Miracle-dz/UniFAR-FTUs huggingface dataset:
Detection of Legionellae in Hospital Water Samples by Quantitative Real-Time LightCycler PCR

ABSTRACT Contamination of hospital water systems with legionellae is a well-known cause of nosocomial legionellosis. We describe a new real-time LightCycler PCR assay for quantitative determination of legionellae in potable water samples. Primers that amplify both a 386-bp fragment of the 16S rRNA gene from Legionellaspp. and a specifically cloned fragment of the phage lambda, added to each sample as an internal inhibitor control, were used. The amplified products were detected by use of a dual-color hybridization probe assay design and quantified with external standards composed ofLegionella pneumophila genomic DNA. The PCR assay had a sensitivity of 1 fg of Legionella DNA (i.e., less than one Legionella organism) per assay and detected 44Legionella species and serogroups. Seventy-seven water samples from three hospitals were investigated by PCR and culture. The rates of detection of legionellae were 98.7% (76 of 77) by the PCR assay and 70.1% (54 of 77) by culture; PCR inhibitors were detected in one sample. The amounts of legionellae calculated from the PCR results were associated with the CFU detected by culture (r= 0.57; P < 0.001), but PCR results were mostly higher than the culture results. Since L. pneumophila is the main cause of legionellosis, we further developed a quantitativeL. pneumophila-specific PCR assay targeting the macrophage infectivity potentiator (mip) gene, which codes for an immunophilin of the FK506 binding protein family. All but one of the 16S rRNA gene PCR-positive water samples were also positive in the mip gene PCR, and the results of the two PCR assays were correlated. In conclusion, the newly developedLegionella genus-specific and L. pneumophila species-specific PCR assays proved to be valuable tools for investigation of Legionella contamination in potable water systems.
Study on DEM Reconstruction for Spaceborne Parasitic InSAR

DEM (Digital Elevation Model) reonstruction is an important step in signal processing of spaceborne parasitic InSAR(Interferometric Synthetic Aperture Radar). It uses interferograms and satellite parameters to solve elevation and position of the Earth surface. Spaceborne parasitic InSAR is bistatic, this character should be involved in DEM reconstruction. DEM reconstruction precision is sensitive to baseline error. This paper discusses using Ground Control Point (GCP) to reduce the influence of baseline error on reconstruction precision.
Face recognition based on graph kernels

The problem of face recognition was considered the most popular topic in artificial intelligence and computer vision. In this paper, we investigate face recognition based on graph kernels. We define the concept of max spanning tree, six graph kernels and a complicated kernel based on graph kernel and gray kernel. The result of our experiment shows that our spanning-tree kernels have significantly higher classification accuracy than walk-based kernels.
Comparison of charge pumping and 1/ƒ noise in irradiated Ge pMOSFETs

Irradiated Ge pMOSFETs have been characterized via charge pumping (I<inf>CP</inf>) and 1/ƒ-noise. The noise increases much more with irradiation than I<inf>CP</inf>, showing that bulk oxide traps affect the noise more than interface traps.
Heat Shock 70‐kDa Protein 8 Isoform 1 Is Expressed on the Surface of Human Embryonic Stem Cells and Downregulated upon Differentiation

