gebhart/patrepeval huggingface dataset:
Community‐Associated Methicillin‐ResistantStaphylococcus aureus:The Way to the Wound Is through the Nose (2005)

time, ∼30% of all persons are colonized with S. aureus, with the anterior nares serving as its critical niche [3]. Although colonization typically precedes infection, relatively few colonized individuals develop staphylococcal infections. There are, undoubtedly, a variety of host-organism interactions that play a role in this symbiosis; yet, much of what is known has been derived from the study of persons with clinical disease, not those in
Evaluation of 2′-hydroxyl protection in RNA-synthesis using the H-phosphonate approach (1994)

A number of different protecting groups were compared with respect to their usefulness for protection of 2'-hydroxyl functions during synthesis of oligoribonucleotides using the H-phosphonate approach. The comparison was between the t-butyldimethylsilyl (t-BDMSi), the o-chlorobenzoyl (o-CIBz), the tetrahydropyranyl (THP), the 1-(2-fluorophenyl)-4-methoxypiperidin-4-yl (Fpmp), the 1-(2-chloro-4-methylphenyl)-4-methoxypiperidin-4-yl (Ctmp), and the 1-(2-chloroethoxy)ethyl (Cee) protecting groups. All these groups were tested in synthesis of dodecamers, (Up)11U and (Up)11A, using 5'-O-(4-monomethoxytrityl) or (4,4'-dimethoxytrityl) uridine H-phosphonate building blocks carrying the respective 2'-protection. The performance of the t-BDMSi and o-CIBz derivatives were also compared in synthesis of (Up)19U. The most successful syntheses were clearly those where the t-butyldimethylsilyl group was used. The o-chlorobenzoyl group also gave satisfactory results but seems somewhat limited with respect to synthesis of longer oligomers. The results with all tested acetal derivatives (Fpmp, Ctmp, Cee, THP) were much less successful due to some accompanying cleavage of internucleotidic H-phosphonate functions during removal of 5'-O-protection (DMT).
Identification and Characterization of an RNA-Dependent RNA Polymerase Activity within the Nonstructural Protein 5B Region of Bovine Viral Diarrhea Virus (1998)

Nonstructural protein 5B (NS5B) of bovine viral diarrhea virus (BVDV) contains sequence motifs that are predictive of an RNA-dependent RNA polymerase activity. We describe the expression and purification of the BVDV NS5B protein derived from an infectious cDNA clone of BVDV (NADL strain). BVDV NS5B protein was active in an in vitro RNA polymerase assay using homopolymeric RNA or BVDV minigenomic RNA templates. The major product was a covalently linked double-stranded molecule generated by a "copy-back" mechanism from the input template RNA. In addition, a nucleotide-nonspecific and template-independent terminal nucleotidyl transferase activity was observed with the BVDV NS5B preparation.
Stress enhances the sensitivity of Salmonella enterica serovar Typhimurium to bacteriocins (2015)

Food preservation methods sensitized Gram-negative bacteria to bacteriocins activity, which demonstrate the potential of nisin and bovicin HC5 to inhibit the growth of Salmonella.
Influences of tissue absorption and scattering on diffuse correlation spectroscopy blood flow measurements (2011)

In this study we evaluate the influences of optical property assumptions on near-infrared diffuse correlation spectroscopy (DCS) flow index measurements. The optical properties, absorption coefficient (µ(a)) and reduced scattering coefficient (µ(s)'), are independently varied using liquid phantoms and measured concurrently with the flow index using a hybrid optical system combining a dual-wavelength DCS flow device with a commercial frequency-domain tissue-oximeter. DCS flow indices are calculated at two wavelengths (785 and 830 nm) using measured µ(a) and µ(s)' or assumed constant µ(a) and µ(s)'. Inaccurate µ(s)' assumptions resulted in much greater flow index errors than inaccurate µ(a). Underestimated/overestimated µ(s)' from -35%/+175% lead to flow index errors of +110%/-80%, whereas underestimated/overestimated µ(a) from -40%/+150% lead to -20%/+40%, regardless of the wavelengths used. Examination of a clinical study involving human head and neck tumors indicates up to +280% flow index errors resulted from inter-patient optical property variations. These findings suggest that studies involving significant µ(a) and µ(s)' changes should concurrently measure flow index and optical properties for accurate extraction of blood flow information.
Synthesis of novel conjugated polymers comprising modified cyclopentadithiophene units in the main chain (2017)

