Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular Fine-Specificity Analysis of Antibody Responses to Human Cytomegalovirus and Design of Novel Synthetic-Peptide-Based Serodiagnostic Assays

ABSTRACT To identify single immunodominant marker proteins which can replace complex virion antigen in serodiagnostic assays, we investigated in detail the molecular fine specificity of antibody responses in different individuals with latent or active human cytomegalovirus (HCMV) infection. An overview of the HCMV proteins recognized by human antibodies was obtained by immunoblotting. For selected immunodominant proteins the epitope fine specificity of the antibody response was determined by a peptide-scanning enzyme-linked immunosorbent assay (ELISA). Epitope clusters were synthesized as combination peptides and were used for further serologic analysis of immunoglobulin M (IgM) and IgG reactivities with panels of sera from different groups of patients in comparison to those with cytomegalovirus (CMV) virion antigen. Several serum samples had significantly higher reactivities with peptides than with the CMV virion antigen. However, individual serum samples occasionally recognized diverse peptide epitopes, stressing the importance of using combinations of peptides in serologic assays. From these studies we were able to define a specific combination of peptides derived from pp52 (UL44) and pp150 (UL32) for the specific and highly sensitive early detection of HCMV IgM, whereas a combination of peptides from pp150 (UL32), gB (UL55), and pp28 (UL99) was selected to give optimal and specific reactivity with HCMV IgG. On the basis of the results obtained with these peptide combinations, new, highly specific serodiagnostic assays were constructed. These assays had sensitivities of 98.9 and 96.4% for IgG and IgM, respectively, in comparison with the results obtained with the “gold standard,” the virion antigen-based ELISA. From the results of this study we conclude that specific combinations of highly defined synthetic peptides can replace complex HCMV virion extracts used in current serodiagnostics and may add to further standardization of HCMV serology.
Coordinate Changes in Histone Modifications, mRNA Levels, and Metabolite Profiles in Clonal INS-1 832/13 β-Cells Accompany Functional Adaptations to Lipotoxicity*

Background: Epigenetic regulation may mediate lipotoxic effects on β-cells in type 2 diabetes. Results: Lipotoxicity impairs insulin secretion, and alters metabolism, gene expression, and histone marks in INS-1 832/13 β-cells. Conclusion: Perturbed insulin secretion results from epigenetic, genetic, and metabolic adaptations to increased fatty acid metabolism in β-cells. Significance: Elucidation of the link between lipotoxicity and insulin secretion is crucial for understanding the pathogenesis of type 2 diabetes. Lipotoxicity is a presumed pathogenetic process whereby elevated circulating and stored lipids in type 2 diabetes cause pancreatic β-cell failure. To resolve the underlying molecular mechanisms, we exposed clonal INS-1 832/13 β-cells to palmitate for 48 h. We observed elevated basal insulin secretion but impaired glucose-stimulated insulin secretion in palmitate-exposed cells. Glucose utilization was unchanged, palmitate oxidation was increased, and oxygen consumption was impaired. Halting exposure of the clonal INS-1 832/13 β-cells to palmitate largely recovered all of the lipid-induced functional changes. Metabolite profiling revealed profound but reversible increases in cellular lipids. Glucose-induced increases in tricarboxylic acid cycle intermediates were attenuated by exposure to palmitate. Analysis of gene expression by microarray showed increased expression of 982 genes and decreased expression of 1032 genes after exposure to palmitate. Increases were seen in pathways for steroid biosynthesis, cell cycle, fatty acid metabolism, DNA replication, and biosynthesis of unsaturated fatty acids; decreases occurred in the aminoacyl-tRNA synthesis pathway. The activity of histone-modifying enzymes and histone modifications of differentially expressed genes were reversibly altered upon exposure to palmitate. Thus, Insig1, Lss, Peci, Idi1, Hmgcs1, and Casr were subject to epigenetic regulation. Our analyses demonstrate that coordinate changes in histone modifications, mRNA levels, and metabolite profiles accompanied functional adaptations of clonal β-cells to lipotoxicity. It is highly likely that these changes are pathogenetic, accounting for loss of glucose responsiveness and perturbed insulin secretion.
Bone Remodeling Increases Substantially in the Years After Menopause and Remains Increased in Older Osteoporosis Patients

