Miracle-dz/UniFAR-FTUs huggingface dataset:
ProbMetab: an R package for Bayesian probabilistic annotation of LC–MS-based metabolomics

Summary: We present ProbMetab, an R package that promotes substantial improvement in automatic probabilistic liquid chromatography–mass spectrometry-based metabolome annotation. The inference engine core is based on a Bayesian model implemented to (i) allow diverse source of experimental data and metadata to be systematically incorporated into the model with alternative ways to calculate the likelihood function and (ii) allow sensitive selection of biologically meaningful biochemical reaction databases as Dirichlet-categorical prior distribution. Additionally, to ensure result interpretation by system biologists, we display the annotation in a network where observed mass peaks are connected if their candidate metabolites are substrate/product of known biochemical reactions. This graph can be overlaid with other graph-based analysis, such as partial correlation networks, in a visualization scheme exported to Cytoscape, with web and stand-alone versions. Availability and implementation: ProbMetab was implemented in a modular manner to fit together with established upstream (xcms, CAMERA, AStream, mzMatch.R, etc) and downstream R package tools (GeneNet, RCytoscape, DiffCorr, etc). ProbMetab, along with extensive documentation and case studies, is freely available under GNU license at: http://labpib.fmrp. usp.br/methods/probmetab/. Contact: rvencio@usp.br Supplementary information: Supplementary data are available at Bioinformatics online.
Böhm trees as higher-order recursion schemes

Higher-order recursive schemes (HORS) are schematic representations of functional programs. They generate possibly inﬁnite ranked labelled trees and, in that respect, are known to be equivalent to a restricted fragment of the λY -calculus consisting of ground-type terms whose free variables have types of the form o → ⋯ → o (with o being a special case). In this paper, we show that any λY -term (with no restrictions on term type or the types of free variables) can actually be represented by a HORS. More precisely, for any λY -term M , there exists a HORS generating a tree that faithfully represents M ’s ( η -long) Böhm tree. In particular, the HORS captures higher-order binding information contained in the Böhm tree. An analogous result holds for ﬁnitary PCF. As a consequence, we can reduce a variety of problems related to the λY -calculus or ﬁnitary PCF to problems concerning higher-order recursive schemes. For instance, Böhm tree equivalence can be reduced to the equivalence problem for HORS. Our results also enable MSO model-checking of Böhm trees, despite the general undecidability of the problem.
Emphysema‐induced reductions in locomotory skeletal muscle contractile function

Patients with COPD suffer from locomotory skeletal muscle contractile dysfunction. This may be due to the disease per se or as a result of some confounding factor. Therefore, the purpose of this investigation was to determine whether emphysema: (1) reduces force production; (2) increases fatigability; and (3) impairs the speed of recovery in locomotory skeletal muscle in an accepted animal model in which many confounding variables can be controlled. To explore this issue, in situ mechanical properties of gastrocnemius were measured in Syrian Golden hamsters 8 months after intratracheal instillation of either saline (control, n= 5) or elastase (emphysema, n= 7). Emphysema increased excised lung volume (80%; P < 0.01), increased fatigability (control, 25% reduction in maximal strength after 4 min of repeated contractions; emphysema, 55% reduction; P < 0.05) and decreased the recovery rate (half‐times of recovery: control, 7 ± 7 s; emphysema, 92 ± 92 s; P < 0.05) of gastrocnemius muscle. In contrast, emphysema had no effect on maximal force, whether related to body mass or muscle mass, or force–velocity characteristics of gastrocnemius muscle. These data demonstrate that emphysema, independent of physical activity levels, pharmacological intervention, and/or nutritional status, can increase fatigability and impair the speed of recovery of locomotory skeletal muscle contractile function which may contribute to exercise intolerance of COPD patients.
Correction for Conserved Actin Cysteine Residues Are Oxidative Stress Sensors That Can Regulate Cell Death in Yeast

