gebhart/patrepeval huggingface dataset:
Vascular and inflammatory stresses mediate atherosclerosis via RAGE and its ligands in apoE–/– mice (2008)

Endothelial dysfunction is a key triggering event in atherosclerosis. Following the entry of lipoproteins into the vessel wall, their rapid modification results in the generation of advanced glycation endproduct epitopes and subsequent infiltration of inflammatory cells. These inflammatory cells release receptor for advanced glycation endproduct (RAGE) ligands, specifically S100/calgranulins and high-mobility group box 1, which sustain vascular injury. Here, we demonstrate critical roles for RAGE and its ligands in vascular inflammation, endothelial dysfunction, and atherosclerotic plaque development in a mouse model of atherosclerosis, apoE-/- mice. Experiments in primary aortic endothelial cells isolated from mice and in cultured human aortic endothelial cells revealed the central role of JNK signaling in transducing the impact of RAGE ligands on inflammation. These data highlight unifying mechanisms whereby endothelial RAGE and its ligands mediate vascular and inflammatory stresses that culminate in atherosclerosis in the vulnerable vessel wall.
CpG motif‐independent activation of TLR9 upon endosomal translocation of “natural” phosphodiester DNA (2006)

Endosomally translocated host (self) DNA activates Toll-like receptor 9 (TLR9), while extracellular self-DNA does not. This inconsistency reflects poor endosomal DNA translocation but also implies that host DNA contains DNA sequences that function as ligands for TLR9. Herein we report that contrary to phosphorothioate (PS)-stabilized oligonucleotides (ODN), "natural" phosphodiester (PD) ODN lacking CpG motifs activate TLR9. CpG motif-independent TLR9 activation of Flt3-L-induced dendritic cells (DC) was dependent on enforced endosomal translocation and triggered upregulation of CD40 and CD69 as well as production of IL-6 and IFN-alpha. Binding studies utilizing surface plasmon resonance technology (Biacore) revealed low TLR9 binding to single-stranded (ss) PD-ODN lacking CpG motifs. At higher concentrations their TLR9 binding activity compared well with TLR9 binding of canonical ss PD CpG-ODN. These results imply that both the chemical modification of the DNA backbone as well as the amount of endosomally translocated DNA represent determining factors that allow CpG motif-independent activation of TLR9 by ss PD-DNA.
Isolation and Amino Acid Sequences of Tropoelastin Peptides (1973)

Seventeen peptides have been isolated from a tryptic digest of soluble elastin by ion exchange chromatography and gel filtration. Molecular weights range from approximately 1,700 to 10,500. Partial or complete amino acid sequences of the peptides were obtained and provide the first extensive data on the primary sequence of elastin. Several important findings stand out. First, the sequences obtained reveal an elastin primary structure quite distinct from collagen and possessing repeats of a tetrapeptide, Gly-Gly-Val-Pro, a pentapeptide, Pro-Gly-Val-Gly-Val, and a hexapeptide, Pro-Gly-Val-Gly-Val-Ala. Second, several of the peptides contain a partial hydroxylation of proline residues thereby definitely establishing hydroxyproline as a real constituent of the elastin chain.
Metrology for the Sub-100 NM Domain Via Fiducial Grids (2003)

Abstract : The supported research sought to apply interference lithography technology as a tool for metrology in the sub-100 nm critical dimension (CD) linewidth regime. Semiconductor industry roadmaps show CDs shrinking to under 35 nm within 15 years. This requires mask image placement metrology accuracy of 2 nm by 2014. There are currently no industry length-scale calibration standards at any level of accuracy that may be used to ensure metrology tool accuracy. Instead, the industry relies on various self-referencing schemes which are inaccurate, expensive, time consuming, and ineffective. MIT developed technology to produce image placement metrology standards that achieved sub-5 nm accuracy by the end of this Grant. MIT developed a new tool, called scanning-beam interference lithography (SBIL), which is used to pattern super-accurate grids that will serve as length scale standards. MIT built and tested Phase 1 of the SBIL tool, proving the concept, and then went on to design, build, and test Phase 2 of the tool. The tool was successfully used to pattern 300 mm wafers with 400 nm period gratings which has repeatability of under 3 nanometers.
Pharmacological and X-Ray Structural Characterization of a Novel Selective Androgen Receptor Modulator: Potent Hyperanabolic Stimulation of Skeletal Muscle with Hypostimulation of Prostate in Rats (2006)

