Miracle-dz/UniFAR-FTUs huggingface dataset:
Iterative Non-Sequential protein Structural Alignment

Structural similarity between proteins gives us insights into their evolutionary relationships when there is low sequence similarity. In this paper, we present a novel approach called SNAP for non-sequential pair-wise structural alignment. Starting from an initial alignment, our approach iterates over a two-step process consisting of a superposition step and an alignment step, until convergence. We propose a novel greedy algorithm to construct both sequential and non-sequential alignments. The quality of SNAP alignments were assessed by comparing against the manually curated reference alignments in the challenging SISY and RIPC datasets. Moreover, when applied to a dataset of 4410 protein pairs selected from the CATH database, SNAP produced longer alignments with lower rmsd than several state-of-the-art alignment methods. Classification of folds using SNAP alignments was both highly sensitive and highly selective. The SNAP software along with the datasets are available online at http://www.cs. rpi.edu/~zaki/software/SNAP.
Enzyme-linked immunosorbent assay for shigella toxin

An enzyme-linked immunosorbent assay (ELISA) was developed for the detection of shigella toxin. For the assay, a mouse monoclonal antibody against the B subunit of the toxin and a rabbit polyclonal antibody against the holotoxin were employed. The monoclonal antibody was used to coat wells of a microtiter plate, and the polyclonal antibody preparation was used as the detecting antibody. The amount of bound polyclonal antibody was determined by using a goat anti-rabbit immunoglobulin G-alkaline phosphatase conjugate and substrate. The ELISA was able to detect as little as 12 pg (0.06 ng/ml) of shigella toxin. The assay was specific for shigella toxin, not detecting a variety of other bacterial enterotoxins and lethal toxins. The ELISA values correlated well with cytotoxin activity during toxin purification. Shigella toxin was detected by ELISA and by immunoblot analysis in human fecal specimens from persons with S. dysenteriae infections, demonstrating that this toxin is produced in vivo.
Development of an acrylate monolith in a cyclo‐olefin copolymer microfluidic device for chip electrochromatography separation

An acrylate monolith has been synthesized into a cyclic olefin copolymer microdevice for reversed‐phase electrochromatography purposes. Microchannels, designed by hot embossing, were filled up with an acrylate monolith to serve as a hydrophobic stationary phase. A lauryl acrylate monolith was formulated to suit the hydrophobic material, by implementing 100% organic porogenic solvent. This new composition was tested in capillary prior to its transfer into the microfluidic device. Surface functionalization of the cyclic olefin copolymer surface was applied using UV‐grafting technique to improve the covalent attachment of this monolith to the plastic walls of the microfluidic chip. The on‐chip performances of this monolith were evaluated in detail for the reversed‐phase electrochromatographic separation of polycyclic aromatic hydrocarbons, with plate heights reaching down to 10 μm when working at optimal velocity.
TLabel: A New OLAP Aggregation Operator in Text Cubes

Data Warehousing technologies and On-Line Analytical Processing OLAP feature a wide range of techniques for the analysis of structured data. However, these techniques are inadequate when it comes to analyzing textual data. Indeed, classical aggregation operators have earned their spurs in the online analysis of numerical data, but are unsuitable for the analysis of textual data. To alleviate this shortcoming, on-line analytical processing in text cubes requires new analysis operators adapted to textual data. In this paper, the authors propose a new aggregation operator named Text Label TLabel, based on text categorization. Their operator aggregates textual data in several classes of documents. Each class is associated with a label that represents the semantic content of the textual data of the class. TLabel is founded on a tailoring of text mining techniques to OLAP. To validate their operator, the authors perform an experimental study and the preliminary results show the interest of their approach for Text OLAP.
Two-dimensional imaging of OH in flames by use of polarization spectroscopy.

