Miracle-dz/UniFAR-FTUs huggingface dataset:
Toward Pervasive Gait Analysis With Wearable Sensors: A Systematic Review

After decades of evolution, measuring instruments for quantitative gait analysis have become an important clinical tool for assessing pathologies manifested by gait abnormalities. However, such instruments tend to be expensive and require expert operation and maintenance besides their high cost, thus limiting them to only a small number of specialized centers. Consequently, gait analysis in most clinics today still relies on observation-based assessment. Recent advances in wearable sensors, especially inertial body sensors, have opened up a promising future for gait analysis. Not only can these sensors be more easily adopted in clinical diagnosis and treatment procedures than their current counterparts, but they can also monitor gait continuously outside clinics - hence providing seamless patient analysis from clinics to free-living environments. The purpose of this paper is to provide a systematic review of current techniques for quantitative gait analysis and to propose key metrics for evaluating both existing and emerging methods for qualifying the gait features extracted from wearable sensors. It aims to highlight key advances in this rapidly evolving research field and outline potential future directions for both research and clinical applications.
Generating Edit Operations for Profiled UML Models

Since many tools for model-driven engineering (MDE) can only process consistent models, the consistency must be guaranteed by all tools which modify models, such as model editors, transformers, merge tools, etc. This is a recurring challenge for tool developers. An obvious solution of this challenge is to use a common library of consistency-preserving edit operations for modifying models. Typical meta-models lead to several 1000 edit operations, i.e. it is hardly possible to manually specify and implement so many edit operations. This problem is aggravated by UML profiles: Stereotyped model elements are implemented as complex data structures. This paper discusses several approaches to implementing edit operations on profiled models. Furthermore, it canvasses how to generate complete sets of specifications and implementations of edit operations.
Skin Matters: Identifying Pain Mechanisms and Predicting Treatment Outcomes

The skin acts as a complex sensory organ. The emerging new data on peripheral pain mechanisms from within the skin is presented. This data has led to new insights into the potential pain mechanisms for various pain conditions including neuropathic pain (from small fiber neuropathies) and Complex Regional Pain Syndrome. The somatosensory neurons that innervate our skin constantly update our brains on the objects and environmental factors that surround us. Cutaneous sensory neurons expressing nociceptive receptors such as transient receptor potential vanilloid 1 channels and voltage-gated sodium channels are critical for pain transmission. Epidermal cells (such as keratinocytes, Langerhans cells, and Merkel cells) express sensor proteins and neuropeptides; these regulate the neuroimmunocutaneous system and participate in nociception and neurogenic inflammation. In the past two decades, there has been widespread use of modalities such as punch skin biopsies, quantitative sensory testing, and laser-evoked potentials to evaluate small caliber nerve fibers. This paper explores these laboratory techniques as well as the phenomenon of small fiber neuropathy. Treatment using transdermal drug delivery is discussed. There is potential for these findings to predict treatment outcomes in clinical practice and to develop new therapies for different pain conditions. These findings should enhance the physician's ability to evaluate and treat diverse types of pain.
An Android Application Sandbox system for suspicious software detection

Smartphones are steadily gaining popularity, creating new application areas as their capabilities increase in terms of computational power, sensors and communication. Emerging new features of mobile devices give opportunity to new threats. Android is one of the newer operating systems targeting smartphones. While being based on a Linux kernel, Android has unique properties and specific limitations due to its mobile nature. This makes it harder to detect and react upon malware attacks if using conventional techniques. In this paper, we propose an Android Application Sandbox (AASandbox) which is able to perform both static and dynamic analysis on Android programs to automatically detect suspicious applications. Static analysis scans the software for malicious patterns without installing it. Dynamic analysis executes the application in a fully isolated environment, i.e. sandbox, which intervenes and logs low-level interactions with the system for further analysis. Both the sandbox and the detection algorithms can be deployed in the cloud, providing a fast and distributed detection of suspicious software in a mobile software store akin to Google's Android Market. Additionally, AASandbox might be used to improve the efficiency of classical anti-virus applications available for the Android operating system.
Methodological Reflections on the Use of Asynchronous Online Focus Groups in Health Research

The Internet is increasingly used as a tool in qualitative research. In particular, asynchronous online focus groups are used when factors such as cost, time, or access to participants can make conducting face-to-face research difficult. In this article we consider key methodological issues involved in using asynchronous online focus groups to explore experiences of health and illness. The written nature of Internet communication, the lack of physical presence, and the asynchronous, longitudinal aspects enable participants who might not normally contribute to research studies to reflect on their personal stories before disclosing them to the researcher. Implications for study design, recruitment strategies, and ethics should be considered when deciding whether to use this method.
TRIM38 Negatively Regulates TLR3-Mediated IFN-β Signaling by Targeting TRIF for Degradation

