gebhart/patrepeval huggingface dataset:
Interaction of Non-Aggregated Boar AWN-1 and AQN-3 with Phospholipid Matrices. A Model for Coating of Spermadhesins to the Sperm Surface (1995)

Boar spermadhesins are 12-14 kDa lectins which coat the entire acrosomal cap sperm head surface. The large amount of spermadhesins AQN-1, AQN-2, AQN-3, and AWN-1 present on in vitro capacitated spermatozoa (approximately 7 x 10(6) molecules of each spermadhesin per cell) suggested that they may bind to major component(s) of the sperm surface. We have investigated both the aggregation state of spermadhesins in seminal plasma using gel filtration chromatography, and their ability to bind to the major phospholipids of the boar sperm plasma membrane, i.e. phosphorylcholine and phosphorylethanolamine. The bulk (90%) of spermadhesins AQN-3 and AWN-1 were eluted as aggregated proteins (Mr > 50,000) with the void volume of a Sephadex G-50 column; the remaining 10% of the total amount of seminal plasma AWN-1 and AQN-3 were recovered, together with the whole amount of AQN-1 and AQN-2, in a fraction containing low-molecular-mass proteins (Mr 16,000-30,000). None spermadhesin of either gel-filtration fraction bound to a phosphorylcholine affinity matrix. On the other hand, low-molecular-mass (monomeric or dimeric) AQN-3 and AWN-1 were the only spermadhesins retained in a phosphorylethanolamine affinity column. Both AQN-3 and AWN-1 purified from seminal plasma by reverse-phase HPLC retained their lipid-binding capability. In addition, immobilization of AQN-3 and AWN-1 onto a phosphorylethanolamine matrix did not interfere with the ability of the proteins to bind bovine glycoprotein PDC-109, indicating that the structural determinants for the binding lipid and carbohydrates lay on different structural domains.(ABSTRACT TRUNCATED AT 250 WORDS)
THE UNIVERSAL CLOSE-RANGE ROAD/VEHICLE COMMUNICATION SYSTEM CONCEPT - THE NUMEROUS APPLICATIONS OF THE ENHANCED AVI (1991)

When the Automatic Vehicle Identification Concept (AVI) started it was simply an Electronic Tag. Today, with a 2 way communication capability, programmability and intelligence, it has graduated to a full fledged Close-Range Road/Vehicle Communication System (CRCS). Its applications include vehicle identification, vehicle location, 2 way vehicle communication, fleet management and more. This paper, the first in a series of complementary papers that cover the enhanced AVI system/CRCS concept and describe a number of the different applications of this low cost, high impact technology that is revolutionizing the road transportation system. This paper gives an overall view of the CRCS concept and representative applications from every area of IVHS. (A) For the covering abstract of the conference see IRRD Abstract no. 807788.
A 1.8 V, 5.4 mW, digital-audio ΣΔ modulator in 1.2 μm CMOS (2002)

This experimental switched-capacitor /spl Sigma//spl Delta/ modulator achieves 92 dB dynamic range for a signal bandwidth of dc to 25 kHz while operating from 1.8 V supply. The supply voltage is consistent with the end-of-life of two battery cells in series. The fully-differential circuit has been integrated in a 5 V, 1.2 /spl mu/m CMOS technology with poly-n/sup +/ capacitors.
M-Studio: An Authoring Tool For Context-Aware Mobile Storytelling (2002)

Thesis (M.Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, February 2003.
The genetics of obesity: FTO leads the way (2010)

In 2007, an association of single nucleotide polymorphisms (SNPs) in the fat mass and obesity-associated (FTO) gene region with body mass index (BMI) and risk of obesity was identified in multiple populations, making FTO the first locus unequivocally associated with adiposity. At the time, FTO was a gene of unknown function and it was not known whether these SNPs exerted their effect on adiposity by affecting FTO or neighboring genes. Therefore, this breakthrough association inspired a wealth of in silico, in vitro, and in vivo analyses in model organisms and humans to improve knowledge of FTO function. These studies suggested that FTO plays a role in controlling feeding behavior and energy expenditure. Here, we review the approaches taken that provide a blueprint for the study of other obesity-associated genes in the hope that this strategy will result in increased understanding of the biological mechanisms underlying body weight regulation.
Planarized Be δ-Doped Heterostructure Bipolar Transistor Fabricated Using Doping Selective Contact and Selective Hole Epitaxy (1991)

