gebhart/patrepeval huggingface dataset:
Novel PI(4)P 5-kinase homologue, Fab1p, essential for normal vacuole function and morphology in yeast. (1995)

The FAB1 gene of budding yeast is predicted to encode a protein of 257 kDa that exhibits significant sequence homology to a human type II PI(4)P 5-kinase (PIP5K-II). The recently cloned human PIP5K-II specifically converts PI(4)P to PI(4,5)P2 (Boronenkov and Anderson, 1995). The region of highest similarity between Fab1p and PIP5K-II includes a predicted nucleotide binding motif, which is likely to correspond to the catalytic domain of the protein. Interestingly, neither PIP5K-II nor Fab1p exhibit significant homology with cloned PI 3-kinases or PI 4-kinases. fab1 mutations result in the formation of aploid and binucleate cells (hence the name FAB). In addition, loss of Fab1p function causes defects in vacuole function and morphology, cell surface integrity, and cell growth. Experiments with a temperature conditional fab1 mutant revealed that their vacuoles rapidly (within 30 min) enlarge to more than double the size upon shifting cells to the nonpermissive temperature. Additional experiments with the fab1 ts mutant together with results obtained with fab1 vps (vacuolar protein sorting defective) double mutants indicate that the nuclear division and cell surface integrity defects observed in fab1 mutants are secondary to the vacuole morphology defects. Based on these data, we propose that Fab1p is a PI(4)P 5-kinase and that the product of the Fab1p reaction, PIP2, functions as an important regulator of vacuole homeostasis perhaps by controlling membrane flux to and/or from the vacuole. Furthermore, a comparison of the phenotypes of fab1 mutants and other yeast mutants affecting PI metabolism suggests that phosphoinositides may serve as general regulators of several different membrane trafficking pathways.
A Well-Posed, Embedded Constraint Representation of Joint Moments From Kinesiological Measurements (2000)

Joint moment estimation using the traditional inverse dynamics analysis presents two challenging problems, which limit its reliability. First, the quality of the computed moments depends directly on unreliable estimates of the segment accelerations obtained numerically by differentiating noisy marker measurements. Second, the representation of joint moments from combined video and force plate measurements belongs to a class of ill-posed problems, which does not possess a unique solution. This paper presents a well-posed representation derived from an embedded constraint equation. The proposed method, referred to as the embedded constraint representation (ECR), provides unique moment estimates, which satisfy all measurement constraints and boundary conditions and require fewer acceleration components than the traditional inverse dynamics method. Specifically, for an n-segment open chain planar system, the ECR requires n-3 acceleration components as compared to 3(n-1) components required by the traditional (from ground up) inverse dynamics analysis. Based on a simulated experiment using a simple three-segment model, the precision of the ECR is evaluated at different noise levels and compared to the traditional inverse dynamics technique. At the lowest noise levels, the inverse dynamics method is up to 50 percent more accurate while at the highest noise levels the ECR method is up to 100 percent more accurate. The ECR results over the entire range of noise levels reveals an average improvement on the order 20 percent in estimating the moments distal to the force plate and no significant improvement in estimating moments proximal to the force plate. The new method is particularly advantageous in a combined video, force plate, and accelerometery sensing strategy.
Passivation of GaAs surface recombination with organic thiols (1991)

Exposure of GaAs crystals to solutions of organic thiols resulted in substantial reductions in nonradiative GaAs surface recombination rates. This process yielded improvements in steady state photoluminescence signals that were comparable to those obtained after a Na2S⋅9H2O (aqueous) treatment. Use of a series of thiols indicated that the chemically important surface electrical trap levels behaved as a polarizable, electron deficient center. X-ray photoelectron spectroscopy indicated that the thiols did not remove excess As0 nor form detectable levels of As2S3-like phases, implying that neither of these factors is required for effective surface passivation chemistry.
Recent developments in adeno‐associated virus vector technology (2008)