Actin's functional complexity makes it a likely target of oxidative stress but also places it in a prime position to coordinate the response to oxidative stress. We have previously shown that the NADPH oxidoreductase Oye2p protects the actin cytoskeleton from oxidative stress. Here we demonstrate that the physiological consequence of actin oxidation is to accelerate cell death in yeast. Loss of Oye2p leads to reactive oxygen species accumulation, activation of the oxidative stress response, nuclear fragmentation and DNA degradation, and premature chronological aging of yeast cells. The oye2Delta phenotype can be completely suppressed by removing the potential for formation of the actin C285-C374 disulfide bond, the likely substrate of the Oye2p enzyme or by treating the cells with the clinically important reductant N-acetylcysteine. Because these two cysteines are coconserved in all actin isoforms, we theorize that we have uncovered a universal mechanism whereby actin helps to coordinate the cellular response to oxidative stress by both sensing and responding to oxidative load.
Possible role of the multidrug resistance‐associated protein (MRP) in chemoresistance of human melanoma cells

Human malignant melanoma is characterised by unresponsiveness to conventional chemotherapy. Melanoma‐derived cell lines are often markedly chemoresistant, suggesting that cellular mechanisms mediate the multidrug resistance (MDR) phenotype. The multidrug resistance‐associated protein (MRP) is a drug transporter protein associated with resistance to a broad spectrum of lipophilic drugs. To investigate whether MRP is involved in intrinsic drug resistance of human melanoma, we analysed expression and functional activity of MRP as well as its impact on chemoresistance in 40 melanoma cell lines (35 established by us from primary and metastatic lesions and 5 obtained from international sources), as well as in one dysplastic naevus‐derived cell line and in normal melanocytes. By reverse transcriptase‐polymerase chain reaction various levels of MRP mRNA were detected in all melanoma cell lines, and by immunoblot the corresponding protein in a high percentage of them. Functional activity of MRP was assayed by analysing cellular accumulation of 3H‐daunomycin (3H‐DM) and calcein in response to MRP‐modulators by β‐spectrometric and fluorescence‐activated cell sorter analysis, respectively. Probenecid (PRO), N‐eth‐ylmaleimide (NEM) and benzbromarone (BB) moderately (≤ 1.43‐fold) but significantly enhanced intracellular accumulation of MRP substrate probes corresponding to MRP expression. Moreover, the sensitivity of melanoma cell lines to daunomycin (DM) and doxorubicin (DOX), but not to vinblastine (VBL), etoposide (VP‐16) and cisplatin (CDDP), analysed by an MTT‐based survival assay, were inversely correlated with MRP‐gene expression. Our results imply that MRP may be a component of the intrinsic chemoresistance phenotype characteristic of human malignant melanoma. Int. J. Cancer, 71:108–115, 1997. © 1997 Wiley‐Liss, Inc.
Optimal Resource Allocation for Batch Testing

Batch resource allocation problem arises in the context of executing a sequence of automated system tests or distributed computations where resources are pooled together and flexibly matched with requests. Minimizing resource allocation for a batch of processes reduces the resource management (e.g., setup) cost for the batch while allowing more users to share the resource pool simultaneously. The salient characteristic of the batch resource allocation problem is that while resources can be reused across different processes they are subject to mutually exclusive use for any individual process. We show that resource allocation for a single process can be solved in polynomial time whereas the general optimization problem is NP-complete. This motivates us to consider heuristics that can yield close to optimum solutions in polynomial time. We design several such heuristics and present their experimental comparison. Our experiments show that a technique based on a min-cost max-flow algorithm combined with ranked removal yields the best solution while having smallest running time.
Design development of two phase transverse flux linear motor with permanent-magnet excitation

This paper presents design development of permanent magnet two phase transverse flux linear motor with inner mover type. Infolytica©'s electromagnetic field simulation software, MagNet® is used to analyze the field distribution of the motor by using three-dimensional finite-element analysis method. The effect of geometrical and electrical parameters on the traction and normal force are studied and an optimum design is proposed by achieving the maximum possible traction force. The ripple effect of the traction force is minimized as compared to single phase model.
Correlations between screw hole preparation, torque of insertion, and pullout strength for spinal screws.