We have synthesized novel copolymers P1–P3 comprising fluorene units alternating with cyclopentadithiophene fragments modified at the bridge positions with cyanovinyl or imine groups. Optoelectronic properties of the polymers were investigated in solution and in solid films. A potential of using these materials in organic electronics was considered.
Impact of technology scaling in the clock system power (2003)

The clock distribution and generation circuitry is known to consume more than a quarter of the power budget of existing microprocessors. A previously derived clock energy model is briefly reviewed while a comprehensive framework for the estimation of systemwide (chip level) and clock sub-system power as function of technology scaling is presented. This framework is used to study and quantify the impact that various intensifying concerns associated with scaling (i.e., increased leakage currents, increased interwire capacitance) will have on clock energy and their relative impact on the overall system energy. The results obtained indicate that clock power will remain a significant contributor to the total chip power, as long as techniques are used to limit leakage power consumption.
Interleukin-12 augments cytolytic activity of peripheral blood lymphocytes from patients with hematologic and solid malignancies (1993)

Interleukin-12 (IL-12) is a heterodimeric 70-kD cytokine that can enhance the activity of cytotoxic effector cells. Although IL-12 shares some functional properties with interleukin-2 (IL-2), it appears to act via a distinct mechanism. In this report, we examined the effects of IL- 12 on the cytolytic activity and proliferation of peripheral blood mononuclear cells (PBMC) obtained from patients with malignant disease. PBMC from two groups of patients were evaluated. The first group consisted of 12 individuals with metastatic solid tumors. PBMC from these patients demonstrated a marked defect in their ability to lyse natural killer (NK)-sensitive targets (K562) compared with normal volunteers. Overnight incubation with IL-12 (35 pmol/L) corrected this defect. The effect of 35 pmol/L of IL-12 on cytotoxicity was similar to that of 3 nmol/L of IL-2. In contrast, this concentration of IL-12 had little effect on cytolytic activity against an NK-resistant cell line (COLO 205). When IL-12 was added to PBMC obtained from cancer patients who were being treated with low-dose IL-2 in vivo, a dramatic increase in cytolytic activity against both NK-sensitive and -resistant tumor targets was observed. Unlike IL-2, IL-12 failed to stimulate proliferation of resting PBMC from cancer patients significantly. The second group of patients we studied comprised 13 patients who had recently undergone allogeneic bone marrow transplantation (BMT) for hematologic malignancy. In resting PBMC from these transplant recipients, IL-12 was capable of enhancing cytotoxicity against both NK- sensitive and -resistant tumor targets. Our findings indicate that IL- 12 can restore defective NK activity of PBMC from patients with metastatic cancer, as well as enhance cytolytic function of PBMC from patients after allogeneic BMT. The clinical use of IL-12 as an immunomodulator in patients with malignancy merits further consideration.
A 1-V integrated current-mode boost converter in standard 3.3/5-V CMOS technologies (2005)

A 1-V integrated CMOS current-mode boost converter implemented in a standard 3.3/5-V 0.6-/spl mu/m CMOS technology (V/sub TH//spl ap/0.85 V), providing power-conversion efficiency of higher than 85% at 100-mA output current, is presented in this paper. The high-performance boost converter is successfully developed due to three proposed low-voltage circuit structures, including an inductor-current sensing circuit for current-mode operation with accuracy of higher than 94%, a precision V-I converter for compensation-ramp generation in current-mode control, and a VCO providing supply-independent clock and ramp signals. Moreover, a proposed startup circuit enables proper converter startup within a sub-1-V supply condition.
Pyrophosphoryl Derivatives of 1-(2-Deoxy-3-O-Phosphonomethyl-β-and-α-D-Erythro-Pentofuranosyl)Thymine: Synthesis and Substrate Properties Towards Some DNA Polymerases (2000)

