Miracle-dz/UniFAR-FTUs huggingface dataset:
Validation of High Resolution Melting Analysis (HRM) of the Amplified ITS2 Region for the Detection and Identification of Yeasts from Clinical Samples: Comparison with Culture and MALDI-TOF Based Identification

Aim Candida species are known as opportunistic pathogens, and a possible cause of invasive infections. Because of their species-specific antimycotic resistance patterns, reliable techniques for their detection, quantification and identification are needed. We validated a DNA amplification method for direct detection of Candida spp. from clinical samples, namely the ITS2-High Resolution Melting Analysis (direct method), by comparing it with a culture and MALDI-TOF Mass Spectrometry based method (indirect method) to establish the presence of Candida species in three different types of clinical samples. Materials and Methods A total of 347 clinical samples, i.e. throat swabs, rectal swabs and vaginal swabs, were collected from the gynaecology/obstetrics, intensive care and haematology wards at the Ghent University Hospital, Belgium. For the direct method, ITS2-HRM was preceded by NucliSENS easyMAG DNA extraction, directly on the clinical samples. For the indirect method, clinical samples were cultured on Candida ID and individual colonies were identified by MALDI-TOF. Results For 83.9% of the samples there was complete concordance between both techniques, i.e. the same Candida species were detected in 31.1% of the samples or no Candida species were detected in 52.8% of the samples. In 16.1% of the clinical samples, discrepant results were obtained, of which only 6.01% were considered as major discrepancies. Discrepancies occurred mostly when overall numbers of Candida cells in the samples were low and/or when multiple species were present in the sample. Discussion Most of the discrepancies could be decided in the advantage of the direct method. This is due to samples in which no yeast could be cultured whereas low amounts could be detected by the direct method and to samples in which high quantities of Candida robusta according to ITS2-HRM were missed by culture on Candida ID agar. It remains to be decided whether the diagnostic advantages of the direct method compensate for its disadvantages.
Effectiveness of yearly, register based screening for chlamydia in the Netherlands: controlled trial with randomised stepped wedge implementation

Objective To evaluate the effectiveness of register based, yearly chlamydia screening. Design Controlled trial with randomised stepped wedge implementation in three blocks. Setting Three regions of the Netherlands: Amsterdam, Rotterdam, and South Limburg. Participants 317 304 women and men aged 16-29 years listed on municipal registers at start of trial. Intervention From March 2008 to February 2011, the Chlamydia Screening Implementation programme offered yearly chlamydia screening tests. Postal invitations asked people to use an internet site to request a kit for self collection of samples, which would then be sent to regional laboratories for testing. Treatment and partner notification were done by the general practitioner or at a sexually transmitted infection clinic. Main outcome measures Primary outcomes were the percentage of chlamydia tests positive (positivity), percentage of invitees returning a specimen (uptake), and estimated chlamydia prevalence. Secondary outcomes were positivity according to sex, age, region, and sociodemographic factors; adherence to screening invitations; and incidence of self reported pelvic inflammatory disease. Results The participation rate was 16.1% (43 358/269 273) after the first invitation, 10.8% after the second, and 9.5% after the third, compared with 13.0% (6223/48 031) in the control block invited at the end of round two of the intervention. Chlamydia positivity in the intervention blocks at the first invitation was the same as in the control block (4.3%) and 0.2% lower at the third invitation (odds ratio 0.96 (95% confidence interval 0.83 to 1.10)). No substantial decreases in positivity were seen after three screening rounds in any region or sociodemographic group. Among the people who participated three times (2.8% of all invitees), positivity fell from 5.9% to 2.9% (odds ratio 0.49 (0.47 to 0.50)). Conclusions There was no statistical evidence of an impact on chlamydia positivity rates or estimated population prevalence from the Chlamydia Screening Implementation programme after three years at the participation levels obtained. The current evidence does not support a national roll out of this register based chlamydia screening programme. Trial registration NTR 3071 (Netherlands Trial Register, www.trialregister.nl).
Vav1 and Vav3 Have Critical but Redundant Roles in Mediating Platelet Activation by Collagen*

