Miracle-dz/UniFAR-FTUs huggingface dataset:
On the Masking Effect

Machine learning approaches to knowledge compilation seek to improve the perfonnance of problem-solvers by storing solutions to previously solved problems in an efficient, generalized fonn. The problem-solver retrieves these learned solutions in appropriate later situations to obtain results more efficiently. However, by relying on its learned knowledge to provide a solution, the problem-solver may miss an alternative solution of higher quality - one that could have been generated using the original (non-learned) problem-solving knowledge. This phenomenon is referred to as the ITUlSking effect of learning. In this paper, we examine a sequence of possible solutions for the masking effect. Each solution refines and builds on the previous one. The fmal solution is based on cascaded filters. When learned knowledge is retrieved, these filters alert the system about the inappropriateness of this knowledge so that the system can then derive a better alternative solution. We analyze conditions under which this solution will perfonn better than the others, and present experimental data supportivt: of the analysis. This investigation is based on a simulated robot domain called Groundworld.
Comparative micro-epidemiology of pathogenic avian influenza virus outbreaks in a wild bird population

Understanding the epidemiological dynamics of highly pathogenic avian influenza virus (HPAIV) in wild birds is crucial for guiding effective surveillance and control measures. The spread of H5 HPAIV has been well characterized over large geographical and temporal scales. However, information about the detailed dynamics and demographics of individual outbreaks in wild birds is rare and important epidemiological parameters remain unknown. We present data from a wild population of long-lived birds (mute swans; Cygnus olor) that has experienced three outbreaks of related H5 HPAIVs in the past decade, specifically, H5N1 (2007), H5N8 (2016) and H5N6 (2017). Detailed demographic data were available and intense sampling was conducted before and after the outbreaks; hence the population is unusually suitable for exploring the natural epidemiology, evolution and ecology of HPAIV in wild birds. We show that key epidemiological features remain remarkably consistent across multiple outbreaks, including the timing of virus incursion and outbreak duration, and the presence of a strong age-structure in morbidity that likely arises from an equivalent age-structure in immunological responses. The predictability of these features across a series of outbreaks in a complex natural population is striking and contributes to our understanding of HPAIV in wild birds. This article is part of the theme issue ‘Modelling infectious disease outbreaks in humans, animals and plants: approaches and important themes’. This issue is linked with the subsequent theme issue ‘Modelling infectious disease outbreaks in humans, animals and plants: epidemic forecasting and control’.
A centralized optimal energy management system for microgrids

The issue of controlled and reliable integration of distributed energy resources into microgrids and large power grids has recently gained considerable attention. The microgrid concept, which basically corresponds to the coordinated operation of a cluster of loads, distributed generators and energy storage systems, is quite appealing due to its flexibility, controllability and energy management capabilities. In order to provide uninterruptible power supply to the loads, microgrids are expected to operate in both grid-connected and stand-alone modes, and economically meet the demand on an instantaneous basis. The problem of optimal management of the resources in a microgrid is being widely investigated and recent studies have proposed the application of both centralized and distributed control schemes by using multi-agent systems, heuristic methods and optimization algorithms. This paper elaborates on the conceptual design of a centralized energy management system (EMS) and its desirable attributes for a microgrid in stand-alone mode of operation. A number of test protocols are proposed to analyze the performance of the system, as well as the impacts of relevant parameters.
Exanthema following a spider bite mimicking baboon syndrome

Baboon syndrome (BS) is characterized by V-shaped erythema in inguinal and perianal areas with exanthema in other flexural areas, occurring after systemic exposure to contact allergens (1). The non-contact allergic variant of BS is referred as symmetrical drug-related intertriginous and flexural exanthema (SDRIFE) (2). We report an unprecedented case of exanthema following a spider bite mimicking the BS and misdiagnosed as SDRIFE caused by cotrimoxazole. This article is protected by copyright. All rights reserved.
Early versus late salvage abdominoperineal resection for anal squamous cell carcinoma: Is there a difference in survival?