A novel, highly potent, orally active, nonsteroidal tissue selective androgen receptor (AR) modulator (BMS-564929) has been identified, and this compound has been advanced to clinical trials for the treatment of age-related functional decline. BMS-564929 is a subnanomolar AR agonist in vitro, is highly selective for the AR vs. other steroid hormone receptors, and exhibits no significant interactions with SHBG or aromatase. Dose response studies in castrated male rats show that BMS-564929 is substantially more potent than testosterone (T) in stimulating the growth of the levator ani muscle, and unlike T, highly selective for muscle vs. prostate. Key differences in the binding interactions of BMS-564929 with the AR relative to the native hormones were revealed through x-ray crystallography, including several unique contacts located in specific helices of the ligand binding domain important for coregulatory protein recruitment. Results from additional pharmacological studies effectively exclude alternative mechanistic contributions to the observed tissue selectivity of this unique, orally active androgen. Because concerns regarding the potential hyperstimulatory effects on prostate and an inconvenient route of administration are major drawbacks that limit the clinical use of T, the potent oral activity and tissue selectivity exhibited by BMS-564929 are expected to yield a clinical profile that provides the demonstrated beneficial effects of T in muscle and other tissues with a more favorable safety window.
Diagnosis of Magnesium-Induced Diarrhea (1991)

Quantitative fecal analysis for soluble magnesium is an accurate method of diagnosing magnesium-induced diarrhea. Some patients with chronic diarrhea ingest excessive amounts of magnesium (in antacids or food supplements), and physicians may fail to discover this before embarking on an expensive and invasive diagnostic evaluation.
Evidence that production and release of amyloid beta-protein involves the endocytic pathway (1994)

Amyloid beta-protein (A beta), the 40-43-amino acid polypeptide that is the principal constituent of senile plaques found in Alzheimer's disease, is constitutively produced and released into medium of cultured cells by an unclear mechanism. In this study, we report that one route of A beta generation involves the internalization of cell surface amyloid precursor protein (beta PP) via the coated pit-mediated endocytic pathway. Radiolabeled A beta can be recovered in medium following selective cell surface radioiodination, indicating that cell surface beta PP is a direct precursor to A beta. In addition, deletion of the cytoplasmic domains of beta PP or depletion of potassium in medium, both of which resulted in reduced beta PP internalization, significantly diminished A beta release. Moreover, pulse-chase experiments after surface radioiodination showed that the kinetics of beta PP secretion and A beta release was different, with the latter occurring at a significantly slower rate. We therefore hypothesize that the internalization of cell surface beta PP via coated pit-mediated endocytosis is one pathway leading to A beta generation and release into medium.
DzyNA-PCR: Use of DNAzymes to Detect and Quantify Nucleic Acid Sequences in a Real-Time Fluorescent Format (2000)

DzyNA-PCR is a simple, rapid, and sensitive technique for homogeneous amplification and quantification of nucleic acids in clinical specimens.
Pixel based illumination compensation for inter prediction in HEVC (2011)

Weighted prediction and illumination compensation are key technologies for inter prediction in a video codec. They increase coding efficiency when the brightness of objects in a sequence fluctuates. Since most conventional methods compensate for illumination changes at slice-level, they are not effective to code general sequences which have no illumination change. Proposed is a pixel based illumination compensation (PBIC) scheme which is applied to the selected pixels adaptively. The optimal IC parameters are calculated considering characteristics of each block whereas parameters of the conventional schemes are optimised for a slice. From the simulation results, it is concluded that the proposed PBIC improves the coding efficiency of high efficiency video coding (HEVC).
Laser-induced tissue hyperthermia mediated by gold nanoparticles: toward cancer phototherapy (2009)

We describe an application of plasmonic silica/gold nanoshells to produce a controllable laser hyperthermia in tissues with the aim of the enhancement of cancer photothermal therapy. Laser irradiation parameters are optimized on the basis of preliminary experimental studies using a test-tube phantom and laboratory rats. Temperature distributions on the animal skin surface at hypodermic and intramuscular injection of gold nanoparticle suspensions and affectations by the laser radiation are measured in vivo with a thermal imaging system. The results of temperature measurements are compared with tissue histology.
Multiple timescale dispatch and scheduling for stochastic reliability in smart grids with wind generation integration (2011)