The bone-screw interface is critical in the use of spinal instrumentation. The purpose of these experiments described here was twofold. First, to determine whether a correlation existed between torque generated during screw insertion and the pullout strength. Second, to determine how differing surgical methods of screw hole preparation influenced torque of insertion and screw pullout strength. A series of experiments were carried out in which screws were inserted into synthetic bone (experiment 1) and into calf vertebrae (experiment 2). The method of screw hole preparation (i.e., diameter of entrance hole and pilot hole) was varied while the resulting torque of insertion and the pullout strength of the screw was measured in each case. A torque screwdriver was used to measure the torque of insertion of the screws. Screw pullout strength was measured using a materials testing machine. Two important results emerged from these experiments. First, a higher torque of insertion correlated with a higher screw pullout force. This correlation may be useful intraoperatively in evaluating fixation. Second, torque of insertion and pullout force were more influenced by cortex over-drill diameter than pilot hole diameter. These experiments show the importance of the dorsal cortex in pedicle screw fixation.
Color Constrained ICP for Registration of Large Unstructured 3D Color Data Sets

In this paper, we address the problem of pair-wise registration of large unstructured 3D/color datasets. Our purpose is to improve the classical ICP (Iterative closest point) algorithm by using color information, in order to deal with large datasets and with objects for which the geometric information is not significant enough. After a brief presentation of classical ICP (iterative closest point) algorithm and of the research works developed to improve its performance, we propose a new strategy to improve the selection of points. Color information is used to reduce the search space during the matching step. Experimental results obtained with real range images show that the algorithm provides an accurate estimation of the rigid transformation
The Set-Valued Run-to-Run Controller in Semiconductor Manufacturing Processes

In semiconductor manufacturing, run-to-run (RtR) control is paid more and more attention. In this paper a set-valued RtR control scheme is introduced. Di erent from conventional RtR control methods, the set-valued method rst calculates the feasible parameter set at the beginning of each run, then estimates the model parameters within this set. Compared to other RtR control schemes, it does not assume any statistical property of the noises. In simulation it was shown that it is robust to model and sensor errors, and it has the potential to be applied to highly nonlinear processes. Furthermore the set-valued method can be applied to other elds such as signal processing and chemical processes.
The Host Defense Peptide Cathelicidin Is Required for NK Cell-Mediated Suppression of Tumor Growth

Tumor surveillance requires the interaction of multiple molecules and cells that participate in innate and the adaptive immunity. Cathelicidin was initially identified as an antimicrobial peptide, although it is now clear that it fulfills a variety of immune functions beyond microbial killing. Recent data have suggested contrasting roles for cathelicidin in tumor development. Because its role in tumor surveillance is not well understood, we investigated the requirement of cathelicidin in controlling transplantable tumors in mice. Cathelicidin was observed to be abundant in tumor-infiltrating NK1.1+ cells in mice. The importance of this finding was demonstrated by the fact that cathelicidin knockout mice (Camp −/−) permitted faster tumor growth than wild type controls in two different xenograft tumor mouse models (B16.F10 and RMA-S). Functional in vitro analyses found that NK cells derived from Camp −/− versus wild type mice showed impaired cytotoxic activity toward tumor targets. These findings could not be solely attributed to an observed perforin deficiency in freshly isolated Camp −/− NK cells, because this deficiency could be partially restored by IL-2 treatment, whereas cytotoxic activity was still defective in IL-2-activated Camp −/− NK cells. Thus, we demonstrate a previously unrecognized role of cathelicidin in NK cell antitumor function.
Semantic Object Maps for robotic housework - representation, acquisition and use