Two-dimensional imaging of OH radicals in a premixed CH4/O2 flame by polarization spectroscopy is reported. Polarization spectroscopy was applied in a copropagating geometry with linearly polarized pump and probe beams. The images were measured with the laser frequency tuned to resonance with the Q1(9) A2Σ−X2Π(0, 0) transition of OH. The signal dependence on the crossing angle between the pump and probe beams was also studied. The possibilities for two-dimensional temperature mapping were demonstrated by measuring images at two different rotational lines and by extracting the temperature map from these measurements.
Localization and Navigation of Mobile Robots

This dissertation approaches the localization and navigation problems for a differential mobile robot. Thus, the robot’s architecture was updated, so that it could use the local localization system based on odometry. It was also developed a global localization system based on vision in order to correct the local localization system, iGPS (indoor Global Positioning System [1]). To identify the robot in the Y CbCr color space it was used two targets and the statistical Mahalanobis distance. A Kalman filter (KF) did robot’s position tracking. Intrinsic camera parameters were obtained [2]. Robot’s localization was corrected by a Kalman filter (KF), which combines the information from both localization systems. Robot and iGPS were integrated in a service oriented architecture through the development of an interface between MATLAB®and Web Services. A proportional integral (PI) and a time-varying non linear controllers were presented as solutions to the navigation problem. Three trajectories were defined for acquiring simulation and experimental results, in order to validate the proposed methodologies. Experimental results shows that the relocaliztion system can indeed correct the odometry error, while not destabilizing the robot’s navigation.
Characterisation and airborne deployment of a new counterflow virtual impactor inlet

Abstract. A new counterflow virtual impactor (CVI) inlet is introduced with details of its design, laboratory characterisation tests and deployment on an aircraft during the 2011 Eastern Pacific Emitted Aerosol Cloud Experiment (E-PEACE). The CVI inlet addresses three key issues in previous designs; in particular, the inlet operates with: (i) negligible organic contamination; (ii) a significant sample flow rate to downstream instruments (∼15 l min−1) that reduces the need for dilution; and (iii) a high level of accessibility to the probe interior for cleaning. Wind tunnel experiments characterised the cut size of sampled droplets and the particle size-dependent transmission efficiency in various parts of the probe. For a range of counter-flow rates and air velocities, the measured cut size was between 8.7–13.1 μm. The mean percentage error between cut size measurements and predictions from aerodynamic drag theory is 1.7%. The CVI was deployed on the Center for Interdisciplinary Remotely Piloted Aircraft Studies (CIRPAS) Twin Otter for thirty flights during E-PEACE to study aerosol-cloud-radiation interactions off the central coast of California in July and August 2011. Results are reported to assess the performance of the inlet including comparisons of particle number concentration downstream of the CVI and cloud drop number concentration measured by two independent aircraft probes. Measurements downstream of the CVI are also examined from one representative case flight coordinated with shipboard-emitted smoke that was intercepted in cloud by the Twin Otter.
Structural Equation Modeling, A Bayesian Approach

would have been much more helpful to use graphical methods to display the data sets, perhaps along the lines of the elegant Trellis/Lattice graphics implemented by the nlme package in R and S, and described by Pinheiro and Bates (2004). Much material is devoted to explaining basic statistical inference topics like ML estimation, basic distributions, confidence intervals, and the like. Anyone contemplating working with mixed modeling should already have a good understanding of these concepts. There is no need to clutter an otherwise wonderful book with this material, especially when the zeal for simplicity stretches technical accuracy, as with the confidence intervals (Chap. 4), where the general approach given is β̂ ± SE β̂ , where β̂ is the point estimate and SE β̂ is its standard error. The author does not use a multiple (e.g., 2) of the standard error, so the confidence intervals have approximately 68% coverage, not the usual 95% coverage. There is no discussion of this fundamental issue, even though (unnecessary) detail is given on the background of interval estimation. Overall, this book would be useful for anyone who uses GenStat and/or R desiring an introduction to applied mixed modeling, and they should certainly have a look. But it should not be the sole resource.
Increasing membrane contrast by means of imidazole‐osmium post‐fixation as exemplified by skeletal muscle fiber