Integrating volatile renewable energy resources into the bulk power grid is challenging, due to the reliability requirement that the load and generation in the system remain balanced all the time. In this study, we tackle this challenge for smart grid with integrated wind generation, by leveraging multi-timescale dispatch and scheduling. Specifically, we consider smart grids with two classes of energy users - traditional energy users and opportunistic energy users (e.g., smart meters or smart appliances), and investigate pricing and dispatch at two timescales, via day-ahead scheduling and real-time scheduling. In day-ahead scheduling, with the statistical information on wind generation and energy demands, we characterize the optimal procurement of the energy supply and the day-ahead retail price for the traditional energy users; in real-time scheduling, with the realization of wind generation and the load of traditional energy users, we optimize real-time prices to manage the opportunistic energy users so as to achieve system-wide reliability. More specifically, when the opportunistic users are non-persistent, we obtain closed-form solutions to the two-level scheduling problem. For the persistent case, we treat the scheduling problem as a multi-timescale Markov decision process. We show that it can be recast, explicitly, as a classic Markov decision process with continuous state and action spaces, the solution to which can be found via standard techniques.
Stability of Se passivation layers on Si(001) surfaces characterized by time-of-flight positron annihilation induced Auger electron spectroscopy (2005)

The stability of the selenium passivation layer on the Si(001) surface was investigated using a nondestructive surface-sensitive technique: time-of-flight positron annihilation induced Auger electron spectroscopy. After 10days of exposure in the air, the Se passivation layer was observed to incorporate some oxygen but to remain largely intact. Part of the adsorbed oxygen was desorbed during annealing up to 400°C in the ultrahigh-vacuum environment. However, some oxygen remained on the surface until high-temperature annealing at 1030°C. We posit that the oxygen that remained after the low-temperature anneals was chemisorbed on the Si surface at defects in the Se passivation layer. The Se passivation layer was stable up to an annealing temperature of ∼800°C before desorbing from the surface. The stability of the Se-passivated Si(001) surface is attributed to the saturation of the Si dangling bonds on the surface and to the strong Se–Si bonds.
A risk score to predict the probability of postoperative vomiting in adults (1998)

The data suggest that the probability of PV following ENT surgery under inhalational anaesthesia with low-dose opioids can be predicted by a score mainly based upon patient-related risk factors.
Localization of murine Igh-1a allotypic determinants by using a panel of mouse myeloma variant immunoglobulins. (1983)

A number of monoclonal antibodies are available that are reactive with distinct mouse immunoglobulin allotypic determinants. By determining which ones are present on a panel of hybrid IgG2b-IgG2a immunoglobulins, we have localized some of the allotypic determinants present on the IgG2a heavy chain of the "a" allotype (Igh-1a proteins). In particular, one group of determinants--Ig(1a)9.8 (20.6B8), 17.2 (20.19.2), and 14.4 (21.74.4)--has been placed in the CH2 domain. A second group--Ig(1a)8.3 (20.8.3), 21.2 (20.11.2), and 15.3 (21.66.3)--is located in a segment spanning the C terminal 8 residues of the CH2 domain and the complete CH3 domain.
Segregation of altered parental properties in fusions between Saccharomyces cerevisiae and the D-xylose fermenting yeasts Candida shehatae and Pichia stipitis (1992)

A prototrophic strain of Saccharomyces cerevisiae CSIR Y190 MATa xyl-, resistant to high levels of ethanol, was hybridized with xylose-fermenting, auxotrophic mutants of Candida shehatae and Pichia stipitis through polyethylene glycol-induced protoplast fusion in an attempt to produce ethanol-tolerant, xylose-fermenting hybrids. Mononucleate fusants were obtained, but these dissociated into a mixture of parental-type segregants. Purified Candida- and Pichia-resembling segregants failed to acquire improved ethanol tolerance but expressed other novel properties of S. cerevisiae, suggesting that karyogamy was impaired after internuclear gene transfer.
Aminoacyl derivatives of nucleosides, nucleotides, and polynucleotides. XXII. Substrate specificity of ribosomal peptidyltransferase. Effect of modification in the heterocyclic, carbohydrate and amino acid moiety of 2'(3')-O-L-phenylalanyladenosine (1975)

