gebhart/patrepeval huggingface dataset:
Laser photobioactivation mechanisms: In vitro studies using ascorbic acid uptake and hydroxyproline formation as biochemical markers of irradiation response (1990)

Clinical investigations of laser photobioactivation, or biostimulation, might be differently designed and more fruitful if knowledge of basic biochemical mechanisms were better understood. In this investigation, biochemical events identified as responses to 904 nm irradiation included increased ascorbic acid uptake by fibroblasts. These cells also showed increased hydroxyproline formation, and this was increased several-fold by the addition of proline to the medium. Maximum biochemical responses were observed at a pulse frequency of 67 Hz and a pulse width of 150 nsec with an energy density of approximately 7 mJ/cm2 per exposure. Elements in the mitochondrial cytochrome system are proposed as the radiation absorbing chromophore(s). Hypothetically, the energy generated is linked to ascorbic acid uptake, which in turn stimulates collagen synthesis.
Nonstructural Proteins 1 and 2 of Respiratory Syncytial Virus Suppress Maturation of Human Dendritic Cells (2008)

Human respiratory syncytial virus (RSV) is the most important agent of serious pediatric respiratory tract disease worldwide. One of the main characteristics of RSV is that it readily reinfects and causes disease throughout life without the need for significant antigenic change. The virus encodes nonstructural protein 1 (NS1) and NS2, which are known to suppress type I interferon (IFN) production and signaling. In the present study, we monitored the maturation of human monocyte-derived myeloid dendritic cells (DC) following inoculation with recombinant RSVs bearing deletions of the NS1 and/or NS2 proteins and expressing enhanced green fluorescent protein. Deletion of the NS1 protein resulted in increased expression of cell surface markers of DC maturation and an increase in the expression of multiple cytokines and chemokines. This effect was enhanced somewhat by further deletion of the NS2 protein, although deletion of NS2 alone did not have a significant effect. The upregulation was largely inhibited by pretreatment with a blocking antibody against the type I IFN receptor, suggesting that suppression of DC maturation by NS1/2 is, at least in part, a result of IFN antagonism mediated by these proteins. Therefore, this study identified another effect of the NS1 and NS2 proteins. The observed suppression of DC maturation may result in decreased antigen presentation and T-lymphocyte activation, leading to incomplete and/or weak immune responses that might contribute to RSV reinfection.
Editorial Statement (2007)

APSA is pleased to announce the next editorial team for American Political Science Review . The new team, to be located at UCLA, will begin their term on July 1, 2007. Their Editorial Statement follows. Lee Sigelman, the current APSR editor, and his team at George Washington University will conclude their term in August 2007. The transition from the Sigelman's GWU team to the UCLA team will be complete by the end of the calendar year, and the change will be reflected on the APSR masthead commencing with the first issue of Volume 102 in February of 2008.
Neutrophils in innate host defense against Staphylococcus aureus infections (2011)

Staphylococcus aureus has been an important human pathogen throughout history and is currently a leading cause of bacterial infections worldwide. S. aureus has the unique ability to cause a continuum of diseases, ranging from minor skin infections to fatal necrotizing pneumonia. Moreover, the emergence of highly virulent, drug-resistant strains such as methicillin-resistant S. aureus in both healthcare and community settings is a major therapeutic concern. Neutrophils are the most prominent cellular component of the innate immune system and provide an essential primary defense against bacterial pathogens such as S. aureus. Neutrophils are rapidly recruited to sites of infection where they bind and ingest invading S. aureus, and this process triggers potent oxidative and non-oxidative antimicrobial killing mechanisms that serve to limit pathogen survival and dissemination. S. aureus has evolved numerous mechanisms to evade host defense strategies employed by neutrophils, including the ability to modulate normal neutrophil turnover, a process critical to the resolution of acute inflammation. Here we provide an overview of the role of neutrophils in host defense against bacterial pathogens and discuss strategies employed by S. aureus to circumvent neutrophil function.
Fewer thymic changes in MuSK antibody‐positive than in MuSK antibody‐negative MG (2005)

