gebhart/patrepeval huggingface dataset:
Apolipoprotein AIMilano. Disulfide-linked dimers increase high density lipoprotein stability and hinder particle interconversion in carrier plasma. (1990)

The in vitro metabolism of high density lipoproteins (HDL) in carriers of the apolipoprotein AIMilano (apoAIM) mutant was investigated during incubation of whole plasma and isolated lipoprotein fractions. A reduced cholesterol esterification (16.5 versus 25.0% for controls) and a decreased exchange of lipids between HDL and lower density lipoproteins was observed during incubation (6 h at 37 degrees C) of AIM plasma. Control HDL3 were converted to larger, faster-floating HDL particles, whereas only a fraction of AIM HDL3 followed the same pathway. Incubations were also carried out by mixing HDL3 from controls and AIM carriers with a lipoprotein-depleted plasma fraction in the presence of triglyceride-rich particles isolated from Intralipid. AIM HDL3 again showed a reduced capacity for lipid exchange; some HDL3 particles followed a "normal" conversion to faster-floating, larger HDL, whereas the small AIM HDL3 were not modified, indicating that AIM HDL3 are a mixture of metabolically functional and nonfunctional particles. Following transformation of the apoAIM homo- and heterodimers into their normal counterparts, i.e. monomeric apoAI and -AII, by reduction and carboxamidomethylation of AIM HDL3, the modified HDL3 behave like control HDL3 during incubation with lipoprotein-depleted plasma and triglyceride-rich particles. The presence of AIM dimers is most likely responsible for the increased HDL3 stability in the AIM carriers, indicating that apolipoprotein composition plays a major role in HDL particle interconversion.
Observations, legends, and conjectures concerning restricted T-cell receptor usage and autoimmune disease. (1992)

It has become clear over the past few years that a variety of experimental autoimmune conditions are mediated by T cells bearing a highly restricted subset of antigen receptors. This restricted TcR usage raises important questions concerning not only the recognition of autoantigens, but also the pathogenic mechanisms underlying many models of autoimmunity. Furthermore, the extension of these findings in certain cases to human disease has raised the possibility of specific therapeutic immune intervention. In this review, we examine the available data on restricted T-cell receptor usage in autoimmune disorders and explore the interpretations and the theoretical and practical implications of these findings.
Thickness Dependence of the Solvent-Induced Glass Transition in Polymer Brushes (1999)

We have investigated the sorption behavior of polystyrene brushes with thicknesses of 10−200 nm in toluene vapor. The sorption curve displays a kink, which is attributed to the solvent-induced glass transition. The derivative of the sorption curve with respect to solvent activity (“osmotic capacity”) shows a glass step at a certain characteristic activity ag. This is the analogue of the glass step observed in the heat capacity at Tg with differential scanning calorimetry. Both ag and the height of the glass step decrease with decreasing film thickness. The glass step is most pronounced after annealing the films at elevated temperatures in a vacuum. Due to accumulation of solvent in the film, the step disappears after repeated swelling/drying cycles.
Using dynamic cache management techniques to reduce energy in general purpose processors (2000)

The memory hierarchy of high-performance and embedded processors has been shown to be one of the major energy consumers. For example, the Level-1 (L1) instruction cache (I-Cache) of the StrongARM processor accounts for 27% of the power dissipation of the whole chip, whereas the instruction fetch unit (IFU) and the I-Cache of Intel's Pentium Pro processor are the single most important power consuming modules with 14% of the total power dissipation [2]. Extrapolating current trends, this portion is likely to increase in the near future, since the devices devoted to the caches occupy an increasingly larger percentage of the total area of the chip. In this paper, we propose a technique that uses an additional mini cache, the LO-Cache, located between the I-Cache and the CPU core. This mechanism can provide the instruction stream to the data path and, when managed properly, it can effectively eliminate the need for high utilization of the more expensive I-Cache. We propose, implement, and evaluate five techniques for dynamic analysis of the program instruction access behavior, which is then used to proactively guide the access of the LO-Cache. The basic idea is that only the most frequently executed portions of the code should be stored in the LO-Cache since this is where the program spends most of its time. We present experimental results to evaluate the effectiveness of our scheme in terms of performance and energy dissipation for a series of SPEC95 benchmarks. We also discuss the performance and energy tradeoffs that are involved in these dynamic schemes. Results for these benchmarks indicate that more than 60% of the dissipated energy in the I-Cache subsystem can be saved.
Homeotic factor ATBF1 induces the cell cycle arrest associated with neuronal differentiation (2005)

