gebhart/patrepeval huggingface dataset:
Regulation of intestinal Th17 and Treg cells by gut microbiota (2015)

Dysbiosis, an imbalance in the gut microbiota composition, is significantly associated with inflammatory bowel disease and other immune disorders. Dysbiosis can dysregulate immune system, compromise mucosal barrier integrity, and perpetuate chronic inflammation. Therefore, gut microbiota manipulation could be potentially used for treating various inflammatory diseases. Various intestinal bacteria differentially regulate the development and function of different immune cell populations. In particular, bacterial species falling within clusters VI and XIVa of the class Clostridia affect the generation and function of mucosal regulatory T cells, whereas segmented filamentous bacteria are the strong inducers for T helper 17 cells. This review discusses how the components of the gut microbiota affect the host immune system and disease susceptibility.
Laser-Grooved Backside Contact Solar Cells With 680-mV Open-Circuit Voltage (2004)

In this paper, we demonstrate for the first time the use of the laser-grooved solar cell technology, a proved commercial technology, for the implementation of the rear junction backside contact solar cells. Laser-grooved backside contact solar cells, designated as interdigitated backside buried contact (IBBC) solar cells, have been fabricated on planar, n-type, 1 /spl Omega//spl middot/cm wafers with a single layer SiO/sub 2/ anti-reflection coating, achieving 17% efficiency with open-circuit voltage (V/sub oc/) of more than 680 mV. Front and rear surface recombination velocities of 350 cm/s and 4800 cm/s, and more than 1 ms of post-processing bulk lifetime confirm that commercial laser-grooved solar cell fabrication process is capable of obtaining the efficiency advantages of the rear junction, backside contact design. Moreover, this paper presents a side-by-side comparison between the more conventional double-sided buried contact solar cell and the IBBC solar cell. The advantages of higher short-circuit current in the latter design due to no contact shading loss, and higher V/sub oc/ due to inherently lower surface recombination velocity of the IBBC structure are demonstrated.
Bayesian Pursuit algorithm for sparse representation (2009)

In this paper, we propose a Bayesian pursuit algorithm for sparse representation. It uses both the simplicity of the pursuit algorithms and optimal Bayesian framework to determine active atoms in sparse representation of a signal. We show that using Bayesian Hypothesis testing to determine the active atoms from the correlations leads to an efficient activity measure. Simulation results show that our suggested algorithm has better performance among the algorithms which have been implemented in our simulations in most of the cases.
SWDM PAM4 Transmission Over Next Generation Wide-Band Multimode Optical Fiber (2016)

Two system transmission experiments are reported which indicate the feasibility of transmitting an aggregated speed of >200 Gb/s over a single next-generation wide-band multimode optical fiber (NG-WBMMF) using a shortwave wavelength division multiplexing (SWDM) and a four-level pulse amplitude modulation (PAM4), using optics rated for 25 Gb/s NRZ operation. The first experiment leverages predistorted KR4 51.5625 Gb/s electrical PAM4 signaling generated by an arbitrary waveform generator to drive SWDM TOSAs at 850, 880, 910, and 940 nm. The received optical PAM4 signals are then post processed offline with linear equalizers to improve the eye quality. Detailed analysis of the height and width of the received optical eyes indicates an aggregated 206.25 Gb/s speed is achievable on a single NGWBMMF beyond 150 m. In the second experiment, a commercial PAM4 IC evaluation kit with real-time digital signal processing is adopted to generate and detect PAM4 signals at KP4 FEC rate of 53.125 Gb/s per wavelength. The SWDM wavelength range is extended with additional tests at 980 nm. Pre-FEC BER below threshold of 2.4 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-4</sup> is achieved up to 300 m across all five wavelengths demonstrating an aggregated speed of 265.625 Gb/s over a single MMF.
Peptide Binding and Presentation by Mouse CD1 (1995)

CD1 molecules are distantly related to the major histocompatibility complex (MHC) class I proteins. They are of unknown function. Screening random peptide phage display libraries with soluble empty mouse CD1 (mCD1) identified a peptide binding motif. It consists of three anchor positions occupied by aromatic or bulky hydrophobic amino acids. Equilibrium binding studies demonstrated that mCD1 binds peptides containing the appropriate motif with relatively high affinity. However, in contrast to classical MHC class I molecules, strong binding to mCD1 required relatively long peptides. Peptide-specific, mCD1-restricted T cell responses can be raised, which suggests that the findings are of immunological significance.
Clinical Efficacy of Pimobendan Versus Benazepril for the Treatment of Acquired Atrioventricular Valvular Disease in Dogs (2006)