Vav family proteins are guanine nucleotide exchange factors for the Rho/Rac family of small GTP-binding proteins. In addition, they have domains that mediate protein-protein interactions, including one Src homology 2 (SH2) and two Src homology 3 (SH3) domains. Vav1, Vav2, and Vav3 play a crucial role in the regulation of phospholipase Cγ (PLCγ) isoforms by immuno-tyrosine-based activation motif (ITAM)-coupled receptors, including the T- and B-cell antigen receptors. We have reported in platelets, however, that Vav1 and Vav2 are not required for activation of PLCγ2 in response to stimulation of the ITAM-coupled collagen receptor glycoprotein VI (GPVI). Here we report that Vav3 is tyrosinephosphorylated upon activation of GPVI but that Vav3-deficient platelets also exhibit a normal response upon activation of the ITAM receptor. In sharp contrast, platelets deficient in both Vav1 and Vav3 show a marked inhibition of aggregation and spreading upon activation of GPVI, which is associated with a reduction in tyrosine phosphorylation of PLCγ2. The phenotype of Vav1/2/3 triple-deficient platelets is similar to that of Vav1/3 double-deficient cells. These results demonstrate that Vav3 and Vav1 play crucial but redundant roles in the activation of PLCγ2 by GPVI. This is the first time that absolute redundancy between two protein isoforms has been observed with respect to the regulation of PLCγ2 in platelets.
Phosphorylation of Retinoblastoma-Related Protein by the Cyclin D/Cyclin-Dependent Kinase Complex Is Activated at the G1/S-Phase Transition in Tobacco Online version contains Web-only data. Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.0025

In mammals, D-type cyclin-associated kinases mainly regulate the G1/S transition by phosphorylating the retinoblastoma (Rb) protein. We previously demonstrated that in tobacco, cyclin D (Nicta; CycD3;3) is complexed with the PSTAIRE-containing cyclin-dependent kinase (CDKA) from tobacco. Here, we show that Nicta; CycD3;3–associated kinases phosphorylate both the tobacco Rb-related protein (NtRb1) and histone H1. Although NtRb1 kinase activity was detected only during the middle G1- to early S-phase, histone H1 kinase activity was observed as two peaks in G1- to S-phase and G2/M- to M-phase. Importantly, we show that the proportion of cells in the G1-phase was reduced in transgenic Bright Yellow-2 cells overexpressing Nicta; CycD3;3-GFP. Mutational analyses revealed that phosphorylation of Thr-191 in Nicta; CycD3;3 possibly is required for both full kinase activity and localization predominantly to the nucleus. These data suggest that Nicta; CycD3;3 acts as a rate-limiting regulator in the G1/S transition by forming active complexes with CDKA or its related kinases to phosphorylate Rb-related protein and potentially plays a novel role during G2/M and mitosis.
Unsupervised learning for long-term autonomy

This thesis investigates methods to enable a robot to build and maintain an environment model in an automatic manner. Such capabilities are especially important in long-term autonomy, where robots operate for extended periods of time without human intervention. In such scenarios we can no longer assume that the environment and the models will remain static. Rather changes are expected and the robot needs to adapt to the new, unseen, circumstances automatically. The approach described in this thesis is based on clustering the robot’s sensing information. This provides a compact representation of the data which can be updated as more information becomes available. The work builds on affinity propagation (Frey and Dueck, 2007), a recent clustering method which obtains high quality clusters while only requiring similarities between pairs of points, and importantly, selecting the number of clusters automatically. This is essential for real autonomy as we typically do not know “a priori” how many clusters best represent the data. The contributions of this thesis are three fold. First, a self-supervised method is presented that automatically builds a visual appearance model of the environment with traversability information of objects within the environment. The model allows the detection of obstacles in new observations for safe navigation. Improvements over existing large scale affinity propagation extensions are made with meta-point affinity propagation, reducing computational time and improving robustness to noise. Experiments on indoor and outdoor data demonstrate the quality of the model as well as the ability to recognise obstacles. The usefulness in long-term autonomy is demonstrated on outdoor data captured months apart. Second, an extension of affinity propagation capable of clustering multiple data sources automatically is described. The method only requires information on a per sensor basis, which is automatically combined into a single clustering solution. This is of particular interest in robotics, as robots generally obtain data from different sensors. Experiments on indoor and outdoor RGB-D data demonstrate the advantage of combining multiple sensor modalities and the quality obtained by the proposed method in tasks such as segmentation and clustering. Third, joint clustering and anomaly detection is formulated as a generic integer program to which two optimisation methods are proposed. The formulation
Analyzing heterogeneous system architectures by means of cost functions: A comparative study for basic operations