The first‐line treatment for anal squamous cell carcinoma is Nigro protocol chemoradiotherapy. Some patients will fail curative intent chemoradiotherapy and have persistent disease while others may have an initial response followed by disease recurrence. The goal of this study is to investigate survival in anal squamous cell carcinoma patients who fail first‐line treatment.
Of mice and men: Interaction of Corynebacterium diphtheriae strains with murine and human phagocytes

ABSTRACT Seven non-toxigenic C. diphtheriae strains and one toxigenic strain were analyzed with regard to their interaction with murine macrophages (BMM) and human THP-1 macrophage-like cells. Proliferation assays with BMM and THP-1 revealed similar intracellular CFUs for C. diphtheriae strains independent of the host cell. Strain ISS4060 showed highest intracellular CFUs, while the toxigenic DSM43989 was almost not detectable. This result was confirmed by TLR 9 reporter assays, showing a low signal for DSM43989, indicating that the bacteria are not endocytosed. In contrast, the non-pathogenic C. glutamicum showed almost no intracellular CFUs independent of the host cell, but was recognized by TLR9, indicating that the bacteria were degraded immediately after endocytosis. In terms of G-CSF and IL-6 production, no significant differences between BMM and THP-1 were observed. G-CSF production was considerably higher than IL-6 for all C. diphtheriae strains and the C. glutamicum did not induce high cytokine secretion in general. Furthermore, all corynebacteria investigated in this study were able to induce NFκB signaling but only viable C. diphtheriae strains were able to cause host cell damage, whereas C. glutamicum did not. The absence of Mincle resulted in reduced G-CSF production, while no influence on the uptake of the bacteria was observed. In contrast, when MyD88 was absent, both the uptake of the bacteria and cytokine production were blocked. Consequently, phagocytosis only occurs when the TLR/MyD88 pathway is functional, which was also supported by showing that all corynebacteria used in this study interact with human TLR2.
Validity and Test-Retest Reliability of the Dutch Version of the Chronic Otitis Media Benefit Inventory.

OBJECTIVES We aimed to test the validity and test-retest reliability of the Dutch translation of the Chronic Otitis Media Benefit Inventory (COMBI) questionnaire. MATERIALS AND METHODS In total, 30 chronic otitis media (COM) patients with a previous ear surgery completed the questionnaire; 30 patients with a negative medical history of COM complaints and with previous non-otologic surgery as the control group completed the questionnaire. For estimating the test-retest reliability, patients of the COM group completed the questionnaire twice; the scores were compared to those of the control group to test the validity. RESULTS The overall COMBI score ranged as 32-60 in the patient test group, 32-60 in the patient retest group, and 35-40 in the control group. A mean (standard deviation) score of 43.87 (6.81) in the patient test group, 44.4 (6.83) in the patient retest group, and 36.7 (1.29) in the control group was noted. Post-intervention, the COM patients had a significantly higher absolute COMBI score compared to the control group. The diagnostic accuracy was investigated, and a cut-off score of 38.5 was found to have a high sensitivity and specificity in distinguishing a significant positive change from an insignificant change after the intervention. The average-measures intra-class correlation coefficient for absolute agreement (ICCAA) was 0.985 (95% confidence interval: 0.969-0.993), indicating an excellent test-retest reliability in the control group. CONCLUSION The Dutch version of the COMBI questionnaire has a good validity, diagnostic accuracy, and test-retest reliability.
A self‐monitoring urinary salt excretion level measurement device for educating young women about salt reduction: A parallel randomized trial involving two groups