Seventy-six dogs with clinical acquired atrioventricular valvular disease were evaluated to determine the efficacy of pimobendan (n=41) versus benazepril hydrochloride (n=35) in a randomized, positive-controlled, multicenter study. The study was divided into 56-day and long-term evaluation periods. In a subgroup of dogs with concurrent furosemide treatment (pimobendan [n=31], benazepril [n=25]), the Heart Insufficiency Score improved in favor of pimobendan (P=0.0011), equating to a superior overall efficacy rating (P<0.0001) at day 56. Long-term median survival (i.e., death or treatment failure) for dogs receiving pimobendan was 415 days versus 128 days for dogs not on pimobendan (P=0.0022).
Degradable Disulfide Core-Cross-Linked Micelles as a Drug Delivery System Prepared from Vinyl Functionalized Nucleosides via the RAFT Process (2008)

A nucleosides containing block copolymer, poly(polyethylene glycol methyl ether methacrylate)- block-poly(5'-O-methacryloyluridine) (PPEGMEMA 30- b-PMAU 80) was self-assembled in aqueous medium and cross-linked via RAFT polymerization at 60 degrees C to afford core-cross-linked micelles exhibiting a PPEGMEMA corona and a polynucleotide core. A disulfide cross-linking agent, bis(2-methacryloyloxyethyl)disulfide, was employed to cross-link the structure via the RAFT process resulting in core-shell nanoparticles, which can degrade under reductive conditions. The resulting core-cross-linked micelles readily hydrolyzed into free block copolymers in the presence of dithiothreitol (DTT) in less than 1 h, depending on the concentration of the reducing agent and the amount of cross-linker in the micelle. A small fraction of permanently cross-linked micelle was found as the result of conventional chain transfer to disulfide containing compounds. A model drug, vitamin B 2, was loaded into the micelle. The loading capacity increased with increasing cross-linking degree. The amount of drug released reached 60-70% after 7 h in the presence of DTT (0.65 mM), while the cross-linked micelle in the absence of dithiothreitol shows only a delayed drug release. Cytotoxicity tests confirmed the biocompatibility of the polymers and the residues after reduction.
Synthesis of the Antitumor Agent Aglycon (±)-Calicheamicinone Using an o-Quinone Monoketal Strategy (1998)

Commercially available 5-methoxysalicylic acid 16 was converted into the o-quinone monoketal 21, which was attached to the enediyne 22, resulting in 23. After protection of the tert-alcohol 24 and conversion of the ester 25 to aldehyde 28, treatment with LiN(TMS)2 gave a 1:4 mixture of the 12α- and 12β-ols 29 and 30, respectively. Oxidation of the mixture 29/30 followed by DIBAL-H reduction resulted in exclusive formation of 29. Deprotection of 29 gave 34, which on treatment with Ph2SNH gave the 2-amino adduct 35. Protection of 35 as the tris-Boc derivative 37 followed by intermolecular Wadsworth−Emmons reaction gave the lactone 38. The lactone 38 was converted into the bis-methyl carbamate derivative 52, which was reduced with NaBH4/CeCl3 to give 55. Conversion of the allylic alcohol 55 into the thiol acetate 58 and then to the trisulfide 61 followed previous precedent. Finally, removal of the enol Boc protecting group and the alcohol protecting groups gave (±)-calicheamicinone (2).
Clinicopathological Role of Serum-Derived Hyaluronan-Associated Protein (SHAP)-Hyaluronan Complex in Endometrial Cancer (2011)