Toll-like receptors (TLRs) mediated immune response is crucial for combating pathogens and must be tightly controlled. Tripartite motif (TRIM) proteins are a family of proteins that is involved in a variety of biological and physiological processes. Some members of the TRIM family are important in the regulation of innate immunity. Although it has been shown that TRIM38 negatively regulates innate immunity, the mechanisms by which it does so have not been fully addressed. In this study, we demonstrated that TRIM38 negatively regulates Toll-like receptor 3 (TLR3)-mediated type I interferon signaling by targeting TIR domain-containing adaptor inducing IFN-β (TRIF). We found that overexpression of TRIM38 inhibits TLR3-mediated type I interferon signaling, whereas knockdown of TRIM38 has the reverse effects. We further showed that TRIM38 targets TRIF, a critical adaptor protein downstream of TLR3. TRIF is co-immunoprecipitated with TRIM38, and domain mapping experiments show that PRYSPRY of TRIM38 interacts with the N-terminus of TRIF. Overexpression of TRIM38 decreased expression of overexpressed and endogenous TRIF. This effect could be inhibited by MG132 treatment. Furthermore, the RING/B-box domain of TRIM38 is critical for K48-linked polyubiquitination and proteasomal degradation of TRIF. Collectively, our results suggest that TRIM38 may act as a novel negative regulator for TLR3-mediated type I interferon signaling by targeting TRIF for degradation.
The Significance of Fellow Patients for the Patient With Cancer: WHAT CAN NURSES DO?

Based on two qualitative studies, this article describes the significance of fellow patients in cancer wards, and the relevance for health personnel involved in patient–patient relationships is discussed. Using grounded theory, in-depth interviews were conducted in the first study with 21 adult cancer patients and in a follow-up study with 8 patients and 27 health care providers. The findings indicate that the significance of fellow patients for the patient with cancer can be described in terms of three different dimensions: attitudes toward own illness, interpersonal relationships, and environmental factors. Although contact with fellow patients most often seems to engender positive experiences, some negative experiences are reported also. The suggestions in this article for practical implications are meant to help nurses and other health care providers to promote positive and prevent negative consequences in patient–patient relationships in hospitals.
Nodal and BMP2/4 pattern the mesoderm and endoderm during development of the sea urchin embryo

Nodal factors play fundamental roles in induction and patterning of the mesoderm and endoderm in vertebrates, but whether this reflects an ancient role or one that evolved recently in vertebrates is not known. Here, we report that in addition to its primary role in patterning the ectoderm, sea urchin Nodal is crucial for patterning of the endoderm and skeletogenic mesoderm through the regulation of the expression of key transcription factors and signalling molecules, including BMP2/4 and FGFA. In addition, we uncovered an essential role for Nodal and BMP2/4 in the formation and patterning of the non-skeletogenic mesoderm. By comparing the effects of misexpressing Nodal or an activated Nodal receptor in clones of cells, we provide evidence that Nodal acts over a long range in the endomesoderm and that its effects on the blastocoelar cell precursors are likely to be direct. The activity of Nodal and BMP2/4 are antagonistic, and although bmp2/4 is transcribed in the ventral ectoderm downstream of Nodal, the BMP2/4 ligand is translocated to the dorsal side, where it activates signalling in the dorsal primary mesenchyme cells, the dorsal endoderm and in pigment cell precursors. Therefore, correct patterning of the endomesoderm depends on a balance between ventralising Nodal signals and dorsalising BMP2/4 signals. These experiments confirm that Nodal is a key regulator of dorsal-ventral polarity in the sea urchin and support the idea that the ventral ectoderm, like the Spemann organiser in vertebrates, is an organising centre that is required for patterning all three germ layers of the embryo.
Trans-Allelic Model for Prediction of Peptide:MHC-II Interactions

