Miracle-dz/UniFAR-FTUs huggingface dataset:
Epidemiology of Invasive Pneumococcal Disease in Czech Children under 5 Years of Age after Routine Immunisation.

BACKGROUND The introduction of the surveillance of invasive pneumococcal diseases (IPD) in 2007 has helped to monitor changes in serotype occurrence in the Czech population and assess the impact of routine immunisation against IPD on the child population under 5 years of age. METHODS Observational study of childhood IPD in the Czech Republic based on the state public health surveillance data comparing pre-immunisation (2007-2008) and post-immunisation (2012-2013) periods. RESULTS In the child population there was an overall decline in IPD occurrence of 46.6% (95% CI 63.4-21.9) observed during the post-immunisation period. There was even greater decrease of 71.6% (95% CI 50.4-83.8) in vaccinated children. In the post-immunisation period, Prevenar 13 (PCV13) and Synflorix (PCV10) contributed to a vaccine-type IPD reduction of 95.4% (95% CI 67.0-99.4) and 76.9% (95% CI 36.0-91.7), respectively, compared to unimmunised children. The occurrence of 10 serotypes contained in both commercial vaccines also decreased in unvaccinated children by 61.4% (95% CI 14.5-82.6). However, a rise in the risk of non-vaccine and unspecified serotype acquisition by up to 153% was revealed in unimmunised children when comparing post-immunisation and pre-immunisation periods. CONCLUSIONS The findings suggest a shift in IPD caused either by vaccine or non-vaccine serotypes between immunised and unimmunised populations of children, which could result in increased incidence of IPD caused by non-vaccine serotypes. Therefore, routine immunisation using only one vaccine with broader serotype coverage together with a higher vaccination rate could raise hopes of further decrease in IPD in the child population.
Imaging Studies in Focal Dystonias: A Systems Level Approach to Studying a Systems Level Disorder

Focal dystonias are dystonias that affect one part of the body, and are sometimes task-specific. Brain imaging and transcranial magnetic stimulation techniques have been valuable in defining the pathophysiology of dystonias in general, and are particularly amenable to studying focal dystonias. Over the past few years, several common themes have emerged in the imaging literature, and this review summarizes these findings and suggests some ways in which these distinct themes might all point to one common systems-level mechanism for dystonia. These themes include (1) the role of premotor regions in focal dystonia, (2) the role of the sensory system and sensorimotor integration in focal dystonia, (3) the role of decreased inhibition/increased excitation in focal dystonia, and (4) the role of brain imaging in evaluating and guiding treatment of focal dystonias. The data across these themes, together with the features of dystonia itself, are consistent with a hypothesis that all dystonias reflect excessive output of postural control/stabilization systems in the brain, and that the mechanisms for dystonia reflect amplification of an existing functional system, rather than recruitment of the wrong motor programs. Imaging is currently being used to test treatment effectiveness, and to visually guide treatment of dystonia, such as placement of deep brain stimulation electrodes. In the future, it is hoped that imaging may be used to individualize treatments across behavioral, pharmacologic, and surgical domains, thus optimizing both the speed and effectiveness of treatment for any given individual with focal dystonia.
A HowNet-based Feature Selection Method for Chinese Text Representation

Data dimension reduction plays an important role in the field of text representation. An effective dimension reduction method can not only reduce computation complexity, but help to improve the accuracy of text classification. This paper presents a new method of dimension reduction which is based on words semantic similarities. Being different with traditional methods which usually use the statistical information of words, natural language processing knowledge is used in our method which considers semantic information and POS information of feature terms. The experimental results show that our method is effective in dimensionality reduction of text representation and achieves a higher accuracy of text classification. The semantic similarity based method is a suitable method for text representation.
Frontiers in Computational Neuroscience an Inverse Approach for Elucidating Dendritic Function