To prevent and treat hypertension, it is important to restrict salt in one's diet since adolescence. However, an effective salt‐reduction education system has yet to be established. Besides accurate evaluation, we believe that the frequent usage of a measurement device may motivate individuals to avoid high salt intake. The present study evaluated the use of a urinary salt excretion measurement device for salt‐reduction education in a parallel randomized trial of two groups. The sample comprised 100 university students who provided consent to participate. A survey with 24‐hour home urine collection and blood pressure measurement was conducted. Participants in the self‐monitoring group measured their own urinary salt excretion level for 4 weeks, using the self‐measurement device. Analyses were conducted on 51 participants in the control group and 49 in the self‐monitoring group. At baseline, there was no significant difference between the two groups in terms of their characteristics and 24‐hour urinary salt excretion levels. After intervention, 24‐hour urinary sodium/potassium ratio showed no change in the control group [baseline score: 4.1 ± 1.5; endline score: 4.2 ± 2.0; P = 0.723], but it decreased significantly in the self‐monitoring group [baseline score: 4.0 ± 1.7; endline score: 3.5 ± 1.4; P = 0.044]. This change was significant even after adjusting for baseline and endline differences between groups using analysis of covariance (P = 0.045). The self‐monitoring urinary salt excretion measurement device improved the 24‐hour urinary sodium/potassium ratio. The device is a useful and practical tool for educating young individuals about dietary salt reduction.
Multilabel Feature Extraction Algorithm via Maximizing Approximated and Symmetrized Normalized Cross-Covariance Operator

Multilabel feature extraction (FE) is an effective preprocessing step to cope with some possible irrelevant, redundant, and noisy features, to reduce computational costs and even improve classification performance. Original normalized cross-covariance operator represents a kernel-based nonlinear dependence measure between features and labels, whose empirical estimator is formulated as a trace operation including two inverse matrices of feature and label kernels with a regularization constant. Due to such a complicated expression, it is impossible to derive an eigenvalue problem for linear FE directly. In this paper, we approximate this measure using Moore–Penrose inverse matrix, linear kernel for feature space, and delta kernel for label space, and then symmetrize the entire matrix in the trace operation, resulting in an effective approximated and symmetrized representation. According to orthonormal projection direction constraints, maximizing such a modified form induces a novel eigenvalue problem for multilabel linear FE. Experiments on 12 data sets illustrate that our proposed method works the best, compared with seven existing FE techniques, according to eight multilabel classification performance metrics and three statistical tests.
Self-applicable partial evaluation for the pi-calculus

In this paper, we are interested in self-applicable partial evaluation for the pi-calculus, a language which models the concurrent behavior of communicating processes. We use the classic three-steps methodology. First, we write a meta-interpreter for the language. Second, we introduce an abstract analysis that determines which operations (communications) can be executed at compile-time. The notion of well-annotatedness of terms is defined. Finally, we exhibit the self-applicable partial evaluator which is applied to well-annotated terms, and we prove its correctness with respect to the interpreter. This approach is compatible with Futamura's projections. Proofs of correctness are baaed on the notion of weak reduction equivalence.
Non-Sulfate-Reducing, Syntrophic Bacteria Affiliated with Desulfotomaculum Cluster I Are Widely Distributed in Methanogenic Environments

ABSTRACT The classical perception of members of the gram-positive Desulfotomaculum cluster I as sulfate-reducing bacteria was recently challenged by the isolation of new representatives lacking the ability for anaerobic sulfate respiration. For example, the two described syntrophic propionate-oxidizing species of the genus Pelotomaculum form the novel Desulfotomaculum subcluster Ih. In the present study, we applied a polyphasic approach by using cultivation-independent and culturing techniques in order to further characterize the occurrence, abundance, and physiological properties of subcluster Ih bacteria in low-sulfate, methanogenic environments. 16S rRNA (gene)-based cloning, quantitative fluorescence in situ hybridization, and real-time PCR analyses showed that the subcluster Ih population composed a considerable part of the Desulfotomaculum cluster I community in almost all samples examined. Additionally, five propionate-degrading syntrophic enrichments of subcluster Ih bacteria were successfully established, from one of which the new strain MGP was isolated in coculture with a hydrogenotrophic methanogen. None of the cultures analyzed, including previously described Pelotomaculum species and strain MGP, consumed sulfite, sulfate, or organosulfonates. In accordance with these phenotypic observations, a PCR-based screening for dsrAB (key genes of the sulfate respiration pathway encoding the alpha and beta subunits of the dissimilatory sulfite reductase) of all enrichments/(co)cultures was negative with one exception. Surprisingly, strain MGP contained dsrAB, which were transcribed in the presence and absence of sulfate. Based on these and previous findings, we hypothesize that members of Desulfotomaculum subcluster Ih have recently adopted a syntrophic lifestyle to thrive in low-sulfate, methanogenic environments and thus have lost their ancestral ability for dissimilatory sulfate/sulfite reduction.
Validity of Natural Language Processing for Ascertainment of EGFR and ALK Test Results in SEER Cases of Stage IV Non-Small-Cell Lung Cancer.

