gebhart/patrepeval huggingface dataset:
Lasing characteristics of high-performance narrow-stripe InGaAs-GaAs quantum-well lasers confined by AlAs native oxide (1996)

High-performance narrow-stripe InGaAs-GaAs quantum-well lasers with integral buried AlAs native-oxide layers have been fabricated. AlAs native-oxide layers above and below waveguide region were employed for current and optical confinement to form narrow-stripe lasers. A low temperature (400/spl deg/C) anisotropic wet oxidation technique was used to selectively oxidize AlAs layers in the epitaxial structure. The devices demonstrated continuous wave threshold currents of 3.5 mA, external quantum efficiencies of 82%, and a characteristic temperature of 133 K for 1.8 μm-wide aperture, 400 μm-long devices. Threshold currents of 1.7 mA were obtained by applying HR/HR coatings.
Negative-Acting Aqueous Base-Developable Photoresist With Submicron Resolution Capabilities Over Topography (1987)

A family of negative-acting "image reversal" photoresists identified as the MacDermid XNR 2000 series is characterized here in some detail. Although its photoresist chemistry is based on the conventional positive resist concept using cresol Novolak resins together with a somewhat novel 2-1-4 naphthoquinone-diazo-oxide-ester, the conversion of the resist to the negative mode is primarily based on the addition of a new generation of thermal crosslinking agents to a typical positive resist formulation. The processing cycle evolved for this series consists of: (a) spin-coat, (b) soft-bake, (c) UV expose,(d) post-exposure-bake (PEB), and then (e) develop with either metal-ion containing or metal-ion-free developer(s) in either immersion or in-line mode(s).
Modulation of Glucose-Induced Insulin Secretion from a Rat Clonal β-Cell Line* (1990)

The present studies demonstrate that the beta-cell line RINr1046-38 (RIN-38) retains the capability to secrete insulin in response to glucose. The maximal effect of glucose was a 5- to 9-fold stimulation of insulin secretion from RIN-38 cells. This glucose-induced insulin secretion was maximal at 0.6 mM and was modulated by other secretagogues. Potassium concentrations of 10 mM, adenylate cyclase activators (glucagon-like peptide-1 and forskolin), and a phosphodiesterase inhibitor (isobutylmethylxanthine) potentiated glucose-induced insulin secretion, but had little or no effect on insulin secretion in the absence of glucose. Potassium concentrations of 20 mM or more, glibenclamide, and carbachol (Cch) stimulated insulin secretion 8- to 12-fold in the absence of glucose, while only Cch potentiated the effect of glucose on insulin secretion. Amino acids (alanine, arginine, leucine, and ketoisocaproate) also stimulated insulin secretion. The alpha 2-adrenergic agonist clonidine (1 microM), low extracellular calcium (less than or equal to 0.5 mM), and extended culture of RIN-38 cells at low glucose concentrations (0.33 mM) inhibited the stimulatory effect of glucose on insulin secretion. Insulin secretion was retained in RIN-38 cells for up to 98 passages. However, extended passage was associated with a decline in cellular insulin content (83% decline over 89 passages). In addition, high passage cells lost the ability to secrete insulin in response to glucose, but continued to respond to other secretagogues (K+, alanine, and carbachol). In fact, in the absence of glucose the effect of Cch on insulin secretion was well maintained in high passage cells (8- and 9.9-fold increase in insulin secretion, passages 9 and 70, respectively). Thus, low passage RIN-38 cells secrete insulin in response to glucose and other insulin secretagogues. High passage cells do not respond to glucose, but continue to respond to other secretagogues. Based on these results we propose that high and low passage RIN-38 cells provide a model for examining molecular mechanisms of glucose-induced insulin secretion. In addition, these findings emphasize that passage information is essential for interpretation of secretion studies with RIN cell lines.
Planning Of Landmark Measurement For The Navigation A Mobile Robot (2005)