In generalized myasthenia gravis (MG) patients without detectable acetylcholine receptor (AChR) antibodies (SNMG), the thymus is often reported as "normally involuted." We analyzed thymic compartments in 67 patients with generalized MG, with AChR antibodies (AChR+, n = 23), with muscle-specific kinase (MuSK) antibodies (MuSK+, n = 14) or with neither (MuSK-, n = 30), and in 11 non-MG controls. Four of 14 MuSK+ thymi had rare small germinal centers, but overall they were not different from age-matched controls. However, approximately 75% MuSK- samples showed lymph node-type infiltrates similar to those in AChR+ patients, but with fewer germinal centers. These variations may explain some apparent differences in responses to thymectomy in SNMG.
Dual-Energy Contrast-enhanced Digital Subtraction Mammography: Feasibility (2003)

A technique for demonstrating breast cancers, dual-energy contrast agent-enhanced digital subtraction mammography, was performed in 26 subjects with mammographic or clinical findings that warranted biopsy. The technique consists of high-energy and low-energy digital mammography after administration of iodinated contrast agent. Weighted subtraction of the logarithmic transform of these images is then performed to obtain an image that preferentially shows iodine. Of the 26 subjects, 13 had invasive cancers. Eleven of these tumors enhanced strongly, one enhanced moderately, and one enhanced weakly. The duct in one patient with ductal carcinoma in situ was weakly enhancing. In the other 12 patients, benign tissue enhanced diffusely in two and weakly focally in two. These results indicate that the technique is feasible and worthy of further study.
Increased Expression of Erythropoiesis Inhibiting Cytokines (IFN-γ, TNF-α, IL-10, and IL-13) by T Cells in Patients Exhibiting a Poor Response to Erythropoietin Therapy (2003)

Resistance to recombinant human erythropoietin occurs in a small but important proportion of hemodialysis patients. This may be due to increased immune activation because pro-inflammatory cytokines inhibit erythropoiesis in vitro. Using FACScan flow cytometry, the proportion of PMA/ionomycin-stimulated T cells expressing cytokines ex vivo was compared in 18 poor responders to erythropoietin, 14 good responders to erythropoietin, and 14 normal controls. CD4(+) T cells from poor responders expressed more interferon-gamma (IFN-gamma; 19 +/- 6%) compared with good responders (11 +/- 6%, P < 0.001) and controls (12 +/- 6%, P < 0.01). Similarly, CD4+ T cells from poor responders expressed more tumor necrosis factor-alpha (TNF-alpha; poor responders: 51 +/- 19% versus good responders: 27 +/- 15% [P < 0.01] and controls: 30 +/- 19% [P < 0.01]). CD4+ expression of IL-10 was also enhanced (poor responders: 1.6 +/- 1.1% versus good responders: 0.7 +/- 0.6% [P < 0.05] and controls: 0.5 +/- 0.2% [P < 0.01]). Likewise, CD4+ expression of interleukin-13 (IL-13) was increased (poor responders: 4.4 +/- 4.2% versus good responders: 1.6 +/- 1.7% [P < 0.05] and controls: 1.6 +/- 1.5% [P < 0.05]). CD8+ T cells from poor responders also showed enhanced expression of cytokines. For IFN-gamma, poor responder expression was 48 +/- 20% compared with 31 +/- 17% (P < 0.05) for good responders and 23 +/- 15% (P < 0.01) for controls. TNF-alpha expression for poor responders was 41 +/- 21% versus 25 +/- 14% for good responders (P < 0.05) and 21 +/- 15% for controls (P < 0.01). IL-10 expression for poor responders was 2.0 +/- 1.2% (good responders: 0.7 +/- 0.6% [P < 0.01]; controls: 0.5 +/- 0.2% [P < 0.001]). These data indicate that T cells from poor responders are in an enhanced activation state possibly as a result of chronic inflammation. In the absence of any other cause (such as iron deficiency), the overproduction of cytokines may account for hyporesponsiveness to erythropoietic therapy in patients with renal failure.
Effect of iron restriction on the outer membrane proteins of Actinobacillus (Haemophilus) pleuropneumoniae (1989)

The outer membrane protein profile of Actinobacillus (Haemophilus) pleuropneumoniae grown under iron-restricted and iron-replete conditions was studied by polyacrylamide gel electrophoresis and immunoblotting. A virulent serotype 1 isolate synthesized a novel protein with an apparent molecular weight of 105,000 (105K) and increased the synthesis of a 76K protein under iron-restricted conditions. Both proteins were synthesized within 15 min of establishment of iron-restricted conditions. Proteins of equivalent molecular weights could also be induced by iron restriction in serotype 2, 3, 4, 5, and 7 isolates of A. pleuropneumoniae. Convalescent-phase sera from serotype 1-infected pigs contained antibodies which recognized both the 105K and 76K proteins from all six serotypes examined, indicating that these proteins were expressed in vivo and were immunologically conserved. Cells expressing the 105K and 76K proteins also displayed an enhanced ability to bind Congo red and hemin, suggesting that one or both of these proteins functioned to acquire complexed iron during in vivo growth.
A conformal Bayesian network for classification of Mycobacterium tuberculosis complex lineages (2010)