The synthesis of 1-(2-deoxy-3-O-phosphonomethyl-beta-D-erythropentofuranosyl)thymine (17) and its alpha-anomer 18 is described. Attempts to prepare 1-[2-deoxy-3-O-(pyrophosphoryl)phosphonomethyl-beta-D-erythro-pentofuranosyl]thymine (19) by an activation of the respective phosphonate 17 with 1,1'-carbonyldiimidazole (Im2CO) resulted in the quantitative formation of the corresponding pyrophosphonate derivative 21 (Scheme 2). Activation of inorganic pyrophosphate with Im2CO followed by the condensation with the phosphonates 17 and 18 afforded the desired analogues of nucleoside triphosphate 19 (35%) and its alpha-anomer 20 (27%) along with the respective pyrophosphonate derivatives 21 (37%) and 24 (38%) (Scheme 3). It was found that compounds 19 and 20 display (i) no substrate properties toward calf thymus terminal deoxynucleotidyl transferase (TDT) and AMV reverse transcriptase, and (ii) moderate substrate activity with E. coli DNA polymerase I (Klenow fragment).
Identification of cell adhesive active sites in the N-terminal domain of thrombospondin-1 (1997)

Using a series of fusion proteins that span almost all of the thrombospondin-1 (TSP-1) molecule, we observed in this study that Chinese hamster ovary (CHO) K1 cells strongly attached to the N-terminus but not to the other domains of TSP-1 (e.g. the C-terminus, and type 1, type 2 and type 3 repeats). In addition, attachment to the N-terminus of CHO S745 cells defective in cell-surface glycosaminoglycans (GAGs) was decreased by 47% compared with that observed with CHO K1 cells, indicating the presence of GAG-dependent cell adhesive sites. With the aim of identifying these cell adhesive sites, a series of synthetic peptides, overlapping heparin-binding sequences ARKGSGRR (residues 22-29), MKKTRG (residues 79-84) and TRDLASIARLRIAKGVNDNF (residues 170-189), were synthesized and tested for their ability to support CHO cell attachment. Using both centrifugation and cell-attachment assays, MKKTRG-containing peptides promoted CHO K1 cell adhesion, while ARKGSGRR-containing peptides and peptide TRDLASIARLRIAKGVNDNF did not. CHO S745 cell attachment to MKKTRG-containing peptides was partially decreased. A 36% decrease in CHO K1 cell attachment to the N-terminus was also observed when the heparin-binding consensus sequence KKTR was mutated to QNTR. In addition, peptide MKKTRG partially inhibited (25% inhibition) CHO K1 cell attachment to the N-terminus. However, peptide MKKTRG was not sufficient to fully promote cell attachment to the N-terminus of TSP-1. Peptides VDAVRTEKGFLLLASLRQ and TLLALERKDHS also supported CHO K1 cell attachment in a GAG-dependent and -independent manner respectively. Moreover, CHO K1 cell attachment to MKKTRG was found to be markedly enhanced when flanked with the sequences VDAVRTEKGFLLLASLRQ and TLLALERKDHS. Peptide VDAVRTEKGFLLLASLRQMKKTRG nearly abolished (98% inhibition) CHO K1 cell attachment to the N-terminus, while peptides MKKTRG, MKKTRGTLLALERKDHS and VDAVRTEKGFLLLASLRQ had only a moderate inhibitory effect (25, 27 and 53% inhibition respectively). These data indicate that the sequence VDAVRTEKGFLLLASLRQMKKTRGTLLALERKDHS (residues 60-94) constitutes a GAG-dependent cell adhesive site in the N-terminus of TSP-1. Moreover, a GAG-independent site, encompassing residues 189-200 (FQGVLQNVRFVF), has been identified. These two adhesive sites supported the attachment of a wide variety of cells (human breast carcinoma, melanoma and osteosarcoma cells), and a high degree of sequence homology was found between TSP-1 and TSP-2 between residues 60 and 94 (48% identity) and 189-200 (67% identity), further suggesting the functional importance of these two cell adhesive sites in the N-terminus of TSP-1.
Novel Pharmacologic Strategies in the Treatment of Experimental Traumatic Brain Injury: 1998 (1998)

The mechanisms underlying secondary or delayed cell death following traumatic brain injury are poorly understood. Recent evidence from experimental models suggests that widespread neuronal loss is progressive and continues in selectively vulnerable brain regions for months to years after the initial insult. The mechanisms underlying delayed cell death are believed to result, in part, from the release or activation of endogenous "autodestructive" pathways induced by the traumatic injury. The development of sophisticated neurochemical, histopathological and molecular techniques to study animal models of TBI have enabled researchers to begin to explore the cellular and genomic pathways that mediate cell damage and death. This new knowledge has stimulated the development of novel therapeutic agents designed to modify gene expression, synthesis, release, receptor or functional activity of these pathological factors with subsequent attenuation of cellular damage and improvement in behavioral function. This article represents a compendium of recent studies suggesting that modification of post-traumatic neurochemical and cellular events with targeted pharmacotherapy can promote functional recovery following traumatic injury to the central nervous system.
Induction of split tolerance and clinical cure in high-responding hemophiliacs with factor IX antibodies. (1986)