In this article we investigate the representation and acquisition of Semantic Objects Maps (SOMs) that can serve as information resources for autonomous service robots performing everyday manipulation tasks in kitchen environments. These maps provide the robot with information about its operation environment that enable it to perform fetch and place tasks more efficiently and reliably. To this end, the semantic object maps can answer queries such as the following ones: “What do parts of the kitchen look like? ”, “How can a container be opened and closed? ”, “Where do objects of daily use belong? ”, “What is inside of cupboards/drawers? ”, etc. The semantic object maps presented in this article, which we call SOM+, extend the first generation of SOMs presented by Rusu et al. [1] in that the representation of SOM+ is designed more thoroughly and that SOM+ also include knowledge about the appearance and articulation of furniture objects. Also, the acquisition methods for SOM+ substantially advance those developed in [1] in that SOM+ are acquired autonomously and with low-cost (Kinect) instead of very accurate (laser-based) 3D sensors. In addition, perception methods are more general and are demonstrated to work in different kitchen environments.
Sensitivity to visual motion in amblyopic macaque monkeys

Amblyopia is usually considered to be a deficit in spatial vision. But there is evidence that amblyopes may also suffer specific deficits in motion sensitivity as opposed to losses that can be explained by the known deficits in spatial vision. We measured sensitivity to visual motion in random dot displays for strabismic and anisometropic amblyopic monkeys. We used a wide range of spatial and temporal offsets and compared the performance of the fellow and amblyopic eye for each monkey. The amblyopes were severely impaired at detecting motion at fine spatial and long temporal offsets, corresponding to fine spatial scale and slow speeds. This impairment was also evident for the untreated fellow eyes of strabismic but not anisometropic amblyopes. Motion sensitivity functions for amblyopic eyes were shifted toward large spatial scales for amblyopic compared to fellow eyes, to a degree that was correlated with the shift in scale of the spatial contrast sensitivity function. Amblyopic losses in motion sensitivity, however, were not correlated with losses in spatial contrast sensitivity. This, combined with the specific impairment for detecting long temporal offsets, reveals a deficit in spatiotemporal integration in amblyopia which cannot be explained by the lower spatial resolution of amblyopic vision.
Multimodal fusion: a new hybrid strategy for dialogue systems

This is a new hybrid fusion strategy based primarily on the implementation of two former and differentiated approaches to multimodal fusion [11] in multimodal dialogue systems. Both approaches, their predecessors and their respective advantages and disadvantages will be described in order to illustrate how the new strategy merges them into a more solid and coherent solution. The first strategy was largely based on Johnston's approach [5] and implies the inclusion of multimodal grammar entries and temporal constraints. The second approach implied the fusion of information coming from different channels at dialogue level. The new hybrid strategy hereby described requires the inclusion of multimodal grammar entries and temporal constraints plus the additional information at dialogue level utilized in the second strategy. Within this new approach therefore, the fusion process will be initiated at grammar level and will be culminated at dialogue level.
Comparing interval estimates for small sample ordinal CFA models

Robust maximum likelihood (RML) and asymptotically generalized least squares (AGLS) methods have been recommended for fitting ordinal structural equation models. Studies show that some of these methods underestimate standard errors. However, these studies have not investigated the coverage and bias of interval estimates. An estimate with a reasonable standard error could still be severely biased. This can only be known by systematically investigating the interval estimates. The present study compares Bayesian, RML, and AGLS interval estimates of factor correlations in ordinal confirmatory factor analysis models (CFA) for small sample data. Six sample sizes, 3 factor correlations, and 2 factor score distributions (multivariate normal and multivariate mildly skewed) were studied. Two Bayesian prior specifications, informative and relatively less informative were studied. Undercoverage of confidence intervals and underestimation of standard errors was common in non-Bayesian methods. Underestimated standard errors may lead to inflated Type-I error rates. Non-Bayesian intervals were more positive biased than negatively biased, that is, most intervals that did not contain the true value were greater than the true value. Some non-Bayesian methods had non-converging and inadmissible solutions for small samples and non-normal data. Bayesian empirical standard error estimates for informative and relatively less informative priors were closer to the average standard errors of the estimates. The coverage of Bayesian credibility intervals was closer to what was expected with overcoverage in a few cases. Although some Bayesian credibility intervals were wider, they reflected the nature of statistical uncertainty that comes with the data (e.g., small sample). Bayesian point estimates were also more accurate than non-Bayesian estimates. The results illustrate the importance of analyzing coverage and bias of interval estimates, and how ignoring interval estimates can be misleading. Therefore, editors and policymakers should continue to emphasize the inclusion of interval estimates in research.
Improving the Adoption of Dynamic Web Security Vulnerability Scanners