Until now, the interpretation of findings derived from investigations on membrane structures (T tubules, sarcoplasmic reticulum, the Golgi apparatus) in thick sections of mammalian muscle tissue has been limited in TEM due to the lack of sharp resolution of the membrane contours. This article shows how the imidazol‐osmium post‐fixation of tissue blocks can be used to achieve well‐contrasted, sharply defined membrane contours. Therefore, unstained sections from imidazol‐osmium post‐fixed tissue can be examined immediately. But protein structures (e.g., ribosomes) remain uncontrasted with this technique. If needed, it is possible to visualize the protein structures by conventional section staining with uranyl acetate and lead citrate. This method is suitable for both ultrathin and thick sections (>150 nm). Microsc. Res. Tech. 58:121–124, 2002. © 2002 Wiley‐Liss, Inc.
Association between cirrhosis and Helicobacter pylori infection: a meta-analysis

Cirrhosis is a severe threat to public health. Some studies have suggested that cirrhosis is associated with Helicobacter pylori infection, but the results remain controversial. This meta-analysis was conducted to quantify the association between cirrhosis and H. pylori infection. Published articles on H. pylori prevalence in patients with cirrhosis were collected to assess the potential associations between H. pylori infection and cirrhosis risk. Twenty-one eligible studies were included for the analysis. Data on publication year, geographic region, and etiology were summarized. Metaregression models and subgroup analyses were established to screen the factors for heterogeneity. Of the 322 articles retrieved, 21 met the inclusion criteria. These studies involved 6135 cases, with a total H. pylori infection rate of 52.26%. This meta-analysis showed significant difference in H. pylori infection between patients with cirrhosis and controls [odd ratio (OR)=2.05, 95% confidence interval (CI): 1.33–3.18, P<0.0001]. The subgroup analysis revealed, in contrast to Asia (OR=0.90, 95% CI: 0.48–1.66, P<0.0001), Europe (OR=2.98, 95% CI: 2.02–4.39, P<0.0001), and America (OR=4.75, 95% CI: 1.42–15.95, P=0.249), a significantly higher prevalence of H. pylori infection in patients with cirrhosis. On the basis of etiology, there was a higher prevalence of H. pylori infection due to primary biliary cirrhosis (OR=1.75, 95% CI: 1.15–2.64, P=0.147) and viral cirrhosis (OR=2.66, 95% CI: 1.24–5.71, P<0.0001) compared with alcohol cirrhosis (OR=0.77, 95% CI: 0.04–16.59, P<0.0001). The pooled data suggest that there is a significantly high prevalence of H. pylori infection in patients with cirrhosis. Large-scale and multicenter studies are needed to further investigate the relation between cirrhosis and H. pylori infection.
Microtubule disruption leads to cellular contraction in human trabecular meshwork cells.

PURPOSE To determine whether microtubule- and actin-altering drugs, which have been shown to increase aqueous humor outflow, cause cellular contraction in human trabecular meshwork (HTM) cells. METHODS HTM cells were plated in culture dishes containing a polymerized deformable silicone substrate. After 48 hours, the dishes were placed on an inverted microscope and treated with ethacrynic acid, colchicine, vinblastine, cytochalasin B, or 1-(5-isoquinolinylsulfonyl)-2-methylpiperazine (H-7) and then recorded on videotape for 15 minutes. An increase in silicone substrate wrinkle size and/or number indicated a contraction. Sham controls were used. RESULTS Cellular contraction was observed with ethacrynic acid, colchicine, and vinblastine in the 10(-5) to 10(-4) M dosage range. Pretreatment with H-7 blocked these effects. Cytochalasin B did not produce cellular contraction. CONCLUSIONS Microtubule disruption causes cellular contraction in HTM cells, and this effect depends on an intact actin cytoskeleton network. Contraction of trabecular meshwork cells in response to various stimuli is an attractive hypothesis for possible homeostatic mechanisms in the outflow pathway, and this may serve as a focus for novel glaucoma drug development.
Nonlinear Observer-based Chaos Control for SPMSM with Both Uncertain Parameters and External Disturbances