CBN conforms to the available PCR-based biological markers and achieves high performance in identifying major lineages of MTBC. The method can be readily extended as new biomarkers are introduced for TB tracking and control. An online tool (http://www.cs.rpi.edu/~bennek/tbinsight/tblineage) makes the CBN model available for TB control and research efforts.
In Vitro and In Vivo Activities of Macrolide Derivatives against Mycobacterium tuberculosis (2005)

Existing macrolides have never shown definitive clinical efficacy in tuberculosis. Recent reports suggest that ribosome methylation is involved in macrolide resistance in Mycobacterium tuberculosis, a mechanism that newer macrolides have been designed to overcome in gram-positive bacteria. Therefore, selected macrolides and ketolides (descladinose) with substitutions at positions 9, 11,12, and 6 were assessed for activity against M. tuberculosis, and those with MICs of < or = 4 microM were evaluated for cytotoxicity to Vero cells and J774A.1 macrophages. Several compounds with 9-oxime substitutions or aryl substitutions at position 6 or on 11,12 carbamates or carbazates demonstrated submicromolar MICs. For the three macrolide-ketolide pairs, macrolides demonstrated superior activity. Four compounds with low MICs and low cytotoxicity also effected significant reductions in CFU in infected macrophages. Active compounds were assessed for tolerance and the ability to reduce CFU in the lungs of BALB/c mice in an aerosol infection model. A substituted 11,12 carbazate macrolide demonstrated significant dose-dependent inhibition of M. tuberculosis growth in mice, with a 10- to 20-fold reduction of CFU in lung tissue. Structure-activity relationships, some of which are unique to M. tuberculosis, suggest several synthetic directions for further improvement of antituberculosis activity. This class appears promising for yielding a clinically useful agent for tuberculosis.
Resonant optical transmission and coupling in phase-locked diode laser arrays of antiguides: The resonant optical waveguide array (1989)

Uniform linear arrays of antiguides have 100% optical transmission between elements when the interelement spacing is an integer number of leaky wave half-wavelengths in the lateral direction. Resonant in-phase-mode and out-of-phase-mode coupling occurs when the number of half-wavelengths is odd and even, respectively. Such devices are called resonant optical waveguide (ROW) arrays. The discrimination between the resonant array mode and adjacent array modes reaches a maximum in close proximity to the resonance. An AlGaAs/GaAs ROW diode laser array operating close to resonance is demonstrated. Devices with virtually uniform near-field intensity profiles operate in stable, diffraction-limited in-phase modes to drive levels in excess of three times threshold.
Push-Sum Distributed Dual Averaging for convex optimization (2012)

Recently there has been a significant amount of research on developing consensus based algorithms for distributed optimization motivated by applications that vary from large scale machine learning to wireless sensor networks. This work describes and proves convergence of a new algorithm called Push-Sum Distributed Dual Averaging which combines a recent optimization algorithm [1] with a push-sum consensus protocol [2]. As we discuss, the use of push-sum has significant advantages. Restricting to doubly stochastic consensus protocols is not required and convergence to the true average consensus is guaranteed without knowing the stationary distribution of the update matrix in advance. Furthermore, the communication semantics of just summing the incoming information make this algorithm truly asynchronous and allow a clean analysis when varying intercommunication intervals and communication delays are modelled. We include experiments in simulation and on a small cluster to complement the theoretical analysis.
Cas-Database: web-based genome-wide guide RNA library design for gene knockout screens using CRISPR-Cas9 (2016)

Supplementary data are available at Bioinformatics online.
High-Temperature Seedless Synthesis of Gold Nanorods (2006)

We demonstrate seedless synthesis of gold nanorods at high temperatures up to 97 degrees C. Using the correct silver nitrate concentration is crucial for formation of rod-shaped particles at all temperatures. We observed a decrease of nanorod length with increasing temperature, while the width stays constant throughout the temperature range. From kinetics studies, we show 3 orders of magnitude increase in nanorod growth rate when the temperature is raised from room temperature to 97 degrees C. From the temperature dependence of the growth rate, we obtain a average activation energy for growth on all facets of 90 +/- 10 kJ mol(-1). High-temperature synthesis of gold nanorods presents a more attractive method for scalable flow-based production of gold nanorods.
Synthesis of a Site-Specific Deuterium Substituted Methyl β-D-Glucan Decasaccharide (1993)