The chemical synthesis of 2'(3')-O-L-phenylalanyl derivatives of nebularine (Ld), 6-methoxynebularine (Ih), N6,N6-dimethyladenosine (Lk), 6-methylthionebularine (Lo), 8-bromoadenosine (Lr), tubercidin (Iu), and 3'-O-L-phenylalanyl derivatives of 1-(beta-D-arabinofuranosyl)cytosine (IIIg) and 9-(beta-D-arabinofuranosyl)adenine (IIIl) is described. 2'(3')-O-(3-Phenyl)propionyladenosine (Iv) was obtained by reaction of adenosine with ethyl 3-phenylorthopropionate and subsequent hydrolysis of the orthoester intermediate IV with formic acid. Compounds Id, Ih, Ik, Io, and Iu were active in the release of Ac-Phe from N-Ac-Phe-tRNA-poly(U)-70S ribosome complex: at 0.01 mM the release of Ac-Phe was 50-100% of that of A-Phe. At 1 mM, compounds Ir and IIIg released 30 and 25% of Ac-Phe relative to A-Phe whereas derivatives Iv and IIIl were virtually inactive. The results indicate the following conclusions regarding ribosomal peptidyltransferase activity of 2'(3')-O-aminoacyl nucleosides: (a) the presence of the 2'-hydroxy group in the ribo configuration is more important for a highly active substrate (A-Phe) than for one of moderate activity (C-Phe); (b) the heterocyclic (purine) residue is in the anti conformation although this requirement is not absolute; (c) the presence of the amino group of the aminoacyl moiety is required; (d) acceptor activity is dependent upon the substituent in the position 6 of the purine moiety.
Clustering of scientific journals (1973)

Abstract A cluster analysis procedure is described in which 288 journals in the disciplines of physics, chemistry and molecular biology are grouped into clusters. Most of the clusters are easily identified as subdisciplinary subject areas. The data source was the cross citing amongst the journals derived from the Journal Citation Index (JCI) , a file derived in turn from the Science Citation Index (SCI) ®. The JCI consists of journal by journal tabulation of citings to and from each journal processed in the SCI. Two‐step citation maps linking the clusters are presented for each discipline. Within the disciplines the clusters of journals form fully transitive hierarchies with very few relational conflicts.
Stability of Extruded 17β-Estradiol Solid Dispersions (2001)

Recrystallization is one of the main problems concerning the stability of solid dispersions. Different analytical methods were applied showing that no recrystallization occurred after treating melt extruded solid dispersions with 17 beta-Estradiol as the model drug with heat or water vapor. A skillful choice of excipients--a combination of polymers and additives--could be the reason for improving the stability. The requirements of the USP 23 for Estradiol tablets of 75% dissolved drug after 60 min were fulfilled after storing the tablets for 6 months at 40 degrees C/75% RH. By observing the change in glass transition temperature, DSC analysis showed that the solid dispersions were stable against thermal stress. Isothermal microcalorimetry as well as moisture absorption gravimetry were methods to prove the stability of the solid dispersions against water vapor.
Mudding: Social phenomena in text-based virtual realities. (1997)

A MUD (Multi-User Dungeon or, sometimes, Multi-User Dimension) is a network-accessible, multi-participant, user-extensible virtual reality whose user interface is entirely textual. Participants (usually called players) have the appearance of being situated in an artificially-constructed place that also contains those other players who are connected at the same time. Players can communicate easily with each other in real time. This virtual gathering place has many of the social attributes of other places, and many of the usual social mechanisms operate there. Certain attributes of this virtual place, however, tend to have significant effects on social phenomena, leading to new mechanisms and modes of behavior not usually seen ‘IRL’ (in real life). In this paper, I relate my experiences and observations from having created and maintained a MUD for over a year.
Monolithic IO-Technology - Modulators and Switches Based on InP (1986)

Waveguiding devices, like modulators and switches, realized with InGaAsP lattice matched to InP are discussed. Basic phenomena, such as optical absorption, electro- and elasto-optic effect as well as the impact of free carriers on absorption and refractive index, are considered and described in their use with actually realized devices. Whereas the optical absorption seems not to be a main obstacle, the relatively large length of the devices will restrict their employment to the most essential functions.
Effect of Phytate in Soy Protein on the Serum and Liver Cholesterol Levels and Liver Fatty Acid Profile in Rats (2003)

