intervention, and 4 months after the end of it, by means of three endocrine plasma markers: cortisol, prolactin and testosterone. In both study groups the prolactin levels increased in women during the starting phase of the intervention, whereas in men prolactin levels remained stable with a tendency (p=0.06) towards lowered prolactin levels during the end phase of the intervention in the active group. Cortisol levels increased markedly in the passive group and tended to decrease in the active group during the intervention (two-way interaction p=0.003), particularly in men. These findings may be indicative of feelings of uneasiness. Tes.
Achieving empowerment using the Empowerment Strategy Grid

To survive in an increasingly competitive environment, companies today are searching for innovative ways to enhance the creative potential of their workforce. Like total quality management (TQM) and re‐engineering, empowerment has become a 1990s mantra. Yet empowerment in practice is more than just a current buzzword: it is a significant leadership challenge. To confront this challenge, we have developed the Empowerment Strategy Grid, an assessment tool which can help companies avoid the implementation pitfalls associated with group differences, variations in the definition and degree of empowerment across an organization, and human‐resource interventions which unintentionally disempower. Comprehensively describes the Empowerment Strategy Grid and its practical application in facilitating a leading US multinational’s transition to empowered work teams and potential achievement of empowerment benefits. Also presents implications for companies managing similar change.
Effective and Efficient: Large-Scale Dynamic City Express

Due to the large number of requirements for city express services in recent years, the current city express system is found to be unsatisfactory for both the service providers and customers. In this paper, we are the first to systematically study the large-scale dynamic city express problem. We aim to increase both the effectiveness and the efficiency of the scheduling algorithm. The challenges of the problem stem from the highly dynamic environment, the NP-completeness with respect to the number of requests, and real-time demands for the scheduling result. We introduce a basic algorithm to assign a request to a courier on a first-come, first-served basis. To improve the effectiveness of the basic algorithm, we adopt a batch assignment strategy that computes the pickup-delivery routes for a group of requests received in a short period rather than dealing with each request individually. To improve the efficiency of the algorithm, we further design a two-level priority queue structure to reduce redundant shortest distance calculation and repeated candidate generation. We develop a simulation system and conduct extensive performance studies on the real road network of Beijing city. The experimental results demonstrate the high effectiveness and efficiency of our algorithms. Remarkably, our system can achieve much better service quality and largely reduce the operation cost of a city express company simultaneously.
Quantitative Förster resonance energy transfer efficiency measurements using simultaneous spectral unmixing of excitation and emission spectra

Abstract. Accurate quantification of Förster resonance energy transfer (FRET) using intensity-based methods is difficult due to the overlap of fluorophore excitation and emission spectra. Consequently, mechanisms are required to remove bleedthrough of the donor emission into the acceptor channel and direct excitation of the acceptor when aiming to excite only the donor fluorophores. Methods to circumvent donor bleedthrough using the unmixing of emission spectra have been reported, but these require additional corrections to account for direct excitation of the acceptor. Here we present an alternative method for robust quantification of FRET efficiencies based upon the simultaneous spectral unmixing of both excitation and emission spectra. This has the benefit over existing methodologies in circumventing the issue of donor bleedthrough and acceptor cross excitation without the need for additional corrections. Furthermore, we show that it is applicable with as few as two excitation wavelengths and so can be used for quantifying FRET efficiency in microscope images as easily as for data collected on a spectrofluorometer. We demonstrate the accuracy of the approach by reproducing efficiency values in well characterized FRET standards: HEK cells expressing a variety of linked cerulean and venus fluorescent proteins. Finally we describe simple ImageJ plugins that can be used to calculate and create images of FRET efficiencies from microscope images.
Memory deduplication as a threat to the guest OS

Memory deduplication shares same-content memory pages and reduces the consumption of physical memory. It is effective on environments that run many virtual machines with the same operating system. Memory deduplication, however, is vulnerable to memory disclosure attacks, which reveal the existence of an application or file on another virtual machine. Such an attack takes advantage of a difference in write access times on deduplicated memory pages that are re-created by Copy-On-Write. In our experience on KSM (kernel samepage merging) with the KVM virtual machine, the attack could detect the existence of sshd and apache2 on Linux, and IE6 and Firefox on WindowsXP. It also could detect a downloaded file on the Firefox browser. We describe the attack mechanism in this paper, and also mention countermeasures against this attack.
A graph-theoretic network security game