The present study aimed to elucidate the function of AT motif-binding factor 1 (ATBF1) during neurogenesis in the developing brain and in primary cultures of neuroepithelial cells and cell lines (Neuro 2A and P19 cells). Here, we show that ATBF1 is expressed in the differentiating field in association with the neuronal differentiation markers beta-tubulin and MAP2 in the day E14.5 embryo rat brain, suggesting that it promotes neuronal differentiation. In support of this, we show that ATBF1 suppresses nestin expression, a neural stem cell marker, and activates the promoter of Neurod1 gene, a marker for neuronal differentiation. Furthermore, we show that in Neuro 2A cells, overexpressed ATBF1 localizes predominantly in the nucleus and causes cell cycle arrest. In P19 cells, which formed embryonic bodies in the floating condition, ATBF1 is mainly cytoplasmic and has no effect on the cell cycle. However, the cell cycle was arrested when ATBF1 became nuclear after transfer of P19 cells onto adhesive surfaces or in isolated single cells. The nuclear localization of ATBF1 was suppressed by treatment with caffeine, an inhibitor of PI(3)K-related kinase activity of ataxa-telangiectasia mutated (ATM) gene product. The cytoplasmic localization of ATBF1 in floating/nonadherent cells is due to CRM1-dependent nuclear export of ATBF1. Moreover, in the embryonic brain ATBF1 was expressed in the cytoplasm of proliferating stem cells on the ventricular zone, where cells are present at high density and interact through cell-to-cell contact. Conversely, in the differentiating field, where cell density is low and extracellular matrix is dense, the cell-to-matrix interaction triggered nuclear localization of ATBF1, resulting in the cell cycle arrest. We propose that ATBF1 plays an important role in the nucleus by organizing the neuronal differentiation associated with the cell cycle arrest.
c‐MYB oncogene‐like genes encoding three MYB repeats occur in all major plant lineages (2000)

Since the identification of the first plant MYB-like protein, the Zea mays factor C1, the number of MYB-related genes described has greatly increased. All of the more than 150 plant MYB-like proteins known so far contain either two or only one sequence-related helix-turn-helix motif in their DNA-binding domain. Animal c-MYB genes contain three such helix-turn-helix motif-encoding repeats (R1R2R3 class genes). It has therefore been concluded that R2R3-MYB genes are the plant equivalents of c-MYB and that there are significant differences in the basic structure of MYB genes of plants and animals. Here, we describe expressed R1R2R3-MYB genes from Physcomitrella patients++ and Arabidopsis thaliana, designated PpMYB3R-1 and AtMYB3R-1. The amino acid sequences of their DNA-binding domains show high similarity to those of animal MYB factors, and less similarity to R2R3-MYB proteins from plants. In addition, R1R2R3-MYB genes were identified in different plant evolutionary lineages including mosses, ferns and monocots. Our data show that a DNA-binding domain consisting of three MYB repeats existed before the divergence of the animal and plant lineages. R1R2R3-MYB genes may have a conserved function in eukaryotes, and R2R3-MYB genes may predominantly regulate plant-specific processes which evolved during plant speciation.
A Weak Attractive Interaction between Organic Fluorine and an Amide Group (2004)

A combination of a chemical double-mutant cycle and a linear free energy relationship has demonstrated that a weak attractive interaction (−0.8 to −1.5 kJ mol−1) exists between an organic fluorine substituent and the face of an amide functional group (see picture). This study supports recent results that have suggested that such an attraction may be operative in enzyme–inhibitor interactions. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2004/z460781_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Highly Stretchable Piezoelectric‐Pyroelectric Hybrid Nanogenerator (2013)