Security vulnerabilities remain present in many web applications despite the improving knowledge base on vulnerabilities. Attackers can exploit such security vulnerabilities to extract critical data from web applications and their users. Many dynamic security vulnerability scanners exist that try to automatically find such security vulnerabilities. We studied the adoption of these tools and found out they are rarely used by web developers during the development process of a web application. Through interviews, we investigated the main cause of the lack of adoption is the difficulty to use such tools. In order to improve the adoption of dynamic security vulnerability scanners, we introduce the Universal Penetration Testing Robot (UPeTeR). UPeTeR is a class library that allows web developers to easily set relevant data for many dynamic vulnerability scanners by providing them with an abstraction of required configuration data. Plugins, ideally created by experts of the scanners, transform this abstraction into an optimal setup of such scanners. A prototype has been created which was used to validate UPeTeR’s acceptance by web developers at the Software Improvement Group, a software consultancy company in the Netherlands. The acceptance experiment demonstrated that web developers are willing to try out and work with UPeTeR.
Implicit Surface Modeling Suitable for Inside/Outside Tests with Radial Basis Functions

We describe a method for computing an implicit function that represents a surface by its zero level set, given a set of points scattered over the surface and associated with surface normal vectors. This implicit function is defined as a linear combination of compactly supported radial basis functions. Our method is suitable for testing whether a given point is interior or exterior to the surface, previously only associated with globally supported or globally regularized radial basis functions. We use a two-level interpolation approach. In the coarse scale interpolation, we set basis function centers by a grid that covers the enlarged bounding box of the given point set and compute their signed distances to the underlying surface using local quadratic approximations of the nearest surface points. Then a fitting to the residual errors on the surface points and additional off-surface points is performed with fine scale basis functions. The final function is the sum of the two intermediate functions and is a good approximation of the signed distance field to the surface in the bounding box. Examples of surface reconstruction and set operations between shapes are provided.
Association of Reports of Childhood Abuse and All-Cause Mortality Rates in Women.

IMPORTANCE Research has linked childhood abuse to a variety of adult psychiatric problems, but little is known about associations of child abuse with adult mortality. OBJECTIVE To test associations of retrospective reports of physical and emotional abuse in childhood with all-cause mortality rates in adulthood. DESIGN, SETTING, AND PARTICIPANTS National sample of 6285 adults (aged 25-74 years at baseline) from the survey of Midlife Development in the United States. Baseline psychosocial data were collected in 1995 and 1996, with follow-up mortality data collected through October 2015. MAIN OUTCOMES AND MEASURES Participants completed questionnaires at baseline about self-report of childhood emotional abuse, moderate physical abuse, and severe physical abuse. Mortality data during the next 20 years was tracked using the National Death Index. RESULTS Of the 6285 participants included in the study sample, 2987 were men (48%) and 5581were white (91%), with a mean (SD) age of 46.9 (12.95) years. Women who reported childhood emotional abuse (hazard ratio [HR], 1.22; 95% CI, 1.01-1.49; P = .04), moderate physical abuse (HR, 1.30; 95% CI, 1.05-1.60; P = .02), or severe physical abuse (HR, 1.58; 95% CI, 1.20-2.08; P = .001) were at increased risk for all-cause mortality during the follow-up period. Reports of more types of childhood abuse were also associated with a greater risk of all-cause mortality in women (all vs none HR, 1.68; 95% CI, 1.24-2.30; P = .001; some vs none HR, 1.24; 95% CI, 1.01-1.52; P = .04). These effects could not be accounted for by childhood socioeconomic status, personality traits, or adult depression. No associations were observed in men. CONCLUSIONS AND RELEVANCE These results suggest that in addition to the established psychiatric consequences of abuse, women who report childhood abuse also remain vulnerable to premature mortality into adulthood. Thus, reported childhood abuse may have long-term ramifications for health and longevity in women.