Optimum partitioning plays a crucial role in the implementation of systems on heterogeneous target architectures. Typical target architectures for such systems include FPGAs, semi-custom or physically optimized ASICs as well as programmable digital signal or general purpose processors. The goal was to provide an estimation for implementation specific parameters like throughput rate, power dissipation and required silicon area by means of cost functions. Considering normalization we provide implementation parameters of selected basic operations like linear and nonlinear filtering, exemplary arithmetic operation and simple matching operations which all are required in the digital video processing domain. These operations were optimized for each architecture block. We show quantitatively that the cost ratio between different architecture blocks highly depends on the operation to be performed. This information is essential in order to find the optimum partitioning for implementing a system.
Faster Cognitive and Functional Decline in Dysexecutive versus Amnestic Alzheimer's Subgroups: A Longitudinal Analysis of the National Alzheimer's Coordinating Center (NACC) Database

Objective To compare the rate of cognitive and functional decline in dysexecutive, typical and amnestic subgroups of Alzheimer’s disease. Methods 943 participants from the National Alzheimer’s Coordinating Center (NACC) database who had a diagnosis of probable AD were followed for a mean of 2.3 years. A dysexecutive subgroup (n = 165) was defined as having executive performance >1.5 SD worse than memory performance, an amnestic subgroup (n = 157) was defined as having memory performance >1.5 SD worse than executive performance and a typical subgroup (n = 621) was defined as having a difference in executive and memory performance of <1.5 SD. Generalized estimating equations (GEE) were used to model decline on the Folstein Mini Mental Status Exam (MMSE), rise on the Clinical Dementia Rating (CDR) sum of boxes and rise on the total Functional Assessment Questionnaire (FAQ). Results Compared with the amnestic subgroup, the dysexecutive subgroup declined 2.2X faster on the Folstein MMSE (p<.001), rose 42% faster on the CDR sum of boxes (p = .03) and rose 33% faster on the total FAQ (p = .01). Rate of change for the typical subgroup fell between that of the amnestic and dysexecutive subgroups for the MMSE, CDR sum of boxes and total FAQ. Among a subset of participants (n = 129) who underwent autopsy, the dysexecutive, amnestic and typical subgroups did not differ in odds of having an AD pathologic diagnosis, suggesting that variation in non-AD pathologies across subtypes did not lead to the observed differences. Conclusions A dysexecutive subgroup of AD has a unique disease course in addition to cognitive phenotype.
Antwort auf den Kommentar von Link und Lüdecke zu "On the Meaning of Feedback Parameter, Transient Climate Response, and the Greenhouse Effect: Basic Considerations and the Discussion of Uncertainties"

Da mittlerweile verschiedene Versionen des zitierten Kommentars von Link und Ludecke existieren, haben wir uns entschlossen, zunachst nur auf die erste Version dieses Kommentars zu antworten, die am 15. Dezember 2010 auf der EIKE-Webseite erschien. Zwischenzeitlich existierte auf der Webseite des Autors Link eine dritte Version, die am 16. Dezember 2010 verfugbar war, nun aber wiederum durch eine andere Version ersetzt wurde. Hinzu kommt noch, das eine weitere Version auf der EIKE-Webseite existiert, die als Version 14 bezeichnet wird. Da dieses vorerst die jungste Version zu sein scheint, werden wir kurz darauf eingehen. Wir uberlassen es dem Leser, dieses merkwurdige Verhalten der Autoren Link und Ludecke zu wurdigen.
Implications for a Wireless, External Device System to Study Electrocorticography

