Miracle-dz/UniFAR-FTUs huggingface dataset:
TraK and TraB Are Conserved Outer Membrane Proteins of the Neisseria gonorrhoeae Type IV Secretion System and Are Expressed at Low Levels in Wild-Type Cells

ABSTRACT Neisseria gonorrhoeae uses a type IV secretion system (T4SS) to secrete chromosomal DNA into the medium, and this DNA is effective in transforming other gonococci via natural transformation. In addition, the T4SS is important in the initial stages of biofilm development and mediates intracellular iron uptake in the absence of TonB. To better understand the mechanism of type IV secretion in N. gonorrhoeae, we examined the expression levels and localization of two predicted T4SS outer membrane proteins, TraK and TraB, in the wild-type strain as well as in overexpression strains and in a strain lacking all of the T4SS proteins. Despite very low sequence similarity to known homologues, TraB (VirB10 homolog) and TraK (VirB9 homolog) localized similarly to related proteins in other systems. Additionally, we found that TraV (a VirB7 homolog) interacts with TraK, as in other T4SSs. However, unlike in other systems, neither TraK nor TraB required the presence of other T4SS components for proper localization. Unlike other gonococcal T4SS proteins we have investigated, protein levels of the outer membrane proteins TraK and TraB were extremely low in wild-type cells and were undetectable by Western blotting unless overexpressed or tagged with a FLAG3 triple-epitope tag. Localization of TraK-FLAG3 in otherwise wild-type cells using immunogold electron microscopy of thin sections revealed a single gold particle on some cells. These results suggest that the gonococcal T4SS may be present in single copy per cell and that small amounts of T4SS proteins TraK and TraB are sufficient for DNA secretion.
Concordance study between Miniplex assays and a commercial STR typing kit.

TABLE 1—Summary of 15 discordant STR profiling results observed in this study between the Identifiler kit and our Miniplex assays for 12 different African American (AA) and 3 Hispanic (H) samples. PowerPlex 16 (PP16) results all agree with the Identifiler results for these 15 samples. Sigle allele shifts of 1 repeat in the D13S317 heterozygotes are likely due to a 4 base pair deletion in the flanking region outside of the Miniplex primer binding site (see Ref 2). Allele dropout at D5S818 (see Ref 2), D13S317, and vWA (see Ref 3) are likely due to primer binding site mutations at specific alleles.
Development and evaluation of a recombinant DNA vaccine candidate expressing porcine circovirus 2 structural protein 1

Silva Júnior A. , Castro L.A. , Chiarelli Neto O. , Silva F.M. F. , Vidigal P.M.P., Moraes M.P. & Almeida M.R. 2009. Development and evaluation of a recombinant DNA vaccine candidate expressing porcine circovirus 2 structural protein. Pesquisa Veterinária Brasileira 29(1):76-82. Laboratório de Infectologia Molecular Animal, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Av. PH Rolfs s/n, Campus Universitário, Viçosa, MG 36570-000, Brazil. E-mail: marcia@ufv.br Porcine circovirus 2 (PCV2) is generally associated with the porcine circovirosis syndrome, which is considered an important disease of swine and has potentially serious economic impact on the swine industry worldwide. This article describes the construction of a recombinant plasmid expressing the PCV2 structural protein and the evaluation of cellular and humoral immune responses produced by this recombinant vaccine in BALB/c mice. The vaccine candidate was obtained and analyzed in vivo, in an effort to determine the ability to induce a specific immune response in mice. DNA was extracted from a Brazilian PCV2 isolate and the gene coding for Cap protein was amplified by PCR and inserted into an expression plasmid. Groups of BALB/c mice were inoculated intra-muscularly and intradermally in a 15-day interval, with 100 μg and 50 μg of the vaccine construct, respectively. Another group was inoculated intramuscularly with 100 μg of empty plasmid, corresponding to the control group. Seroconversion and cellular response in BALB/c mice were compared and used for vaccine evaluation. Seroconversion was analyzed by ELISA. After a series of 3 immunizations the spleen cells of the immunized animals were used to perform lymphocyte proliferation assays. Seroconversion to PCV2 was detected by ELISA in the animals inoculated with the vaccine construct when compared with control groups. Lymphocyte proliferation assays showed a stronger cell proliferation in the inoculated animals compared with the control group. Thus, the vaccine candidate construct demonstrated to be able to induce both humoral and cellular responses in inoculated mice.
Comparative virulence of porcine Haemophilus bacteria.