What Feynman noted for physics is even more true for biology with its confusing zoo of phenomena, namely that a different perspective of a phenomenon can lead to novel insights. We have recently attempted to find a novel perspective on dendritic function– structure relationships (Stiefel and Sejnowski, 2007; Torben-Nielsen and Stiefel, 2009). Specifically, we are using an inverse approach where we pick a computational function and then use computer simulations to generate dendrites optimized for the chosen function. We thus go in the opposite direction of conventional studies, where the neural theorist starts with a known dendritic morphology and aims to find out the computational function: we start with the computational function and aim to find the corresponding morphology. This inverse approach can be used in two ways (Figure 2). First, we can choose a computational function of neurobiologi-cal relevance, and find the optimized dendrites for performing that function. Then, by comparing the resultant artificial dendrites to the known dendritic morphologies of real neurons, we can gain novel hypotheses about the functions of their dendrites: If dendrites of a neural type resemble the artificial, optimized, dendrites, then they will likely fulfill a similar function. We call this approach the " hypothesis generator ". Second, we can start our reasoning with a real neuron and its hypothesized computational function. We then optimize dendrites for that hypothesized function, and compare the outcome to the original neuron. If the dendrites are similar, this results provides additional support for the hypothesis that the neuron in fact performs that function. In addition, if the artificial dendrites have features which have not been determined yet in the biological system, such as distributions of conductances, these constitute predictions about these features in real neurons. We call this second approach the " function confirmation ". DenDrites Neurons possess two types of cellular appendages, axons and den-drites. While axons serve to deliver the output of their computations to other neurons via synapses, dendrites receive the synaptic inputs from other neurons. The dendrites of neurons are highly diverse, both between and within classes of neurons (Soltesz, 2005; and see Figure 1). Furthermore, the distributions of voltage sensitive conductances (Migliore and Shepherd, 2002) and synapses of different polarity (excitatory/inhibitory) and presynaptic origin are distinct between different types of neurons (Stuart et al., 2008). What is the function of this great cellular diversity? Dendrites have been shown to support a diversity of …
Coliform Bacteria for Bioremediation of Waste Hydrocarbons

Raw, domestic sewage of Kuwait City contained about 106 ml−1 colony forming units of Enterobacter hormaechei subsp. oharae (56.6%), Klebsiella spp. (36%), and Escherichia coli (7.4%), as characterized by their 16S rRNA-gene sequences. The isolated coliforms grew successfully on a mineral medium with crude oil vapor as a sole source of carbon and energy. Those strains also grew, albeit to different degrees, on individual n-alkanes with carbon chains between C9 and C36 and on the individual aromatic hydrocarbons, toluene, naphthalene, phenanthrene, and biphenyl as sole sources of carbon and energy. These results imply that coliforms, like other hydrocarbonoclastic microorganisms, oxidize hydrocarbons to the corresponding alcohols and then to aldehydes and fatty acids which are biodegraded by β-oxidation to acetyl CoA. The latter is a well-known key intermediate in cell material and energy production. E. coli cells grown in the presence of n-hexadecane (but not in its absence) exhibited typical intracellular hydrocarbon inclusions, as revealed by transmission electron microscopy. Raw sewage samples amended with crude oil, n-hexadecane, or phenanthrene lost these hydrocarbons gradually with time. Meanwhile, the numbers of total and individual coliforms, particularly Enterobacter, increased. It was concluded that coliform bacteria in domestic sewage, probably in other environmental materials too, are effective hydrocarbon-biodegrading microorganisms.
Parametric solutions to rectangular high-order Sylvester equations—Case of F arbitrary

In this paper a class of high-order rectangular Sylvester equations are considered. It is first shown that this type of Sylvester equations cover many such types of equations appeared in the literature. Then, based on Smith form reduction of polynomial matrices, a general complete parametric solution to the proposed type of Sylvester equations are proposed, which possesses a very neat explicit closed form. The primary feature of this solution is that the matrix F does not need to be in any canonical form, or may be even unknown a priori, and thus may be set undetermined and used as degrees of freedom beyond the completely free parameter matrix Z. For the nonhomogeneous case, the matrix R is also allowed to be set undetermined and used as a part of the degrees of freedom.
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
Towards formal model-based analysis and testing of Android's security mechanisms

This article reports on our experiences in applying formal methods to verify the security mechanisms of Android. We have developed a comprehensive formal specification of Android's permission model, which has been used to state and prove properties that establish expected behavior of the procedures that enforce the defined access control policy. We are also interested in providing guarantees concerning actual implementations of the mechanisms. Therefore we are following a verification approach that combines the use of idealized models on which fundamental properties are formally verified with testing of actual implementations using lightweight model-based techniques. We describe the formalized model, present security properties that have been verified using the Coq proof assistant and discuss a testing technique that relies on the use of certified algorithms.
CrowdWiFi: efficient crowdsensing of roadside WiFi networks

In this paper, we present CrowdWiFi, a novel vehicular middleware to identify and localize roadside WiFi APs that are located outside or inside buildings. Our work is motivated by the recent surge in availability of open WiFi access points (APs) that are enabling opportunistic data services to moving vehicles. Two key elements of CrowdWiFi that provide vehicles with opportunistic WiFi access include (a) an online compressive sensing component and (b) an offline crowdsourcing module. Online compressive sensing (CS) techniques are primarily used to for the coarse-grained estimation of nearby APs along the driving route; here, the received signal strength (RSS) values are recorded at runtime, and the number and locations of APs are recovered immediately based on limited RSS readings. The offline crowdsourcing mechanism assigns the online CS tasks to crowd-vehicles and aggregates answers using a bipartite graphical model. This offline crowdsourcing executes at a crowd-server that iteratively infers the reliability of each crowd-vehicle from the aggregated sensing results and refines the estimation of APs using weighted centroid processing. Extensive simulation results and real testbed experiments confirm that CrowdWiFi can successfully reduce the number of measurements needed for AP recovery, while maintaining satisfactory counting and localization accuracy. In addition, the impact of CrowdWiFi middleware on WiFi handoff and data transmission applications is examined.
NEATfields: evolution of neural fields