Adeno-associated virus (AAV), a single-stranded DNA parvovirus, is emerging as one of the leading gene therapy vectors owing to its nonpathogenicity and low immunogenicity, stability and the potential to integrate site-specifically without known side-effects. A portfolio of recombinant AAV vector types has been developed with the aim of optimizing efficiency, specificity and thereby also the safety of in vitro and in vivo gene transfer. More and more information is now becoming available about the mechanism of AAV/host cell interaction improving the efficacy of recombinant AAV vector (rAAV) mediated gene delivery. This review summarizes the current knowledge of the infectious biology of AAV, provides an overview of the latest developments in the field of AAV vector technology and discusses remaining challenges.
Bistable conditions for low-temperature silicon epitaxy (1990)

We report on the role of hydrogen surface passivation in achieving low-temperature silicon epitaxy by chemical vapor deposition processes. Upon insertion of an HF-etched silicon wafer into an epitaxial silicon deposition apparatus, residual contamination of the Si surface is negligible. Si 2p core level photoemission spectra demonstrate that the silicon surface is stable in air and free of SiO2 for a time period of minutes. The predominant passivating species is found to be silicon hydride. We demonstrate that hydrogen passivation by HF pretreatment leads to two divergent temperature ranges where epitaxy is successful, those being a low-temperature range, 425≲T≲650 °C, and a high-temperature regime, T≳750 °C. Additionally, we employ temperature-programmed desorption techniques to elucidate the role of hydrogen in the transition to a steady-state growth process, employing ultrahigh vacuum/chemical vapor deposition as the model system.
NTDB: Thermodynamic Database for Nucleic Acids (2001)

A new thermodynamic database for normal and modified nucleic acids has been developed. This Thermodynamic Database for Nucleic Acids (NTDB) includes sequence, structure and thermodynamic information as well as experimental methods and conditions. In this release, there are 1851 sequences containing both normal and modified nucleic acids. A user-friendly web-based interface has been developed to allow data searching under different conditions. Useful thermodynamic tools for the study of nucleic acids have been collected and linked for easy usage. NTDB is available at http://ntdb.chem.cuhk.edu.hk.
Integrated optics erbium ytterbium amplifier system in 10 Gb/s fiber transmission experiment (1996)

We report the full characterization of a pigtailed erbium-ytterbium co-doped planar glass waveguide laser amplifier module. With a single 980 nm diode pump, this ion-exchanged 4.5 cm long device delivers signal gain of 16.5 dB, noise figure of 4.5 dB, and saturated power of a 12.5 dBm. To confirm its stability, we tested this module as a power booster in a 10 Gb/s transmission system experiment at the 1534 nm wavelength, and demonstrated successful bit error rate (BER<10/sup -12/) transmission over 72.5 km of dispersion shifted fiber.
Estrogen receptor-mediated and cytotoxic effects of the antiestrogens tamoxifen and 4-hydroxytamoxifen. (1984)

The triphenylethylene antiestrogen tamoxifen (TAM) is believed to exert its antitumor effect via the estrogen receptor (ER). To test this hypothesis and to differentiate between ER-mediated and general cytotoxic effects of TAM, the growth-inhibitory effects of TAM and its in vivo metabolite 4-hydroxytamoxifen (OH-TAM) have been studied in five continuous human cancer cell lines, MCF7 and T47D (mammary carcinoma, ER positive), BT20 and MDA-MB-231 (mammary carcinoma, ER negative), and ME8 (melanoma, ER negative). All five cell lines are completely killed by concentrations of TAM and OH-TAM above 10(-6) M, regardless of ER status. TAM and OH-TAM have little effect on the ER-negative lines at concentrations below 10(-6) M, whereas the ER-positive lines are highly sensitive to TAM at 10(-7) M and to OH-TAM at 10(-9) M. Inhibition of growth parallels the relative affinity of these drugs for the ER. We conclude that, above 10(-6) M, the growth-inhibitory effects of TAM and OH-TAM in tissue culture are the results of a mechanism other than that via the ER system and that only at lower concentrations are the true ER-mediated effects seen. Plasma concentrations of TAM and OH-TAM in breast cancer patients treated with TAM are in the same range as the concentrations in vivo at which growth inhibition is seen, leading to the conclusion that both compounds contribute to the overall effect of TAM in vivo.
Quantitative Thermal Imaging of Single-Walled Carbon Nanotube Devices by Scanning Joule Expansion Microscopy (2012)