Recognition of its current location is im- portant for a mobile robot to follow a planned path. Landmarks, which are assumed in the environment around the robot, are used to support this recognition. In this paper we propose a method for the robot to select the most suitable landmark among the measur- able landmarks from its current position by evaluating the error covariance update of the position estimation. We use the extended Kalman filter to update the po- sition estimation. We show the update behaviors of two types of landmarks : line type and point type. For the criteria of the evaluation we use the widths of the error ellipses, perpendicular to the direction of the course. Through the simulation of navigating a robot along the center lines of corridors the effectiveness of the proposed method is confirmed. ing landmarks the position estimation is updated in the same way. The behaviors of using two types of landmarks, a line type landmark and a point type one, are examined. The position estimation using a particular landmark is ex- pressed by an error ellipse which is derived from the error covariance update and which shows the directional error distribution of the estimated position error. Though it is favorable if the radius of the error ellipse is small in all di- rections, we think the width of the ellipse along the course is important and propose to use it as the criterion for the selection of the landmark. By the simulation of navigating a robot along the center lines of corridors the effectiveness of navigation based on the proposed landmark selection method is shown.
High speed scientific data transfers using software defined networking (2015)

The massive data volumes acquired, simulated, processed and analyzed by globally distributed scientific collaborations continue to grow exponentially. One leading example is the LHC program, now at the start of its second three year data taking cycle, searching for new particles and interactions in a previously inaccessible range of energies, which has experienced a 70% growth in peak data transfer rates over the last 12 months alone. Other major science programs such as LSST and SKA, and other disciplines ranging from earth observation to genomics, are expected to have similar or great needs than the LHC program within the next decade. The development of new methods for fast, efficient and reliable data transfers over national and global distances, and a new generation of intelligent, software-driven networks capable of supporting multiple science programs with diverse needs for high volume and/or real-time data delivery, are essential if these programs are to continue to progress, and meet their goals. In this paper we describe activities of the Caltech High Energy Physics team and collaborators, related to the use Software Defined Networking to help achieve fast and efficient data distribution and access. Results from Supercomputing 2014 are presented together with our work on the Advanced Network Services for the Experiments project, and a new project developing a Next Generation Integrated SDN Architecture, as well as our plans for Supercomputing 2015.
Differential roles of protein kinase C and pertussis toxin-sensitive G-binding proteins in modulation of melanoma cell proliferation and motility by thrombospondin 1. (1998)

Thrombospondin 1 (TSP1) is an angiogenesis inhibitor that decreases tumor growth. We now report that TSP1 directly inhibits the proliferation of human melanoma cells. TSP1, peptides, and a recombinant fragment from the type I repeats, but not peptides that bind CD36 or CD47, inhibit the proliferation of A2058 melanoma cells. In contrast, chemotaxis is mediated by peptides or recombinant fragments from the procollagen, type I, type II, and cell-binding domains. The antiproliferative activity of TSP1 is mediated by a different signal transduction pathway than those mediating motility responses to the same protein. Activators of protein kinase A and protein kinase C inhibit chemotaxis but not the antiproliferative activity of TSP1, whereas the antiproliferative activity is reversed by inhibiting the tyrosine kinase or phosphatase activities. TSP1-mediated chemotaxis is partially dependent on a pertussis toxin (PT)-sensitive G-binding protein, whereas haptotaxis is not. Chemotaxis stimulated by the procollagen domain and the CD47-binding sequences from the COOH-terminal domain are also sensitive to PT, but responses to the type I and type III domains are not sensitive to PT. Residual chemotaxis to TSP1 in the presence of PT may therefore be mediated by the activities of the type I or type III repeats. Thus, TSP1 elicits several intracellular signals in melanoma cells that result from interactions with several domains of this protein and differentially affect growth and motility.
Enediyne antibiotics as antitumor agents (1995)

Enediyne Antitumor Antibiotics, Terrence W. Doyle and Donald B. Borders Calicheamicins The Biochemical Induction Assay and Its Application in the Detection of the Calicheamicins, Michael Greenstein, Mary Jo Wildey, and William M. Maiese Taxonomy, Fermentation, and Yield Improvement, Amedeo A. Fantini and Raymond T. Testa Identification, Isolation, and Structure Determination, May D. Lee Disulfide Calicheamicins and the Chemistry of the Allylic Trisulfide Group, William J. McGahren, Wei-Dong Ding, and George A. Ellestad Preparation of Conjugates to Monoclonal Antibodies, Lois M. Hinman, Philip R. Hamann, and Janis Upeslacis Genetic Analysis of Calicheamicin Biosynthesis, David M. Rothstein Biological Activities of Calicheamicin, Frederick E. Durr, Roslyn E. Wallace, Raymond T. Testa, and Nydia A. Kuck DNA-Cleaving Properties of Calicheamicing, George A. Ellestad, Wei-Dong ding, Nada Zein, and Craig A. Townsend Esperamicins Fermentation and Isolation of Esperamicins, Kin Sing Lam and Salvatore Forenza Structure Determination of the Esperamicins, Jerzy Golik Biosynthesis of Esperamicin, Kin Sing Lam and Judith A. Veitch Mechanism of Action and Molecular Modeling for Esperamicin A1, Calicheamicing, and Dynemicin A, David R. Langley Biological Properties of Esperamicin and Other Enediyne Antibodies, Anna Maria Casazza and Susan L. Kelley Dynemicins Dynemicin, Masataka Konishi and Toshikazu Oki Neocarzinostatin Neocarzinostatin: Chemical and Biological Basis of Oxidative DNA Damage, Irving H. Goldberg and Lizzy S. Kappen The Clinical Effects of Neocarzinostatin and Its Polymer Conjugate, SMANCS, Hiroshi Maeda Synthetic Methodologies Synthetic Studies of the Enediyne Antibiotics, Randall L. Halcomb
Risk of Human Immunodeficiency Virus Infection in Herpes Simplex Virus Type 2–Seropositive Persons: A Meta‐analysis (2002)

