Miracle-dz/UniFAR-FTUs huggingface dataset:
Superior immune response to protein-conjugate versus free pneumococcal polysaccharide vaccine in chronic obstructive pulmonary disease.

RATIONALE Debate exists about the immunogenicity and protective efficacy of antibodies produced by the 23-valent pneumococcal polysaccharide vaccine (PPSV23) in chronic obstructive pulmonary disease (COPD). The 7-valent diphtheria-conjugated pneumococcal polysaccharide vaccine (PCV7) induces a more robust immune response than PPSV23 in healthy elderly adults. OBJECTIVES We hypothesized that serotype-specific IgG antibody concentration and functional antibody activity would be superior after PCV7 vaccination compared with PPSV23 in moderate to severe COPD. We also posited that older age and prior PPSV23 vaccination would be associated with reduced vaccine responsiveness. METHODS One hundred twenty patients with COPD were randomized to PPSV23 (63 subjects) or PCV7 (57 subjects). IgG concentrations were determined by ELISA; functional antibody activity was assayed with a standardized opsonophagocytosis assay and reported as an opsonization killing index (OPK). Increases in serotype-specific IgG and OPK at 1 month post vaccination were compared within and between vaccine groups. MEASUREMENTS AND MAIN RESULTS Both vaccines were well tolerated. Within each study group, postvaccination IgG and OPK were higher than baseline (P < 0.01) for all serotypes. Adjusted for baseline levels, postvaccination IgG was higher in the PCV7 group than the PPSV23 group for all seven serotypes, reaching statistical significance for five (P < 0.05). PCV7 resulted in a higher OPK for six of seven serotypes (statistically greater for four) compared with PPSV23. In multivariate analyses, younger age, vaccine naivety, and receipt of PCV7 were associated with increased OPK responses. CONCLUSIONS PCV7 induces a superior immune response at 1 month post vaccination compared with PPSV23 in COPD. Older age and prior PPSV23 reduce vaccine responsiveness. Clinical trial registered with www.clinicaltrials. gov (NCT00457977).
Identification of yeast DNA topoisomerase II mutants resistant to the antitumor drug doxorubicin: implications for the mechanisms of doxorubicin action and cytotoxicity.

Doxorubicin is a therapeutically useful anticancer drug that exerts multiple biological effects. Its antitumor and cardiotoxic properties have been ascribed to anthracycline-mediated free radical damage to DNA and membranes. Evidence for this idea comes in part from the selection by doxorubicin from stationary phase yeast cells of mutants (petites) deficient in mitochondrial respiration and therefore defective in free radical generation. However, doxorubicin also binds to DNA topoisomerase II, converting the enzyme into a DNA damaging agent through the trapping of a covalent enzyme-DNA complex termed the 'cleavable complex. ' We have used yeast to determine whether stabilization of cleavable complexes plays a role in doxorubicin action and cytotoxicity. A plasmid-borne yeast TOP2 gene was mutagenized with hydroxylamine and used to transform drug-permeable yeast strain JN394t2-4, which carries a temperature-sensitive top2-4 mutation in its chromosomal TOP2 gene. Selection in growth medium at the nonpermissive temperature of 35 degrees in the presence of doxorubicin resulted in the isolation of plasmid-borne top2 mutants specifying functional doxorubicin-resistant DNA topoisomerase II. Single-point changes of Gly748 to Glu or Ala642 to Ser in yeast topoisomerase II, which lie in and adjacent to the CAP-like DNA binding domain, respectively, were identified as responsible for resistance to doxorubicin, implicating these regions in drug action. None of the mutants selected in JN394t2-4, which has a rad52 defect in double-strand DNA break repair, was respiration-deficient. We conclude that topoisomerase II is an intracellular target for doxorubicin and that the genetic background and/or cell proliferation status can determine the relative importance of topoisomerase II- versus free radical-killing.
Exploit Every Bit: Effective Caching for High-Dimensional Nearest Neighbor Search