An approach to the problem of inducing tolerance in patients with hemophilia complicated by high-responding antibodies is described. Thus, in four patients with severe hemophilia B and high-responding antibodies against factor IX, it has been possible to modify the immune response by giving high doses of intravenous IgG in combination with cyclophosphamide and factor IX, followed by regular factor IX treatment. In three of the patients, the in vivo recovery and half-life of infused factor IX coagulant activity (IX:C) are now normal, while the fourth patient has been converted to a low responder. Hip replacement surgery has been performed successfully in one patient. The tolerant state in these four patients is characterized, and they have all been found to have complexes between factor IX antigen and a "new" antibody without IX:C inhibitory activity. The disappearance rate of the complexed factor IX antigen (i.e., lacking IX:C activity) is considerably prolonged, and the persistence in the circulation of this (probably modified) factor IX molecule may be crucial, since tolerance to factor IX treatment was only induced when immunocomplexes were produced. Since earlier treatment of the patients with cyclophosphamide and factor IX, but without IgG, failed to induce tolerance, it appears to be the IgG that is the prerequisite.
A universal, vector-based system for nucleic acid reading-frame selection (2002)

The identification of a nucleic acid sequence's correct reading frame has important implications for homology-independent protein engineering techniques such as incremental truncation and SCRATCHY. We report the development and experimental implementation of a general in-frame selection system, pSALect, a plasmid vector that utilizes two marker sequences flanking the DNA of interest. This dual selection approach overcomes inconsistencies observed with traditional C-terminally fused reporter proteins. In the pSALect vector, sequences of interest are positioned between an N-terminal Tat-signal sequence and a C-terminal beta-lactamase reporter. In-frame selection of the resulting three-domain protein is performed by growing colonies on ampicillin-containing plates, requiring full-length translation in order to link covalently the signal sequence to the lactamase for export into the periplasm. This dual selection scheme has been validated successfully using defined sequences of glycinamide ribonucleotide formyltransferases (GARTs) from Escherichia coli and human and, in contrast to C-terminal fusion systems, proved effective when applied towards the selection of in-frame constructs in an incremental truncation library.
Peptide-based vaccination: where do we stand? (2005)

The manipulation of peptide epitopes may provide a strategy for the rational design of peptide allergy vaccines further improving safety and efficacy.
Preliminary study on helical CT algorithms for patient motion estimation and compensation (1995)

Helical computed tomography (helical/spiral CT) has replaced conventional CT in many clinical applications. In current helical CT, a patient is assumed to be rigid and motionless during scanning and planar projection sets are produced from raw data via longitudinal interpolation. However, rigid patient: motion is a problem in some cases (such as in the skull base and temporal bone imaging). Motion artifacts thus generated in reconstructed images can prevent accurate diagnosis. Modeling a uniform translational movement, the authors address how patient motion is ascertained and how it may be compensated. First, mismatch between adjacent fan-beam projections of the same orientation is determined via classical correlation, which is approximately proportional to the patient displacement projected onto an axis orthogonal to the central ray of the involved fan-beam. Then, the patient motion vector (the patient displacement per gantry rotation) is estimated from its projections using a least-square-root method. To suppress motion artifacts, adaptive interpolation algorithms are developed that synthesize full-scan and half-scan planar projection data sets, respectively. In the adaptive scheme, the interpolation is performed along inclined paths dependent upon the patient motion vector. The simulation results show that the patient motion vector can be accurately and reliably estimated using the authors' correlation and least-square-root algorithm, patient motion artifacts can be effectively suppressed via adaptive interpolation, and adaptive half-scan interpolation is advantageous compared with its full-scan counterpart in terms of high contrast image resolution.
Nitric oxide neurotoxicity in neurodegenerative diseases (2004)