The role of hyaluronan (HA), serum-derived HA-associated protein (SHAP)-HA complex and hyaluronan synthase (HAS) in endometrial carcinomas was investigated. The relationship of metalloproteinase (MMP) and its inhibitor (TIMP) with HA and the SHAP-HA complex was also examined. The expression of HAS1 was related to the depth of myometrial invasion and lymph-vascular space involvement. The serum levels of HA, SHAP-HA complex, MMP-9, and TIMP-1 were increased in related with the depth of myometrial invasion, histological grade and lymph-vascular space involvement. They were also higher in the HAS1-positive group compared to -negative group. The serum concentrations of HA and SHAP-HA complex had a significant correlation with the MMP-9 and TIMP-1. The patients with elevated SHAP-HA complex had the shorter disease-free survival. The multivariate analysis revealed that the SHAP-HA complex was the independent variable for disease-free survival of endometrial cancer patients. In conclusion, the elevation of serum SHAP-HA complex depended on the HAS1 expression and the SHAP-HA complex is a useful marker to predict disease recurrence in endometrial cancer patients. The SHAP-HA complex may promote the lymph-vascular space involvement and the synthesis and activation of MMP-9 and TIMP-1 in the progression of endometrial cancer.
A general model for the simulation of room acoustics based on hierachical radiosity (1997)

No abstract available.
Aptamer-Conjugated Nanoparticles for Selective Collection and Detection of Cancer Cells (2006)

We have developed a method for the rapid collection and detection of leukemia cells using a novel two-nanoparticle assay with aptamers as the molecular recognition element. An aptamer sequence was selected using a cell-based SELEX strategy in our laboratory for CCRF-CEM acute leukemia cells that, when applied in this method, allows for specific recognition of the cells from complex mixtures including whole blood samples. Aptamer-modified magnetic nanoparticles were used for target cell extraction, while aptamer-modified fluorescent nanoparticles were simultaneously added for sensitive cell detection. Combining two types of nanoparticles allows for rapid, selective, and sensitive detection not possible by using either particle alone. Fluorescent nanoparticles amplify the signal intensity corresponding to a single aptamer binding event, resulting in improved sensitivity over methods using individual dye-labeled probes. In addition, aptamer-modified magnetic nanoparticles allow for rapid extraction of target cells not possible with other separation methods. Fluorescent imaging and flow cytometry were used for cellular detection to demonstrate the potential application of this method for medical diagnostics.
A compilation technique for software pipelining of loops with conditional jumps (1987)

We describe a compilation algorithm for efficient software pipelining of general inner loops, where the number of iterations and the time taken by each iteration may be unpredictable, due to arbitrary if-then- else statements and conditional exit statements within the loop. As our target machine, we assume a wide instruction word architecture that allows multi-way branching in the form of if-then-else trees, and that allows conditional register transfers depending on where the microinstruction branches to (a hardware implementation proposal for such a machine is briefly described in the paper). Our compilation algorithm, which we call the pipeline scheduling technique, produces a software- pipelined version of a given inner loop, which allows a new iteration of the loop to begin on every cycle whenever dependencies and resources permit. The correctness and termination properties of the algorithm are studied in the paper.
N-ACETYLCYSTEINE ATTENUATES THE INCREASE IN ??-GLUTATHIONE S-TRANSFERASE AND CIRCULATING ICAM-1 AND VCAM-1 AFTER REPERFUSION IN HUMANS UNDERGOING LIVER TRANSPLANTATION1 (2001)

NAC attenuated the increase in alpha-glutathione S-transferase and circulating ICAM-1 and VCAM-1 after reperfusion of the donor liver, indicating possible cytoprotective effects of NAC.
New strategy for chemical modification of hyaluronic acid: Preparation of functionalized derivatives and their use in the formation of novel biocompatible hydrogels (1999)

Biodegradable materials for spatially and temporally controlled delivery of bioactive agents such as drugs, growth factors, or cytokines are key to facilitating tissue repair. We have developed a versatile method for chemical crosslinking high-molecular-weight hyaluronic acid under physiological conditions yielding biocompatible and biodegradable hydrogels. The method is based on the introduction of functional groups onto hyaluronic acid by formation of an active ester at the carboxylate of the glucuronic acid moiety and subsequent substitution with a side chain containing a nucleophilic group on one end and a (protected) functional group on the other. We have formed hyaluronic acid with amino or aldehyde functionality, and subsequently hydrogels with these hyaluronic acid derivatives and bifunctional crosslinkers or mixtures of the hyaluronic acid derivatives carrying different functionalities using active ester- or aldehyde-mediated reactions. Size analysis of the hyaluronic acid derivatives showed that the chemical modification did not lead to fragmentation of the polysaccharide. Hydrogels formed with hyaluronic acid derivatized to a varying degree and crosslinked with low- or high-molecular-weight crosslinkers were evaluated for biodegradability by digestion with hyaluronidase and for biocompatibility and ectopic bone formation by subcutaneous implantation in rats. Several hydrogel formulations showed excellent cell infiltration and chondro-osseous differentiation when loaded with bone morphogenetic protein-2 (BMP-2). Synergistic action of insulin-like growth factor-1 with BMP-2 promoted cartilage formation in this model, while addition of transforming growth factor-beta and BMP-2 led to rapid replacement of the matrix by bone.
Fluorescence Energy Transfer as a Spectroscopic Ruler (1978)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
Charge Migration in DNA: Ion-Gated Transport (2001)

