Miracle-dz/UniFAR-FTUs huggingface dataset:
The Czech Surveillance System for Invasive Pneumococcal Disease, 2008-2013: A Follow-Up Assessment and Sensitivity Estimation

Background Invasive pneumococcal disease (IPD) is caused by Streptococcus pneumoniae and mostly presents as pneumonia, sepsis or meningitis. A notable portion of IPD cases is vaccine preventable and the pneumococcal conjugate vaccine (PCV) was introduced into the routine childhood immunization programs in many countries during the last decades. Objectives Before PCV introduction in the Czech Republic in 2010, a national surveillance system for IPD was implemented in 2008 and further improved in 2011. In this study, we describe the new surveillance system for the first time and measure its sensitivity between 2010 and 2013 using the capture-recapture method. Furthermore, we describe the recent epidemiological trend of IPD, taking sensitivity estimates into account. Results and Conclusions Between 2010 and 2013 the estimated sensitivity of the overall IPD surveillance increased from 81% to 99%. The sensitivity of individual reporting sources increased from 72% to 87% for the laboratory system and from 31% to 89% for the epidemiological notification system. Crucial for this improvement was the introduction of quarterly report reminders in 2011. Due to positive source dependency, the presented sensitivity estimates are most probably overestimated and reflect the upper limit of reporting completeness. Stratification showed variation in sensitivity of reporting particularly according to region.An effect of the PVC vaccination in the Czech Republic is visible in the incidence of IPD in target age groups (<5y). This influence was not evident in the total IPD incidence and may interfere with increasing sensitivity of reporting. In 2013, an increase in the IPD incidence was observed. This finding requires further observation and a detailed vaccine impact analysis is needed to assess the current immunization strategy.
Melodic Similarity: A Re-examination of the MIREX2005 Data

Despite a considerable body of research, there is no clarity about the basic properties of melodic similarity, such as whether or not it constitutes a metric space, or whether it is a more complex phenomenon. An experiment conducted by Typke et al., used as a basis for the MIREX2005 melodic-similarity modelling contest, represents a particularly rich source of data. In the experiment, for each of eleven queries (melodies taken from RISM A/II), about 25 experts ranked some of about 50 candidates for similarity with the query. A ‘Monte Carlo’ approach has been taken in re-examining this data, simulating data in the same form on the basis of simple assumptions about the nature of melodic similarity. Statistical properties of the actual data were compared with the same properties for 10,000 sets of simulated data, allowing estimation of the significance of differences found. In terms of overall measures such as the ranking profile for each candidate, quite good simulations (i.e., sets of simulated data in which the original falls within the second and third quartiles in the measured property) arose from stochastic ranking based only on the mean and variance of the actual ranking for each candidate and on the likelihood of the candidate being selected for ranking. However, the simulations did show evidence, in a substantial minority of cases, of an effect for some candidates to be ranked higher or lower dependent on the presence of another candidate, and of the influence of similarity between candidates.
Biology of chemokine and classical chemoattractant receptors: differential requirements for adhesion-triggering versus chemotactic responses in lymphoid cells