Major histocompatibility complex class two (MHC-II) molecules are trans-membrane proteins and key components of the cellular immune system. Upon recognition of foreign peptides expressed on the MHC-II binding groove, CD4+ T cells mount an immune response against invading pathogens. Therefore, mechanistic identification and knowledge of physicochemical features that govern interactions between peptides and MHC-II molecules is useful for the design of effective epitope-based vaccines, as well as for understanding of immune responses. In this article, we present a comprehensive trans-allelic prediction model, a generalized version of our previous biophysical model, that can predict peptide interactions for all three human MHC-II loci (HLA-DR, HLA-DP, and HLA-DQ), using both peptide sequence data and structural information of MHC-II molecules. The advantage of this approach over other machine learning models is that it offers a simple and plausible physical explanation for peptide–MHC-II interactions. We train the model using a benchmark experimental dataset and measure its predictive performance using novel data. Despite its relative simplicity, we find that the model has comparable performance to the state-of-the-art method, the NetMHCIIpan method. Focusing on the physical basis of peptide–MHC binding, we find support for previous theoretical predictions about the contributions of certain binding pockets to the binding energy. In addition, we find that binding pocket P5 of HLA-DP, which was not previously considered as a primary anchor, does make strong contribution to the binding energy. Together, the results indicate that our model can serve as a useful complement to alternative approaches to predicting peptide–MHC interactions.
Electrostatic potential at the retinal of three archaeal rhodopsins: Implications for their different absorption spectra

The color tuning mechanism of the rhodopsin protein family has been in the focus of research for decades. However, the structural basis of the tuning mechanism in general and of the absorption shift between rhodopsins in particular remains under discussion. It is clear that a major determinant for spectral shifts between different rhodopsins are electrostatic interactions between the chromophore retinal and the protein. Based on the Poisson‐Boltzmann equation, we computed and compared the electrostatic potential at the retinal of three archaeal rhodopsins: bacteriorhodopsin (BR), halorhodopsin (HR), and sensory rhodopsin II (SRII) for which high‐resolution structures are available. These proteins are an excellent test case for understanding the spectral tuning of retinal. The absorption maxima of BR and HR are very similar, whereas the spectrum of SRII is considerably blue shifted—despite the structural similarity between these three proteins. In agreement with their absorption maxima, we find that the electrostatic potential is similar in BR and HR, whereas significant differences are seen for SRII. The decomposition of the electrostatic potential into contributions of individual residues, allowed us to identify seven residues that are responsible for the differences in electrostatic potential between the proteins. Three of these residues are located in the retinal binding pocket and have in fact been shown to account for part of the absorption shift between BR and SRII by mutational studies. One residue is located close to the β‐ionone ring of retinal and the remaining three residues are more than 8 Å away from the retinal. These residues have not been discussed before, because they are, partly because of their location, no obvious candidates for the spectral shift among BR, HR, and SRII. However, their contribution to the differences in electrostatic potential is evident. The counterion of the Schiff base, which is frequently discussed to be involved in the spectral tuning, does not contribute to the dissimilarities between the electrostatic potentials. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Schwinger-Dyson equation approach to chiral symmetry breaking in an external magnetic field.

We develop a method for using the nonperturbative Schwinger-Dyson equation to study chiral symmetry breaking in an external field. We apply it to massless QED in a constant magnetic field and obtain a nontrivial solution for the fermion self-energy at weak coupling, suggesting that chiral symmetry is dynamically broken. {copyright} {ital 1996 The American Physical Society. }
A miniaturized GaAs MMIC bandpass filter for the 5 GHz band

Novel miniaturized GaAs based bandpass filters for 5GHz band WLAN using diagonally end-shorted coupled lines and lumped capacitors are proposed. The new filter has a compact size, as small as a few degrees, and shows wider stopband characteristic over 35dB up to 60 GHz. A two-stage band pass filter with planar structure was designed and fabricated at a center frequency of 5.5 GHz, with chip surface area only 0.54× 0.78 mm. The fabricated filter has been implemented using Knowledge*on GaAs process. Index terms — GaAs filters, miniaturization, parallel coupled lines
Observación y evaluación del ambiente de aprendizaje en educación infantil : dimensiones y variables a considerar

The goal of this paper is to describe the type of key indicators that must be considered in the analysis of the learning environment created in a classroom of childhood education.The research is connected to the assumptions established in a previous paper by the author. In that paper, the organization of space and time was studied, along with the activities and the performance of female teachers in twenty-one schools in Galicia (Spain) and northern Portugal. The paper is focused on the process of observation and evaluation of learning environments by analyzing the concept of «learning environment» and the spheres that are involved in it, and its differences with the concept of «school space». Finally, we will present a few guidelines for evaluating a learning environment of childhood education, pointing out which spheres and variables must be observed.
Synthetic Genistein Glycosides Inhibiting EGFR Phosphorylation Enhance the Effect of Radiation in HCT 116 Colon Cancer Cells