Dietary soy protein, in comparison with casein, generally lowers the serum cholesterol concentration in rats fed on a cholesterol-enriched diet, while mixed results were observed in rats fed on a diet free of cholesterol. Soy protein also suppresses the conversion of linoleic acid to arachidonic acid in the rat liver. The present study examines whether phytate, a minor component of a soy protein isolate, is responsible for these beneficial effects of soy protein. Weanling male rats were fed for 4 weeks on a purified diet containing a 20% level of protein (either casein (CAS), soy protein (SOY), phytate-depleted SOY (PDSOY) or phytate-replenished PDSOY (PRSOY)) and cholesterol (0 or 0.5%). The dietary protein source and phytate level only affected the serum and liver cholesterol concentrations when the animals were fed on the cholesterol-enriched diet, being significantly lower in those rats fed on the SOY and PRSOY diets than in those fed on the CAS diet, while the concentrations in the rats fed on the PDSOY diet were intermediate. When the animals were fed on the cholesterol-free diet, the ratio of (20:3n-6 + 20:4n-6)/18:2n-6 in liver phosphatidylcholine, a delta6 desaturation index, was significantly lower in the SOY diet group than in the CAS, PDSOY and PRSOY diet groups. Dietary cholesterol significantly depressed the ratio, but neither depletion nor replenishment of phytate affected the ratio. These results suggest that phytate in soy protein played a limited role in the cholesterol-lowering effect of soy protein and was not involved in the metabolism of linoleic acid.
Transcription factors GATA-4 and GATA-6 in normal and neoplastic human gastrointestinal mucosa (2008)

The results suggest differential but overlapping functions for GATA-4 and GATA-6 in the normal gastrointestinal mucosa. Furthermore, GATA-4, GATA-6 and Ihh expression is altered in premalignant dysplastic lesions and reduced in overt cancer.
Dislocation reduction in MOVPE grown GaN layers on (111)Si using SiNxand AlGaN layers (2010)

Growth of GaN on Si(111) potentially enables cost efficient manufacturing of optoelectronic devices due to the possibility of using cheap large area substrates. However, GaN layers grown on Si(111) substrates suffer from high tensile stress that can lead to cracking at layer thicknesses exceeding 1 μm. Another challenge is the high dislocation density of GaN layers grown on Si(111) which is detrimental to device performance. In this paper we show that a step graded AlGaN buffer layer can compensate tensile stress, avoiding cracking, and at the same time reduce the dislocation density. An additional SiNx interlayer in the GaN layer is shown to further reduce the dislocation density down to the high 108 /cm2. Weak beam dark field TEM was used to study the dislocation reduction in cross sectional samples and for comparison of the step graded AlGaN buffer layer structure to a continuously graded one. STEM ADF was used to determine the exact location of dislocation bending with respect to the position of the interface.
A lattice-ladder structure for multipulse linear predictive coding of speech (1987)

This correspondence presents an order-recursive algorithm for the computation of the model parameters required in multipulse linear predictive coding (LPC) or speech in the case of autocorrelation method. Its computational complexity is 2p <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> + 4p multiplications and divisions, where p + 1 is the number of the model parameters. It is also shown that the developed algorithm leads, in a natural way, to lattice-ladder structures for multipulse linear predictive coding of speech.
Inhibition of Localized Adhesion of Enteropathogenic Escherichia coli to HEp-2 Cells by Immunoglobulin and Oligosaccharide Fractions of Human Colostrum and Breast Milk (1991)

Secretory IgA (sIgA) purified from colostrum and breast milk obtained from 14 women inhibited the localized adherence of an enteropathogenic Escherichia coli (EPEC) to HEp-2 cells. Inhibition decreased as lactation continued even when the concentration of sIgA was maintained constant at 1 mg/ml. sIgA responded to a 94-kDa plasmid-encoded outer membrane protein implicated as the EPEC adherence factor. An oligosaccharide-enriched fraction (OEF) from these samples also inhibited the attachment of this EPEC. Inhibition by OEFs decreased as lactation continued because of a general reduction in oligosaccharide content. Localized adherence of six other EPEC was also inhibited by sIgA and OEF, whereas attachment of isolates with diffuse or aggregative adherence was not inhibited by these fractions. Experiments with purified oligosaccharide fractions revealed that EPEC attach to HEp-2 cells through a carbohydrate-mediated mechanism based on the preferential recognition of fucosylated residues in human milk.