Several chemoattractant receptors can support agonist-induced, integrin- dependent arrest of rolling neutrophils in inflamed venules in vivo, as well as subsequent crawling into tissues. It has been hypothesized that receptors of the Galpha(i)-linked chemoattractant subfamilies, especially receptors for chemokines, may mediate parallel activation- dependent arrest of homing lymphocyte subsets. However, although several chemokines can attract subsets of B or T cells, robust chemoattractant triggering of resting lymphocyte adhesion to vascular ligands has not been observed. To study the biology of individual leukocyte chemoattractant receptors in a defined lymphoid environment, mouse L1/2 pre-B cells and/or human Jurkat T cells were transfected with alpha (IL-8 receptor A) or beta (MIP-1alpha/CC-CKR-1) chemokine receptors, or with the classical chemoattractant C5a (C5aR) or formyl peptide receptors (fPR). All receptors supported robust agonist- dependent alpha4beta1 integrin-mediated adhesion of lymphocytes to VCAM- 1. L1/2 cells cotransfected with fPR and beta7 integrin were also induced to bind MAdCAM-1, suggesting common mechanisms coupling chemoattractant receptors to activation of distinct integrins. Adhesion was rapid but transient, with spontaneous reversion to unstimulated levels within 5 min after peak binding. When observed under flow conditions, alpha4beta1-mediated arrest occurred within seconds after initiation of contact and rolling of IL-8RA transfectants on VCAM-1/IL- 8 co-coated surface; and arrest reversed spontaneously after a mean of 5 min with a return to rolling behavior. Each of the receptors also conferred agonist-specific chemotaxis; however, whereas strong adhesion required simultaneous occupancy of many receptors with maximal responses above the Kd, chemotaxis in each case was suppressed at high agonist concentrations. The findings indicate that alpha and beta chemokine as well as classical chemoattractant receptors can trigger robust adhesion as well as directed migration of lymphoid cells, but that the requirements for and kinetics of adhesion triggering and chemotaxis are distinct, thus permitting their independent regulation. They suggest that the discordance between proadhesive and chemoattractant responses of circulating lymphocytes to many chemokines may reflect quantitative aspects of receptor expression and/or coupling rather than qualitative differences in receptor signaling.
Give GPs more time with patients, urges RCGP chair

GPs need more time to care for their patients, the chair of the Royal College of General Practitioners has said, adding that she would call on the four UK governments to cut bureaucracy to allow this. Speaking at the college’s annual conference in Liverpool on 12 October, Helen Stokes-Lampard also said, “GPs see patients, many of whom are widowed, who have multiple health problems like diabetes, hypertension, and depression. But often their main problem isn’t medical: …
An Amine‐Functionalized Iron(III) Metal–Organic Framework as Efficient Visible‐Light Photocatalyst for Cr(VI) Reduction

The photocatalytic reduction of Cr(VI) is investigated over iron(III)‐based metal–organic frameworks (MOFs) structured as MIL‐88B. It is found that MIL‐88B (Fe) MOFs, containing Fe3‐μ3‐oxo clusters, can be used as photocatalyst for the reduction of Cr(VI) under visible light irradiation, which is due to the direct excitation of Fe3‐μ3‐oxo clusters. The amine‐functionalized MIL‐88B (Fe) MOFs (denoted as NH2–MIL‐88B (Fe)) shows much higher efficiency for the photocatalytic Cr(VI) reduction under visible‐light irradiation compared with MIL‐88B (Fe). It is revealed that in addition to the direct excitation of Fe3‐μ3‐oxo clusters, the amine functionality in NH2–MIL‐88B (Fe) can also be excited and then transferred an electron to Fe3‐μ3‐oxo clusters, which is responsible for the enhanced photocatalytic activity for Cr(VI) reduction. The enhanced photocatalytic activity for Cr(VI) reduction is also achieved for other two amine‐functionalized iron(III)‐based MOFs (NH2–MIL‐53 (Fe) and NH2–MIL‐101 (Fe)).
Conditions for fibronectin fibril formation in the early Xenopus embryo

Fibronectin fibril formation on a multilayered cohesive cell sheet is studied in the Xenopus embryo. In the blastula, secreted fibronectin accumulates in the blastocoel, where it associates with mucous material. At the onset of gastrulation, a fibrillar fibronectin matrix develops on the blastocoel roof. Cells engage in this process stochastically within a 2‐hr period. Fibril network formation requires more than 60 μg/ml of fibronectin, but the timing of fibrillogenesis is not regulated through the availability of fibronectin. With the exception of a few isolated mesoderm cells, only the cells of the blastocoel roof are able to form fibronectin fibrils. However, this requires that cells are provided with a free surface and, at the same time, with lateral adhesive cell contacts, i.e. fibril assembly occurs only on the surface of cohesive cells aggregates. This explains the observed restriction of fibronectin matrix formation to the inner surface of the blastocoel roof in the embryo. In addition, a minimum blastocoel roof size is required for fibril formation. Dev. Dyn. 1998;212:335–345. © 1998 Wiley‐Liss, Inc.
Syntheses and Selective Inhibitory Activities of Terphenyl‐Bisamidines for Serine Proteases