To determine the contribution of herpes simplex type 2 (HSV-2) infection to the risk of human immunodeficiency virus (HIV) acquisition, a systematic review of literature and data synthesis were done. Thirty-one studies addressed the risk of HIV infection in HSV-2-seropositive persons. For 9 cohort and nested case-control studies that documented HSV-2 infection before HIV acquisition, the risk estimate was 2.1 (95% confidence interval, 1.4-3.2). Thus, the attributable risk percentage of HIV to HSV-2 was 52%, and the population attributable risk percentage was 19% in populations with 22% HSV-2 prevalence but increased to 47% in populations with 80% HSV-2 prevalence. For 22 case-control and cross-sectional studies, the risk estimate was 3.9 (95% confidence interval, 3.1-5.1), but the temporal sequence of the 2 infections cannot be documented. Control strategies for HSV-2 need to be incorporated into control of sexually transmitted infections as a strategy for HIV prevention.
Evidence against either a premature stop codon or the absence of obese gene mRNA in human obesity. (1995)

Obese (ob) gene expression in abdominal subcutaneous adipocytes from lean and obese humans was examined. The full coding region of the ob gene was isolated from a human adipocyte cDNA library. Translation of the insert confirmed the reported amino acid sequence. There was no difference in the sequence of an reverse transcription PCR product of the coding region from five lean and five obese subjects. The nonsense mutation in the ob mouse which results in the conversion of arginine 105 to a stop codon was not present in human obesity. In all 10 human cDNAs, arginine 105 was encoded by CGG, consequently two nucleotide substitutions would be required to result in a stop codon. To compare the amount of ob gene expression in lean and obese individuals, radiolabed primer was used in the PCR reaction with beta-actin as a control. There was 72% more ob gene expression (P < 0.01) in eight obese subjects (body mass index, BMI = 42.8 +/- 2.7) compared to eight lean controls (BMI = 22.4 +/- 0.8). Regression analysis indicated a positive correlation between BMI and the amount of ob message (P < 0.005). There was no difference in the amount of beta-actin expression in the two groups. These results provide evidence that ob gene expression is increased in human obesity; furthermore, the mutations present in the mouse ob gene were not detected in the human mRNA population.
The Adele configuration manager (1995)

This article proposes an overview of the Adele system and also discusses other approaches and other systems. While most of our work on Configuration Management is covered, we have deliberately chosen to discuss in greater depth the Work Space aspect and the relationship between the Repository Space and the WSs
A Self-Reducible and Alcohol-Soluble Copper-Based Metal–Organic Decomposition Ink for Printed Electronics (2014)

We report a novel method for the synthesis of a self-reducible (thermally reducible without a reducing atmosphere) and alcohol-soluble copper-based metal-organic decomposition (MOD) ink for printed electronics. Alcohol-solvent-based conductive inks are necessary for commercial printing processes such as reverse offset printing. We selected copper(II) formate as a precursor and alkanolamine (2-amino-2-methyl-1-propanol) as a ligand to make an alcohol-solvent-based conductive ink and to assist in the reduction reaction of copper(II) formate. In addition, a co-complexing agent (octylamine) and a sintering helper (hexanoic acid) were introduced to improve the metallic copper film. The specific resistivity of copper-based MOD ink (Cuf-AMP-OH ink) after heat treatment at 350 °C is 9.46 μΩ·cm, which is 5.5 times higher than the specific resistivity of bulk copper. A simple stamping transfer was conducted to demonstrate the potential of our ink for commercial printing processes.
Bacillus subtilis Contains Four Closely Related Type I Signal Peptidases with Overlapping Substrate Specificities (1997)