High-dimensional $k$ nearest neighbor (kNN) search has a wide range of applications in multimedia information retrieval. Existing disk-based $k$ NN search methods incur significant I/O costs in the candidate refinement phase. In this paper, we propose to cache compact approximate representations of data points in main memory in order to reduce the candidate refinement time during $k$ NN search. This problem raises two challenging issues: (i) which is the most effective encoding scheme for data points to support $k$ NN search? and (ii) what is the optimal number of bits for encoding a data point? For (i), we formulate and solve a novel histogram optimization problem that decides the most effective encoding scheme. For (ii), we develop a cost model for automatically tuning the optimal number of bits for encoding points. In addition, our approach is generic and applicable to exact / approximate $k$ NN search methods. Extensive experimental results on real datasets demonstrate that our proposal can accelerate the candidate refinement time of $k$ NN search by at least an order of magnitude.
Inhibition of microbial pathogens using fruit and vegetable peel extracts

Abstract The aim of the present work is to evaluate the antimicrobial potency of some vegetable and fruit peels. The extraction was done by individual cold percolation method using various solvents with increasing polarity (Hexane, ethyl acetate, acetone, methanol and aqueous). The antimicrobial activity was done by agar well diffusion assay against five Gram positive bacteria, five Gram negative bacteria and four fungi. All extracts demonstrated varied level of antimicrobial activity. The peel extracts showed highest zone of inhibition against Gram negative bacteria as compared to Gram positive bacteria and fungi. Amongst studied peel extracts Citrus limon followed by Manilkara zapota and Carica papaya showed good antimicrobial activity indicating its potency as a promising source of natural antimicrobics. The results confirm the belief that agro waste can be therapeutically used.
An Investigation of the Potential Benefits in Trading Energy Resolution for Timing Resolution in Time-of-Flight Positron Emission Tomography

Recent developments in scintillators and photodetectors have renewed the interest in time-of-flight positron emission tomography (TOF-PET). In this paper, we demonstrated that exact image reconstruction can be achieved with TOF-PET data generated by using coincidence windows that are smaller than the subject size. With this new possibility in TOF-PET imaging, we demonstrated the potential benefit of placing more emphasis on the timing resolution when developing TOF-PET systems, even though the energy resolution of the system may be sub-optimal. This observation can create more options in selecting scintillation materials and photodetector technologies that would otherwise be considered inappropriate for building TOF-PET systems.
The carriage of the type 1 diabetes‐associated R262W variant of human LNK correlates with increased proliferation of peripheral blood monocytes in diabetic patients

Lavrikova EY, Nikitin AG, Kuraeva TL, Peterkova VA, Tsitlidze NM, Chistiakov DA, Nosikov VV. The carriage of the type 1 diabetes‐associated R262W variant of human LNK correlates with increased proliferation of peripheral blood monocytes in diabetic patients.
Concurrent infection with WSSV and MBV in Tiger prawn, Penaeus monodon (Fabricious) in West Bengal and their detection using PCR and DNA Dot-blot hybridization technique

Prevalence status of white spot disease (WSD), caused by white spot syndrome virus (WSSV) and Monodon baculovirus (MBV), was studied in different prawn farms in North and South-24 paragana districts of West Bengal, specifically in the areas previously affected by WSD. In total 283 samples of giant tiger prawn Penaeus monodon, Indian white prawn P. indicus and giant freshwater prawn Macrobrachium rosenbergii from 12 different farms were screened and presence of MBV occlusion-bodies (Obs) were detected. Of samples screened, 30 samples showed multiple spherical Obs typical of MBV infection. Of 80 samples screened using PCR, 17 (21.25%) were positive for MBV and 51 samples (63.75%) were positive for WSSV, and amplified DNA of 674 bp and 643 bp, respectively was visualized on 1% agarose gel electrophoresis. Significantly all samples showing positive reaction with MBV were also positive for WSSV in PCR, indicating co-infection of prawns with both MBV and WSSV. However, none of the M. rosenbergii samples were positive of MBV-Obs but 5 samples were positive for WSSV in PCR. Both MBV and WSSV amplified DNA were labeled with alkaline phosphatase using Alkphos DNA labeling reagent kit and samples were screened using DNA dot-blot and slot-blot hybridization. All samples showing positive PCR reaction were also found positive in DNA hybridization
Synthesis of Heterobifunctional Protein Fusions Using Copper-Free Click Chemistry and the Aldehyde Tag