A highly stretchable hybrid nanogenerator has been developed using a micro-patterned piezoelectric polymer P(VDF-TrFE), PDMS-CNT composite, and graphene nanosheets. Mechanical and thermal energies are simultaneously harvested from a single cell of the device. The hybrid nanogenerator exhibits high robustness behavior even after 30% stretching and generates very stable piezoelectric and pyroelectric power outputs due to micro-pattern designing.
TrueSkill™: A Bayesian Skill Rating System (2007)

We present a new Bayesian skill rating system which can be viewed as a generalisation of the Elo system used in Chess. The new system tracks the uncertainty about player skills, explicitly models draws, can deal with any number of competing entities and can infer individual skills from team results. Inference is performed by approximate message passing on a factor graph representation of the model. We present experimental evidence on the increased accuracy and convergence speed of the system compared to Elo and report on our experience with the new rating system running in a large-scale commercial online gaming service under the name of TrueSkill.
Molecular cloning and characterization of protective outer membrane protein P.69 from Bordetella pertussis. (1989)

Protein P.69 is localized on the outer membrane of Bordetella pertussis and is one of the virulence factors believed to contribute to the disease state of whooping cough. We demonstrate that protein synthesis of P.69 is under genetic control of the vir locus. Using oligonucleotide probes derived from the protein sequence of a cyanogen bromide fragment, we have cloned the gene for P.69 from B. pertussis CN2992. Analysis of the DNA sequence reveals a G + C-rich gene capable of encoding a protein of 910 amino acids with a Mr of 93,478, suggesting that P.69 is a processed form of a larger precursor. In common with some of the genes in the pertussis toxin operon, the sequence CCTGG was found 5' to the ATG initiation codon. At the 3' end, 29 bases after the TAA stop codon, the sequence GTTTTTCCT was found and may have some function in transcription termination. A full-length clone of the gene for P.69 carried by the cosmid pBPI69 was unable to direct the expression of P.69 protein in an Escherichia coli host. The generation of P.69-fusion products allowed the detection of P.69-specific protein products synthesized in E. coli.
Electronic cigarettes for smoking cessation and reduction (2012)

This is a protocol for a Cochrane Review (Intervention). The objectives are as follows: The primary objective is to evaluate the efficacy of electronic cigarettes (ECs) for helping people who smoke to achieve long‐term cessation. The secondary objectives are to evaluate the efficacy of ECs for helping smokers to substantially reduce cigarette use and to assess potential adverse effects.
Improved μc-Si p-layer and a-Si i-layer materials using VHF plasma deposition (2002)

Microcrystalline Si p-layers have been widely used in a-Si solar cell technology to achieve high efficiency. To improve the solar cell performance further, the authors have studied the deposition of high quality /spl mu/c-Si p-layer material using a modified VHF plasma enhanced CVD process and consequently have improved the solar cell current. This improvement was primarily in the blue response which leads to a 6-10% improvement in the overall solar cell efficiency. In addition, they have explored the deposition of a-Si at high rates using VHF plasma and compared these VHF i-layers with RF plasma deposited i-layers. With improved deposition conditions, VHF intrinsic layers deposited at a rate up to 15 /spl Aring//s show similar device performance and light stability to VHF and RF i-layers deposited at low rates and show higher stability than RF i-layers deposited at high rates in the same deposition system. A 10.9% efficient single-junction solar cell was fabricated using a VHF deposited i-layer.
Comparison of Maximum Induced Current and Electric Field fromTranscranial Direct Current and Magnetic Stimulations of a Human HeadModel (2007)

As important non-invasive techniques in brain stimulation, transcranial direct cur- rent stimulation (tDCS) and transcranial magnetic stimulation (TMS) have been studied and compared in this paper by employing impedance method and a 3D human head model. The quantitative analysis of distributions of current density and electric fleld by tDCS and TMS have been presented. Results are compared and potential applications are discussed. DOI: 10.2529/PIERS060906193504 In this paper we use a 3D human head model obtained from Brooks Air Force Laboratory, USA. The model which has 24 difierent tissues is based on anatomical slices from a male cadaver and it is originally obtained from the Visible Human Project. The electrical properties are modeled using the 4-Cole-Cole model (5). Typical sliced layer in the head model and tissue colour palette for part of the tissues are shown in Fig. 1. Conductivities of some important tissues used in the present paper are given in Table 1.
[Sacral neuromodulation is effective in the treatment of fecal incontinence with intact sphincter muscles; a prospective study]. (2002)