Electron hole (radical cation) migration in DNA, where the quantum transport of an injected charge is gated in a correlated manner by the thermal motions of the hydrated counterions, is described here. Classical molecular dynamics simulations in conjunction with large-scale first-principles electronic structure calculations reveal that different counterion configurations lead to formation of states characterized by varying spatial distributions and degrees of charge localization. Stochastic dynamic fluctuations between such ionic configurations can induce correlated changes in the spatial distribution of the hole, with concomitant transport along the DNA double helix. Comparative ultraviolet light-induced cleavage experiments on native B DNA oligomers and on ones modified to contain counterion (Na(+))-starved bridges between damage-susceptible hole-trapping sites called GG steps show in the latter a reduction in damage at the distal step. This reduction indicates a reduced mobility of the hole across the modified bridge as predicted theoretically.
Blind OFDM symbol synchronization in ISI channels (2002)

We present a new algorithm for blind symbol synchronization in orthogonal frequency division multiplexing (OFDM) systems. Unlike the previously proposed algorithms, the new algorithm guarantees correct symbol synchronization, even in the presence of ISI. Also, it does not assume data in an OFDM symbol to be i.i.d. The increased complexity of the algorithm would be acceptable for systems, such as fixed receiver broadcast systems, that require guaranteed synchronization under all conditions.
Phosphorylation of TPX2 by Plx1 enhances activation of Aurora A (2009)

Entry into mitosis requires the activation of mitotic kinases, including Aurora A and Polo-like kinase 1 (Plk1). Increased levels of these kinases are frequently found associated with human cancers, and therefore it is imperative to understand the processes leading to their activation. We demonstrate that TPX2, but neither Ajuba nor Inhibitor-2, can activate Aurora A directly. Moreover, Plx1 can induce Aurora A T-loop phosphorylation indirectly in vivo during oocyte maturation. We identify Ser204 in TPX2 as a Plx1 phosphorylation site. Mutating Ser204 to alanine decreases activation of Aurora A, whereas a phosphomimetic Asp mutant exhibits enhanced activating ability. Finally, we show that phosphorylation of TPX2 with Plx1 increases its ability to activate Aurora A. Taken together, our data indicate that Plx1 promotes activation of Aurora A, most likely through TPX2. In light of the current literature, we propose a model in which Plx1 and Aurora A activate each other in a positive feedback loop.
Persistent elimination of ErbB-2/HER2-overexpressing tumors using combinations of monoclonal antibodies: Relevance of receptor endocytosis (2009)

Monoclonal antibodies (mAbs) to ErbB-2/HER2 or to its sibling, the epidermal growth factor receptor (EGFR), prolong survival of cancer patients, especially when combined with cytotoxic therapies. However, low effectiveness of therapeutic mAbs and the evolution of patient resistance call for improvements. Here we test in animals pairs of anti-ErbB-2 mAbs and report that pairs comprising an antibody reactive with the dimerization site of ErbB-2 and an antibody recognizing another distinct epitope better inhibit ErbB-2-overexpressing tumors than other pairs or the respective individual mAbs. Because the superiority of antibody combinations extends to tumor cell cultures, we assume that nonimmunological mechanisms contribute to mAb synergy. One potential mechanism, namely the ability of mAb combinations to instigate ErbB-2 endocytosis, is demonstrated. Translation of these lessons to clinical applications may enhance patient response and delay acquisition of resistance.
Microfabricated Microneedles: A Novel Approach to Transdermal Drug Delivery (1998)