The need to find new EGFR inhibitors for use in combination with radiotherapy in the treatment of solid tumors has drawn our attention to compounds derived from genistein, a natural isoflavonoid. The antiproliferative potential of synthetic genistein derivatives used alone or in combination with ionizing radiation was evaluated in cancer cell lines using clonogenic assay. EGFR phosphorylation was assessed with western blotting. Genistein derivatives inhibited clonogenic growth of HCT 116 cancer cells additively or synergistically when used in combination with ionizing radiation, and decreased EGFR activation. Our preclinical evaluation of genistein-derived EGFR inhibitors suggests that these compounds are much more potent sensitizers of cells to radiation than the parent isoflavonoid, genistein and indicate that these compounds may be useful in the treatment of colon cancer with radiation therapy.
Improving Classification of Protein Interaction Articles Using Context Similarity-Based Feature Selection

Protein interaction article classification is a text classification task in the biological domain to determine which articles describe protein-protein interactions. Since the feature space in text classification is high-dimensional, feature selection is widely used for reducing the dimensionality of features to speed up computation without sacrificing classification performance. Many existing feature selection methods are based on the statistical measure of document frequency and term frequency. One potential drawback of these methods is that they treat features separately. Hence, first we design a similarity measure between the context information to take word cooccurrences and phrase chunks around the features into account. Then we introduce the similarity of context information to the importance measure of the features to substitute the document and term frequency. Hence we propose new context similarity-based feature selection methods. Their performance is evaluated on two protein interaction article collections and compared against the frequency-based methods. The experimental results reveal that the context similarity-based methods perform better in terms of the F1 measure and the dimension reduction rate. Benefiting from the context information surrounding the features, the proposed methods can select distinctive features effectively for protein interaction article classification.
Latitudinal Clines of the Human Vitamin D Receptor and Skin Color Genes

The well-documented latitudinal clines of genes affecting human skin color presumably arise from the need for protection from intense ultraviolet radiation (UVR) vs. the need to use UVR for vitamin D synthesis. Sampling 751 subjects from a broad range of latitudes and skin colors, we investigated possible multilocus correlated adaptation of skin color genes with the vitamin D receptor gene (VDR), using a vector correlation metric and network method called BlocBuster. We discovered two multilocus networks involving VDR promoter and skin color genes that display strong latitudinal clines as multilocus networks, even though many of their single gene components do not. Considered one by one, the VDR components of these networks show diverse patterns: no cline, a weak declining latitudinal cline outside of Africa, and a strong in- vs. out-of-Africa frequency pattern. We confirmed these results with independent data from HapMap. Standard linkage disequilibrium analyses did not detect these networks. We applied BlocBuster across the entire genome, showing that our networks are significant outliers for interchromosomal disequilibrium that overlap with environmental variation relevant to the genes’ functions. These results suggest that these multilocus correlations most likely arose from a combination of parallel selective responses to a common environmental variable and coadaptation, given the known Mendelian epistasis among VDR and the skin color genes.
Providencia stuartii Genes Activated by Cell-to-Cell Signaling and Identification of a Gene Required for Production or Activity of an Extracellular Factor

ABSTRACT By utilizing reporter transposons, five Providencia stuartii genes that are activated by the accumulation of self-produced extracellular signals have been identified. These genes have been designated cma for conditioned medium activated. The presence of conditioned medium from stationary-phase cultures grown in rich media resulted in the premature activation of each gene in cells at early log phase, with activation values ranging from 6- to 26-fold. Preparation of conditioned medium from an M9 salts medium and fractionation by gel filtration chromatography resulted in fractions within the included volume which activated three of the cmafusions. In addition, depending on the reporter fusion, peak activity was found in different fractions. The partially purified factors activated in a dose-dependent manner. Characterization of the factors activating the cma fusions indicated that they were stable to heat, alkali, and acid. Furthermore, for each cmafusion, factor activity was not reproduced by the addition of homoserine lactone, homocysteine thiolactone, pyruvate, Casamino Acids, or α-ketoglutarate. The identities of three cma genes have been determined and revealed physiological roles in amino acid biosynthesis and nutrient import. To begin to address the pathways for production of or response to the extracellular factors, we have identified a locus, aarA, that is required for the activation of four cma fusions. The AarA product was required for factor activity in extracellular supernatants, indicating a possible role in biosynthesis or export.
Implementing Hpsg with Modular Tools for Fast Compiling and Parsing

We describe a modular HPSG implementation , based on a set of tools rather than a single monolithic engine such as ALE. With these tools we can use techniques for much faster compiling and parsing than ALE. We use two-stage grammar compilation with partial execution and a concurrent process implementation of the chart for fast parsing. We compile HPSG lexical rules into Prolog rules used at run-time by the morphological preprocess, thus eliminating lexical rule expansion at compile-time as in ALE. This gives fast lexicon compilation, and also allows further exploitation of lexical rules to eliminate empty categories.