Heterobifunctional protein fusions are gaining interest as next-generation biopharmaceuticals.1–5 Combining proteins with disparate functions can enable multidrug therapy with a single chemical entity,6, 7 add a targeting element to an otherwise nonspecific therapeutic,8, 9 or improve the pharmacokinetic profile of a rapidly cleared molecule.10, 11 Indeed, heterobifunctional proteins, such as immunoglobulin G (IgG) Fc domain fusions, are among the top-selling biotherapeutics on the market today.12 These biomolecules are primarily generated as genetic fusions. The DNA sequences that encode the individual protein components are fused in tandem to direct the expression of a single polypeptide that comprises the two proteins joined together at their N and C termini, respectively. However, this limited topology is not ideal for every protein combination, as some polypeptides require unmodified termini for optimal bioactivity13 or can suffer from expression difficulties as a result of folding and processing issues.3, 14, 15
Low Triiodothyronine (T3) or Reverse Triiodothyronine (rT3) Syndrome Modifies Gene Expression in Rats With Congestive Heart Failure

Heart failure (HF) is frequently associated with euthyroid “sick” syndrome (low T3 and elevated rT3). We investigated if altered thyroid hormone in HF could affect expression of the TH receptor (TRα1), and alpha and beta myosin heavy chains (α-MHC, β-MHC). HF was provoked in rats by aortic stenosis. We showed that rT3 generated from liver and kidney deiodination significantly increased and T3 decreased in HF; there was significantly higher TRα1 expression, no α-MHC expression, but β-MHC expression. Changes in TRα1 could be compensating for low T3 from HF.
Space-Time Body Pose Estimation in Uncontrolled Environments

We propose a data-driven, multi-view body pose estimation algorithm for video. It can operate in uncontrolled environments with loosely calibrated and low resolution cameras and without restricting assumptions on the family of possible poses or motions. Our algorithm first estimates a rough pose estimation using a spatial and temporal silhouette based search in a database of known poses. The estimated pose is improved in a novel pose consistency step acting locally on single frames and globally over the entire sequence. Finally, the resulting pose estimation is refined in a spatial and temporal pose optimization consisting of novel constraints to obtain an accurate pose. Our method proved to perform well on low resolution video footage from real broadcast of soccer games.
On adapting migration parameters for multi-population genetic algorithms

In recent years, multi-population genetic algorithms (MGAs) have been recognized as being more effective both in speed and solution quality than single-population genetic algorithms (SGAs). Despite of these advantages, the behavior and performance of MGAs, like SGAs, are still heavily affected by a judicious choice of parameters, such as connection topology, migration method, migration interval, migration rate, population number, etc. In this paper, the issue of adapting migration parameters for MGAs is investigated. We examine, in particular, the effect of adapting the migration interval as well as migration rate on the performance and solution quality of MGAs. Thereby, we propose an adaptive scheme to evolve the appropriate migration interval and migration rate for MGAs. Experiments on the 0/1 knapsack problem showed that our approach can compete with MGAs with static migration parameters.
Author ' s personal copy Chronic stress , salivary cortisol , and a-amylase in children with asthma and healthy children

The present study examined whether chronic stress is related to daily life levels of salivary a-amylase (sAA), a marker for sympathetic activity, and cortisol in healthy children versus children with asthma. Children’s sAA and cortisol levels were measured repeatedly over 2 days. Chronic stress measures included interviews with children about chronic home life stress and interviews with parents about one marker of socioeconomic status, parental education. Among children with asthma, higher chronic stress was associated with lower daily sAA output, while among healthy children, higher chronic stress was associated with flatter cortisol slopes. In conclusion, chronically stressed children with asthma showed lower salivary a-amylase output, indicating lower sympathetic activity, and implying a possible mechanism for increased susceptibility to symptom exacerbations. In contrast, higher cortisol levels in healthy children with chronic stress may indicate, for example, an increased risk for infectious diseases. This dichotomy emphasizes the different biological effects of chronic stress depending on illness status. # 2007 Elsevier B.V. All rights reserved.
Detection of Rhodococcus Equi by Polymerase Chain Reaction Using Species-Specific Nonproprietary Primers