Most biological membranes contain one or two type I signal peptidases for the removal of signal peptides from secretory precursor proteins. In this respect, the Gram-positive bacterium Bacillus subtilis seems to be exceptional, because it contains at least four chromosomally-encoded type I signal peptidases, denoted SipS, SipT, SipU, and SipV. Here, we report the identification of the sipT and sipV genes, and the functional characterization of SipT, SipU, and SipV. The four signal peptidases have similar substrate specificities, as they can all process the same beta-lactamase precursor. Nevertheless, they seem to prefer different pre-proteins, as indicated by studies on the processing of the pre-alpha-amylase of Bacillus amyloliquefaciens in strains lacking SipS, SipT, SipU, or SipV. The sipU and sipV genes are constitutively transcribed at a low level, suggesting that they are required for processing of (pre-)proteins secreted during all growth phases. In contrast, the transcription of sipS and sipT is temporally controlled, in concert with the expression of the genes for most secretory proteins, which suggests that SipS and SipT serve to increase the secretory capacity of B. subtilis. Taken together, our findings suggest that SipS, SipT, SipU, and SipV serve different functions during the exponential and post-exponential growth phase of B. subtilis.
Stereodefined Phosphorothioate Analogues of DNA:  Relative Thermodynamic Stability of the Model PS-DNA/DNA and PS-DNA/RNA Complexes (2002)

Thermodynamic data regarding the influence of P-chirality on stability of duplexes formed between phosphorothioate DNA oligonucleotides (of either stereo-defined all-R(P) or all-S(P) or random configuration at the P atoms) and complementary DNA or RNA strands are presented. Measured melting temperatures and calculated DeltaG(37)(o) values showed that duplexes formed by PS-DNA oligomers with DNA strands are less stable than their unmodified counterparts. However, relative stability of the duplexes ([all-R(P)]-PS-DNA/DNA vs [all-S(P)]-PS-DNA/DNA) depends on their sequential composition rather than on the absolute configuration of PS-oligos, contrary to the results of theoretical considerations and molecular modeling reported in the literature. On the other hand, for all six analyzed pairs of diastereomers, the [all-R(P)]-PS isomers form more stable duplexes with RNA templates, but the origin of stereodifferentiation depends on the sequence with more favorable entropy and enthalpy factors which correlated with dT-rich and dA/dG-rich PS-oligomers, respectively.
Magnetotactic Bacteria (1975)

Bacteria with motility directed by the local geomagnetic field have been observed in marine sediments. These magnetotactic microorganisms possess flagella and contain novel structured particles, rich in iron, within intracytoplasmic membrane vesicles. Conceivably these particles impart to cells a magnetic moment. This could explain the observed migration of these organisms in fields as weak as 0.5 gauss.
Molecular characterization of the 4-hydroxyphenylacetate catabolic pathway of Escherichia coli W: engineering a mobile aromatic degradative cluster (1996)

We have determined and analyzed the nucleic acid sequence of a 14,855-bp region that contains the complete gene cluster encoding the 4-hydroxyphenylacetic acid (4-HPA) degradative pathway of Escherichia coli W (ATCC 11105). This catabolic pathway is composed by 11 genes, i.e., 8 enzyme-encoding genes distributed in two putative operons, hpaBC (4-HPA hydroxylase operon) and hpaGEDFHI (meta-cleavage operon); 2 regulatory genes, hpaR and hpaA; and the gene, hpaX, that encodes a protein related to the superfamily of transmembrane facilitators and appears to be cotranscribed with hpaA. Although comparisons with other aromatic catabolic pathways revealed interesting similarities, some of the genes did not present any similarity to their corresponding counterparts in other pathways, suggesting different evolutionary origins. The cluster is flanked by two genes homologous to the estA (carbon starvation protein) and tsr (serine chemoreceptor) genes of E. coli K-12. A detailed genetic analysis of this region has provided a singular example of how E. coli becomes adapted to novel nutritional sources by the recruitment of a catabolic cassette. Furthermore, the presence of the pac gene in the proximity of the 4-HPA cluster suggests that the penicillin G acylase was a recent acquisition to improve the ability of E. coli W to metabolize a wider range of substrates, enhancing its catabolic versatility. Five repetitive extragenic palindromic sequences that might be involved in transcriptional regulation were found within the cluster. The complete 4-HPA cluster was cloned in plasmid and transposon cloning vectors that were used to engineer E. coli K-12 strains able to grow on 4-HPA. We report here also the in vitro design of new biodegradative capabilities through the construction of a transposable cassette containing the wide substrate range 4-HPA hydroxylase, in order to expand the ortho-cleavage pathway of Pseudomonas putida KT2442 and allow the new recombinant strain to use phenol as the only carbon source.
5-Chloro-3-(phenylsulfonyl)indole-2-carboxamide: a novel, non-nucleoside inhibitor of HIV-1 reverse transcriptase (1993)

