Miracle-dz/UniFAR-FTUs huggingface dataset:
Immunogenicity, adalimumab levels and clinical response in ankylosing spondylitis patients during 24 weeks of follow-up

Background Immunogenicity influences adalimumab levels and therefore clinical response in patients with rheumatic diseases. Objectives To study the relationship between clinical response, adalimumab levels and antidrug antibodies (ADAb) in ankylosing spondylitis (AS). Methods Observational cohort study of 115 consecutive AS patients treated with adalimumab in the Netherlands (n=85) and Taiwan (n=30), monitored during 24 weeks. Adalimumab levels and ADAb titres were determined using an ELISA and an antigen binding test (ABT), respectively, designed by Sanquin Research, Amsterdam. Response to adalimumab treatment was defined as a Bath Ankylosing Spondylitis Disease Activity Index (BASDAI) response, and disease activity was measured using the Ankylosing Spondylitis Disease Activity Score using C-reactive protein (CRP) (ASDAS). Results At baseline, median BASDAI (IQR) was 6.4 (4.5–7.6) and mean ASDAS (SD) was 3.5 (1.0). After 24 weeks, 49 (42.6%) patients were BASDAI50 responders and mean ASDAS (SD) for responders was 1.5 (1.0) vs 2.6 (1.0) for non-responders (p<0.001). Thirty-one (27.0%) patients had detectable ADAb. After 24 weeks, adalimumab levels (mg/L) (IQR) were significantly higher in ADAb-negative patients than in ADAb-positive patients (12.7 (8.2–18.0) vs 1.2 (0.0–2.0), (p<0.001)). A significant association was demonstrated between adalimumab levels and ASDAS (p=0.02; RC −1.1; 95% CI −2.0 to −0.2). Eleven (9.6%) patients had no detectable adalimumab levels and high detectable ADAb titres (>100 AU/mL). In these patients, CRP and erythrocyte sedimentation rate remained elevated during treatment. Conclusions Adalimumab levels are related to clinical response in AS patients measured with ASDAS and are influenced by ADAb detectable with an ABT.
Dietary magnesium and calcium intake and risk of depression in the general population: A meta-analysis

Objective: Several epidemiological studies have evaluated the associations between dietary magnesium (Mg) and calcium (Ca) intake and the risk of depression. However, the results of these studies remain controversial. Thus, we performed a meta-analysis to explore these associations and to investigate the possible dose–response relationship between dietary Mg intake and risk of depression. Methods: MEDLINE, Web of Science, Embase, Cochrane CENTRAL, CINAHL database, Chinese National Knowledge Infrastructure, Wan fang databases and Databases of Chinese Scientific and Technical Periodicals were searched for eligible publications up to September 2016. Pooled relative risks with 95% confidence intervals were calculated using random-effects model. Publication bias was estimated using Egger’s test and the funnel plot. Dose–response relationship was assessed by restricted cubic spline functions. Results: A total of 17 epidemiological studies from 12 articles were included in the present meta-analysis. Among these studies, 11 studies evaluated the association between dietary Mg intake and risk of depression and 6 studies evaluated the association between dietary Ca intake and risk of depression. When comparing the highest with the lowest intake, the pooled relative risks of depression were 0.81 (95% confidence interval = [0.70, 0.92]) for Mg and 0.66 (95% confidence interval = [0.42, 1.02]) for Ca. Dietary Mg intake was significantly associated with a reduced risk of depression among studies conducted in Asia (relative risk = 0.57; 95% confidence interval = [0.44, 0.74]) and in studies adjusting for energy intake (relative risk = 0.73; 95% confidence interval = [0.58, 0.92]). For dose–response analysis, evidence of a nonlinear relationship was found between dietary Mg intake and risk of depression, and the largest risk reductions were observed for 320 mg/day. Conclusion: This meta-analysis indicated that moderate Mg intake may be inversely associated with the risk of depression, which still needs to be confirmed by larger prospective cohort studies.
Haptic display of micro surface undulation based on discrete mechanical stimuli to whole fingers