The virulence of strains of Haemophilus pleuropneumoniae serotype 1, 2, 3, 7 and strains of the "minor-group" and Haemophilus parasuis were compared by inoculating specific pathogen-free pigs into the lower airways with specified doses of bacteria. Haemophilus pleuropneumoniae, strain W, serotype 1, given in 1 X 10(8) colony-forming units, produced a lethal acute pleuropneumonia in four pigs. Nonlethal localized pulmonary necrosis was induced in four groups of two pigs given 1 X 10(7), 1 X 10(6), 1 X 10(5) and 1 X 10(4) respectively of the same strain. Two groups of four pigs developed chronic lesions when inoculated with 1 X 10(7) colony-forming units of H. pleuropneumoniae, strain Shope 4074, serotype 1 and 1 X 10(7) colony-forming units of H. pleuropneumoniae, strain WF83, serotype 7, respectively. Of 20 pigs given 1 X 10(8) colony-forming units of strain 1536, serotype 2, two died of acute pleuropneumonia and 18 had lesions of pulmonary necrosis or abscessation and pleuritis. A dose of 4 X 10(9) colony-forming units of strain BC181, serotype 3, induced pulmonary necrosis similar to the lesions in pigs given 10(7) colony-forming units or less of strain W, serotype 1, suggesting that the serotype 3 strain is less virulent. No clinical signs, but focal areas of pulmonary fibrosis and pleural adhesions were induced in four pigs inoculated with 4 X 10(9) colony-forming units of the "minor-group" strain 7ATS. Similarly, four pigs inoculated with "minor-group" strain 33PN did not show clinical signs, but had focal necrotic and fibrotic pulmonary lesions and pleural adhesions. (ABSTRACT TRUNCATED AT 250 WORDS)
Thai sentiment terms construction using the Hourglass of Emotions

Most of the current sentiment analysis techniques classifies emotions into two classes which are positive and negative. Some works classify them as positive, negative and objective (neutral). In fact, there are many kinds of emotions in human mind. Recently, psychological viewpoints have influenced most of the works in sentiment analysis. This psychology perspective was adopted to classify human emotions into a wider range, and in a more accurate manner. This paper reviews the adopted computational representation of emotions the so-called Hourglass of Emotion. This paper also proposes a construction of Thai sentiment resource based on such representation for Thai sentiment term tagging. A preliminary sentiment text tagging result shows that the resource as an ontology can be successfully used to tag sentiment text in Thai children stories.
Classifying breast cancer microscopic images using fractal dimension and ensemble classifier

To improve the performance of the computer-aided systems for breast cancer diagnosis, the ensemble classifier is proposed for classifying the histological structures in the breast cancer microscopic images into three region types: positive cancer cells, negative cancer cells and non-cancer cell (stromal cells and lymphocyte cells) image. The bagging and boosting ensemble techniques are used with the decision tree (DT) learner. They are also compared with the single classifier, DT. The feature used as an input of classifiers is the fractal dimension (FD) based 12 color channels. It is computed from the image datasets, which are manually prepared in small cropped image with 3 window sizes including 128×128 pixels, 192×192 pixels and 256×256 pixels. The results show that the boosting ensemble classifier gives the best accuracy about 80% from window size of 256, although it is the lowest when using the single DT as classifier. The results indicated that the ensemble method is capable of improving the accuracy in the classification compared to the single classifier. The classification model using FD and the ensemble classifier would be applied to develop the computer-aided systems for breast cancer diagnosis in the future.
Prediction of the outcome of orthodontic treatment of Class III malocclusion.