We report a heterostructure bipolar transistor (HBT) in which the base is δ-doped with Be to a concentration of 1×10 14 cm -2 and the Be is spatially confined to within 15 Å. To fabricate the HBT without inducing Be redistribution and avoid critical emitter mesa etching, we have developed a new low-temperature base-contacting procedure ( T max =420°C) which requires no base-emitter etching. A 50 µm diameter δ-HBT shows a current gain of 20. Upon reducing the size of the emitter to 3×8 µm, the current gain of the δ-HBT increases to 30. This, we belive, is due to our new processing technique which eliminates the critical base-emitter etch and hence reduces surface recombination. In addition, we grew and fabricated HBT's in holes that have been pre-etched into the substrates. High quality material has been achieved in the holes.
Mitochondrial Dysfunction in Friedreich’s Ataxia (2001)

Friedreich ataxia (FRDA) is an autosomal recessive degenerative disorder caused in the vast majority of cases by a GAA triplet expansion in the FRDA gene on chromosome 9q13. The FRDA gene product, frataxin, is a widely expressed mitochondrial protein which is severely reduced in FRDA patients. Loss of the homologue of frataxin in yeast is associated with mitochondrial iron overload, increased sensitivity to oxidative stress and profound deficit of oxidative phosphorylation. The demonstration that the human pathology of FRDA is also characterised by mitochondrial iron accumulation, deficit of respiratory chain complex activities and in vivo deficit of tissue energy metabolism establishes FRDA as a 'new' nuclear encoded mitochondrial disease.
New Green and Red Phosphors for White LEDs (2008)

High-luminous green phosphors and a red phosphor have been newly developed for white LEDs. The developed green phosphors are Ca3(Sc,Mg)2Si3O12:Ce made by replacing with Mg a part of Sc of green phosphor Ca3Sc2Si3O12:Ce, a new green phosphor CaSc2O4:Ce, and a new host material doped with a rare-earth element, Ba3Si6O12N12:Eu. The new red phosphor is (Sr,Ca)AlSiN3:Eu made by replacing a part of Ca of CaAlSiN3:Eu with Sr.
Murine tumor antigens: is it worth the search? (1996)

Standardized techniques that allow the direct identification of tumor antigens are now available. Several murine antigens recognized by T cells have already been identified. So far, the majority of these antigens derive from cellular proteins similar to those that give rise to human tumor antigens. While many of the known human tumor antigens are widely shared, most of the murine tumor antigens appear to be unique to the individual tumor from which they were isolated. Nonetheless, common features between murine and human tumor antigens are emerging, suggesting that these murine antigens will provide essential tools in the evaluation of antigen-based vaccines for the future treatment of cancer.
Lysophosphatidic Acid Protects Cancer Cells from Histone Deacetylase (HDAC) Inhibitor-induced Apoptosis through Activation of HDAC (2008)

Histone deacetylases (HDACs) catalyze the removal of acetyl groups from histones and contribute to transcriptional repression. In addition, the HDAC inhibitors induce apoptosis in cancer cells through alterations in histone acetylation and activation of the tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) apoptotic pathway. Lysophosphatidic acid (LPA) is a growth factor that promotes survival of cancer cells through activation of G protein-coupled receptors. Here we show that HDAC inhibitors can induce apoptosis through activation of the TRAIL apoptotic pathway, and LPA prevented HDAC inhibitor-induced apoptosis and increased TRAIL receptor DR4 (death receptor 4) protein expression. This was associated with increased HDAC1 recruitment to the DR4 promoter following LPA treatment and a reduction in HDAC inhibitor-induced histone acetylation in the DR4 promoter. In addition, LPA induces HDAC enzyme activity in a dose- and time-dependent manner, and this is associated with HDAC1 activation and increased binding of HDAC1 to HDAC2. Reducing the expression of HDAC1 significantly lowered LPA-induced HDAC activity and increased histone acetylation. LPA induction of HDAC activity was blocked by the LPA receptor antagonist, Ki16425, or by inhibiting receptor activation with pertussis toxin. Reducing the expression of the LPA receptor LPA(1) also blocked LPA-induced HDAC activation. In addition, LPA reduced histone acetyltransferase enzymatic activity. Finally, LPA attenuated the ability of the HDAC inhibitor to reduce HDAC activity. Thus, LPA enhances survival of cancer cells by increasing HDAC activity and reducing histone acetylation.
The Nuclear Factor-κB Signaling Network: Insights from Systems Approaches (2014)