Graphical Abstract Humans can perceive a wide and small surface undulation that is hundreds micrometers in height and hundreds millimeters in width by scanning the surface with their whole fingers and palm in the distal and proximal directions. We developed a wearable haptic device that presents a surface undulation to the hand. The device is composed of nine independent stimulator units that control the heights of nine finger pads of the index finger, the middle finger, and the ring finger (three units on each finger) according to the virtual surface. Three experiments are carried out to evaluate the haptic perception by the haptic device. A first experiment shows that the perceived dimensions are diminished as compared to the dimensions applied by the haptic device. On the basis of this result, the applied dimensions are calibrated to match the virtual surface undulation to the real surface undulation. A second experiment shows that the shape of gently-curved surfaces can be estimated with the haptic display. A third experiment shows that the discrimination threshold is not different between the virtual surface undulation and the real surface undulation. These experimental results show the applicability of the haptic device as a haptic interface.
Compression of electrocardiogram signals using JPEG2000

JPEG2000 is the latest international standard for compression of still images. Although the JPEG2000 codec is designed to compress images, we illustrate that it can also be used to compress other signals. As an example, we illustrate how the JPEG2000 codec can be used to compress electrocardiogram (ECG) data. Experiments using the MIT-BIH arrhythmia database illustrate that the proposed approach outperforms many existing ECG compression schemes. The proposed scheme allows the use of existing hardware and software JPEG2000 codecs for ECG compression, and can be especially useful in eliminating the need for specialized hardware development. The desirable characteristics of the JPEG2000 codec, such as precise rate control and progressive quality, are retained in the presented scheme. The goal of this paper is to demonstrate the ECG application as an example. This example can be extended to other signals that exist within the consumer electronics realm.
Constructing Semantic Space Models from Parsed Corpora

Traditional vector-based models use word co-occurrence counts from large corpora to represent lexical meaning. In this paper we present a novel approach for constructing semantic spaces that takes syntactic relations into account. We introduce a formalisation for this class of models and evaluate their adequacy on two modelling tasks: semantic priming and automatic discrimination of lexical relations.
Intraoperative mass spectrometry mapping of an onco-metabolite to guide brain tumor surgery

Significance The diagnosis of tumors during surgery still relies principally on an approach developed over 150 y ago: frozen section microscopy. We show that a validated molecular marker—2-hydroxyglutarate generated from isocitrate dehydrogenase 1 mutant gliomas—can be rapidly detected from tumors using a form of ambient MS that does not require sample preparation. We use the Advanced Multimodality Image Guided Operating Suite at Brigham and Women’s Hospital to demonstrate that desorption electrospray ionization MS could be used to detect residual tumor that would have been left behind in the patient. The approach paves the way for the clinical testing of MS-based intraoperative monitoring of tumor metabolites, an advance that could revolutionize the care of surgical oncology patients. For many intraoperative decisions surgeons depend on frozen section pathology, a technique developed over 150 y ago. Technical innovations that permit rapid molecular characterization of tissue samples at the time of surgery are needed. Here, using desorption electrospray ionization (DESI) MS, we rapidly detect the tumor metabolite 2-hydroxyglutarate (2-HG) from tissue sections of surgically resected gliomas, under ambient conditions and without complex or time-consuming preparation. With DESI MS, we identify isocitrate dehydrogenase 1-mutant tumors with both high sensitivity and specificity within minutes, immediately providing critical diagnostic, prognostic, and predictive information. Imaging tissue sections with DESI MS shows that the 2-HG signal overlaps with areas of tumor and that 2-HG levels correlate with tumor content, thereby indicating tumor margins. Mapping the 2-HG signal onto 3D MRI reconstructions of tumors allows the integration of molecular and radiologic information for enhanced clinical decision making. We also validate the methodology and its deployment in the operating room: We have installed a mass spectrometer in our Advanced Multimodality Image Guided Operating (AMIGO) suite and demonstrate the molecular analysis of surgical tissue during brain surgery. This work indicates that metabolite-imaging MS could transform many aspects of surgical care.
Revisiting Visibility in the Plane