Species-specific primers for the polymerase chain reaction (PCR) for the detection of Rhodococcus equi were developed. These primers were based on unique DNA fragments produced from R. equi reference strains and field isolates. Following random amplification of polymorphic DNA from R. equi and R. rhodochrous with a set of 40 arbitrary 10–base pair (bp) primers, a pair of species-specific primers was designed to detect a unique 700-bp fragment of R. equi chromosomal DNA. This PCR product was limited to R. equi and was not detectable in other Rhodococcus species or in a panel of additional gram-positive and gram-negative bacteria.
Organizing principles of cortical integration in the rat neostriatum: Corticostriate map of the body surface is an ordered lattice of curved laminae and radial points

The neuroanatomic organizing principles underlying integrative functions in the striatum are only partially understood. Within the three major subdivisions of the striatum—sensorimotor, associative, and limbic—longitudinal zones of axonal plexuses from the cerebral cortex end in bands and clusters that innervate cell groups. To identify organizing principles of the corticostriate bands and clusters, we localized somatosensory cortical cells receptive to light touch on the hindlimb, forelimb, or vibrissae by extracellular recording, and we labeled their projections by iontophoretic application of dextran anterograde tracers. The results show that cortical cells in columnar groups project to the striatum in the form of successive strips, or laminae, that parallel the curve of the external capsule. The vibrissae somatosensory cortex projects to the most lateral lamina. Just medial to the vibrissae projection, the major axonal arborizations arising from hindlimb and forelimb somatosensory cortex are organized within a common lamina, where they interdigitate and overlap as well as remain separate. In addition, the hindlimb and forelimb cortex send small projections to the vibrissae lamina, and vice versa, forming broken, radially oriented lines of points across the laminar strips. The major somatosensory projections are in the dorsolateral, calbindin‐poor sensorimotor striatum, whereas the radially oriented projection points extend into the medial, calbindin‐rich associative striatum. Extending previous studies of corticostriate projections, this report shows a grid translation of columnar somatosensory cortical inputs into striatum and a detailed map for the rat sensorimotor zone. The lattice‐like grid is a novel functional/neuroanatomic organization that is ideal for distributing, combining, and integrating information for sensorimotor and cognitive processing. J. Comp. Neurol. 392:468–488, 1998. © 1998 Wiley‐Liss, Inc.
Increased expression of HIV co-receptor CXCR4 on CD4+ T-cells in patients with active visceral leishmaniasis

Enhanced expression of the human immunodeficiency virus (HIV) co-receptor CXCR4 renders T-lymphocytes more susceptible for infection with HIV. We demonstrate that patients with active visceral leishmaniasis have a higher proportion of circulating CD4+ T-cells expressing CXCR4 than healthy controls, suggesting that Leishmania may facilitate HIV infection of CD4+ lymphocytes.
How do non-R&D-based innovations affect SMEs' performance? The mediating role of dynamic capabilities

Non-R&D-based innovations as effective ways to promote firms' growth and performance have gradually been recognized in recent years. However, the reason why those innovations generate benefits is still underexplored and mixed, particularly for small and medium enterprises (SMEs) in the context of emerging economies like China. Using quantitative data from 506 SMEs in China, we analyze five kinds of non-R&D-based innovative activities and explore how those non-R&D-based innovations contribute to SMEs' performance from dynamic capabilities view. Our results provide evident support that SMEs' dynamic capabilities mediate the relationships between three kinds of non-R&D-based innovations, namely product and service customization, marketing innovation and organizational innovation, and business performance. We contribute to enriching dynamic capabilities research in non-R&D-based innovation context, on one hand, which is relatively neglected in previous research. On the other hand, we call for more attention on non-R&D-based innovative activities, which could complement the picture of innovation processes in SMEs in emerging economies.
The Large‐Scale Digital Cell Analysis System: an open system for nonperturbing live cell imaging