This chapter reviews the nature of bipartite nuclear factor-κB (NF-κB) regulatory pathways activated in response to monokines produced as a consequence of viral infection, and those involved in mediating RNA viral infection. The chapter discusses work using mRNA profiling studies to determine the genetic networks downstream of NF-κB in response to monokines and RNA virus replication. Inhibition of reactive oxygen species (ROS) formation blocks Ser-276 phosphorylation and NF-κB-dependent gene expression without affecting NF-κB translocation. It was also found that RelA Ser-276 phosphorylation allows complex formation with the cyclin-dependent kinases (CDK)-9/Ccn T1, known as positive transcription elongation factor-b (PTEF-b). Reovirus is a segmented double-stranded RNA (dsRNA) virus that induces cellular apoptosis in an NF-κB-dependent manner. In a study, the tTA-IκB-α Mut cell system was exposed to reovirus for various times from 0 to 10 h in the presence or absence of functional NF-κB signaling. The major pathways are now understood to be composed of bipartite signaling modules whose actions affect nuclear translocation and, separately, transcription factor activation. The chapter also reviews systematic approaches to understanding the signaling pathway, including proteomics, mathematical modeling, real-time imaging, and gene network analyses.
A novel endothelial-specific heat shock protein HspA12B is required in both zebrafish development and endothelial functions in vitro (2006)

A zebrafish transcript dubbed GA2692 was initially identified via a whole-mount in situ hybridization screen for vessel specific transcripts. Its mRNA expression during embryonic development was detected in ventral hematopoietic and vasculogenic mesoderm and later throughout the vasculature up to 48 hours post fertilization. Morpholino-mediated knockdown of GA2692 in embryos resulted in multiple defects in vasculature, particularly, at sites undergoing active capillary sprouting: the intersegmental vessels, sub-intestinal vessels and the capillary sprouts of the pectoral fin vessel. During the course of these studies, a homology search indicated that GA2692 is the zebrafish orthologue of mammalian HspA12B, a distant member of the heat shock protein 70 (Hsp70) family. By a combination of northern blot and real-time PCR analysis, we showed that HspA12B is highly expressed in human endothelial cells in vitro. Knockdown of HspA12B by small interfering RNAs (siRNAs) in human umbilical vein endothelial cells blocked wound healing, migration and tube formation, whereas overexpression of HspA12B enhanced migration and accelerated wound healing - data that are consistent with the in vivo fish phenotype obtained in the morpholino-knockdown studies. Phosphorylation of Akt was consistently reduced by siRNAs against HspA12B. Overexpression of a constitutively active form of Akt rescued the inhibitory effects of knockdown of HspA12B on migration of human umbilical vein endothelial cells. Collectively, our data suggests that HspA12B is a highly endothelial-cell-specific distant member of the Hsp70 family and plays a significant role in endothelial cells during development and angiogenesis in vitro, partially attributable to modulation of Akt phosphorylation.
PI3K/mTOR Dual Inhibitor VS-5584 Preferentially Targets Cancer Stem Cells (2014)

Cancer stem cells (CSC) have been implicated in disease recurrence, metastasis, and therapeutic resistance, but effective targeting strategies for these cells are still wanting. VS-5584 is a potent and selective dual inhibitor of mTORC1/2 and class I PI 3-kinases. Here, we report that VS-5584 is up to 30-fold more potent in inhibiting the proliferation and survival of CSC compared with non-CSC in solid tumor cell populations. VS-5584 preferentially diminished CSC levels in multiple mouse xenograft models of human cancer, as evidenced by marked reduction of tumor-initiating capacity in limiting dilution assays. Likewise, VS-5584 treatment ex vivo preferentially reduced CSC in surgically resected breast and ovarian patient tumors. In contrast, chemotherapeutics such as paclitaxel and cisplatin were less effective in targeting CSC than bulk tumor cells. Mechanistic investigations revealed that preferential targeting of CSC required inhibition of multiple components of the PI3K-mTOR pathway: coordinate RNAi-mediated silencing of PI3Kα, PI3Kβ, and mTOR phenocopied the effect of VS-5584, exhibiting the strongest preferential targeting of CSC, while silencing of individual PI3K isoforms or mTOR failed to replicate the effect of VS-5584. Consistent with CSC ablation, VS-5584 delayed tumor regrowth following chemotherapy in xenograft models of small-cell lung cancer. Taken together, the preferential targeting of CSC prompts a new paradigm for clinical testing of VS-5584: clinical trials designed with CSC-directed endpoints may facilitate demonstration of the therapeutic benefit of VS-5584. We suggest that combining VS-5584 with classic chemotherapy that debulks tumors may engender a more effective strategy to achieve durable remissions in patients with cancer.
An Escherichia coli protein consisting of a domain homologous to FK506-binding proteins (FKBP) and a new metal binding motif. (1994)