Bone remodeling rates (Ac.f) were measured in transilial biopsy specimens from 50 healthy premenopausal women before and 1 year after menopause, in 34 healthy women 13 years past menopause, and in 89 women with untreated osteoporosis. Ac.f nearly doubled 1 year after menopause, tripled 13 years after menopause, and remained elevated in women with osteoporosis.
A probabilistic approach to detecting network scans

This paper presents a probabilistic approach for detecting network scans in real-time. Unlike previous approaches, our model takes into consideration both the number of destinations or ports accessed by a source, as well as how unusual these accesses are. We demonstrate the effectiveness of our approach in terms of accuracy and throughput, based on an analysis of the unusual sources that were found in real-life packet trace files.
Toward a 6 DOF body state estimator for a hexapod robot with dynamical gaits

We report on a continuous time full body state estimator for a hexapod robot operating in the dynamical regime (entailing a significant aerial phase) on level ground that combines a conventional rate gyro with a novel leg strain based body pose estimator. We implement this estimation procedure on the robot RHex and evaluate its performance using a visual ground truth measurement system. As an independent assessment of our estimator's quality we also compare its odometry performance to sensorless averaged open loop distance-per-stride estimates.
The Dartmouth Database of Children’s Faces: Acquisition and Validation of a New Face Stimulus Set

Facial identity and expression play critical roles in our social lives. Faces are therefore frequently used as stimuli in a variety of areas of scientific research. Although several extensive and well-controlled databases of adult faces exist, few databases include children’s faces. Here we present the Dartmouth Database of Children’s Faces, a set of photographs of 40 male and 40 female Caucasian children between 6 and 16 years-of-age. Models posed eight facial expressions and were photographed from five camera angles under two lighting conditions. Models wore black hats and black gowns to minimize extra-facial variables. To validate the images, independent raters identified facial expressions, rated their intensity, and provided an age estimate for each model. The Dartmouth Database of Children’s Faces is freely available for research purposes and can be downloaded by contacting the corresponding author by email.
Object Disambiguation for Augmented Reality Applications

The broad deployment of wearable camera technology in the foreseeable future offers new opportunities for augmented reality applications ranging from consumer (e.g. games) to professional (e.g. assistance). In order to span this wide scope of use cases, a markerless object detection and disambiguation technology is needed that is robust and can be easily adapted to new scenarios. Further, standardized benchmarking data and performance metrics are needed to establish the relative success rates of different detection and disambiguation methods designed for augmented reality applications. Here, we propose a novel object recognition system that fuses stateof-the-art 2D detection with 3D context. We focus on assisting a maintenance worker by providing an augmented reality overlay that identifies and disambiguates potentially repetitive machine parts. In addition, we provide an annotated dataset that can be used to quantify the success rate of a variety of 2D and 3D systems for object detection and disambiguation. Finally, we evaluate several performance metrics for object disambiguation relative to the baseline success rate of a human.
N-version design Versus one Good Version