The cell‐surface markers used routinely to define the undifferentiated state and pluripotency of human embryonic stem cells (hESCs) are those used in mouse embryonic stem cells (mESCs) because of a lack of markers directly originated from hESC itself. To identify more hESC‐specific cell‐surface markers, we generated a panel of monoclonal antibodies (MAbs) by immunizing the irradiated cell clumps of hESC line Miz‐hES1, and selected 26 MAbs that were able to bind to Miz‐hES1 cells but not to mESCs, mouse embryonic fibroblast cells, and STO cells. Most antibodies did not bind to human neural progenitor cells derived from the Miz‐hES1 cells, either. Of these, MAb 20‐202S (IgG1, κ) immunoprecipitated a cell‐surface protein of 72‐kDa from the lysate of biotin‐labeled Miz‐hES1 cells, which was identified to be heat shock 70‐kDa protein 8 isoform 1 (HSPA8) by quadrupole time‐of‐flight tandem mass spectrometry. Immunocytochemical analyses proved that the HSPA8 protein was also present on the surface of hESC lines Miz‐hES4, Miz‐hES6, and HSF6. Two‐color flow cytometric analysis of Miz‐hES1 and HSF6 showed the coexpression of the HSPA8 protein with other hESC markers such as stage‐specific embryonic antigen 3 (SSEA3), SSEA4, TRA‐1‐60, and TRA‐1‐81. Flow cytometric and Western blot analyses using various cells showed that MAb 20‐202S specifically bound to the HSPA8 protein on the surface of Miz‐hES1, contrary to other anti‐HSP70 antibodies examined. Furthermore, the surface expression of the HSPA8 protein on Miz‐hES1 was markedly downregulated upon differentiation. These data indicate that a novel MAb 20‐202S recognizes the HSPA8 protein on the surface of hESCs and suggest that the HSPA8 protein is a putative cell‐surface marker for undifferentiated hESCs.
Too Sick Not to Exercise: Using a 6-Week, Home-Based Exercise Intervention for Cancer-Related Fatigue Self-management for Postsurgical Non–Small Cell Lung Cancer Patients

Background: Two prevalent unmet supportive care needs reported by the non–small cell lung cancer (NSCLC) population include the need to manage fatigue and attain adequate exercise to meet the physical demands of daily living. Yet, there are no guidelines for routine rehabilitative support to address fatigue and exercise for persons with NSCLC during the critical transition from hospital to home after thoracotomy. Objective: The objective of this study was to evaluate the feasibility, acceptability, safety, and changes in study end points of a home-based exercise intervention to enhance perceived self-efficacy for cancer-related fatigue (CRF) self-management for persons after thoracotomy for NSCLC transitioning from hospital to home. Interventions/Methods: Guided by the principles of the Transitional Care Model and the Theory of Symptom Self-management, a single-arm design composed of 7 participants with early-stage NSCLC performed light-intensity walking and balance exercises in a virtual reality environment with the Nintendo Wii Fit Plus. Exercise started the first week after hospitalization for thoracotomy and continued for 6 weeks. Results: The intervention positively impacted end points such as CRF severity; perceived self-efficacy for fatigue self-management, walking, and balance; CRF self-management behaviors (walking and balance exercises); and functional performance (number of steps taken per day). Conclusions: A home-based, light-intensity exercise intervention for patients after thoracotomy for NSCLC is feasible, safe, well tolerated, and highly acceptable showing positive changes in CRF self-management. Implications for Practice: Beginning evidence suggests that a light-intensity in-home walking and balance intervention after hospitalization for thoracotomy for NSCLC is a potentially effective rehabilitative CRF self-management intervention. Next steps include testing of this health-promoting self-management intervention in a larger-scale randomized controlled trial.
Evolution of Hepatitis C Virus Quasispecies during Ribavirin and Interferon-Alpha-2b Combination Therapy and Interferon-Alpha-2b Monotherapy

Objective: Ribavirin and interferon combination therapy is more effective than interferon monotherapy in patients with chronic hepatitis C virus (HCV) infection. To test the hypothesis that ribavirin induces nucleotide substitutions in the viral genome and reduces viral load by forcing it into error catastrophe in the combination therapy, we investigated the molecular evolution of HCV quasispecies in 3 patients who received combination therapy and 2 patients who received interferon monotherapy. Methods: The quasispecies were analyzed before and after therapy by sequencing at least 8 clones in five regions of the HCV genome; 5′ untranslated region, EI, E2, NS5A and NS5B. Results: Marked genetic drift was observed in the NS5A and NS5B regions in patients treated with combination therapy. However, genetic distances between clones obtained after therapy were closer than those obtained before therapy. Conclusion: Our results suggest that the combination therapy modified HCV quasispecies, but that this did not reflect the induction of error catastrophe by ribavirin. Modification of quasispecies by this therapy requires further investigation in a larger number of patients to elucidate the possible mechanism of viral resistance against the combination therapy.
Abstract O.27: The Role Of CD40L And CD40 In The Pathogenesis Of Kawasaki Disease