Consider a network vulnerable to viral infection, where the security software can guarantee safety only to a limited part of it. We model this practical network scenario as a non-cooperative multi-player game on a graph, with two kinds of players, a set of attackers and a protector player, representing the viruses and the system security software, respectively. We are interested in the associated Nash equilibria, where no network entity can unilaterally improve its local objective. We obtain the following results: for certain families of graphs, mixed Nash equilibria can be computed in polynomially time. These families include, among others, regular graphs, graphs with perfect matchings and trees. The corresponding price of anarchy for any mixed Nash equilibria of the game is upper and lower bounded by a linear function of the number of vertices of the graph. (We define the price of anarchy to reflect the utility of the protector). Finally, we introduce a generalised version of the game. We show that the existence problem of pure Nash equilibria here is NP complete.
Discrimination of Liver Diseases from CT Images Based on Gabor Filters

In this paper, a liver disease diagnosis based on Gabor filters is proposed. Three kinds of liver diseases are identified: cyst, hepatoma and cavernous hemangioma. The diagnosis scheme includes two steps: features extraction and classification. The features derived from Gabor filters are obtained from the ROIs among the normal and abnormal CT images. In the classification step the SVM classifier is used to discriminate the different liver disease types. Finally the receiver operating characteristic curve is employed to evaluate the performance of the diagnosis system. The effectiveness of the proposed method is demonstrated through experimental results on CT images including 76 liver cysts, 30 hepatomas, and 40 cavernous hemangiomas. From the results, we can observe that the discrimination rate of cyst is higher than the other diseases, and the classification accuracy decreases slightly between cavernous hemangiomas and hepatomas. However, a normal region can be discriminated from all of these diseases entirely
A Next-Generation Cleaved, Soluble HIV-1 Env Trimer, BG505 SOSIP.664 gp140, Expresses Multiple Epitopes for Broadly Neutralizing but Not Non-Neutralizing Antibodies

A desirable but as yet unachieved property of a human immunodeficiency virus type 1 (HIV-1) vaccine candidate is the ability to induce broadly neutralizing antibodies (bNAbs). One approach to the problem is to create trimeric mimics of the native envelope glycoprotein (Env) spike that expose as many bNAb epitopes as possible, while occluding those for non-neutralizing antibodies (non-NAbs). Here, we describe the design and properties of soluble, cleaved SOSIP.664 gp140 trimers based on the subtype A transmitted/founder strain, BG505. These trimers are highly stable, more so even than the corresponding gp120 monomer, as judged by differential scanning calorimetry. They are also homogenous and closely resemble native virus spikes when visualized by negative stain electron microscopy (EM). We used several techniques, including ELISA and surface plasmon resonance (SPR), to determine the relationship between the ability of monoclonal antibodies (MAbs) to bind the soluble trimers and neutralize the corresponding virus. In general, the concordance was excellent, in that virtually all bNAbs against multiple neutralizing epitopes on HIV-1 Env were highly reactive with the BG505 SOSIP.664 gp140 trimers, including quaternary epitopes (CH01, PG9, PG16 and PGT145). Conversely, non-NAbs to the CD4-binding site, CD4-induced epitopes or gp41ECTO did not react with the trimers, even when their epitopes were present on simpler forms of Env (e.g. gp120 monomers or dissociated gp41 subunits). Three non-neutralizing MAbs to V3 epitopes did, however, react strongly with the trimers but only by ELISA, and not at all by SPR and to only a limited extent by EM. These new soluble trimers are useful for structural studies and are being assessed for their performance as immunogens.
A new experimental method for behavioral finance

This article introduces a new instrument for financial experiment called Investor Behavior Test and Analysis Platform (IBTAF), trying to establish a more scientific system for experimental studies in behavioral finance. This method creates a new way to do researches in trading behavioral characteristics of individuals and groups, particularly some extreme cases in real market can be simulated once and once again. Our platform is an independent trading matching and executing system with flexible and multi-functional controlling conditions. Here, we describe how to design the experiment under controlled conditions. Finally, we share an empirical experiment focusing on how the investor's behavior influenced by the changes of prices; also the experimental results are reported.
Insulin Secretory Defect and Insulin Resistance in Isolated Impaired Fasting Glucose and Isolated Impaired Glucose Tolerance