Sir In the latest issue of the European Journal of Orthodontics the readers can find a systematic review article by Fudalej et al. (2011) on prediction models for the outcomes of orthodontic treatment of Class III malocclusions. We would like to express several concerns regarding this article. First of all, in the review that Fudalej and associates have conducted …
Typical impulses in power electronics and their EMI characteristics

Electromagnetic interference (EMI) characteristics are one of the most important aspects of a power converter. For purpose of topology evaluation and EMI filter design, the spectrum of the current and voltage impulses, which are sources of the conduction EMI, should be analysed. To calculate the spectrum of an impulse signal, Fourier analysis is commonly used. But with this method it is not easy to obtain simple and clear symbolic results for the syntheses of EMI filters. Using a graphical method, simple and clear results can be obtained which describe the upper limit of the spectrum envelope. Therefore, the typical current and voltage impulses in power electronics are analysed by using this graphic approach. Equations, which describe their spectrum envelope upper limit, are derived. Using these results, the EMI characteristics of the common topologies can be compared easily. Furthermore, the method enables an efficient EMI filter design.
Supplemental – Semantic Word Clusters Using Signed Spectral Clustering 1 Gold Standard

For GloVe we used pretrained 200 dimensional vector embeddings1 trained using Wikipedia 2014 + Gigaword 5 (6B tokens). Eigenwords were trained on English Gigaword with no lowercasing or cleaning. Finally, we used 50 dimensional vector representations from Huang et al. (2012), which used the April 2010 snapshot of the Wikipedia corpus (Lin, 1998; Shaoul, 2010), with a total of about 2 million articles and 990 million tokens.
Onion graphs: aesthetics and layout

In many engineering disciplines it is interesting to use diagrams which combine a graph notation with an onion notation. It is observed that such onion graphs lend themselves easily to some kinds of sophisticated tool support, but also that the need for tool support is significantly larger than for ordinary graphs. Most notably there is a need for supporting automatic layout to a much larger extent than for traditional graphs, particularly of the incremental kind. Some aesthetics and algorithms are outlined for the layout of onion graphs. <<ETX>>
Identification of Thr29 as a Critical Phosphorylation Site That Activates the Human Proton Channel Hvcn1 in Leukocytes*

Voltage-gated proton channels and NADPH oxidase function cooperatively in phagocytes during the respiratory burst, when reactive oxygen species are produced to kill microbial invaders. Agents that activate NADPH oxidase also enhance proton channel gating profoundly, facilitating its roles in charge compensation and pHi regulation. The “enhanced gating mode” appears to reflect protein kinase C (PKC) phosphorylation. Here we examine two candidates for PKC-δ phosphorylation sites in the human voltage-gated proton channel, HV1 (Hvcn1), Thr29 and Ser97, both in the intracellular N terminus. Channel phosphorylation was reduced in single mutants S97A or T29A, and further in the double mutant T29A/S97A, by an in vitro kinase assay with PKC-δ. Enhanced gating was evaluated by expressing wild-type (WT) or mutant HV1 channels in LK35.2 cells, a B cell hybridoma. Stimulation by phorbol myristate acetate enhanced WT channel gating, and this effect was reversed by treatment with the PKC inhibitor GF109203X. The single mutant T29A or double mutant T29A/S97A failed to respond to phorbol myristate acetate or GF109203X. In contrast, the S97A mutant responded like cells transfected with WT HV1. We conclude that under these conditions, direct phosphorylation of the proton channel molecule at Thr29 is primarily responsible for the enhancement of proton channel gating. This phosphorylation is crucial to activation of the proton conductance during the respiratory burst in phagocytes.
P1B-4 Characterization of a HIFU Field at High Intensity

Accurate quantification of HIFU fields has been hampered by the inability of traditional hydrophones to survive the high pressures encountered. We present a set of data at high intensities taken with a hydrophone capable of surviving this environment, which included 5 MPa maximum rarefactional pressure, pulse-average-spatial-peak intensity of 3760 W/cm2, and a total power of 101 Watts. Comparisons are made to predictions of a KZK model and an independent measurement of total power via radiation force balance, and are found to be favorable. Beamplots show more than 50% reduction in the -3 dB beam area measured at low power, in agreement with KZK predictions.
Geographically Varying Effects of Weather on Tobacco Consumption: Implications for Health Marketing Initiatives

Weather and its fluctuations have been found to influence the consumption of negative hedonic goods. However, such findings are of limited use to health marketers who cannot control the weather, and hence, its effects. The current research utilizes data obtained at the zip-code level to study geographical variations in the effect of weather on tobacco consumption across the entire continental United States. The results allow health marketers to identify areas that will be most responsive to marketing efforts aimed at curtailing negative hedonic consumption and thus implement more effective, region-specific initiatives.
Effects of intraruminal and intra-abomasal additions of cod-liver oil on milk fat production in the cow.