We have developed a novel extension of the NEAT neuroevolution method, termed NEATfields, to solve problems with large input and output spaces. NEATfields networks are layered into two-dimensional fields of identical or similar subnetworks with an arbitrary topology. The subnetworks are evolved with genetic operations similar to those used in the NEAT neuroevolution method. We show that information processing within the neural fields can be organized by providing suitable building blocks to evolution. NEATfields can solve a number of visual discrimination tasks and a newly introduced multiple pole balancing task.
CMOS LC quadrature oscillator with phase mismatch compensation circuit for UWB application

This paper presents a quadrature voltage controlled oscillator (QVCO) with phase mismatch compensation circuit implemented in 0. 18µm technology. The implemented LC-QVCO, working from 4.1GHz to 5.2GHz, targets UWB application. Using on-chip mixer, a post-compensation image band rejection of 45dB was achieved, which is an indirect measure of quadrature phase accuracy. A low phase noise of −116dBc/Hz at 1MHz offset away from the carrier frequency of 4.51GHz is demonstrated. For a power consumption of 9mW, a figure of merit (FoM) of 181dB is obtained.
Development of a simple and highly sensitive mutation screening system by enzyme mismatch cleavage with optimized conditions for standard laboratories

Efficient screening of unknown DNA variations is one of the substantive matters of molecular biology even today. Historically, SSCP and heteroduplex analysis (HA) are the most commonly used methods for detecting DNA variations everywhere in the world because of their simplicity. However, the sensitivity of these methods is not satisfactory for screening purpose. Recently, several new PCR‐based mutation screening methods have been developed, but most of them require special instruments and adjustment of conditions for each DNA sequence to attain the maximum sensitivity, eventually becoming as inconvenient as old methods. Enzyme mismatch cleavage (EMC) is potentially an ideal screening method. With high‐performance nucleases and once experimental conditions are optimized, it requires only conventional staff and conditions remain the same for each PCR product. In this study we tested four commercially available endonucleases for EMC and optimized the electrophoresis and developing conditions. We prepared 25 known DNA variations consisting of 18 single base substitutions (8 transitions and 10 transversions, including all possible sets of mismatches) and 7 small deletions or insertions. The combination of CEL nuclease, 12% PAGE and rapid silver staining can detect all types of mutations and achieved 100% sensitivity.
Profiling individuals based on email analysis and ego networks: A visualization technique

Nowadays, communication between people is mediated by technology and more specifically via Internet either by using email or social networking sites. Since any online activity generates an electronic trace, creating an automated tool to collect and analyze the communication between people can be valuable for extracting useful information about their behavioral characteristics. Combining these characteristics, with the ego network of each person within the network, additional analysis can be performed to detect the sphere of influence of the individual, identify other individuals in the network with similar behavioral characteristics and so on. In this paper, an automated tool has been designed and developed with the purpose to identify potential malevolent persons inside the organization. With this tool, we are able to analyze the communication between the employees of any given organization, build the behavioral profile of each individual, as well as their ego network.
Displacement structure and maximum entropy

The study of matrices with a displacement structure is mainly concerned with recursions for the so-called generator matrices. The recursion usually involves free parameters, which can be chosen in several ways so as to simplify the resulting algorithm. In this correspondence we present a choice for the parameters that is motivated by a maximum-entropy formulation, This choice further motivates the introduction of the so-called generalized reflection coefficients which are, in general, different from the better known Schur coefficients.
Migration of monocytes across endothelium and passage through extracellular matrix involve separate molecular domains of PECAM-1

During the inflammatory response, the adhesion molecule PECAM plays a crucial role in transendothelial migration, the passage of leukocytes across endothelium. We report here an additional role for PECAM in the subsequent migration of monocytes through the subendothelial extracellular matrix. PECAM has six immunoglobulin (Ig) superfamily domains. Monoclonal antibodies whose epitopes map to domains 1 and/or 2 selectively block monocyte migration through the endothelial junction, whereas those that map to domain 6 block only the migration through the extracellular matrix, trapping the monocyte between the endothelium and its basal lamina. Therefore, transendothelial migration (diapedesis) and passage through extracellular matrix (interstitial migration) are distinct and separable phases of monocyte emigration. Furthermore, distinct and separate Ig domains of PECAM are involved in mediating these two steps.
High-Yield Soluble Expression and Simple Purification of the Antimicrobial Peptide OG2 Using the Intein System in Escherichia coli