Sacral neuromodulation was of therapeutic value in most of the patients treated for faecal incontinence without sphincter damage.
Doppler asymmetric spatial heterodyne spectroscopy (DASH): concept and experimental demonstration (2007)

We describe the concept of Doppler asymmetric spatial heterodyne spectroscopy (DASH) and present a laboratory Doppler-shift measurement using an infrared laser line. DASH is a modification of spatial heterodyne spectroscopy optimized for high precision, high accuracy Doppler-shift measurements of atmospheric emission lines either from the ground or a satellite. We discuss DASH design considerations, field widening, thermal stability and tracking, noise propagation, advantages, and trade-offs. DASH interferometers do not require moving optical parts and can be built in rugged, compact packages, making them suitable for space flight and mobile ground instrumentation.
Synthesis and Hydrogen Sorption Properties of Carborane Based Metal−Organic Framework Materials (2007)

The synthesis and hydrogen uptake properties of metal−organic framework (MOFs) materials based on carboranes have been investigated. These are the first MOFs to make use of boron-rich components as building blocksspecifically, the deprotonated form of 1,12-dihydroxycarbonyl-1,12-dicarba-closo-dodecaborane. In evacuated form the initially obtained compound, featuring zinc-coordinated solvent molecules, displays modest H2 uptake at 77 K and 1 atm. Upon removal of the coordinated solvent, however, the uptake triples (2.1 wt. %), the heat of adsorption substantially increases, and the structure adjusts such that the pore size decreases.
Prospects for TIM3-Targeted Antitumor Immunotherapy (2011)

New insights into the control of T-cell activation and proliferation have led to the identification of checkpoint proteins that either up- or downmodulate T-cell reactivity. Monoclonal antibody immunotherapies that are reactive with cytotoxic T lymphocyte antigen 4 or programmed death receptor 1 have shown promising therapeutic outcomes in mice and humans with established cancer, highlighting the fact that cancer immunotherapy using T-cell checkpoint inhibitors is one of the most promising new therapeutic approaches. T-cell immunoglobulin and mucin domain 3 (TIM3) is one of many similar inhibitory molecules that are gaining attention as targets, but it remains relatively poorly studied in oncology. This review discusses our recent probing of the mechanism of action of anti-TIM3 antibody against established spontaneous and experimental tumors in mice, in the context of the exciting possibility of rationally combining agents that promote tumor-specific T-cell activation, proliferation, effector function, and survival.
ESR Studies of Free Radical Decay in Irradiated Polyethylene (1962)

A study has been made of the temperature and rates at which molecular hydrogen is evolved and free radical decay occurs when semicrystalline polyethylene, irradiated at liquid-nitrogen temperature, is warmed to room temperature. Hydrogen evolution and free radical decay roughly parallel each other. The temperature of half reaction is the same as the temperature of the gamma-maximum in the mechanical dispersion temperature curve. At constant temperature over the temperature range —71° to 41°C, the free radical decay is first order and the free radical concentration seems to decrease to a limiting value at each temperature. The first-order decay constants are approximately constant with temperature. The data are interpreted in terms of free radicals decaying in spurs. If a constant activation energy of 15 kcal mole—1 is assumed, the frequency factors decrease with rise of temperature. This decrease is interpreted on the basis of a decreasing probability of reaction for those free radicals that escape reaction at low temperatures, but react at higher and higher temperatures. An alternative model based upon the release of free radicals from traps as the temperature is raised is also discussed. The reaction rate constant for free radical decay calculated from D—H exchange experiments agrees with that deduced from the ESR measurements. It is also concluded that the persistent free radical in polyethylene irradiated to moderate doses is the allyl free radical.
Mad Proteins Contain a Dominant Transcription Repression Domain (1996)