PURPOSE SEER registries do not report results of epidermal growth factor receptor (EGFR) and anaplastic lymphoma kinase (ALK) mutation tests. To facilitate population-based research in molecularly defined subgroups of non-small-cell lung cancer (NSCLC), we assessed the validity of natural language processing (NLP) for the ascertainment of EGFR and ALK testing from electronic pathology (e-path) reports of NSCLC cases included in two SEER registries: the Cancer Surveillance System (CSS) and the Kentucky Cancer Registry (KCR). METHODS We obtained 4,278 e-path reports from 1,634 patients who were diagnosed with stage IV nonsquamous NSCLC from September 1, 2011, to December 31, 2013, included in CSS. We used 855 CSS reports to train NLP systems for the ascertainment of EGFR and ALK test status (reported v not reported) and test results (positive v negative). We assessed sensitivity, specificity, and positive and negative predictive values in an internal validation sample of 3,423 CSS e-path reports and repeated the analysis in an external sample of 1,041 e-path reports from 565 KCR patients. Two oncologists manually reviewed all e-path reports to generate gold-standard data sets. RESULTS NLP systems yielded internal validity metrics that ranged from 0.95 to 1.00 for EGFR and ALK test status and results in CSS e-path reports. NLP showed high internal accuracy for the ascertainment of EGFR and ALK in CSS patients-F scores of 0.95 and 0.96, respectively. In the external validation analysis, NLP yielded metrics that ranged from 0.02 to 0.96 in KCR reports and F scores of 0.70 and 0.72, respectively, in KCR patients. CONCLUSION NLP is an internally valid method for the ascertainment of EGFR and ALK test information from e-path reports available in SEER registries, but future work is necessary to increase NLP external validity.
Dirac operators on cobordisms: degenerations and surgery

We investigate the Dolbeault operator on a pair of pants, i.e., an elementary cobordism between a circle and the disjoint union of two circles. This operator induces a canonical selfadjoint Dirac operator $D_t$ on each regular level set $C_t$ of a fixed Morse function defining this cobordism. We show that as we approach the critical level set $C_0$ from above and from below these operators converge in the gap topology to (different) selfadjoint operators $D_\pm$ that we describe explicitly. We also relate the Atiyah-Patodi-Singer index of the Dolbeault operator on the cobordism to the spectral flows of the operators $D_t$ on the complement of $C_0$ and the Kashiwara-Wall index of a triplet of finite dimensional lagrangian spaces canonically determined by $C_0$.
M2R: Enabling Stronger Privacy in MapReduce Computation