Electrical generation of heat in single-walled carbon nanotubes (SWNTs) and subsequent thermal transport into the surroundings can critically affect the design, operation, and reliability of electronic and optoelectronic devices based on these materials. Here we investigate such heat generation and transport characteristics in perfectly aligned, horizontal arrays of SWNTs integrated into transistor structures. We present quantitative assessments of local thermometry at individual SWNTs in these arrays, evaluated using scanning Joule expansion microscopy. Measurements at different applied voltages reveal electronic behaviors, including metallic and semiconducting responses, spatial variations in diameter or chirality, and localized defect sites. Analytical models, validated by measurements performed on different device structures at various conditions, enable accurate, quantitative extraction of temperature distributions at the level of individual SWNTs. Using current equipment, the spatial resolution and temperature precision are as good as ∼100 nm and ∼0.7 K, respectively.
Dendritic cells and immune regulation in the liver (2003)

Hepatic dendritic cells (DC) unquestionably play important roles in the induction and regulation of immune responses. Due to their paucity, functional characterisation of these important antigen presenting cells has been slow but use of DC growth factors (in particular GM-CSF and Flt3L) that markedly enhance their numbers has proved helpful in furnishing adequate study material. While there is growing evidence that DC function is affected in the pathogenesis of liver disease, most work to date has been performed on non-hepatic DC. Increasing knowledge of hepatic DC biology is likely to improve our understanding of disease pathogenesis and resistance to and therapy of liver disease.
Induction of cytotoxic T lymphocytes by primary in vitro stimulation with peptides. (1988)

Antigen-specific cytotoxic T cells can be generated by primary in vitro stimulation of spleen cells from C57BL/6 mice with appropriate peptide fragments. This response can be elicited without prior in vivo immunization. Chicken OVA fragmented with either cyanogen bromide (CN OVA) or trypsin (T OVA) was used as a source of mixed peptides. A synthetic peptide, NP365-380, representing the sequence 365-380 from influenza virus A/PR/8 nucleoprotein, was also used, since this contains the main determinants recognized by CTL generated from H-2b mice infected with A/PR/8 virus. The primary in vitro cytotoxic T cell response was peptide specific, since targets were lysed only in the presence of appropriate peptide antigens. Native OVA could not elicit primary effectors in vitro nor could it sensitize targets for lysis by OVA digest-specific CTL. A synthetic peptide corresponding to residues 111-122 within the OVA sequence could sensitize targets for lysis by effectors induced against T OVA. Effectors generated by in vitro stimulation were CD8+, CD4-, and H-2Db-restricted for NP365-380 and T OVA recognition. CN OVA-specific effectors were also CD8+, CD4-, but surprisingly, were able to lyse a range of H-2-different targets in an antigen-specific manner. These effectors failed to lyse a tumor line that does not express class I MHC molecules. This broad MHC restriction pattern was also apparent at the clonal level. In all cases, the antipeptide CTL generated by primary in vitro stimulation were inefficient in lysing target cells expressing endogenous forms of antigens, such as influenza virus-infected cells or cells transfected with the OVA cDNA. However, cytotoxic T cell lines generated in vitro against the NP365-380 peptide did contain a minor population of virus-reactive cells that could be selectively expanded by stimulation with A/PR/8-infected spleen cells. These results are discussed in terms of class I-restricted T cell stimulation in the absence of antigen processing by high surface densities of peptide/MHC complexes.
Multiple regulatory sites in the Bacillus subtilis citB promoter region (1990)