Kawasaki Disease (KD) is characterized by acute, systemic inflammation followed by a persistent immune response localized to the coronary arteries. Lactobacillus Casei Cell Wall Extract (LCWE) contains among its active ingredients a superantigen (SAg) that induces coronary arteritis in mice. LCWE induces massive immune activation followed by apoptosis or anergy. Previous work has shown that co-stimulatory signals can rescue a subset of SAg-reactive T-cells from apoptosis. CD40-CD40L (ligand) are members of the TNF superfamily which play a role in T-cell co-stimulation. Moreover, genome wide association studies have implicated CD40/CD40L as candidate genes in the pathogenesis of KD. We hypothesize that co-stimulation via the CD40 pathway regulates survival of SAg-reactive T-cells during disease development. Using thymidine proliferation assay and flow cytometry we show that activation of CD40 signaling via agonistic anti-CD40 antibody or recombinant soluble CD40L (rsCD40L) upregulates CD86 (ligand responsible for CD28 signaling) expression, reduces active-caspase-3 expression, indicating decreased cell death and promotes lymphocyte proliferation, Additionally, using CD28 deficient mice we show that lymphocytes do not proliferate in response to SAg plus CD40 stimulation indicating that CD28 is the intermediary that mediates the proliferative effects of CD40 activation. Furthermore, platelets, which are markedly elevated in KD, produce approximately 90% of the soluble CD40L in the circulation. We show that activated platelets (CD62P+) express CD40L and promotes cell survival as evidenced by enhanced lymphocyte proliferation. Likewise, the absence of CD40L negates the proliferative effects of platelet mediated proliferation. Lastly, to determine the role of CD40 stimulation on in vivo development of KD, LCWE was injected into B6 and CD40L deficient mice. We show that inflammation in the coronary arteries does not develop in the absence of CD40L. Therefore, CD40L plays a critical role in immune activation via upregulation of CD86 on antigen presenting cells leading to enhanced co-stimulation and T-cell survival.
Comparison of the structure and accuracy of two land change models

This paper compares two land change models in terms of appropriateness for various applications and predictive power. Cellular Automata Markov (CA_Markov) and Geomod are the two models, which have similar options to allow for specification of the predicted quantity and location of land categories. The most important structural difference is that CA_Markov has the ability to predict any transition among any number of categories, while Geomod predicts only a one‐way transition from one category to one alternative category. To assess the predictive power, each model is run several times to predict land change in central Massachusetts, USA. The models are calibrated with information from 1971 to 1985, and then the models predict the change from 1985 to 1999. The method to measure the predictive power: 1) separates the calibration process from the validation process, 2) assesses the accuracy at multiple resolutions, and 3) compares the predictive model vis‐à‐vis a null model that predicts pure persistence. Among 24 model runs, the predictive models are more accurate than the null model at resolutions coarser than two kilometres, but not at resolutions finer than one kilometre. The choice of the options account for more variation in accuracy of runs than the choice of the model per se. The most accurate model runs are those that did not use spatial contiguity explicitly. For this particular study area, the added complexity of CA_Markov is of no benefit.
In Plants, 3-O-Methylglucose Is Phosphorylated by Hexokinase But Not Perceived as a Sugar1

In plants, sugars are the main respiratory substrates and important signaling molecules in the regulation of carbon metabolism. Sugar signaling studies suggested that sugar sensing involves several key components, among them hexokinase (HXK). Although the sensing mechanism of HXK is unknown, several experiments support the hypothesis that hexose phosphorylation is a determining factor. Glucose (Glc) analogs transported into cells but not phosphorylated are frequently used to test this hypothesis, among them 3-O-methyl-Glc (3-OMG). The aim of the present work was to investigate the effects and fate of 3-OMG in heterotrophic plant cells. Measurements of respiration rates, protein and metabolite contents, and protease activities and amounts showed that 3-OMG is not a respiratory substrate and does not contribute to biosynthesis. Proteolysis and lipolysis are induced in 3-OMG-fed maize (Zea mays L. cv DEA) roots in the same way as in sugar-starved organs. However, contrary to the generally accepted idea, phosphorous and carbon nuclear magnetic resonance experiments and enzymatic assays prove that 3-OMG is phosphorylated to 3-OMG-6-phosphate, which accumulates in the cells. Insofar as plant HXK is involved in sugar sensing, these findings are discussed on the basis of the kinetic properties because the catalytic efficiency of HXK isolated from maize root tips is five orders of magnitude lower for 3-OMG than for Glc and Man.
ETIOLOGY OF SUPPURATIVE CORNEAL ULCERS IN RURAL POPULATION OF NORTHERN INDIA