New big-data analysis platforms can enable distributed computation on encrypted data by utilizing trusted computing primitives available in commodity server hardware. We study techniques for ensuring privacy-preserving computation in the popular MapReduce framework. In this paper, we first show that protecting only individual units of distributed computation (e.g. map and reduce units), as proposed in recent works, leaves several important channels of information leakage exposed to the adversary. Next, we analyze a variety of design choices in achieving a stronger notion of private execution that is the analogue of using a distributed oblivious-RAM (ORAM) across the platform. We develop a simple solution which avoids using the expensive ORAM construction, and incurs only an additive logarithmic factor of overhead to the latency. We implement our solution in a system called M2R, which enhances an existing Hadoop implementation, and evaluate it on seven standard MapReduce benchmarks. We show that it is easy to port most existing applications to M2R by changing fewer than 43 lines of code. M2R adds fewer than 500 lines of code to the TCB, which is less than 0.16% of the Hadoop codebase. M2R offers a factor of 1.3× to 44.6× lower overhead than extensions of previous solutions with equivalent privacy. M2R adds a total of 17% to 130% overhead over the insecure baseline solution that ignores the leakage channels M2R addresses.
A Novel Method Makes Concolic System More Effective

Fuzzing is attractive for finding vulnerabilities in binary programs. However, when the application's input space is huge, fuzzing cannot deal with it well. For discovering vulnerabilities more effective, researchers came up concolic testing, and there are much researches on it recently. A common limitation of concolic systems designed to create inputs is that they often concentrate on path-coverage and struggle to exercise deeper paths in the executable under test, but ignore to find those test cases which can trigger the vulnerabilities. In this paper, we present TSM, a novel method for finding potential vulnerabilities in concolic systems, which can help concolic systems more effective for hunting vulnerabilities. We implemented TSM method on a wide-used concolic testing tool-Fuzzgrind, and the evaluation experiments show that TSM can make Fuzzgrind hunt bugs quickly in real-world software, which are hardly found ever before.
Glucose-Independent, Black–White Differences in Hemoglobin A1c Levels

BACKGROUND A previous study of participants with prediabetes found that hemoglobin A(1c) (HbA(1c)) levels differed between black and white participants with no differences in glucose concentration. OBJECTIVE To determine whether black-white differences in HbA(1c) level are present in other populations and across the full spectrum of glycemia. DESIGN Cross-sectional, retrospective. SETTING Outpatient. PARTICIPANTS 1581 non-Hispanic black and white participants between 18 and 87 years of age without known diabetes in the SIGT (Screening for Impaired Glucose Tolerance) study and 1967 non-Hispanic black and white participants older than 40 years without known diabetes in the NHANES III (Third National Health and Nutrition Examination Survey). MEASUREMENTS HbA(1c) levels, anthropometry, and plasma glucose levels during oral glucose tolerance testing. RESULTS Hemoglobin A(1c) levels were higher in black than in white participants with normal glucose tolerance (0.13 percentage point [P < 0.001] in the SIGT sample and 0.21 percentage point [P < 0.001] in the NHANES III sample), prediabetes (0.26 percentage point [P < 0.001] and 0.30 percentage point [P < 0.001], respectively), or diabetes (0.47 percentage point [P < 0.020] and 0.47 percentage point [P < 0.013], respectively) after adjustment for plasma glucose levels and other characteristics known to correlate with HbA(1c) levels. LIMITATION The mechanism for the differences is unknown. CONCLUSION Black persons have higher HbA(1c) levels than white persons across the full spectrum of glycemia, and the differences increase as glucose intolerance worsens. These findings could limit the use of HbA(1c) to screen for glucose intolerance, indicate the risk for complications, measure quality of care, and evaluate disparities in health.
A critical view on conservative mutations.

By analysing the surface composition of a set of protein 3D structures, complemented with predicted surface compositional information for homologous proteins, we have found significant evidence for a layer composition of protein structures. In the innermost and outermost parts of proteins there is a net negative charge, while the middle has a net positive charge. In addition, our findings indicate that the concept of conservative mutation needs substantial revision, e.g. very different spatial preferences were found for glutamic acid and aspartic acid. The alanine screening often used in protein engineering projects involves the substitution of residues to alanine, based on the assumption that alanine is a "neutral" residue. However, alanine has a high negative correlation with all but the non-polar residues. We therefore propose the use of, for example, serine as a substitute for the residues that are negatively correlated with alanine.