Biphenyl nitriles 5a—c, terphenyl dinitriles 11a—d, and naphthalene‐bis(benzonitrile) 11e were prepared by palladium‐catalyzed cross coupling reactions and subsequently converted to biphenyl amidines 8a—c and bis(benzamidines) 4a—e. Among the biphenyl amidines 8 only the meta‐derivative 8b inhibits factor Xa and trypsin (Ki = 10 μM). The terphenyl bisamidine 4c does not inhibit factor Xa, trypsin, thrombin, and plasmin, while 4a and 4d are almost equipotent inhibitors of theses enzymes (Ki 1–6 μM), and 4b and 4e are selective for trypsin (Ki = 0.2 and 0.3 μM; but Ki > 1 μM for factor Xa, thrombin, and plasmin). X‐ray analysis of crystals of 4b complexed with bovine trypsin revealed a unique binding mode: one benzamidino group binds in the S1 site to the side chain carboxylate of Arg189. The central phenyl group is twisted away from the S2/S3 sites and the second amidino group contacts the Asn143 side chain.
An Adaptive Particle Weighting Strategy for ECG Denoising Using Marginalized Particle Extended Kalman Filter: An Evaluation in Arrhythmia Contexts

Model-based Bayesian frameworks have a common problem in processing electrocardiogram (ECG) signals with sudden morphological changes. This situation often happens in the case of arrhythmias where ECGs do not obey the predefined state models. To solve this problem, in this paper, a model-based Bayesian denoising framework is proposed using marginalized particle-extended Kalman filter (MP-EKF), variational mode decomposition, and a novel fuzzy-based adaptive particle weighting strategy. This strategy helps MP-EKF to perform well even when the morphology of signal does not comply with the predefined dynamic model. In addition, this strategy adapts MP-EKF's behavior to the acquired measurements in different input signal to noise ratios (SNRs). At low input SNRs, this strategy decreases the particles’ trust level to the measurements while increasing their trust level to a synthetic ECG constructed with the feature parameters of ECG dynamic model. At high input SNRs, the particles’ trust level to the measurements is increased and the trust level to synthetic ECG is decreased. The proposed method was evaluated on MIT-BIH normal sinus rhythm database and compared with EKF/EKS frameworks and previously proposed MP-EKF. It was also evaluated on ECG segments extracted from MIT-BIH arrhythmia database, which contained ventricular and atrial arrhythmia. The results showed that the proposed algorithm had a noticeable superiority over benchmark methods from both SNR improvement and multiscale entropy based weighted distortion (MSEWPRD) viewpoints at low input SNRs.
Capacity analysis of a wireless backhaul for metering in the Smart Grid

Many application scenarios envisioned as part of the `Smarter' Grid depend on an effective underlying communication infrastructure for power distribution. To this end, a linear chain wireless communication architecture is proposed in this work to meet communication requirements at the distribution level of the power grid. A theoretical study is done to understand the capacity limitations of using such linear chain wireless technologies at the distribution level. The application of advanced metering infrastructure (AMI) that encourages customer participation in energy delivery is used as a case study to understand the implications of any limitations imposed by the proposed communication architecture.
Tragedy Viewers Count Their Blessings

Hypotheses were derived from downward comparison and attachment theory to address the tragedy paradox: more sadness produces greater tragedy enjoyment. Participants (n = 361) watched a tragedy and reported affect, enjoyment, life happiness, and spontaneous thoughts (categorized into self- vs. socio-focused). Greater sadness led to greater enjoyment, mediated by life reflection; specifically, both self- and socio-focused thoughts mediated this sadness impact on tragedy enjoyment. Furthermore, more sadness led to greater life happiness increase during exposure, mediated by socio-focused thoughts only. No parallel effects emerged for positive affect. The present findings suggest that tragedy-induced sadness instigates (a) life reflection that increases tragedy enjoyment as well as (b) specifically thoughts about close relationships that, in turn, raise life happiness, which (c) subsequently increases tragedy enjoyment further.
Sodium, Extracellular Fluid Volume, and Cardiac Output Changes in the Genesis of Mineralocorticoid Hypertension in the Intact Dog