A series of highly potent, structurally novel, non-nucleoside RT inhibitors has been described. Low nanomolar concentrations of 5-chloro-3-(phenylsulfonyl)-indole-2-carboxamide (1) inhibit the HIV-1 RT enzyme in vitro and HTLVIIIb viral spread in MT-4 human T-lymphoid cells. Good oral bioavailability was observed in rhesus monkeys upon oral dosing of 1 as a suspension in methocel. When compared to other non-nucleoside inhibitors (e.g. 15-18), 1 possesses improved inhibitory potency with respect to the wild-type RT, as well as the K103N and Y181C mutant enzymes. Additional studies within this class of inhibitors are in progress.
Osteoclasts, rheumatoid arthritis, and osteoimmunology (2006)

New findings in osteoimmunology will be instrumental in the development of strategies for research into the treatment of various diseases afflicting the skeletal and immune systems.
Synthesis, Structure, and Activity of Diclofenac Analogues as Transthyretin Amyloid Fibril Formation Inhibitors (2001)

Twelve analogues of diclofenac (1), a nonsteroidal antiinflammatory drug and known inhibitor of transthyretin (TTR) amyloid formation, were prepared and evaluated as TTR amyloid formation inhibitors. High activity was exhibited by five of the compounds. Structure-activity relationships reveal that a carboxylic acid is required for activity, but changes in its position as well as the positions of other substituents are tolerated. High-resolution X-ray crystal structures of four of the active compounds bound to TTR were obtained. These demonstrate the significant flexibility with which TTR can accommodate ligands within its two binding sites.
Familial amyloid polyneuropathy: new developments in genetics and treatment. (1996)

Familial amyloid polyneuropathy is an hereditary amyloidosis related to several different genetic errors. It usually presents as a severe peripheral neuropathy. The protein most frequently involved in the disease is transthyretin, a serum transport protein synthesized primarily in the liver. Variable penetrance and variable clinical expression are widely described but the factors that influence such variability are largely unknown. Liver transplantation has been suggested as an effective treatment for this fatal condition. More than 146 patients have undergone this procedure and progression of the disease is halted after surgery. Therefore, it is thought that liver transplantation is an effective treatment for severe forms of familial amyloid polyneuropathy.
Mechanisms of tumor cell capture by activated macrophages: evidence for involvement of lymphocyte function-associated (LFA)-1 antigen. (1986)

The lymphocyte function-associated (LFA)-1 molecule is expressed on certain populations of macrophages that have an augmented capacity to capture tumor cells. Accordingly, we analyzed the role of LFA-1 in the establishment of such cell-cell interactions. F(ab')2 fragments of the M17/4, anti-LFA-1 monoclonal antibody (MAb) inhibited the interaction between activated macrophages and tumor cells by up to 80% in a dose-dependent manner. The anti-LFA-1 MAb reduced (between 55 to 79%) the number of P815, LSTRA, or EL-4 tumor cells bound to trypsin-sensitive structures on bacillus Calmette Guerin activated macrophages. The inhibition appeared selective, because a F(ab')2 fragment of anti-Mac-1 did not inhibit such binding. Inhibition of tumor cell capture could be observed as soon as 15 min after the onset of the cell-cell interaction between activated macrophages and tumor cells. Optimal inhibition occurred when both tumor targets and macrophages were precoated with the MAb. Although P815, LSTRA, EL-4, and BW5147 tumor cells all expressed LFA-1, only the first three but not BW5147 cells were bound by activated macrophages. Furthermore, endotoxin-pulsed macrophages elicited by thioglycollate broth expressed the LFA-1 antigen but did not exhibit selective tumor cell capture. Finally, anti-LFA-1 inhibited the development of weak into strong binding. Taken together, the results suggest that LFA-1 molecules can participate in the interaction between activated macrophages and neoplastic cells.