The Large‐Scale Digital Cell Analysis System (LSDCAS) was designed to provide a highly extensible open source live cell imaging system. Analysis of cell growth data has demonstrated a lack of perturbation in cells imaged using LSDCAS, through reference to cell growth data from cells growing in CO2 incubators. LSDCAS consists of data acquisition, data management and data analysis software, and is currently a Core research facility at the Holden Comprehensive Cancer Center at the University of Iowa. Using LSDCAS analysis software, this report and others show that although phase‐contrast imaging has no apparent effect on cell growth kinetics and viability, fluorescent image acquisition in the cell lines tested caused a measurable level of growth perturbation using LSDCAS. This report describes the current design of the system, reasons for the implemented design, and details its basic functionality. The LSDCAS software runs on the GNU/Linux operating system, and provides easy to use, graphical programs for data acquisition and quantitative analysis of cells imaged with phase‐contrast or fluorescence microscopy (alone or in combination), and complete source code is freely available under the terms of the GNU Public Software License at the project website (http://lsdcas.engineering.uiowa.edu).
Large-Scale Interlaboratory Study to Develop, Analytically Validate and Apply Highly Multiplexed, Quantitative Peptide Assays to Measure Cancer-Relevant Proteins in Plasma*

There is an increasing need in biology and clinical medicine to robustly and reliably measure tens to hundreds of peptides and proteins in clinical and biological samples with high sensitivity, specificity, reproducibility, and repeatability. Previously, we demonstrated that LC-MRM-MS with isotope dilution has suitable performance for quantitative measurements of small numbers of relatively abundant proteins in human plasma and that the resulting assays can be transferred across laboratories while maintaining high reproducibility and quantitative precision. Here, we significantly extend that earlier work, demonstrating that 11 laboratories using 14 LC-MS systems can develop, determine analytical figures of merit, and apply highly multiplexed MRM-MS assays targeting 125 peptides derived from 27 cancer-relevant proteins and seven control proteins to precisely and reproducibly measure the analytes in human plasma. To ensure consistent generation of high quality data, we incorporated a system suitability protocol (SSP) into our experimental design. The SSP enabled real-time monitoring of LC-MRM-MS performance during assay development and implementation, facilitating early detection and correction of chromatographic and instrumental problems. Low to subnanogram/ml sensitivity for proteins in plasma was achieved by one-step immunoaffinity depletion of 14 abundant plasma proteins prior to analysis. Median intra- and interlaboratory reproducibility was <20%, sufficient for most biological studies and candidate protein biomarker verification. Digestion recovery of peptides was assessed and quantitative accuracy improved using heavy-isotope-labeled versions of the proteins as internal standards. Using the highly multiplexed assay, participating laboratories were able to precisely and reproducibly determine the levels of a series of analytes in blinded samples used to simulate an interlaboratory clinical study of patient samples. Our study further establishes that LC-MRM-MS using stable isotope dilution, with appropriate attention to analytical validation and appropriate quality control measures, enables sensitive, specific, reproducible, and quantitative measurements of proteins and peptides in complex biological matrices such as plasma.
Design of a wideband orthomode transducer

The design of an offset ridge quad-ridged waveguide (QRWG) orthomode transducer (OMT) is presented. By offsetting one of the ridges in the direction of propagation, a much wider single mode operating bandwidth can be achieved than that achievable in a traditional symmetric QRWG OMT's. This wide single mode operating bandwidth ensures that no higher order modes are excited at the feeds of the OMT, which in turn eliminates unwanted resonances often observed in traditional QRWG OMT's. The performance of the OMT is similar to that of traditional types, with reflections below −20 dB and cross coupling below −40 dB across most of the desired 1.7∶1 bandwidth.