Implantable neuronal interfaces to the brain are an important keystone for future medical applications. However, entering this field of research is difficult since such an implant requires components from many different areas of technology. Since the complete avoidance of wires is important due to the risk of infections and other long-term problems, means for wirelessly transmitting data and energy are a necessity which adds to the requirements. In recent literature, many high-tech components for such implants are presented with remarkable properties. However, these components are typically not freely available for such a system. Every group needs to re-develop their own solution. This raises the question if it is possible to create a reusable design for an implant and its external base-station, such that it allows other groups to use it as a starting point. In this article, we try to answer this question by presenting a design based exclusively on commercial off-the-shelf components and studying the properties of the resulting system. Following this idea, we present a fully wireless neuronal implant for simultaneously measuring electrocorticography signals at 128 locations from the surface of the brain. All design files are available as open source.
Discriminative Filters for Depth from Defocus

Depth from defocus (DFD) requires estimating the depth dependent defocus blur at every pixel. Several approaches for accomplishing this have been proposed over the years. For a pair of images this is done by modeling the defocus relationship between the two differently defocused images and for single defocused images by relying on the the properties of the point spread function and the characteristics of the latent sharp image. We propose depth discriminative filters for DFD that can represent many of the widely used models such as the relative blur, Blur Equalization Technique, deconvolution based depth estimation, and subspace projection methods. We show that by optimizing the parameters of this general model we can obtain state-of-the-art result on synthetic and real defocused images with single or multiple defocused images with different apertures.
Chlamydia pneumoniae eradication from carotid plaques. Results of an open, randomised treatment study.

OBJECTIVE to determine the effect of specific antibiotic treatment with roxithromycin in the eradication of Chlamydia pneumoniae from carotid artery plaques. DESIGN prospective open randomised treatment study. PATIENTS AND METHODS we analysed 32 patients (16 females, mean age 70.1+/-14.7 years) who underwent surgery for the removal of atherosclerotic plaques from carotid arteries. During surgery samples of lingual vein and superior thyroid artery were also taken. Before surgery, patients were randomised to receive either roxithromycin 150 mg twice daily or no treatment. Sixteen patients were treated with antibiotic for a mean of 26 days (range 17-35 days). The two groups of patients were comparable in terms of age, sex, risk factors, and seroprevalence for C. pneumoniae. We applied a semi-nested polymerase chain reaction (PCR) technique to the carotid plaques, lingual vein, and thyroid artery samples. Blood samples were obtained from the patients for the determination of C. pneumoniae IgG, IgA, and IgM antibody titres by a microimmunofluorescence technique. RESULTS in twelve out of sixteen non-treated patients we found evidence of C. pneumoniae DNA in the carotid plaques. Conversely, C. pneumoniae DNA was detected in only five out of sixteen treated patients (p=0.034, Chi-squared test). In all cases PCR was negative for the lingual vein and thyroid artery samples. CONCLUSIONS Roxithromycin seems effective in reducing the bacterial burden of C. pneumoniae within atherosclerotic plaques, although extended follow-up is needed to determine whether antibiotic treatment benefits long-term patient outcome.
O-mannosylation of the Mycobacterium tuberculosis Adhesin Apa Is Crucial for T Cell Antigenicity during Infection but Is Expendable for Protection