Transcription repression by the basic region-helix-loop-helix-zipper (bHLHZip) protein Mad1 requires DNA binding as a ternary complex with Max and mSin3A or mSin3B, the mammalian orthologs of the Saccharomyces cerevisiae transcriptional corepressor SIN3. The interaction between Mad1 and mSin3 is mediated by three potential amphipathic alpha-helices: one in the N terminus of Mad (mSin interaction domain, or SID) and two within the second paired amphipathic helix domain (PAH2) of mSin3A. Mutations that alter the structure of the SID inhibit in vitro interaction between Mad and mSin3 and inactivate Mad's transcriptional repression activity. Here we show that a 35-residue region containing the SID represents a dominant repression domain whose activity can be transferred to a heterologous DNA binding region. A fusion protein comprising the Mad1 SID linked to a Ga14 DNA binding domain mediates repression of minimal as well as complex promoters dependent on Ga14 DNA binding sites. In addition, the SID represses the transcriptional activity of linked VP16 and c-Myc transactivation domains. When fused to a full-length c-Myc protein, the Mad1 SID specifically represses both c-Myc's transcriptional and transforming activities. Fusions between the GAL DNA binding domain and full-length mSin3 were also capable of repression. We show that the association between Mad1 and mSin3 is not only dependent on the helical SID but is also dependent on both putative helices of the mSin3 PAH2 region, suggesting that stable interaction requires all three helices. Our results indicate that the SID is necessary and sufficient for transcriptional repression mediated by the Mad protein family and that SID repression is dominant over several distinct transcriptional activators.
Immunization withStaphylococcus aureusiron regulated surface determinant B (IsdB) confers protection via Th17/IL17 pathway in a murine sepsis model (2012)

We have previously shown that IsdB, a conserved protein expressed by Staphylococcus aureus, induces a robust antibody response which correlates with protection in a murine challenge model. Here we investigate the role of cellular immunity in IsdB mediated protection using lymphocyte deficient SCID mice. As opposed to WT CB-17 mice the CB-17 SCID mice were not protected against a lethal challenge of S. aureus after active and passive immunizations with IsdB. Adoptive transfer of in vitro isolated lymphocyte subsets revealed that reconstituting mice with IsdB specific CD3+ or CD4+ T-cells conferred antigen specific protection while CD8(+) T-cells, CD19(+) B-cells and plasma cells (CD138(high)B220(int)CD19(lo)) alone were not protective. A combination of CD3(+) T-cells plus CD19(+) B-cells conferred protection in CB-17 SCID mice, whereas bovine serum albumin (BSA) immune lymphocytes did not confer protection. Active immunization experiments indicated that IsdB immunized Jh mice (B-cell deficient) were protected against lethal challenge, while nude (T-cell deficient) mice were not. In vitro assays indicated that isolated IsdB specific splenocytes from immunized mice produced abundant IL-17A, much less IFN-γ and no detectable IL-4. IL-23 deficient mice were not protected from a lethal challenge by IsdB vaccination, pointing to a critical role for CD4(+) Th17 in IsdB-mediated vaccination. Neutralizing IL-17A, but not IL-22 in vivo significantly increased mortality in IsdB immunized mice; whereas, neutralizing IFN-γ did not alter IsdB-mediated protection. These findings suggest that IL-17A producing Th17 cells play an essential role in IsdB vaccine-mediated defense against invasive S. aureus infection in mice.
A Convenient and Versatile Synthesis of 2' (and 3')-Amino (and azido)-2' (and 3')-deoxyadenosine as Diverse Synthetic Precursors of Cyclic Adenosine Diphosphate Ribose (cADPR) (2004)

As diverse synthetic precursors of cyclic adenosine diphosphate ribose (cADPR), several adenosine derivatives in which azido or amino group is introduced at 2'- or 3'-position of the sugar moiety of adenosine were prepared from readily available adenosine via conventional protocols. These synthetic sequence employs very efficient reactions conditions that proceed at or below ambient temperature with actual yields of >80% for each individual step.