SUMMARY Twenty-four trained, conscious dogs with chronically implanted iliac catheters were used to assess the relative roles of sodium (Na) and volume in the development of mineralocorticoid hypertension. All were maintained on restricted Na diets; supplemental Na was given as slow I.V. infusions of 0.9% NaCl solution. The effect of gradual replenishment of total body sodium on arterial blood pressure (BP), cardiac output (CO), total peripheral resistance (TPR) and extracellular fluid volume (ECFV) was assessed at four separate levels of cumulative Na intake (70,140,420 and 840 mEq). The sequence of changes in 12 metyrapone-treated dogs was compared with 12 untreated controls submitted to the same protocol. Changes in fluid volumes and CO were virtually identical in the two groups; however, only dogs previously treated with metyrapone became significantly hypertensive (AMAP 16 and 28 mm Hg, p < 0.001). Within the metyrapone-treated groups, increases in volume and flow led to markedly different TPR responses dependent on level of cumulative sodium Intake; at levels $ 140 TPR was lowered as output increased, but as levels > 140 TPR and BP rose in the face of increases in output and ECFV that were not greater than those found at 140 mEq cumulative Na intake. These findings suggest that this steroid-induced hypertension in the dog is “resistance-mediated” from its earliest stages, and that restoration of sodium stores rather than volume expansion played the more important role in the initiation of this hypertension.
Solving Transition Independent Decentralized Markov Decision Processes

Formal treatment of collaborative multi-agent systems has been lagging behind the rapid progress in sequential decision making by individual agents. Recent work in the area of decentralized Markov Decision Processes (MDPs) has contributed to closing this gap, but the computational complexity of these models remains a serious obstacle. To overcome this complexity barrier, we identify a specific class of decentralized MDPs in which the agents' transitions are independent. The class consists of independent collaborating agents that are tied together through a structured global reward function that depends on all of their histories of states and actions. We present a novel algorithm for solving this class of problems and examine its properties, both as an optimal algorithm and as an anytime algorithm. To the best of our knowledge, this is the first algorithm to optimally solve a non-trivial subclass of decentralized MDPs. It lays the foundation for further work in this area on both exact and approximate algorithms.
The CGView Server: a comparative genomics tool for circular genomes

The CGView Server generates graphical maps of circular genomes that show sequence features, base composition plots, analysis results and sequence similarity plots. Sequences can be supplied in raw, FASTA, GenBank or EMBL format. Additional feature or analysis information can be submitted in the form of GFF (General Feature Format) files. The server uses BLAST to compare the primary sequence to up to three comparison genomes or sequence sets. The BLAST results and feature information are converted to a graphical map showing the entire sequence, or an expanded and more detailed view of a region of interest. Several options are included to control which types of features are displayed and how the features are drawn. The CGView Server can be used to visualize features associated with any bacterial, plasmid, chloroplast or mitochondrial genome, and can aid in the identification of conserved genome segments, instances of horizontal gene transfer, and differences in gene copy number. Because a collection of sequences can be used in place of a comparison genome, maps can also be used to visualize regions of a known genome covered by newly obtained sequence reads. The CGView Server can be accessed at http://stothard.afns. ualberta.ca/cgview_server/
ONTOMSN: Medical social network ONTOlogy

Recently, the social network has revolutionized the interaction and information exchange between users. Several works have been committed to unify the social network domain, particularly the medical domain through introducing ontology-based modeling of medical social network. Nevertheless, few researches focused on modeling the social network using ontology from the medical side. To overcome this drawback, we propose, in this paper, a medical social network ontology which includes definitions of main entities and describes major attributes of medical social network concepts aiming at sharing common understanding of this domain.
A comparison of serratus anterior muscle activation during a wall slide exercise and other traditional exercises.