We consider two closely related problems: computing the region visible from a point amid simple polygonal obstacles and computing the lower envelope of a set of disjoint segments. Visibility problems such as these were proposed and promptly solved in the late ’80s and early ’90s before the widespread popularity of the word RAM model. All previously published algorithms thus run in Ω(n log n) time, although they can be sped up in the word RAM model to some extent by substituting appropriate word RAM data structures and algorithms. Our main result is a deterministic linear-time algorithm for the case in which endpoints are presorted. Using the fastest known integer sorting algorithm of Han and Thorup [17], we thus obtain an algorithm for the general case that runs in O(n √ log log n) time. We expect our algorithm for the presorted case to be practically efficient. Our algorithm actually solves the more general problem of computing the lower envelope of a set of non-intersecting partial functions defined over intervals. We obtain our results via a novel approach that considers a partial lower envelope problem in which we need only find the lowest partial function at q ≤ 2n x-coordinates. We combine this algorithm with another that exploits the bounded precision of x-coordinates of endpoints and otherwise performs only comparisons to determine the vertical ordering of partial functions. In addition to our word RAM result, we obtain a better understanding of the inherent complexity of our visibility problems, resulting in a pointer machine algorithm that runs in O(nα(n)) time as long as endpoints are appropriately presorted.
Airborne retrievals of snow and ice surface emissivity at millimeter wavelengths

Passive microwave radiometers (24-157 GHz) have been flown over Baltic Sea ice and snow sites in April 1995 and on March 15, 1997. Data from these instruments are analyzed with reference to ground measurements of snow and ice conditions, and emissivity spectra are presented for 12 classifications of surface type. A simple model based on dielectric permittivity can accurately represent the microwave spectra of sea ice, but cannot be extended to the behavior of dry snow above 100 GHz without the addition of an extra term to represent volume scattering. The parameterization presented is intended to provide a background for temperature and humidity retrievals from satellite sounders, but the results will be of interest to the snow and ice remote-sensing communities.
Mechanical behavior of rammed earth walls under Pushover tests

Determining the mechanical behavior of rammed earth walls is a highly important feature giving that there is a renewed interest in the use of the natural material in building construction. On one hand, it contributes to finding suitable and appropriate ways for the conservation and restoration of these building and on another hand, it draws new recommendations for the conception of new rammed earth structures with respect to new building regulations (earthquake building guideline, new thermal regulation). In this context, this thesis investigates the behavior of rammed earth walls subjected to lateral loading. Four unstabilized rammed earth walls were tested under a combination of vertical and monotonic pushover tests up to failure. The shear behavior of these walls is studied along with the failure modes by means of digital image correlation. Results showed that the response of the rammed earth is characterized by significant non-linear behavior with a remarkable ductility. In general, the walls experienced a shear failure due to the failure of diagonal struts. Cracks at the interface between the bottom layers were also observed.The performance of these walls was assessed based on the pushover methodology. The experimental work was completed with the determination of the mechanical characteristics of rammed earth in compression and an investigation of the shear components: cohesion and friction angle of the rammed earth through shear box tests on a different scale. Finally, the relevance of these parameters was tested by performing a numerical model that aims to simulate the experimental tests done on the scale of the walls.
Canadian Multicenter Laboratory Study for Standardized Second-Line Antimicrobial Susceptibility Testing of Mycobacterium tuberculosis

ABSTRACT The purpose of this study was to establish a standardized protocol for second-line antimicrobial susceptibility testing of Mycobacterium tuberculosis using the Bactec MGIT 960 system in Canadian laboratories. Four Canadian public health laboratories compared the susceptibility testing results of 9 second-line antimicrobials between the Bactec 460 and Bactec MGIT 960 systems. Based on the data generated, we have established that the Bactec MGIT 960 system provides results comparable to those obtained with the previous Bactec 460 method. The critical concentrations established for the testing of the antimicrobials used are as follows: amikacin, 1 μg/ml; capreomycin, 2.5 μg/ml; ethionamide, 5 μg/ml; kanamycin, 2.5 μg/ml; linezolid, 1 μg/ml; moxifloxacin, 0.25 μg/ml; ofloxacin, 2 μg/ml; p-aminosalicylic acid, 4 μg/ml; rifabutin, 0.5 μg/ml.
Analyzing the precision of JSW measurements using 3D scans and statistical models