The aconitase (citB) gene of Bacillus subtilis is repressed during growth in a medium that contains a rapidly metabolizable carbon source and a source of 2-ketoglutarate. It is derepressed when either of these nutrient sources becomes limiting. Repression by rapidly metabolizable carbon sources was shown previously to depend at least in part on a DNA sequence located 67 to 84 base pairs upstream of the start point of citB transcription. In the present work, this region and surrounding DNA were mutagenized to identify more precisely the target for carbon catabolite repression. Mutations in a symmetric sequence located between positions -73 and -59 led to constitutive transcription from the citB promoter in media that normally provoke catabolite repression. By gel mobility shift assays, it was shown that at least one protein in extracts of B. subtilis binds to the symmetric sequence and that DNA of constitutive mutants binds to this protein much less effectively. A second sequence located near position -45 was also implicated in this regulation. A second form of regulation of citB was also investigated. This gene is known to be derepressed when cells are induced to sporulate by exhaustion of a nutrient broth medium or limitation of guanine nucleotide synthesis. The mutations that led to constitutivity with respect to the carbon source had no effect on citB expression in nutrient broth medium, indicating that control by catabolite repression and control by components of nutrient broth (presumably amino acids) act by different mechanisms.
Modulation of guanine nucleotides bound to Ras in NIH3T3 cells by oncogenes, growth factors, and the GTPase activating protein (GAP) (1990)

The mitogenic activity of membrane-associated tyrosine kinases such as Src and the PDGF receptor appear to depend on Ras function. Ras biochemical activity involves regulation of a GTP/GDP cycle and the GTPase activating protein (GAP). Recently, PDGF and v-Src have been shown to stimulate tyrosine phosphorylation of GAP, linking these pathways at the biochemical level. To test whether PDGF and v-Src affect the Ras GTP/GDP cycle, we have measured the guanine nucleotides complexed to Ras in NIH3T3 cells and compared the ratio of GTP to total GTP + GDP detected (percent GTP). In normal quiescent NIH3T3 cells, PDGF stimulated the basal amount of GTP complexed to Ras (7%) by 2.1-fold to 15%. The effect was dependent on PDGF concentration and was observed maximally within 10 min following PDGF challenge. Ras was complexed to 22% GTP in NIH3T3 cells transformed by v-src or v-abl. Overexpression of GAP by 110-fold in NIH3T3 cells reduced the basal level of GTP complexed to Ras to 2.4%; upon challenge with PDGF, Ras was complexed to 6.6% GTP. These results indicate that PDGF receptor activation and tyrosine kinase-encoding oncogene products can stimulate Ras into the GTP complex and that GAP in intact mammalian cells can decrease the amount of GTP complexed to Ras.
Depressed tumor necrosis factor alpha and interleukin-12p40 production by peripheral blood mononuclear cells of gastric cancer patients: Association with IL-1R-associated kinase-1 protein expression and disease stage (2004)

Our study investigated the ability of peripheral blood mononuclear cells (PBMCs) isolated from patients with different clinical stages of gastric cancer to produce proinflammatory (tumor necrosis factor alpha [TNFalpha], interleukin 12p40 [IL-12p40] and interleukin 6 [IL-6]) and antiinflammatory (interleukin-10 [IL-10]) cytokines after stimulation with lipopolysaccharide (LPS) or tumor cells, and its correlation with IL-1R-associated kinase-1 (IRAK-1) protein expression. The data showed that TNF production by tumor cell-stimulated PBMCs obtained from patients with advanced gastric cancer was significantly depressed in comparison to the control group. The response to LPS was less affected. IL-12p40 production was depressed in all stages of disease, while the release of IL-10 and IL-6 remained unchanged. Depressed tumor cell-induced TNF and IL-12p40 production was associated with diminished IRAK-1 protein expression in PBMC. These findings may suggest that in advanced gastric cancer (at least in some cancer patients) diminished IRAK-1 protein expression may be a novel mechanism responsible for or facilitating downregulation of innate immune response to tumor cells.
Epigenetic Silencing in Friedreich Ataxia Is Associated with Depletion of CTCF (CCCTC-Binding Factor) and Antisense Transcription (2009)