Glycosylation is the most abundant post-translational polypeptide chain modification in nature. Although carbohydrate modification of protein antigens from many microbial pathogens constitutes important components of B cell epitopes, the role in T cell immunity is not completely understood. Here, using ELISPOT and polychromatic flow cytometry, we show that O-mannosylation of the adhesin, Apa, of Mycobacterium tuberculosis (Mtb) is crucial for its T cell antigenicity in humans and mice after infection. However, subunit vaccination with both mannosylated and non-mannosylated Apa induced a comparable magnitude and quality of T cell response and imparted similar levels of protection against Mtb challenge in mice. Both forms equally improved waning BCG vaccine-induced protection in elderly mice after subunit boosting. Thus, O-mannosylation of Apa is required for antigenicity but appears to be dispensable for its immunogenicity and protective efficacy in mice. These results have implications for the development of subunit vaccines using post-translationally modified proteins such as glycoproteins against infectious diseases like tuberculosis.
Short jute fiber‐reinforced polypropylene composites: Effect of compatibilizer

Jute fibers were chopped to approximately 100 mm in length and then processed through a granulator having an 8-mm screen. Final fiber lengths were up to 10 mm maximum. These fibers along with polypropylene granules and a compatibilizer were mixed in a K-mixer at a fixed rpm, 5500, and dumped at a fixed temperature, 390°F, following single-stage procedure. The fiber loadings were 30, 40, 50, and 60 wt %, and at each fiber loading, compatibilizer doses were 0, 1, 2, 3 and 4 wt %. The K-mix samples were pressed and granulated. Finally, ASTM test specimens were molded using a Cincinnati injection molding machine. At 60% by weight of fiber loading, the use of the compatibilizer improved the flexural strength as high as 100%, tensile strength to 120%, and impact strength (unnotched) by 175%. Remarkable improvements were attained even with 1% compatibilizer only. Interface studies were carried out by SEM to investigate the fiber surface morphology, fiber pull-out, and fiber–polymer interface. © 1998 John Wiley & Sons, Inc. J Appl Polym Sci 69: 329–338, 1998
The Public's Role in the Evaluation of Health Care Technology: The Conflict Over ECT

Abstract The use of electroconvulsive therapy (ECT), controversial since its inception, offers an instructive case study on the challenge of addressing patients' perspectives in the evaluation of health care technology. Despite widespread professional acceptance of ECT, groups of former psychiatric patients have worked through the U.S. legal system to restrict and even ban ECT in the treatment of mental illness. This unusual lay participation in the regulation of health care illustrates how differing conceptions of evidence can affect the evaluation of technology. ECT provides a powerful example of the value of a more complex definition of the significant outcomes of treatment and the growing practice of outcomes assessment, especially as such research is used to shape health policy.
Noise Removal and Structured Data Detection to improve search for personality features

This paper discusses part one of the main work in field of data science, mining and analytics. Family of algorithms is developed to predict the educational relevance of individuals' talents through lens of personality features (unstructured and semi-structured) and academic/career data. The big data (unstructured and semi-structured) contains lots of valuable information that can be mined and analyzed. However, such processing and utilization of data introduce challenges of dealing with noise (irrelevant, unnecessary and redundant data). Regardless of the nature of data processing and utilization for a given problem or an application, noise adds unnecessary time and cost. This paper briefly discusses the overall research work and then presents Noise Removal and Structured Data Detection (NR-and-SDD) algorithm and related math construct. NR-and-SDD detects the noise to reduce the processing cost and improve structured data detection in relevance of personality features. The given results show improved reliability and efficiency of NR and SDD processes. Related study is provided and paper is concluded with final remarks and future works.
Evaluation of cellular distributed power control algorithms in wireless ad hoc networks

We evaluate the performances of existing distributed power control schemes which were originally proposed for cellular networks (i.e. the target-tracking, and the opportunistic algorithms) in wireless ad hoc networks. In contrast to wireless ad hoc networks, there is no need to exchange pricing packets in cellular networks. We demonstrate that these schemes perform satisfactorily in ad hoc networks as well. We also compare their performances in terms of the achieved quality of service, the consumed power, and the outage ratio; and show that the combination of target tracking and opportunistic power control schemes outperforms each individual algorithm in solo in wireless ad hoc networks.