Software Diversity as a way of achieving high reliability of software Software diversity has long been seen as way of achieving higher reliability of software than is attainable by a single software version subjected to a heroic testing. The known experiments with software diversity confirm that indeed fault-tolerant software employing diversity is "on average" more reliable than a single software version. Utilising design diversity when high reliability is required is, nevertheless, problematic. The cost of diverse system, which may increase substantially, is not the only obstacle. The main problem is assessing how much gain in reliability has actually been achieved. It was shown empirically and theoretically that even versions developed by not communicating development teams tend to fail simultaneously more often than they should under if their failures were independent. Quantifying the dependence between failures is no easier than assessing the reliability of the system, very difficult, because the failures of such systems are very rare and putting a reasonable confidence in the assessment results requires a very long observation. The idea that diversity may be a more cost effective way to deliver high diversity is alive and recently it was spelled out by Hatton [Hatton 1997]. His main point, which seems to be shared by many, is that despite the dependence between the failures of the independently developed software versions, for a given target of the system reliability fault-tolerant software, e.g. 2-out-of-3 system, may be a more cost effective solution than a single software version. The key idea is that despite the dependence between the failures of the versions, a fault-tolerant system consisting of versions of 'ordinary' quality will deliver better reliability than if the efforts to develop several channels were used to produce a single 'state-of-the-art' version. Hatton concludes that taking into account the ratio between the reliability of the 'ordinary' and the 'state-of-the-art' software favours the decision to develop diverse software. The interested reader is referred to Hatton's paper for detailed justification of this idea. He goes even further to conclude that if the targeted reliability increases, than the cost benefits of using design diversity increase, too. The implications of the analysis are that when the developer can afford to produce several versions independently this is the way to go-the reliability of the fault-tolerant system is likely to be better than if a single version were developed. We scrutinise Hatton's analysis, which crucially depends on the assumption …
Transform-both-sides nonlinear models for in vitro pharmacokinetic experiments

Transform-both-sides nonlinear models have proved useful in many experimental applications including those in pharmaceutical sciences and biochemistry. The maximum likelihood method is commonly used to fit transform-both-sides nonlinear models, where the regression and transformation parameters are estimated simultaneously. In this paper, an analysis of variance-based method is described in detail for estimating transform-both-sides nonlinear models from randomized experiments. It estimates the transformation parameter from the full treatment model and then the regression parameters are estimated conditionally on this estimate of the transformation parameter. The analysis of variance method is computationally simpler compared with the maximum likelihood method of estimation and allows a more natural separation of different sources of lack of fit. Simulation studies show that the analysis of variance method can provide unbiased estimators of complex transform-both-sides nonlinear models, such as transform-both-sides random coefficient nonlinear regression models and transform-both-sides fixed coefficient nonlinear regression models with random block effects.
ILTERING S YSTEMS

Email systems have suffered from degraded quality of service due to rampant spam, phishing and fraudulent emails. This is partly because the classification speed of email filtering systems falls far behind the requirements of email service providers. We are motivated to address this issue from the perspective of computer architecture support. In this paper, as the first step towards novel architecture designs, we present extensive performance data collected from measurement and profiling experiments using representative email filtering systems including CRM114, DSPAM, SpamAssassin and TREC Bogofilter. We provide detailed analysis of the time consuming functions in the systems under study. We also show how the processor architecture parameters affect the performance of these email filters through simulation experiments.
Regular Paper Computational Game Theory for Security and Sustainability

Security is a critical concern around the world that arises in protecting our ports, airports, transportation and other critical national infrastructure from adversaries, in protecting our wildlife and forests from poachers and smugglers, and in curtailing the illegal flow of weapons, drugs and money; and it arises in problems ranging from physical to cyber-physical systems. In all of these problems, we have limited security resources which prevent full security coverage at all times; instead, security resources must be deployed intelligently taking into account differences in priorities of targets requiring security coverage, the responses of the attackers to the security posture, and potential uncertainty over the types, capabilities, knowledge and priorities of attackers faced. Game theory, which studies interactions among multiple selfinterested agents, is well-suited to the adversarial reasoning required for security resource allocation and scheduling problems. Casting the problem as a Bayesian Stackelberg game, we have developed new algorithms for efficiently solving such games that provide randomized patrolling or inspection strategies. These algorithms have led to some initial successes in this challenging problem arena, leading to advances over previous approaches in security scheduling and allocation, e.g., by addressing key weaknesses of predictability of human schedulers. These algorithms are now deployed in multiple applications: ARMOR has been deployed at the Los Angeles International Airport (LAX) since 2007 to randomize checkpoints on the roadways entering the airport and canine patrol routes within the airport terminals [17]; IRIS, a game-theoretic scheduler for randomized deployment of the US Federal Air Marshals (FAMS) requiring significant scaleup in underlying algorithms, has been in use since 2009 [17]; PROTECT, which schedules the US Coast Guard’s randomized patrolling of ports using a new set of algorithms based on modeling bounded-rational human attackers, has been deployed in the
Effect of antiretroviral therapy on the diagnostic accuracy of symptom screening for intensified tuberculosis case finding in a South African HIV clinic.