Background: A prospective, interventional, comparative study carried out in rural population of northern India in western UP. Fungal keratitis studies available in literature were also reviewed. Methods: Patients presenting in eye OPD of UPRIMS & R Saifai, Etawah, UP with suspected microbial keratitis were recruited to the study. Corneal ulceration was defined as loss of corneal epithelium with clinical evidence of infection in form of corneal infiltrate with or without hypopyon. Microscopy and culture were performed on all corneal specimens. Results: A total of 105 patients presenting with suppurative keratitis were enrolled in the study from Jan 2014 to April 2015. Fungi were identified as the dominant causative agent of infection (including mixed infections) in 52 patients (49.52%). Bacteria were isolated from 32 cases (30.47%). Mixed infection was present in 9 cases (8.57%). In each case of mixed infection a single bacterial species was associated with a single fungal species. In 21 cases (20%) had no definitive laboratory diagnosis. The principal causative micro- organisms noted in rural population were filamentous fungi (Fusarium and Aspergillus species) in 49.52 % cases. The most common bacterial pathogen was gram positive streptococci. Conclusion: Infections of the cornea due to filamentous fungi are a frequent cause of corneal ulcer in rural population of north India and are very difficult treat. Corneal scrapping is very useful to assess etiology empirically and start anti-fungal drugs earliest. Knowledge of regional etiology will helpful in management of suppurative keratitis for private practitioner when microscopy cannot be performed. Keywords: Corneal uclcer, Fungal corneal ulcer, Rural area, Suppurative keratitis.
An Improved Lempel-Ziv Algorithm for Sequential Data Compression

The importance of data compression has been increasing of late due to the increasing demand put on the networks by applications consuming high amount of network bandwidth. Thus compressing data to at least a particular level becomes mandatory for applications to avoid congestion in the network. Recently there has been an interest in increasing the capacity of storage systems, which employ lossless data compression. In this paper, we have proposed two improved algorithms for data compression. These algorithms are tested and compared with best known existing algorithms of data compression. It has been observed that compression rate of our proposed algorithms reaches up to 99% for huge files like swap files.
The Effect of Rosiglitazone on Insulin Sensitivity, Beta Cell Function, Bone Mineral Density, and Body Composition in HIV-positive Patients on Highly-active Antiretroviral Therapy (HAART)

Highly active antiretroviral therapy (HAART) leads to lipodystrophy and is associated with detrimental changes in glucose and lipid metabolism. This study investigated the impact of rosiglitazone on insulin sensitivity, beta cell function, bone mineral density, and body composition in HIV+ nondiabetic subjects under HAART. In this randomized, double blind, placebo controlled parallel group study, 40 HIV+ subjects were treated with rosiglitazone 4 mg/day (R, n=23) or placebo (P, n=17) for 6 months. Glucose, insulin and C peptide concentrations were analyzed for assessing insulin sensitivity and secretion. Adiponectin and leptin were evaluated. Body fluid compartments were measured with bioelectrical impedance spectroscopy, and bone mineral density and body composition with Dual X Ray absorptiometry. Rosiglitazone improved peripheral insulin sensitivity (+36.7+/-15.7 ml/min/m (2), p=0.03, means+/-SEM), while no change was observed in P (+4.5+/-19.5 ml/min/m (2), p=0.55). Liver insulin resistance, beta cell activity, and hepatic insulin clearance did not change. Plasma adiponectin increased (R: +2.47+/-0.86 microg/ml, p=0.01 vs. P: +0.45+/-0.60, p=0.28). Rosiglitazone had no influence on body composition, fat distribution and bone mineral density but expanded extra-cellular fluid volume in HIV infected persons (R: +0.50+/-0.21 l, p=0.02 vs. P: 0.10+/-0.25 l, p=0.32). Lipid metabolism in P remained unchanged, in R total cholesterol and LDL cholesterol levels increased significantly (p<0.05). Rosiglitazone treatment resulted in improved peripheral insulin sensitivity with increased circulating adiponectin in HIV patients under HAART. No effect was seen on body fat distribution, bone mineral density, and weight. These side effects and their potential for cardiac risk must be weighed against the beneficial effects on glucose metabolism.
A 150 MS/s 133$~\mu$W 7 bit ADC in 90 nm Digital CMOS