Four Holstein cows were used in a modified switchback design to show the effect on milk-fat synthesis of (1) control diet, (2) 29.23, 3.92, 6.48, 30.65, 3.44 control diet plus 255 g/day of cod-liver oil in rumen, and (3) control diet plus 225 g/day of cod-liver oil in abomasum. Mean milk yield (kg/day), fat production (kg/day), and milk-fat percentage were (1) 21.87, . 79, 3.63; (2) 22.99, . 70, 3.05; and (3) 23.02, . 75, 3.28. Compared to the post-treatment control period, only one cow decreased in milk-fat percentage on 3 while all cows decreased in milk-fat percentage on 2. Proportions of carbons 16:0, 16:1, 18:0, 18:1, 18:2, and trans-monoene fatty acids of the milk fat were (1) 30.31, 3.24, 10.15, 30.48, 2.59, 7.91; (2) 26.37; and (3) 26.30, 3.72, 10.56, 30.10, 2.96, 9.84. Proportions of rumen volatile fatty acids were not significantly affected by treatment. Proportions of carbons 16:0, 18:0, 18:1, 18:2, and 18:3 fatty acids in the rumen ingesta were (1) 17.28, 47.92, 21.71, 10.59, 2.46; (2) 19.55, 25.90, 37.21, 11.97, 5.39; and (3) 16.90, 50.80, 19.66, 9.11, and 3.23. Fatty acid composition of blood-serum phospholipids were affected by treatment.
Protein-specific manipulation of ejaculate composition in response to female mating status in Drosophila melanogaster

Female promiscuity can generate postcopulatory competition among males, but it also provides the opportunity for exploitation of rival male ejaculates. For example, in many insect species, male seminal fluid proteins (Sfps) transferred in a female's first mating stimulate increased fecundity and decreased receptivity to remating. Subsequent mates of females could potentially take advantage of the effects of the first male's Sfps and strategically reduce investment in their own ejaculate. We compared postmating responses (fecundity and sexual receptivity) of Drosophila melanogaster females after their first (virgin) matings (V), to the responses of females remating (M) 24 h after their first mating. The results show that M matings fail to boost fecundity and, thus, males are unlikely to gain fitness from transferring Sfps whose sole function—in V matings—is fecundity-stimulation. However, males can protect their likelihood of paternity in M matings through the transfer of receptivity-inhibiting Sfps. The levels of a fecundity-stimulating Sfp (ovulin) were significantly lower in M females relative to V females, at the same time point shortly after the end of mating. In contrast, the levels of a key receptivity-inhibiting Sfp (sex peptide) were the same in M and V females. These results support the hypothesis that males can adaptively tailor the composition of proteins in the ejaculate, allowing a male to take advantage of the fecundity-stimulating effects of the previous male's ovulin, yet maintaining investment in sex peptide. Furthermore, our results demonstrate sophisticated protein-specific ejaculate manipulation.
Image-guided endoscopic ventriculostomy with a new frameless armless neuronavigation system.

OBJECTIVE Complications resulting from imprecise placement of the ventriculoscope and reduced visibility through the endoscopic lens under certain conditions during third ventriculostomy have been reported in the literature. The following is a report of our first experience with image-guided endoscopic ventriculostomy. MATERIALS AND METHODS Between September 1996 and October 1997, 11 patients diagnosed with aqueduct stenosis were found to be eligible for image-guided neuroendoscopy. The image-guided system (BrainLab, Heimstetten, Germany) links a freehand probe, tracked by a passive-marker sensor system, to a virtual computer image space. A 4-mm rigid ventriculoscope (Storz Instruments GMBH, Tuttlingen, Germany) was used. RESULTS Eight patients improved clinically directly after surgery, two patients stabilized, and one patient improved only after insertion of an additional ventriculo-peritoneal shunt. The computer- calculated registration accuracy ranged from 1. 1 to 3.1 mm (median 1.4 mm) using 3-mm computed tomographic slices. The accuracy of the tool tip calibration for the endoscope was in the range of 0.35-0.9 mm (mean = 0.47 +/- 0.21). The described technique provided maximal flexibility for the surgeon and helped in performing a safe and accurate endoscopical procedure. CONCLUSIONS Although not all cases of ventriculostomy require additional image guidance, we found the technique to be helpful in patients with atypical or large ventricles, in cases where orientation became difficult owing to bloody or blurry cerebrospinal fluid, and in patients with small foramina of Monroe, where the entrance angle of the endoscope needs precise definition for an atraumatic procedure to be performed.
Conventional NMA as a better standard for evaluating elastic network models