Abstract Synthesis of a (β-D-glucan decasaccharide, with alternating (β-1,3 and (β-1,4-linkages, is described. The decasaccharide is fully C-deuterated except for the central cellobiose residue. The main glycosylation methods used were activation of glycosyl bromides with silver triflate or activation of thioglycosides with dimethyl(methylthio)sulfonium triflate (DMTST). In order to establish the anomeric configuration of the various oligosaccharide derivatives, a fully C-protonated decasaccharide was also synthesized by a parallel route.
Transfer of clinically relevant gene expression signatures in breast cancer: from Affymetrix microarray to Illumina RNA-Sequencing technology (2014)

To our knowledge, this is the first study to report a systematic comparison of RNA-Seq to microarray for the evaluation of single genes and GES clinically relevant to BC. According to our results, the vast majority of single gene biomarkers and well-established GES can be reliably evaluated using the RNA-Seq technology.
Expression of heparanase mRNA in bovine placenta during gestation (2001)

This study reports the identification and sequence of a partial cDNA for bovine heparanase and the expression of its mRNA in the placenta during gestation. The 364 amino acid residues deduced from the 1092 bp cDNA fragment share 81.9% and 80.5% identity with amino acid sequences of human and rat heparanase, respectively. Northern blot hybridization showed that two mRNAs (2.0 and 3.5 kb) are strongly expressed in placenta, and weakly expressed in the kidney, lung, spleen and non-pregnant uterus. In the placenta, these transcripts were detected in the cotyledon at all stages of gestation examined, and in the intercotyledonary fetal membrane and caruncle on day 60, day 120 and day 260. Quantitative real-time RT-PCR analysis showed very low expression of heparanase mRNA in the conceptus before implantation (day 17), but high expression in the cotyledon-containing fetal membrane (days 27-34) after implantation. Furthermore, heparanase mRNA was detected in the cotyledon, intercotyledonary fetal membrane and caruncle after days 60-64 of gestation. However, no significant expression of heparanase mRNA was observed in intercaruncular endometrium at all stages of gestation examined. These results demonstrate that heparanase mRNA is expressed in the placentome, indicating that heparanase may play a role in implantation, and in placental development and function.
Analysis of Human Skin Emanations by Gas Chromatography/Mass Spectrometry. 1. Thermal Desorption of Attractants for the Yellow Fever Mosquito (Aedes aegypti) from Handled Glass Beads (1998)

Handled glass has the ability to collect and concentrate nonaqueous human skin emanations while minimizing the collection of aqueous perspiration. Compounds originating from the skin and collected on glass have previously been found to attract the Aedes aegypti species of mosquito. Therefore, glass beads were used as the medium to collect skin emanations from humans for subsequent chemical analysis. This process consisted of a 5-15-min collection of sample on glass beads, followed by loading the beads into a gas chromatograph (GC) injector insert for subsequent desorption of the collected compounds onto the GC column. After cryofocusing by liquid nitrogen at the head of the column, the thermally desorbed compounds were analyzed by GC/MS. Microscale purge and trap introduction was also used to provide complementary information. In this case, the beads are held in a round-bottom flask, purged with nitrogen, and heated as the concentrator collects the headspace above the beads. The chromatograms produced by both of these sample introduction methods demonstrate good resolution of a complex sample. Cryofocusing volatiles from handled glass allowed identification of lactic acid, aliphatic fatty acids, and other polar to nonpolar compounds of moderate volatility while purge and trap allowed detection of nonpolar to moderately polar compounds of high volatility.
Separation of Fragments up to 570 Bases in Length by Use of 6% T Non-Cross-Linked Polyacrylamide for DNA Sequencing in Capillary Electrophoresis (1994)

Non-cross-linked polyacrylamide is a very convenient medium for the separation of DNA sequencing fragments in capillary electrophoresis. We demonstrate DNA sequencing with this matrix at an electric field of 200 V/cm and at room temperature. Resolution is observed to decrease exponentially with fragment length. Fragments 570 bases in length generate a resolution of 0.5, which is adequate for sequence identification.
Both RNA level and translation efficiency are reduced by anti-sense RNA in transgenic tobacco (1989)