Initially detected as a persistent contaminant in immobilized metal affinity chromatography of recombinant proteins in Escherichia coli, a 196-amino acid protein was isolated, cloned, overexpressed, and characterized. It consists of two domains, of which the first (146 amino acids) shows some homology to the FK506-binding proteins. The second domain (50 amino acids) is extremely rich in potentially metal-binding amino acids, such as histidine, cysteine, and acidic amino acids. The protein binds Ni2+ and Zn2+ tightly with 1:1 stoichiometry, Cu2+ and Co2+ with lower affinity, and Mn2+, Fe2+, Fe3+, Mg2+, and Ca2+ hardly at all.
Additional amplifications of SERSvia an optofluidic CD-based platform (2008)

In this paper, signal amplifications of surface-enhanced Raman scattering (SERS) are realized by an optofluidic compact disc (CD)-based preconcentration method for effective label-free environmental and biomolecular detections. The preconcentration of target molecules is accomplished through the accumulation of adsorbed molecules on SERS-active sites by repeating a 'filling-drying' cycle of the assay solution in the optofluidic CD platform. After 30 cycles, the clear and high SERS signal of rhodamine 6G of 1 nM is readily detected. In addition to the preconcentration-based signal amplification by the optofluidic SERS system on the CD platform, we introduce a controlled precipitation of gold nanoparticles by CuSO4 for SERS substrates. This method provides high-throughput, high-sensitive and large-area uniform SERS substrates on the optofluidic CD platform. The uniform SERS signals from different positions in spots of 3 mm2 on the different CDs gives us confidence in the reliability and stability of our SERS substrates.
Toward a Classification System of Relational Activity in Consumer Electronic Communities: The Moderators’ Tale (2010)

Increasingly, consumers are turning toward electronic community as a form of expression, giving marketers the opportunity to understand and communicate with consumers in specialist fields. Vast differences exist in the nature and performance of electronic communities, making selecting a community difficult. This article proposes a classification system based on in-depth personal construct interviews with experts from a leading European moderating organization. It reports on the empirical results of 10 differentiating features of relational activity across communities: content of discussions, diversity, frequency, quality of interaction, levels of commitment, interpersonal perceptions, reciprocity and complementarity, power and conflict, self-disclosure, and levels of satisfaction reported in community relationships.
The Control of Diabetes Mellitus (NIDDM) in the Morbidly Obese with the Greenville Gastric Bypass (1987)

Since February 1, 1980, the identical standardized Greenville Gastric Bypass has been performed in 397 morbidly obese patients with an operative mortality rate of 0.8%. The operation effectively controlled weight and maintained satisfactory weight loss even after 6 years (mean weights and ranges: Preoperative: 290 lbs (196-535); 18 months: 175 lbs (110-300); 72 months: 205 lbs (140-320). The gastric bypass favorably affected non-insulin-dependent diabetes (NIDDM), hypertension, physical and role functioning, and several measures of mental health. Rigorous follow-up (97.5% over 6 years) revealed that health problems were common in postoperative patients; there were nine late deaths. Abnormal glucose metabolism was present in 141 (36%) of 397 patients before surgery: NIDDM was present in 88 patients (22%) and 53 patients (14%) were glucose impaired. Of these, all but two became euglycemic within 4 months after surgery without any diabetic medication or special diets. The most recent 42 morbidly obese patients with NIDDM were studied intensively. In that cohort, fasting blood glucose, fasting insulin, and glycosylated hemoglobin returned to normal after surgery; insulin release, insulin resistance, and utilization of glucose improved sharply. The normalization of glucose metabolism after gastric bypass may not be related solely to weight loss and restriction of caloric intake, but may also be due to the bypass of the antrum and duodenum.
Excess pore pressure in Mississippi delta front sediments: Initial report (1976)