CTCF depletion constitutes an epigenetic switch that results in increased antisense transcription, heterochromatin formation and transcriptional deficiency in FRDA. These findings provide a mechanistic basis for the transcriptional silencing of the FXN gene in FRDA, and broaden our understanding of disease pathogenesis in triplet-repeat diseases.
Discovering geographical topics in the twitter stream (2012)

Micro-blogging services have become indispensable communication tools for online users for disseminating breaking news, eyewitness accounts, individual expression, and protest groups. Recently, Twitter, along with other online social networking services such as Foursquare, Gowalla, Facebook and Yelp, have started supporting location services in their messages, either explicitly, by letting users choose their places, or implicitly, by enabling geo-tagging, which is to associate messages with latitudes and longitudes. This functionality allows researchers to address an exciting set of questions: 1) How is information created and shared across geographical locations, 2) How do spatial and linguistic characteristics of people vary across regions, and 3) How to model human mobility. Although many attempts have been made for tackling these problems, previous methods are either complicated to be implemented or oversimplified that cannot yield reasonable performance. It is a challenge task to discover topics and identify users' interests from these geo-tagged messages due to the sheer amount of data and diversity of language variations used on these location sharing services. In this paper we focus on Twitter and present an algorithm by modeling diversity in tweets based on topical diversity, geographical diversity, and an interest distribution of the user. Furthermore, we take the Markovian nature of a user's location into account. Our model exploits sparse factorial coding of the attributes, thus allowing us to deal with a large and diverse set of covariates efficiently. Our approach is vital for applications such as user profiling, content recommendation and topic tracking. We show high accuracy in location estimation based on our model. Moreover, the algorithm identifies interesting topics based on location and language.
Polymerizable Living Free Radical Initiators as a Platform To Synthesize Functional Networks (2005)

Photopolymerizations of multifunctional monomers afford spatial and temporal control of cross-linked network formation whereas living radical polymerizations provide a means to synthesize well-defined architectures from monovinyl monomers. By combination of these technologies in a two-stage polymerization process, a novel method is developed to synthesize functional polymer networks, and supporting results are provided for preparing controlled polymer grafts within photo-cross-linked networks. To demonstrate the concept of internal grafting, an alkoxyamine living radical initiator (for nitroxide-mediated polymerization, NMP) and a tertiary bromide initiator (for atom-transfer radical polymerization, ATRP) were functionalized with a methacrylate group and either was copolymerized with mono- and divinyl methacrylic monomers during the initial network formation step. Activation of the living radical initiators within styrene-swollen networks resulted in controlled molecular weight polystyrene grafts covalently bound to the photo-cross-linked methacrylic networks. To demonstrate the applicability of this technology for synthesizing functional networks, hydrogels with nitroxide groups were first photopolymerized, and different concentrations of acetoacetoxy, (i.e., ketoester) functionality were subsequently grafted within the loosely cross-linked networks. When the grafted networks were swollen in aqueous solutions containing Fe3+, the cations coordinated with the grafted ketoester moieties. In general, this robust technology could be applied to a wide array of monomers and functional groups to control the chemical, physical, and mechanical properties of the final grafted network for application in sensors, catalysis, separations, and combinatorial chemistry platforms.
Speech coding based on adaptive mel-cepstral analysis (2002)

We propose an ADPCM coder which uses a backward adaptive predictor based on the adaptive mel-cepstral analysis. The spectrum represented by the mel-cepstral coefficients has frequency resolution similar to that of the human ear which has high resolution at low frequencies. In the coder, since the transfer functions of noise shaping and postfiltering are also defined through the mel-cepstral coefficients, the effects of nose shaping and postfiltering should fit with characteristics of the human auditory sensation. We incorporate a pitch predictor into the ADPCM coder, and evaluate the speech quality based on objective and subjective performance tests. It is shown that the coder at 16 kb/s can produce a high quality speech comparable with that of the CCITT G.721 ADPCM coder at 32 kb/s with no algorithmic delay.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>