BACKGROUND Current symptom screening algorithms for intensified tuberculosis case finding or prior to isoniazid preventive therapy (IPT) in patients infected with human immunodeficiency virus (HIV) were derived from antiretroviral-naive cohorts. There is a need to validate screening algorithms in patients on antiretroviral therapy (ART). METHODS We performed cross-sectional evaluation of the diagnostic accuracy of symptom screening, including the World Health Organization (WHO) algorithm, to rule out tuberculosis in HIV-infected individuals pre-ART and on ART undergoing screening prior to IPT. RESULTS A total of 1429 participants, 54% on ART, had symptom screening and a sputum culture result available. Culture-positive tuberculosis was diagnosed in 126 patients (8.8%, 95% confidence interval [CI], 7.4%-10.4%). The WHO symptom screen in the on-ART compared with the pre-ART group had a lower sensitivity (23.8% vs 47.6%), but higher specificity (94.4% vs 79.8%). The effect of ART was independent of CD4(+) count in multivariable analyses. The posttest probability of tuberculosis following a negative WHO screen was 8.9% (95% CI, 7.4%-10.8%) and 4.4% (95% CI, 3.7%-5.2%) for the pre-ART and on-ART groups, respectively. Addition of body mass index to the WHO screen significantly improved discriminatory ability in both ART groups, which was further improved by adding CD4 count and ART duration. CONCLUSIONS The WHO symptom screen has poor sensitivity, especially among patients on ART, in a clinic where regular tuberculosis screening is practiced. Consequently, a significant proportion of individuals with tuberculosis would inadvertently be placed on isoniazid monotherapy despite high negative predictive values. Until more sensitive methods of ruling out tuberculosis are established, it would be prudent to do a sputum culture prior to IPT where this is feasible.
Group Structure Influence on Group Lasso Consistency

Group Lasso is a recently proposed regression method that can be used to select group variables. When studying the consistency condition of the regularization path of group Lasso, we assume that the groupings of the univariate variables are known and fixed, that is, the group structure is given. In this paper, we address the issue of the influence of group structure on the group Lasso consistency. Based on the analysis of the consistency condition, we argue that the sparsity patterns is the determinant, the different group structures can lead to different consistencies, and the degree of the correlation between the relevant groups and the irrelevant groups is the key factor. Experimental results also demonstrate that the group Lasso is consistent under low correlation conditions.
Anti-Microbial, Anti-Biofilm Activities and Cell Selectivity of the NRC-16 Peptide Derived from Witch Flounder, Glyptocephalus cynoglossus

Previous studies had identified novel antimicrobial peptides derived from witch flounder. In this work, we extended the search for the activity of peptide that showed antibacterial activity on clinically isolated bacterial cells and bacterial biofilm. Pseudomonas aeruginosa was obtained from otitis media and cholelithiasis patients, while Staphylococcus aureus was isolated from otitis media patients. We found that synthetic peptide NRC-16 displays antimicrobial activity and is not sensitive to salt during its bactericidal activity. Interestingly, this peptide also led to significant inhibition of biofilm formation at a concentration of 4–16 μM. NRC-16 peptide is able to block biofilm formation at concentrations just above its minimum inhibitory concentration while conventional antibiotics did not inhibit the biofilm formation except ciprofloxacin and piperacillin. It did not cause significant lysis of human RBC, and is not cytotoxic to HaCaT cells and RAW264.7 cells, thereby indicating its selective antimicrobial activity. In addition, the peptide’s binding and permeation activities were assessed by tryptophan fluorescence, calcein leakage and circular dichroism using model mammalian membranes composed of phosphatidylcholine (PC), PC/cholesterol (CH) and PC/sphingomyelin (SM). These experiments confirmed that NRC-16 does not interact with any of the liposomes but the control peptide melittin did. Taken together, we found that NRC-16 has potent antimicrobial and antibiofilm activities with less cytotoxicity, and thus can be considered for treatment of microbial infection in the future.
Comparison Among Power LEDs for Automotive Lighting Applications