The effect of anti-sense RNA on the expression of the bialaphos resistance (bar) gene which encodes phosphinothricin acetyl transferase (PAT), was analysed in tobacco. Transient expression studies revealed that an anti-bar RNA with sequence complementarity to the complete bar coding region, inhibits PAT synthesis. To quantify the phenomenon, SR1 tobacco cells were transformed twice to introduce first a hybrid bar gene with a reporter gene and in a second instance an anti-bar gene. A first cycle transformant and a double transformant derived herefrom in which PAT synthesis was reduced to only 8%, were studied in detail. The interference of the anti-sense gene with the expression of the bar gene is manifested at least two levels. First, the bar mRNA steady state level is significantly reduced relative to the parental whereas the transcript level of the reporter gene is unchanged. Comparison of bar mRNA levels in total and single stranded (ss) RNA preparations demonstrated that little if any stably base-pairing bar and anti-bar RNA accumulates. Secondly, a three fold reduction of PAT synthesis per bar mRNA is observed. This supposes that because of unstable interactions with the complementary anti-bar RNA either a substantial part of the bar mRNA detected does not enter the cytoplasm and/or that in the cytoplasm the bar mRNA is less efficiently translated. It is not clear if or how the reduced bar mRNA level is related to such unstable interactions.
An Investigation of the Nucleation/Crystallization Kinetics of Nanosized Colloidal Faujasite Zeolites (2002)

A two-stage varying-temperature technique was utilized to study the nucleation/crystallization kinetics of nanosized faujasite zeolites from clear solutions. At 100 °C, the nucleation period of zeolite Y was determined to be about 6.5 days, which extended over almost the whole period of crystal growth. The crystallization kinetics of colloidal zeolite Y differed from those for another clear solution, colloidal zeolite system, namely, TPA−silicalite-1, where the nucleation and crystal growth were found to occur as separate processes. Despite the occurrence of simultaneous nucleation and crystal growth, the colloidal zeolite Y product had a crystal size distribution similar to that for TPA−silicalite-1. In addition, the influence of the growth-limiting nutrient (Na+) on the crystallization of zeolite Y was investigated. The sodium concentration in the synthesis solution could be controlled below a critical level to avoid the nucleation of zeolite A.
PROMINENT AND SUSTAINED UP-REGULATION OF GP130-SIGNALING CYTOKINES AND OF THE CHEMOKINE MIP-2 IN MURINE RENAL ISCHEMIA-REPERFUSION INJURY1 (2000)

Ischemia-reperfusion injury (IRI) is a major cause of renal dysfunction in both native kidneys and renal allografts. To broaden our understanding of the inflammatory mediators involved in IRI, we used multi-probe RNase protection assays to examine the expression of 26 different cytokine genes in a murine model of renal IRI. We observed that, in addition to up-regulation of IL-1beta and to a lesser extent TNF-alpha, IRI was associated with an intense and sustained up-regulation of three gp130-signaling cytokines, IL-6, IL-11, and leukemia inhibitory factor (LIF), as well as with up-regulation of the neutrophil chemotactic and activating mediator macrophage inflammatory protein (MIP)-2. Macrophage colony-stimulating factor (M-CSF) and monocyte chemoattractant protein (MCP)-1 were also moderately up-regulated after IRI, whereas mRNA levels of several other inflammatory mediators including IL-1alpha, IL-2, IL-4, interferon (IFN)-gamma, GM-CSF, and RANTES were minimally increased or remained undetectable. These findings identify MIP-2 as an attractive target for inhibition of leukocyte recruitment in renal IRI and also suggest a potentially novel role for gp130-mediated signals in IRI.
Vertically oriented GaN-based air-gap distributed Bragg reflector structure fabricated using band-gap-selective photoelectrochemical etching (2005)

A three-period vertically oriented GaN-based air-gap distributed Bragg reflector structure was fabricated using band-gap-selective photoelectrochemical (PEC) etching. The epitaxial structure consisted of an Al0.08Ga0.92N∕(In0.04Ga0.96N∕In0.07Ga0.93N) superlattice structure, wherein the InGaN layers served as sacrificial layers during PEC etching. Microreflectance measurements yielded an average enhancement in the reflected signal of ∼12-fold over the wavelength range of 550–650 nm, when compared with the signal from a dry-etched GaN surface.