One of the methods to diagnose rheumatoid arthritis (RA) is measuring joint space narrowing over time. A method is presented to analyze the sensitivity of this measurement to positioning of the hand. Micro-CT scans are used to generate projections of a joint under varying angles of rotation. A semi-automatic method is used to measure the joint space width (JSW) for each projection. A Statistical model is used to investigate whether the rotation can be detected from a 2D radiograph. It is shown that rotation of the hand has a significant influence on the measured JSW.
Efficacy and Safety of Deferasirox in β-Thalassemia Major Patients in Iran: A Prospective Study from a Single referral Center in Iran

Introduction: Herein, the results of a prospective study evaluating the efficacy and safety of treatment with deferasirox are studied in iron-overloaded patients with β-thalassemia major during an 18-month trial. Methods: Thirty patients who were previously chelated with deferoxamine with/without deferiprone, and fulfilled the inclusion criteria were recruited. Patients received an initial dose of 10–30 mg/kg/day. Liver and cardiac MRI T2* were evaluated before and after the trial. In addition, serum ferritin level was assessed every 3 months. Primary endpoint was regarded as significant improvement in the severity of liver and cardiac iron overload in severe and moderate cases, in addition to improvement or maintenance of the grade of severity in patients with mild iron overload or normal iron accumulation. Therapy was considered effective if primary endpoint was met in >50%. Results: Liver MRI values improved significantly (P = .002), achieving a 73.33% success rate. A successful outcome regarding myocardial iron overload was observed in 80%. Finally, an overall of 66.66% of patients met the success criteria. Secondary endpoint, regarded as safety and tolerability was reached by 93.33%. The most common adverse events were skin rash and gastrointestinal disturbance. A dose between 30 and 40 mg/kg/day, tailored to each patient was considered the optimal dose. Conclusion: Deferasirox proved as an efficient and safe chelating agent in our patients, specifically in mild to moderate iron overloaded patients.
SVM-Based Data Editing for Enhanced One-Class Classification of Remotely Sensed Imagery

This paper studies a specific one-class classification problem where the training data are corrupted by significant outliers. Specifically, we are interested in the one-class support vector machine (OCSVM) approach that normally requires good training data. However, perfect training data are usually hard to obtain in most real-world applications due to the inherent data variability and uncertainty. To address this issue, we propose an OCSVM-based data editing and classification method that can iteratively purify the training data and learn an appropriate classifier from the trimmed training set. The proposed method is compared with a general OCSVM approach trained from two types of bootstrap samples, and applied to the mapping and compliance monitoring tasks for the U.S. Department of Agriculture's Conservation Reserve Program using remotely sensed imagery. Experimental results show that the proposed method outperforms the general OCSVM using bootstrap samples at a lower computational load.
Spoligotyping of Mycobacterium tuberculosis Complex Isolates by Use of Ligation-Based Amplification and Melting Curve Analysis

ABSTRACT We report here a ligation-based spoligotyping that can identify unamplified spacers in membrane-based spoligotyping due to asymmetric insertion of IS6110 in the direct repeat locus. Our typing yielded 84.4% (411/487) concordance with traditional typing and 100% (487/487) accuracy when confirmed by DNA sequencing.
Genotoxic Damage Activates the AMPK-α1 Isoform in the Nucleus via Ca2+/CaMKK2 Signaling to Enhance Tumor Cell Survival

Many genotoxic cancer treatments activate AMP-activated protein kinase (AMPK), but the mechanisms of AMPK activation in response to DNA damage, and its downstream consequences, have been unclear. In this study, etoposide activates the α1 but not the α2 isoform of AMPK, primarily within the nucleus. AMPK activation is independent of ataxia-telangiectasia mutated (ATM), a DNA damage-activated kinase, and the principal upstream kinase for AMPK, LKB1, but correlates with increased nuclear Ca2+ and requires the Ca2+/calmodulin-dependent kinase, CaMKK2. Intriguingly, Ca2+-dependent activation of AMPK in two different LKB1-null cancer cell lines caused G1-phase cell-cycle arrest, and enhanced cell viability/survival after etoposide treatment, with both effects being abolished by knockout of AMPK-α1 and α2. The CDK4/6 inhibitor palbociclib also caused G1 arrest in G361 but not HeLa cells and, consistent with this, enhanced cell survival after etoposide treatment only in G361 cells. These results suggest that AMPK activation protects cells against etoposide by limiting entry into S-phase, where cells would be more vulnerable to genotoxic stress. Implications: These results reveal that the α1 isoform of AMPK promotes tumorigenesis by protecting cells against genotoxic stress, which may explain findings that the gene encoding AMPK-α1 (but not -α2) is amplified in some human cancers. Furthermore, α1-selective inhibitors might enhance the anticancer effects of genotoxic-based therapies. Mol Cancer Res; 16(2); 345–57. ©2017 AACR.
Fuzzy-adaptive-thresholding-based exon prediction