The first LED diode was created in 1969. Since then, they have been experiencing a continuous improvement in luminous efficiency and power dissipation, achieving current AIInGaP and InGaN devices for yellow to red, and blue to green, including white, colours respectively. The improvement experienced in both luminous efficiency and power dissipation makes them interesting for lighting application in automotive industry, where the advantages offered are numerous, from a lower time response in brake lights to an operating life much higher than that of the vehicle itself [1], [2]. In the other hand, the improvement experienced in luminous efficiency and power dissipation allows the construction of most of the signal devices using just a few emitters [1]. Due to the points stated above, a comparison among the most efficient red, amber/yellow and white Power LEDs currently available from the leading manufacturers is proposed, offering a comparison in terms of luminous efficiency in nominal test conditions, thermal resistance between the junction and the slug and also giving a comparison about the performance depending on junction temperature between the two most efficient LEDs for each colour.
Elevated Soluble VEGF Receptor sFlt-1 Correlates with Endothelial Injury in IgA Nephropathy

Background Endothelial injury, which may present clinically as hypertension, proteinuria and increased von Willebrand Factor (vWF) level, is a common manifestation in IgA nephropathy (IgAN). However, causal factors for endothelial injury in IgAN are not completely understood. An imbalance of vascular endothelial growth factor/Soluble fms-like tyrosine kinase-1 (VEGF/sFlt-1) has been observed in many diseases with endothelial dysfunction, including pre-eclampsia and diabetic retinopathy, but whether it contributes to endothelial injury in IgAN requires further exploration. Methods Initially, 96 IgAN patients and 22 healthy volunteers were enrolled as a discovery cohort. VEGF/sFlt-1, sFlt-1 and VEGF levels were compared between patients with IgAN and healthy volunteers to explore the underlying factors that contribute to endothelial injury in IgAN. The identified contributor (sFlt-1) was further confirmed in a replication cohort, which included 109 IgAN patients and 30 healthy volunteers. Correlations of sFlt-1 with hypertension, proteinuria, Oxford-E score and plasma vWF were further evaluated in the combined 205 patients with IgAN. Results VEGF/sFlt-1 levels were significantly lower in IgAN patients than healthy volunteers (0.33±0.27 vs. 0.43±0.22, p = 0.02) in the discovery cohort. Within the ratio, plasma sFlt-1 levels were significantly elevated (101.18±25.19 vs. 79.73±18.85 pg/ml, p<0.001), but plasma VEGF levels showed no significant differences. Elevated sFlt-1 levels in the replication cohort were confirmed in IgAN patients (93.40±39.78 vs. 71.92±15.78 pg/ml, p<0.001). Plasma sFlt-1 levels in IgAN patients correlated with proteinuria (severe (>3.5 g/d) vs. moderate (1–3.5 g/d) vs. mild (<1 g/d) proteinuria: 115.95±39.09 vs. 99.89±28.55 vs. 83.24±33.92 pg/ml; severe vs. mild: p<0.001, moderate vs. mild p = 0.001, severe vs. moderate: p = 0.014), hypertension (with vs. without hypertension: 107.87±31.94 vs. 87.32±32.76 pg/ml, p = 0.015) and vWF levels (r = 0.161, p = 0.021). Conclusions The present study found elevated sFlt-1 in IgAN patients and further identified its correlation with proteinuria, hypertension and vWF levels. These results suggested that elevated sFlt-1 contributes to endothelial injury in IgAN.