Normal mode analysis (NMA) is an important tool for studying protein dynamics. Because of the complexity of conventional NMA that uses an all‐atom model and a semi‐empirical force field, many simplified NMA models have been developed, some of which are known as elastic network models. The quality of these simplified NMA models was assessed mostly by evaluating their predictions against experimental B‐factors, and rarely by comparing them with the original NMA. In this work, we take the effort to create a publicly accessible dataset of proteins with their minimized structures, NMA modes, and mean‐square fluctuations. Then, for the first time, we evaluate the quality of individual normal modes of several widely used elastic network models by comparing them with the conventional NMA. Our results demonstrate that the conventional NMA presents a better and more complete evaluation measure of the quality of elastic network models. This realization should be very helpful in improving current or designing new, higher quality elastic network models. Moreover, using the conventional NMA as the standard of evaluation, a number of interesting and significant insights into the elastic network models are gained. Proteins 2015; 83:259–267. © 2014 Wiley Periodicals, Inc.
Requirements-Based Matching Approach to Configurate Cyber-Physical Systems for SMEs

This paper addresses the challenge of modelling individual cyber-physical systems (CPS) for small and medium-sized enterprises (SMEs) in manufacturing industries. CPS are key technology building blocks for the implementation of Industrie 4.0. Especially for SMEs the increase of production efficiency and reduction of manufacturing costs through CPS offer potential to maintain their competitiveness, and innovation capacity. Although SMEs perceive the potential of CPS, they often lack financial and human resources to acquire the necessary CPS-competencies as well as an overview of all the currently available technological solutions. To overcome this issue a matching platform will offer SMEs support in finding suitable CPS-components by letting them express their functional and technical requirements. The matching logic is based on a set of morphologies that encompasses the functional and requirement spectrum of CPS-components. The matching algorith analyses the input for congruence of requirements and available technologies and suggests suitable technology combinations. This paper describes the methodology of the matching platform, and introduces the research work to define and to develop the technology morphologies. The presented results facilitate the selection and configuration of CPS for SMEs.
An Evaluation of the Low-Carbon Effects of Urban Rail Based on Mode Shifts

Urban rail is widely considered to be a form of low-carbon green transportation, but there is a lack of specific quantitative research to support this. By comparing the mode, distance, and corresponding energy consumption of residents before and after the opening of rail transit, this paper establishes a carbon reduction method for rail transit. A measurement model takes the passenger carbon emissions before the line is opened as the baseline and compares them with the standard after the opening, determining the carbon emissions reduction. The model requires a combination of a large amount of research data, transit smart card data, and GIS network measurement tools as measured data and parameters. The model is then applied to rail transit lines that have opened in Beijing in recent years. The emissions reductions of four different routes are estimated and the carbon emissions reduction effect of rail transit is evaluated.
Measuring innovative intensity

Beschrijving van gangbare indicatoren voor de innovatie-intensiteit van een MKB-bedrijf. Ook komt de vraag aan de orde of deze indicatoren tot een samenvattende score gecombineerd kunnen worden. Allereerst wordt een kort overzicht gegeven van eerdere studies naar het meten van innovatie-intensiteit. Vervolgens wordt ingegaan op de resultaten van een empirisch onderzoek.
A New Dynamic Voltage-Var Compensator Based on SVPWM

In this paper, a new dynamic voltage-var compensator is introduced, compared to the traditional SVC, the new voltage source of continuous two-way adjustable SVC has significant advantages. This paper has introduced the fundamental of the SVPWM; SVPWM control technology is an optimized PWM control technology, compared with the traditional PWM technology, SVPWM with a high utilizationrate, less harmonic control simple, easy-to-digital realization of the advantages. The simulink is used to simulation and analysis. The simulation results show this SVC has its own advantage. It can regulate the voltage smoothly and continually.