Thresholding is always critical and decisive in many bioinformatics problems. In this paper, we propose and apply a fuzzy-logic-based adaptive thresholding approach to a well-known solution for the exon prediction problem, which uses a threshold on the frequency component at f = 1/3 in the nucleotide sequence. The proposed approach allows the thresholds to vary along the data set based on the local statistical properties. Experiments and results on the nucleotide data of Saccharomyces cerevisiae (Bakers yeast) illustrate the advantage of our approach. A user-friendly GUI in MATLAB is freely available for academic use at www.cs. iastate.edu/˜ankitag/FATBEP.html.
1,1′-(2-Thienylmethylene)di-2-naphthol ethyl acetate solvate

In the title compound, C25H18O2S·C4H8O2, there are intermolecular O—H⋯O hydrogen bonds between the main molecule and the solvent molecule. The thiophene ring is oriented at dihedral angles of 70.87 (7) and 75.36 (4)° with respect to the mean planes of the two naphthyl ring systems.
Effect of Improving Spatial or Temporal Resolution on Image Quality and Quantitative Perfusion Assessment with k-t SENSE Acceleration in First-Pass CMR Myocardial Perfusion Imaging

k‐t Sensitivity‐encoded (k‐t SENSE) acceleration has been used to improve spatial resolution, temporal resolution, and slice coverage in first‐pass cardiac magnetic resonance myocardial perfusion imaging. This study compares the effect of investing the speed‐up afforded by k‐t SENSE acceleration in spatial or temporal resolution. Ten healthy volunteers underwent adenosine stress myocardial perfusion imaging using four saturation‐recovery gradient echo perfusion sequences: a reference sequence accelerated by sensitivity encoding (SENSE), and three k‐t SENSE–accelerated sequences with higher spatial resolution (“k‐t High”), shorter acquisition window (“k‐t Fast”), or a shared increase in both parameters (“k‐t Hybrid”) relative to the reference. Dark‐rim artifacts and image quality were analyzed. Semiquantitative myocardial perfusion reserve index (MPRI) and Fermi‐derived quantitative MPR were also calculated. The k‐t Hybrid sequence produced highest image quality scores at rest (P = 0.015). Rim artifact thickness and extent were lowest using k‐t High and k‐t Hybrid sequences (P < 0.001). There were no significant differences in MPRI and MPR values derived by each sequence. Maximizing spatial resolution by k‐t SENSE acceleration produces the greatest reduction in dark rim artifact. There is good agreement between k‐t SENSE and standard acquisition methods for semiquantitative and fully quantitative myocardial perfusion analysis. Magn Reson Med, 2010. © 2010 Wiley‐Liss, Inc.
Finding Subgroups in a Flickr Group

Information management systems today face a tremendous challenge considering the growing popularity of social media repositories involving images and video. Considering the growing volume of multimedia content in such online media-sharing communities there is an increasing need for novel ways of organizing content. In this paper we consider the problem of organizing images in a given Flickr Group by discovering latent subgroups. A Flickr Group can be visualized as a collection of such subgroups where each subgroup represents a distinct theme. We model the task of discovering subgroups as that of finding highly correlated topics from a dataset containing images and associated tags. The proposed probabilistic model employs a more flexible prior distribution to model topic-topic correlations and utilizes both tag and image information for discovering such subgroups. Our experiments on Flickr Group data demonstrate that the model is able to successfully discover subgroups without any supervision.