This paper proposed a robust chaos control scheme for surface permanent magnet synchronous motor (SPMSM) drive system considering the uncertain parameters and external disturbances. A nonlinear time delay estimator is utilized to estimate the nonlinearities, uncertain parameters and disturbances of the system on line, so it is not necessarily required the exact model of the system. Then, based on the time delay estimator, a simple feedback controller, which is only related to the system errors and control input, is simple and easy to be constructed. The control gains can be obtained easily using pole placement method. The stability of the proposed control scheme is analyzed according to Lyapunov stability theory. Law-filter is also used to improve the performance of the system. Simulation results illustrate the effectiveness of the presented control method.
Research on the optimization of high-frequency electronic ballast based on the resistance model of the UV-lamp

The parameters of the resistance model are obtained through various experiments under different lamp power in this study. Polynomial fitting curves are obtained for these parameters to get the values under some certain lamp power. Then simulations in PSIM are conducted by using the calculated values to verify the reliability and accuracy of the method adopted. Good agreement is obtained between the experimental results and simulation results. Finally, In order to improve the lifetime of the lamp and increase the UV irradiance at 253.7nm, the double capacitor topology is proposed and studied.
Reconsidering High-Speed Design Criteria for Transmission-Gate-Based Master–Slave Flip-Flops

In this paper we show that, when dealing with transmission-gate-based master-slave (TGMS) flip-flops (FFs), a reconsideration of the classical approach for the delay minimization is worthwhile to improve the performance in high-speed designs. In particular, by splitting such FFs into two sections that are separately optimized and then reconciling the results, the emerging design always outperforms the one resulting from the employment of a classical Logical Effort procedure assuming such FFs as a whole continuous path. Simulations are performed on several well-known TGMS FFs, designed in a 65-nm technology, to validate the correctness of such a procedure and of the underlying assumptions. Significant improvements are found on delay and, remarkably, on energy and area occupation, thus showing that this approach allows to correctly deal with the actual path effort in such circuits and hence to more properly steer the design towards the achievement of energy efficiency in the high-speed region.
Migration within Great Britain and cardiovascular disease: early life and adult environmental factors.

AIM To examine the relative contributions of early life and adult life factors to risk of cardiovascular disease (CVD) in middle-aged men using migration within Great Britain (GB). METHODS Prospective study of 7,735 men (40-59 years) drawn from one group practice in each of 24 British towns. Zones of birth and/or examination: South of England and rest of GB (Midlands and Wales, North of England, and Scotland). RESULTS There were 1,392 coronary heart disease (CHD) events and 1154 cardiovascular deaths during 21.8 years mean follow-up. Regardless of birth zone, men examined in the South showed lower risk of CHD events and CVD mortality than those examined in the rest of GB. Migrants from South to rest of GB showed a small increase in cardiovascular risk. Men born and examined in the rest of GB showed the highest adjusted risk of CHD events (RR = 1.15, 95% CI: 0.96-1.38) and CVD mortality (RR = 1.28, 95% CI: 1.04-1.57). Men born in the rest of GB who moved to the South showed adjusted risks of CHD events and CVD mortality similar to those born and examined in the South. Zone of examination was more strongly associated with CHD events and CVD mortality than zone of birth (RR = 1.23 versus 0.95 for CHD; RR = 1.26 versus 1.04 for CVD mortality). Smokers, irrespective of zone of birth or examination, showed higher risk than non-smokers. CONCLUSION Factors in adult life appear to be dominant in determining cardiovascular risk in middle and older age although this does not exclude early life effects on cardiovascular risk.
Visually Compar ing M ult iple Par ti t ions of Data with Appl icat ions to Cluster ing

Tightly coupled visualization and analysis is a powerful approach to data exploration especially for clustering. We describe such a specific integration of analysis and visualization for the evaluation of multiple partitions of a data set. Partitions are decompositions of a dataset into a family of disjoint subsets. They may be the results of clustering, of groupings of categorical dimensions, of binned numerical dimensions, of predetermined class labeling dimensions, or of prior knowledge structured in mutually exclusive format (one data item associated with one and only one outcome). Partition or cluster stability analysis can be used to identify near-optimal structures, build ensembles, or conduct validation. We extend Parallel Sets to a new visualization tool which provides for the mutual comparison and evaluation of multiple partitions of the same dataset. We describe a novel layout algorithm for informatively rearranging the order of records and dimensions. We provide examples of its application to data stability and correlation at the record, cluster, and dimension levels within a single interactive display.
Modelling the resource implications and budget impact of new reimbursement guidelines for the management of cow milk allergy in Finland