Nitric oxide (nitrogen monoxide; NO) is a simple molecule with diverse biological functions. NO and related reactive nitrogen oxide species (RNOS) mediate intricate physiological and pathophysiological effects in the central nervous system. Depending on environmental conditions, NO and RNOS can initiate and mediate neuroprotection or neurotoxicity either exclusively or synergistically with other effectors. The focus of this review is limited to the neuroprotectant/neurotoxic role of NO in Acquired Immune Deficiency Syndrome (AIDS) Dementia Complex (aka HIV--Associated Dementia; HAD) Amyotrophic Lateral Sclerosis (aka Lou Gehrig's Disease), Alzheimer's Disease, Huntington's Disease, Multiple Sclerosis and Parkinson's Disease. This review will shed light on the question: "How important is NO in neurodegenerative diseases?"
Transparent Triboelectric Nanogenerators and Self-Powered Pressure Sensors Based on Micropatterned Plastic Films (2012)

Transparent, flexible and high efficient power sources are important components of organic electronic and optoelectronic devices. In this work, based on the principle of the previously demonstrated triboelectric generator, we demonstrate a new high-output, flexible and transparent nanogenerator by using transparent polymer materials. We have fabricated three types of regular and uniform polymer patterned arrays (line, cube, and pyramid) to improve the efficiency of the nanogenerator. The power generation of the pyramid-featured device far surpassed that exhibited by the unstructured films and gave an output voltage of up to 18 V at a current density of ∼0.13 μA/cm(2). Furthermore, the as-prepared nanogenerator can be applied as a self-powered pressure sensor for sensing a water droplet (8 mg, ∼3.6 Pa in contact pressure) and a falling feather (20 mg, ∼0.4 Pa in contact pressure) with a low-end detection limit of ∼13 mPa.
Forecasting Time Series Water Levels on Mekong River Using Machine Learning Models (2015)

Forecasting water levels on Mekong river is an important problem needed to be studied for flood warning. In this paper, we investigate the application to forecasting of daily water levels at Thakhek station on Mekong river using machine learning models such as LASSO, Random Forests and Support Vector Regression (SVR). Experimental results showed that SVR was able to achieve feasible results, the mean absolute error of SVR is 0.486(m) while the acceptable error of a flood forecast model required by the Mekong River Commission is between 0.5(m) and 0.75(m).
Mechanisms of cytomegalovirus-mediated myelosuppression: perturbation of stromal cell function versus direct infection of myeloid cells. (1990)

Infection with cytomegalovirus (CMV) continues to be one of the most common complications following allogeneic bone marrow transplantation. To study the role of CMV in the suppression of hemopoiesis that frequently accompanies infection, we investigated the effect of CMV on the growth of isolated committed myeloid progenitors and on hemopoiesis in long-term bone marrow cultures. Laboratory strain AD169 had no effect on the growth and development of progenitor cells. In contrast, 40% of clinical isolates of CMV inhibited colony formation by up to 100%. In long-term bone marrow cultures all CMV isolates resulted in myelosuppression, which in the majority of cases was associated with the infection of stromal elements. Analysis of RNA from stromal cells infected with AD169 and one clinical isolate demonstrated a specific deficiency of granulocyte colony-stimulating factor transcripts. For a small proportion of the clinical isolates tested in long-term bone marrow cultures, suppression of hemopoiesis was correlated with infection of developing granulocytes. These studies suggest that CMV can impair hemopoiesis either through infection of stromal cells and consequent perturbation of growth factor production or by direct infection of myeloid cells.
DNA Sequencing Protocols (2001)

Since the publication of the first edition of DNA Sequencing Protocols in 1993, major advances in its technology have made PCR-based semiautomated fluorescent sequencing the norm and enabled the complete sequencing of complex genomes. In DNA Sequencing Protocols, 2nd Edn., Colin Graham and a team of leading investigators and expert clinical scientists update the first edition with a collection of powerful, up-to-date PCR-based methods for DNA sequencing, many suitable for human genome sequencing and mutation detection in human disease. Each method provides detailed, step-by-step instructions to ensure successful results, and includes helpful notes identifying and addressing potential problems. This second edition offers new material on automated DNA sequencers, capillary DNA sequencers, heterozygote mutation detection, web-based sequencing databases and genome sequencing sites, and the human genome project. State-of-the-art and highly practical, DNA Sequencing Protocols, 2nd Edn. constitutes an essential laboratory handbook for geneticists and molecular biologists, offering concise, easy-to-follow methods that will impact today's genome sequencing projects, improve the accuracy and quality of DNA sequences obtained by smaller laboratories, and help lay the foundation for molecular diagnostics