Although modern biotechnology has produced extremely sophisticated and potent drugs, many of these compounds cannot be effectively delivered using current drug delivery techniques (e.g., pills and injections). Transdermal delivery is an attractive alternative, but it is limited by the extremely low permeability of skin. Because the primary barrier to transport is located in the upper 10-15 micron of skin and nerves are found only in deeper tissue, we used a reactive ion etching microfabrication technique to make arrays of microneedles long enough to cross the permeability barrier but not so long that they stimulate nerves, thereby potentially causing no pain. These microneedle arrays could be easily inserted into skin without breaking and were shown to increase permeability of human skin in vitro to a model drug, calcein, by up to 4 orders of magnitude. Limited tests on human subjects indicated that microneedles were reported as painless. This paper describes the first published study on the use of microfabricated microneedles to enhance drug delivery across skin.
MHC class I-associated peptides produced from endogenous gene products with vastly different efficiencies (1997)

We compared the efficiency of generating antigenic peptides from various polypeptide contexts expressed by recombinant vaccinia viruses. These included full-length influenza virus nucleoprotein (NP(1-498)), two truncated forms, and cytosolic and endoplasmic reticulum-targeted minimal peptides. Two peptides were studied, NP(50-57) (Kk-restricted) and NP(147-155) (Kd-restricted). The efficiency of peptide generation was measured in cytotoxicity assays by determining 1) the kinetics of presentation following infection using brefeldin A to block additional presentation and 2) the concentration of anti-class I mAbs required to block presentation. The two determinants behaved similarly, being presented most efficiently from minigene products, with intermediate efficiency from fragments, and least efficiently from NP(1-498). Direct quantitation of HPLC-purified peptides supported the validity of these simple methods to roughly estimate the efficiency of class I Ag presentation. It also surprisingly revealed that 60- to 90-fold more NP(50-57) than NP(147-155) peptide was present in cells expressing NP(1-498) or a rapidly degraded fragment (for NP(1-498), 1800 peptides/cell of NP(50-57) vs 30 peptides/cell of NP(147-155)). By contrast, nearly identical (and much greater) amounts of peptides were recovered from cells expressing minigene products (55,000 copies of either peptide/cell). These findings demonstrate 1) that immunodominant peptides from the same protein can be generated with vastly different efficiencies, and 2) that cytosolic or endoplasmic reticulum-targeted minigene products are presented far more efficiently than longer polypeptides.
Identification of the gene coding for rhesus cytomegalovirus glycoprotein B and immunological analysis of the protein. (1997)

The nucleotide sequence of the gene encoding glycoprotein B (gB) of rhesus cytomegalovirus (RhCMV) was determined and the protein characterized. The open reading frame of gB encoded a protein of 854 amino acids with 60% identity and 75% similarity at the amino acid level to human cytomegalovirus (HCMV) gB. Cysteine residues in the extraluminal part of the protein are perfectly conserved. Out of the 16 potential N-linked glycosylation sites present in HCMV gB, 15 are conserved in RhCMV gB. Immunoblot analyses with antisera detected three bands of 150 kDa, 90-110 kDa and 55 kDa representing the full-length gB as well as the proteolytic cleavage products. Cross-reactivity and cross-neutralization of a number of HCMV gB-specific monoclonal antibodies with RhCMV gB indicated sharing of immunogenic epitopes between the two molecules. The RhCMV gB regions corresponding to antigenic domains AD-1, 2 and 3 of HCMV gB were immunogenic during natural RhCMV infection with the AD-1 region being the immunodominant domain. The data indicate that RhCMV might represent a useful model to investigate pathogenesis and immune surveillance of cytomegaloviruses.
Current developments in SELDI affinity technology (2003)

The overall history and recent advancements in Surface-Enhanced Laser Desorption/Ionization (SELDI) affinity technology is reviewed. A detailed account of SELDI technology, utilizing Immobilized-Metal Affinity surfaces, pseudo-specific chromatographic surfaces, and biospecific interactive surfaces, is presented with particular emphasis placed upon examination of fundamental characteristics as well as specific applications for each. Finally, a detailed review of the specific use of such affinity surfaces in fundamental aspects of clinical, process, and research proteomics activity is presented.