Objective. To investigate the characteristics of isolated impaired glucose tolerance (IGT) and isolated impaired fasting glucose (IFG), we analyzed the factors responsible for elevation of 2-hour postchallenge plasma glucose (2 h PG) and fasting plasma glucose (FPG) levels. Methods. We investigated the relationship between 2 h PG and FPG levels who underwent 75 g OGTT in 5620 Japanese subjects at initial examination for medical check-up. We compared clinical characteristics between isolated IGT and isolated IFG and analyzed the relationships of 2 h PG and FPG with clinical characteristics, the indices of insulin secretory capacity, and insulin sensitivity. Results. In a comparison between isolated IGT and isolated IFG, insulinogenic index was lower in isolated IGT than that of isolated IFG (0.43 ± 0.34 versus 0.50 ± 0.47, resp.; p < 0.01). ISI composite was lower in isolated IFG than that of isolated IGT (6.87 ± 3.38 versus 7.98 ± 4.03, resp.; p < 0.0001). In isolated IGT group, insulinogenic index showed a significant correlation with 2 h PG (r = −0.245, p < 0.0001) and had the strongest correlation with 2 h PG (β = −0.290). In isolated IFG group, ISI composite showed a significant correlation with FPG (r = −0.162, p < 0.0001) and had the strongest correlation with FPG (β = −0.214). Conclusions. We have elucidated that decreased early-phase insulin secretion is the most important factor responsible for elevation of 2 h PG levels in isolated IGT subjects, and decreased insulin sensitivity is the most important factor responsible for elevation of FPG levels in isolated IFG subjects.
Cholecystectomy deferral in patients with endoscopic sphincterotomy.

BACKGROUND Cholecystectomy is not required in up to 64% of patients who adopt a wait-and-see policy after endoscopic clearance of common bile duct stones. Although reports of retrospective cohort series have shown a higher mortality among patients who defer cholecystectomy, it is not known if this is due to the patients' premorbid health status or due to the deferral of cholecystectomy. Randomised clinical trials of prophylactic cholecystectomy versus wait-and-see have not had sufficient power to demonstrate differences in survival. OBJECTIVES To evaluate the beneficial and harmful effects of cholecystectomy deferral (wait-and-see) versus elective (prophylactic) cholecystectomy in patients who have had an endoscopic biliary sphincterotomy. SEARCH STRATEGY We searched The Cochrane Hepato-Biliary Group Controlled Trials Register, the Cochrane Controlled Trials Register (CENTRAL) in The Cochrane Library, MEDLINE (1966 to 2007), EMBASE (1980 to 2007), and Science Citation Index Expanded without language restrictions until April 2007. SELECTION CRITERIA Randomised clinical trials comparing patients whose gallbladder was left in-situ after endoscopic sphincterotomy (wait-and-see group) versus patients who had cholecystectomy with either endoscopic sphincterotomy or common bile duct exploration (prophylactic cholecystectomy group), irrespective of blinding, language, or publication status. DATA COLLECTION AND ANALYSIS We assessed the impact of a wait-and-see policy on mortality. Secondary outcomes assessed were the incidence of biliary pain, cholangitis, pancreatitis, need for cholangiography, need for cholecystectomy, and the rate of difficult cholecystectomy. We pooled data using relative risk with fixed-effect and random-effects models. MAIN RESULTS We included 5 randomised trials with 662 participants out of 93 publications identified through the literature searches. The number of deaths was 47 in the wait-and-see group (334 patients) compared to 26 in the prophylactic cholecystectomy group (328 patients) for a 78% increased risk of mortality (RR 1.78, 95% CI 1.15 to 2.75, P = 0.010). The survival benefit of prophylactic cholecystectomy was independent of trial design, inclusion of high risk patients or inclusion of any one of the five trials. Patients in the wait-and-see group had higher rates of recurrent biliary pain (RR 14.56, 95% CI 4.95 to 42.78, P < 00001), jaundice or cholangitis (RR 2.53, 95% CI 1.09 to 5.87, P = 0.03), and of repeat ERCP or other forms of cholangiography (RR 2.36, 95% CI 1.29 to 4.32, P = 0.005). Cholecystectomy was eventually performed in 35% (115 patients) of the wait-and-see group. AUTHORS' CONCLUSIONS Prophylactic cholecystectomy should be offered to patients whose gallbladders remain in-situ after endoscopic sphincterotomy and common bile duct clearance.
STRAND SEPARATION AND SPECIFIC RECOMBINATION IN DEOXYRIBONUCLEIC ACIDS: PHYSICAL CHEMICAL STUDIES.