STUDY DESIGN Single-group repeated-measures design. OBJECTIVES To investigate the ability of the wall slide exercise to activate the serratus anterior muscle (SA) at and above 90 degrees of humeral elevation. BACKGROUND Strengthening of the SA is a critical component of rehabilitation for patients with shoulder impingement syndromes. Traditional SA exercises have included scapular protraction exercises such as the push-up plus. These exercises promote activation of the SA near 90 degrees of humeral elevation, but not in positions above 90 degrees where patients typically experience pain. METHODS AND MEASURES Twenty healthy subjects were studied performing 3 exercises: (1) wall slide, (2) plus phase of a wall push-up plus, and (3) scapular plane shoulder elevation. Three-dimensional position of the thorax, scapula, and humerus and muscle activity from the SA, upper and lower trapezius, and latissimus dorsi were recorded. The magnitudes of activation for each muscle at 90 degrees, 120 degrees, and 140 degrees of humeral elevation were quantified from EMG records. Repeated-measures analyses of variance were used to determine the degree to which the different exercises activated the SA at the 3 humeral positions. RESULTS The intensity of SA activity was not significantly different between the 3 exercises at 90 degrees of humeral elevation (P = .40). For the wall slide and scapular plane shoulder elevation exercises, SA activity increased with increasing humeral elevation angle (P = .001), with no significant differences between the 2 exercises (P = .36). CONCLUSION The wall slide is an effective exercise to activate the SA muscle at and above 90 degrees of shoulder elevation. During this exercise, SA activation is not significantly different from SA activation during the push-up plus and scapular plane shoulder elevation, 2 exercises previously validated in the literature.
Parse Tree Database for Information Extraction

Information extraction systems are traditionally implemented as a pipeline of special-purpose processing modules targeting the extraction of a particular kind of information. A major drawback of such approach is that whenever a new extraction goal emerges or a module is improved, extraction has to be re-applied from scratch to the entire text corpus even though only a small part of the corpus might be affected. In this paper, we describe a novel approach for information extraction so that extraction needs are expressed in the form of database queries, which are evaluated and optimized by databases. Using database queries for information extraction enables generic extraction and minimizes reprocessing of data. In addition, our approach provides two different query generation components that can automatically form database queries for extraction from training datasets, as well as from unlabeled data through a mechanism inspired by the pseudo-relevance feedback approach found in protein-protein interactions and drug-protein-metabolic relations from two sets of corpus. Experiments show that our approach achieves a precision of 83.6% and recall of 58.6% (F-measure of 64.2%) for the extraction of protein-protein interactions from the BioCreative 2 corpus, while achieving a precision of 85.0% and recall of 26.0% (F-measure of 39.8%) for drug-protein-metabolic relations.
Behavior of Short and Deep Beams Made of Concrete-Filled Fiber-Reinforced Polymer Tubes

Behavior of short and deep beams made of concrete-filled fiber-reinforced polymer (FRP) tubes (CFFT) was compared experimentally to that of their slender counterparts. Ten specimens made from four types of glass FRP tubes with different fiber architecture and lamina lay-up were tested with shear span to depth ratio between 0.9 and 6.25, diameter to thickness ratio between 16 and 63, and reinforcement index between 0.11 and 2.2. The study extended the test database of CFFTs to the lowest practical limit of shear span to depth ratio. None of the CFFT beams tested, even with the lowest shear span to depth ratio of 0.9, failed in shear. Tensile bending strains at the bottom of the midspan section of the beams always remained higher than the respective diagonal tensile strain at the midpoint of the shear span. Web shear cracks were observed only in the concrete core of deep CFFT beams with high reinforcement index. Following the first flexural crack, the concrete core began to slip relative to the FRP tube. Th.
3D dynamic simulation of crack propagation in extracorporeal shock wave lithotripsy

Some experimental observations of Shock Wave Lithotripsy(SWL), which include 3D dynamic crack propagation, are simulated with the aim of reproducing fragmentation of kidney stones with SWL. Extracorporeal shock wave lithotripsy (ESWL) is the fragmentation of kidney stones by focusing an ultrasonic pressure pulse onto the stones. 3D models with fine discretization are used to accurately capture the high amplitude shear shock waves. For solving the resulting large scale dynamic crack propagation problem, PDS-FEM is used; it provides numerically efficient failure treatments. With a distributed memory parallel code of PDS-FEM, experimentally observed 3D photoelastic images of transient stress waves and crack patterns in cylindrical samples are successfully reproduced. The numerical crack patterns are in good agreement with the experimental ones, quantitatively. The results shows that the high amplitude shear waves induced in solid, by the lithotriptor generated shock wave, play a dominant role in stone fragmentation.