In recent years the energy efficiency of A/D converters has been improved significantly. Only 5 years ago [3] an energy efficiency of 1 pJ/conversion step was considered state-of-the-art. Now power efficiencies are reported in f J/conversion step. In this paper two new converter techniques are presented that further improve upon reported energy efficiencies of A/D converters. The first technique implements the quantization with a comparator-based asynchronous binary search (CABS). The second technique implements the SAR control algorithm on the comparators (SAR-CC) that are also used to do the quantization. Both these techniques have been applied in a fully dynamic 7 bit A/D converter that uses a two-step lb coarse and 6b fine architecture [2]. The 1b coarse converter is implemented using the SAR-CC principle, the 6b fine converter is implemented using the CABS principle. The 7 bit prototype implementation in 90 nm digital CMOS on a 1 V supply achieves 6.4ENOB, 40 dB SNDR at 150 MS/s consuming 133 muW giving 10 fJ/conversion step energy efficiency (FOM). A second prototype implementing a stand-alone 6b CABS converter (the sub-A/D converter of the 7 bit converter) achieves 32 dB SNDR at 250 MS/s with 140 muW of power consumption, which results in a FOM of 15 fJ/conversion step.
Factors associated with neonatal pneumonia in India: protocol for a systematic review and planned meta-analysis

Introduction India accounts for more neonatal deaths than any other country. There is a lack of consolidated evidence from India regarding the determining factors of pneumonia in neonates. This systematic review is aimed to consolidate and appraise the evidence on risk factors and determinants of pneumonia among neonates in India. Methods and analysis This protocol is part of a project consisting of three reviews (two systematic reviews and one scoping review) and a qualitative study on neonatal pneumonia in India. English language observational studies which report risk factors and determinants of neonatal pneumonia in India will be eligible for inclusion. Electronic searching of nine databases, and hand searching will be done. Two authors will independently conduct screening (title, abstract and full-text stages), extract data and assess risk of bias. A meta-analysis is planned to be performed with random-effects model. A narrative synthesis will be used to summarise the characteristics and findings of the review, if a meta-analysis cannot be performed. If there are more than 10 studies, publication bias will be assessed. Sensitivity and subgroup analysis will performed based on data availability. The quality of our review will be assessed by using ‘Assessing the Methodological quality of Systematic Reviews’ and ‘Grades of Recommendation, Assessment, Development and Evaluation’. Ethics and dissemination The protocol of the entire project has been approved by the host institution’s ethics body (Institutional Ethics Committee, Manipal University, Manipal, India), and the ‘Health Ministry Screening Committee’ under the Ministry of Health and Family Welfare, Government of India. The study findings will be disseminated among relevant stakeholders using knowledge dissemination workshops, policy briefs, publications, etc. PROSPERO registration number CRD42016044019.
Investigation of molecular interaction within biological macromolecular complexes by mass spectrometry

The advent of electrospray ionization (ESI) and matrix‐assisted laser desorption ionization (MALDI) has accelerated structural studies of biological macromolecular complexes. At present, mass spectrometry can provide accurate mass values not only of individual biological macromolecules but also of their assemblies. Furthermore, it can also give information on the interface sites of the biological macromolecular complexes. The present article focuses on the role of mass spectrometry in the investigation of biological molecular interactions, such as protein–protein, protein–DNA, and protein–ligand interactions, which play essential roles in various biological events. © 2006 Wiley Periodicals, Inc.
Delivering 100% throughput in a buffered crossbar with round robin scheduling

Buffered crossbars with virtual output queuing are considered an alternative to bufferless crossbars mainly because the latter requires a complex global scheduling algorithm that matches input with output. Buffered crossbars require only simple schedulers that operate independently for each output crosspoint queue column and independently for each port card. In this paper, fluid-model techniques will be utilized to show that the necessary and sufficient speedup for a NxN buffered crossbar with 1-cell crosspoint buffers is 2-1/N to deliver 100% throughput. Round robin scheduling is assumed, both among virtual output queues in port cards and among crosspoint buffers in output columns