Abstract In September 1975, a differential piezometer probe was successfully implanted in the soft seafloor sediments of Block 28, South Pass, Mississippi Delta. The probe sensor is located approximately 6.4 m below the mudline in a water depth of 19 m, and has essentially continuously monitored excess pore pressure (the difference between sediment pore pressure and hydrostatic pressure at that depth) since installation. Excess pore pressure will be monitored until March 1976, when the probe will be recovered. Immediately after deployment, an excess pore pressure of 54 kPa was recorded. An ambient excess pore pressure of approximately 32 kPa remained after dissipation of that developed during probe installation. Because of the possible presence of gas in the sediments in this area, it is not known with certainty whether the measured excess pressure is pore water pressure, pore gas pressure, or some combination of the two. An excess pore pressure of about 32 ±4 kPa was monitored during Hurricane Eloise and subsequent storms. The exact magnitude and time distribution of these pressure fluctuations is presently being evaluated.
Nucleotide sequence of a Sequence of a sendai virus genome region covering the entire M gene and the 3′ proximal 1013 nudeotides of the F gene (1984)

We determined the sequence of the 2,138 nucleotides in the Sendai virus genome just following the 3' proximal 3,686 nucleotides which we had previously reported (Nucleic Acids Res. 11, 7317-7330, 1983). This covers the entire third gene of 1,173 nucleotides and the 3' proximal 1,013 nucleotides of the fourth gene. Like the NP and P+C genes, both the third and fourth genes start from consensus sequence R1 (3'-UCCCAC(or UA)UUUC) at the 3' end and the third gene terminates with consensus sequence R2 (3'-AUUCUUUUU) at the 5' end. The third gene was identified as M, and the deduced 348 amino acids indicated that the M protein is rich in basic residues and has hydrophobic domains near the C-terminal. The fourth gene, although sequencing is not complete yet, was identified as F, since a large open reading frame found in the gene contains the characteristic sequence of 20 amino acids located at the N-terminal of the F1 protein. Analyses of the amino acid sequence suggested that the structure of the F gene product is NH2-signal peptide-F2-F1-COOH.
Molecular Criteria for Defining the Naive Human Pluripotent State (2016)

Recent studies have aimed to convert cultured human pluripotent cells to a naive state, but it remains unclear to what extent the resulting cells recapitulate in vivo naive pluripotency. Here we propose a set of molecular criteria for evaluating the naive human pluripotent state by comparing it to the human embryo. We show that transcription of transposable elements provides a sensitive measure of the concordance between pluripotent stem cells and early human development. We also show that induction of the naive state is accompanied by genome-wide DNA hypomethylation, which is reversible except at imprinted genes, and that the X chromosome status resembles that of the human preimplantation embryo. However, we did not see efficient incorporation of naive human cells into mouse embryos. Overall, the different naive conditions we tested showed varied relationships to human embryonic states based on molecular criteria, providing a backdrop for future analysis of naive human pluripotency.
Power Blurring: Fast Static and Transient Thermal Analysis Method for Packaged Integrated Circuits and Power Devices (2014)

High-temperature and temperature nonuniformity in high-performance integrated circuits (ICs) can significantly degrade chip performance and reliability. Thus, accurate temperature information is a critical factor in chip design and verification. Conventional volume grid-based techniques, such as finite-difference and finite-element methods (FEMs), are computationally expensive. In an effort to reduce the computation time, we have developed a new method, called power blurring (PB), for calculating temperature distributions using a matrix convolution technique in analogy with image blurring. The PB method considers the finite size and boundaries of the chip as well as 3-D heat spreading in the heat sink. PB is applicable to both static and transient thermal simulations. Comparative studies with a commercial FEM tool show that the PB method is accurate within 2%, with orders of magnitude speedup compared with FEM methods. PB can be applied to very fine power maps with a grid size as small as 10 μm for a fully packaged IC or submicrometer heat sources in power electronic transistor arrays. In comparison with architecture-level thermal simulators, such as HotSpot, PB provides much more accurate temperature profiles with reduced computation time.