OG2 is a modified antimicrobial peptide, that is, derived from the frog peptide Palustrin-OG1. It has high antimicrobial activity and low cytotoxicity, and it is therefore promising as a therapeutic agent. Both prokaryotic (Escherichia coli) and eukaryotic (Pichia pastoris) production host systems were used to produce OG2 in our previous study; however, it was difficult to achieve high expression yields and efficient purification. In this study, we achieved high-yield OG2 expression using the intein fusion system. The optimized OG2 gene was cloned into the pTWIN1 vector to generate pTWIN-OG2-intein2 (C-terminal fusion vector) and pTWIN-intein1-OG2 (N-terminal fusion vector). Nearly 70% of the expressed OG2-intein2 was soluble after the IPTG concentration and induction temperature were decreased, whereas only 42% of the expressed of intein1-OG2 was soluble. Up to 75 mg of OG2-intein2 was obtained from a 1 l culture, and 85% of the protein was cleaved by 100 mM DTT. Intein1-OG2 was less amenable to cleavage due to the inhibition of cleavage by the N-terminal amino acid of OG2. The purified OG2 exhibited strong antimicrobial activity against E. coli K88. The intein system is the best currently available system for the cost-effective production of OG2.
Automatic Verification of Security in Payment Protocols for Electronic Commerce

In order to make secure transactions over computer networks, various cryptographic protocols have been proposed but, because of subtleties involved in their design, many of them have been shown to have flaws, even a long time after their publication. For this reason, several automatic verification methods for analyzing these protocols have been devised. The aim of this paper is to present a methodology for verifying security requirements of electronic payment protocols by means of NuSMV, a symbolic model checker. Our work principally focus on formal representation of security requirements. Indeed, we propose an extension of the correspondence property, so far used only for authentication, to other requirements as confidentiality and integrity. These are the basic security requirements of payment protocols for electronic commerce. We illustrate as case study a variant of the SET protocol proposed by Lu & Smolka. This variant has been formally verified by Ly & Smolka and considered secure. Conversely, we have discovered two attacks that allow a dishonest user to purchase a good debiting the amount to another user.
Crossbreed Thresholding Text extraction Procedure for Images using DWT Domain and SVM Classifier

paper proposes a novel crossbreed technique to vigorously extract the texts in images based on Discreet Wavelet Transform (DWT) and Support Vector Machine (SVM). Images on which experimentation has been done are taken from various book covers, newspapers, magazines and commercial products. Database of proposed technique includes 25 images. In addition to that the proposed technique is robust to language selection of the text that is embedded in an image. Experimental database includes images that contain English, Punjabi as well as Hindi font. The proposed technique can be used in the applications such as; keyword- based searching, document retrieving, database collection in an organized manner etc. The projected work is estimated using ICDAR 2013 competition metrics specification and the performance is good as well as results are promising for 3 languages as well.
Preliminary design of a multimodality molecular imaging system

We have designed a multimodality molecular imaging system for small animals. The aim is to develop a system which can perform functional imaging, structural imaging, and molecular imaging. Our multimodality system contains five imaging modalities which are Bioluminescence Tomography (BLT), Fluorescence Molecular Tomography (FMT), Cerenkov Luminescence Tomography (CLT), X-ray Computed Tomography (CT), and Positron Emission Tomography (PET). We have designed both the hardware structure and software to make sure multimodality imaging can be achieved. Here we will report the overall design and work flow of the system.
B2Sim:: a fast micro-architecture simulator based on basic block characterization

State-of-the-art architectural simulators support cycle accurate pipeline execution of application programs. However, it takes days and weeks to complete the simulation of even a moderate- size program. During the execution of a program, program behavior does not change randomly but changes over time in a predictable/periodic manner. This behavior provides the opportunity to limit the use of a pipeline simulator. More precisely, this paper presents a hybrid simulation engine, named B2Sim for (cycle-characterized) Basic Block based Simulator, where a fast cache simulator e.g., sim-cache and a slow pipeline simulator e.g., sim-outorder are employed together. B2Sim reduces the runtime of architectural simulation engines by making use of the instruction behavior within executed basic blocks. We have integrated B2Sim into SimpleScalar and have achieved on average a factor of 3.3 times speedup on the SPEC2000 benchmark and Media-bench programs compared to conventional pipeline simulator while maintaining the accuracy of the simulation results with less than 1% CPI error on average.