ABSTRACT Objective: To assess the impact of the decision by Kela (The Social Insurance Institution) to adopt guidelines for the management of food allergies in children, developed by the Finnish Medical Society Duodecim, as the basis for reimbursing clinical nutrition preparations for the treatment of cow milk allergy (CMA) in Finland. Methods: A decision model was constructed using published clinical outcomes and clinician-derived resource utilisation estimates. The model was used to estimate the net resource implications and associated costs of Kela's new policy for the annual cohort of 1443 new CMA sufferers over the first 6 months following referral to a specialist. The analysis was conducted from the perspective of Kela, patients and Finnish society. Results: Kela's new policy for reimbursing clinical nutrition preparations for the treatment of CMA is expected to increase healthcare resource use, including a 10% increase in the number of specialist visits over the first 6 months following referral. Consequently, Kela's 6-monthly expenditure on 1443 new CMA sufferers following referral is expected to increase by 12% from €889 389 to €992 761. Additionally, parents’ costs are expected to increase by 10% and fathers’ absenteeism from work to increase by 11% within the first 6 months following referral. Conclusion: It is important to validate guidelines in clinical practice before their implementation. Within the limitations of our model, Kela's new criteria for reimbursing clinical nutrition preparations for the treatment of CMA is expected to increase healthcare resource use in paediatric departments in public hospitals in Finland and increase costs to Kela, patients and Finnish society.
An Effective Mining of Exception Class Association Rules from Medical Datasets

Data mining techniques can be applied on medical data to improve quality of decisions in medical field, and to enhance clinician performance. Class Association Rule (CAR) integrates the techniques of association rule mining and classification rules mining. CAR mining is able to find a lot of rules, some important rules are still not discovered. These rules are called Exception Class Association Rules (ECARs), which have high confidence and low support. The goal of ECAR is to discover rare and low support itemsets to generate useful rules from these itemsets and meet the class label (target attribute). Also, ECARs are considered very important by domain's expert in medical field, which lead to improve the performance of analysis and diagnosis. These type of rules cannot be identified easily using traditional algorithms as they focus in frequent itemsets discovery and don't depend on target attribute for diagnosis. In this paper, an effective algorithm is proposed to mine two types of CARs: Precise Class Association Rules (PCARs) and Approximate Class Association Rules (ACARs), and to generate ECAR for each ACAR from medical datasets. The experimental results shows the effectiveness of the proposed algorithm. Keywords— Association Rule Mining; Knowledge Discovery; Medical Data Mining; Class Association Rule; Exception Class Association Rule.
Microwave imaging update: For medical imaging applications

This paper provides an update on the progress of Keysight and various partners on Microwave Medical Imaging products, systems, and their commercialization. I discuss the physical basis for this imaging modality and then provide an update on the progress to date of a number of product trials and commercialization activities from Dune Medical, Micrima, Medfield Diagnostics, EMTensor, and MiWa technologies. Extensive references are included. These are not comprehensive but representative of the research ongoing in Microwave Medical Imaging.
Integrated nanohole array surface plasmon resonance sensing device using a dual-wavelength source

In this paper, we demonstrate a compact integrated nanohole array-based surface plasmon resonance sensing device. The unit includes a LED light source, driving circuitry, CCD detector, microfluidic network and computer interface, all assembled from readily available commercial components. A dual-wavelength LED scheme was implemented to increase spectral diversity and isolate intensity variations to be expected in the field. The prototype shows bulk sensitivity of 266 pixel intensity units/RIU and a limit of detection of 6 × 10−4 RIU. Surface binding tests were performed, demonstrating functionality as a surface-based sensing system. This work is particularly relevant for low-cost point-of-care applications, especially those involving multiple tests and field studies. While nanohole arrays have been applied to many sensing applications, and their suitability to device integration is well established, this is the first demonstration of a fully integrated nanohole array-based sensing device.