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An improved ensemble of variable-rate LDPC codes with precoding

In this paper, we apply the precoding technique developed by Abbasfar et al. for ARA codes to the original rate-compatible LDPC codes introduced in [1] to obtain an improved ensemble of variable-rate LDPC codes, which perform universally well over the AWGN channel in the low to high code-rate region. The proposed codes will be named precoded Kite codes. The Extrinsic Information Transfer (EXIT) chart is used to optimize the code performance. Numerical results show that the precoded Kite codes can achieve a coding gain of up to 0.3 dB over the codes in [1]. A performance comparison is also made between the proposed codes and the Raptor codes over the AWGN channel. It is shown that the proposed codes outperform the Raptor codes universally in a wide code rate range over AWGN channels. Extensive simulation results confirm that precoded Kite codes perform close to capacity within a range of code rates from 0.1 to 0.9.
Complete Genome Sequence of Klebsiella pneumoniae Phage JD001

ABSTRACT Klebsiella pneumoniae is a member of the family Enterobacteriaceae, opportunistic pathogens that are among the eight most prevalent infectious agents in hospitals. The emergence of multidrug-resistant strains of K. pneumoniae has became a public health problem globally. To develop an effective antimicrobial agent, we isolated a bacteriophage, named JD001, from seawater and sequenced its genome. Comparative genome analysis of phage JD001 with other K. pneumoniae bacteriophages revealed that phage JD001 has little similarity to previously published K. pneumoniae phages KP15, KP32, KP34, and phiKO2. Here we announce the complete genome sequence of JD001 and report major findings from the genomic analysis.
Unsupervised technique for robust target separation and analysis of DNA microarray spots through adaptive pixel clustering

MOTIVATION Microarray images challenge existing analytical methods in many ways given that gene spots are often comprised of characteristic imperfections. Irregular contours, donut shapes, artifacts, and low or heterogeneous expression impair corresponding values for red and green intensities as well as their ratio R/G. New approaches are needed to ensure accurate data extraction from these images. RESULTS Herein we introduce a novel method for intensity assessment of gene spots. The technique is based on clustering pixels of a target area into foreground and background. For this purpose we implemented two clustering algorithms derived from k-means and Partitioning Around Medoids (PAM), respectively. Results from the analysis of real gene spots indicate that our approach performs superior to other existing analytical methods. This is particularly true for spots generally considered as problematic due to imperfections or almost absent expression. Both PX(PAM) and PX(KMEANS) prove to be highly robust against various types of artifacts through adaptive partitioning, which more correctly assesses expression intensity values. AVAILABILITY The implementation of this method is a combination of two complementary tools Extractiff (Java) and Pixclust (free statistical language R), which are available upon request from the authors.
Automatic obfuscated cell layout for trusted split-foundry design

We present split-cellTK, a tool that automates the obfuscation of split-foundry layout, in which an untrusted foundry fabricates the devices (FEOL) and a trusted foundry completes the design with metalization (BEOL). split-cellTK does not alter the design netlist for obfuscation - it accepts an arbitrary transistor-level netlist as input. By obfuscating the the organization, placement and connectivity of devices in the FEOL, split-cellTK increases the difficulty of a reverse engineering effort. We evalute two FEOL obfuscation schemes: uniform layout and layout with random spacing. We extend the set of metrics previously defined in the literature to capture the benefits of obfuscation at the cell level. We use these metrics to evaluate the degree of obfuscation provided by our schemes and present the power, area, and throughput overheads for our obfuscation schemes. Finally, we present measured results for an asynchronous FPGA fabricated in a 65 nm split-foundry technology using our tool.