gebhart/patrepeval huggingface dataset:
Relaxed, low threading defect density Si0.7Ge0.3 epitaxial layers grown on Si by rapid thermal chemical vapor deposition (1994)

Relaxed Si0.7Ge0.3 epitaxial layers that possess threading defect densities as low as 5×105 cm−2 have been grown on Si substrates by rapid thermal chemical vapor deposition. The layers were formed in a series of steps of constant Ge content, each step with either 6% or 3% more Ge than the previous one. At the low average grading rates investigated, the number of steps used to reach 30% Ge only slightly affected the density of individual threading dislocations, imaged by electron beam induced current (EBIC). However, the density of dark-line defects seen in EBIC, which are formed from pile-ups of threading dislocations, was strongly influenced only by the average grading rate. Both the dark line density and the dark spot density must be considered when assessing the surface of these relaxed layers.
Identification of Tyrosine Residues Involved in Ligand Recognition by the Phosphatidylinositol 3-Kinase Src Homology 3 Domain:  Circular Dichroism and UV Resonance Raman Studies (2001)

Src homology 3 (SH3) domains are small noncatalytic protein modules capable of mediating protein-protein interactions. We previously demonstrated that the association of a ligand peptide RLP1 (RKLPPRPSK) causes environmental and structural changes of Trp55 and some of seven Tyr residues in the phosphatidylinositol 3-kinase (PI3K) SH3 domain by circular dichroism (CD) and 235-nm excited UV resonance Raman (UVRR) spectroscopies [Okishio, N., et al. (2000) Biopolymers 57, 208-217]. In this work, the affected Tyr residues were identified as Tyr12, Tyr14, and Tyr73 by the CD analysis of a series of mutants, in which every single Tyr residue was replaced by a Phe residue. Among these three residues, Tyr14 was found to be a main contributor to the UVRR spectral change upon the RLP1 binding. Interestingly, CD and UVRR analyses revealed that RLP1 associates with the Y14F and Y14H mutants in different ways. These results suggest that Tyr14 plays a crucial role in the ligand recognition, and the amino acid substitution at Tyr14 affects the mode of PI3K SH3-ligand interaction. Our findings give an insight into how SH3 domains can produce diversity and specificity to transduce signaling within cells.
Copper wafer bonding in three-dimensional integration (2005)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2005.
A database interface for clustering in large spatial databases (1995)

Both the number and the size of spatial databases are rapidly growing because of the large amount of data obtained from satellite images, X-ray crystallography or other scientific equipment. Therefore, automated knowledge discovery becomes more and more important in spatial databases. So far, most of the methods for knowledge discovery in databases (KDD) have been based on relational database systems. In this paper, we address the task of class identification in spatial databases using clustering techniques. We present an interface to the database management system (DBMS), which is crucial for the efficiency of KDD on large databases. This interface is based on a spatial access method, the R*-tree. It clusters the objects according to their spatial neighborhood and supports efficient processing of spatial queries. Furthermore, we propose a method for spatial data sampling as part of the focusing component, significantly reducing the number of objects to be clustered. Thus, we achieve a considerable speed-up for clustering in large databases. We have applied the proposed techniques to real data from a large protein database used for predicting protein-protein docking. A performance evaluation on this database indicates that clustering on large spatial databases can be performed both efficiently and effectively using our approach.
Mexican New York (2005)

Drawing on more than fifteen years of research, Mexican New York offers an intimate view of globalization as it is lived by Mexican immigrants and their children in New York and in Mexico. Robert Courtney Smith's groundbreaking study sheds new light on transnationalism, vividly illustrating how immigrants move back and forth between New York and their home village in Puebla with considerable ease, borrowing from and contributing to both communities as they forge new gender roles; new strategies of social mobility, race, and even adolescence; and new brands of politics and egalitarianism. Smith's deeply informed narrative describes how first-generation men who have lived in New York for decades become important political leaders in their home villages in Mexico. Smith explains how relations between immigrant men and women and their U.S.-born children are renegotiated in the context of migration to New York and temporary return visits to Mexico. He illustrates how U.S.-born youth keep their attachments to Mexico, and how changes in migration and assimilation have combined to transnationalize both U.S.-born adolescents and Mexican gangs between New York and Puebla. Mexican New York profoundly deepens our knowledge of immigration as a social process, convincingly showing how some immigrants live and function in two worlds at the same time and how transnationalization and assimilation are not opposing, but related, phenomena.
Modification of seed oil content and acyl composition in the brassicaceae by expression of a yeast sn-2 acyltransferase gene. (1997)

A putative yeast sn-2 acyltransferase gene (SLC1-1), reportedly a variant acyltransferase that suppresses a genetic defect in sphingolipid long-chain base biosynthesis, has been expressed in a yeast SLC deletion strain. The SLC1-1 gene product was shown in vitro to encode an sn-2 acyltransferase capable of acylating sn-1 oleoyl-lysophosphatidic acid, using a range of acyl-CoA thioesters, including 18:1-, 22:1-, and 24:0-CoAs. The SLC1-1 gene was introduced into Arabidopsis and a high erucic acid-containing Brassica napus cv Hero under the control of a constitutive (tandem cauliflower mosaic virus 35S) promoter. The resulting transgenic plants showed substantial increases of 8 to 48% in seed oil content (expressed on the basis of seed dry weight) and increases in both overall proportions and amounts of very-long-chain fatty acids in seed triacylglycerols (TAGs). Furthermore, the proportion of very-long-chain fatty acids found at the sn-2 position of TAGs was increased, and homogenates prepared from developing seeds of transformed plants exhibited elevated lysophosphatidic acid acyltransferase (EC 2.3.1.51) activity. Thus, the yeast sn-2 acyltransferase has been shown to encode a protein that can exhibit lysophosphatidic acid acyltransferase activity and that can be used to change total fatty acid content and composition as well as to alter the stereospecific acyl distribution of fatty acids in seed TAGs.
IgG2a-Mediated Enhancement of Antibody and T Cell Responses and Its Relation to Inhibitory and Activating Fcγ Receptors (2004)

A number of studies in experimental animal models point to an important role of Fc gamma Rs in autoimmunity and allergy. In this study, we investigate how the production of IgG, an early step in the chain of events leading to inflammation, is regulated by activating and inhibitory Fc gamma Rs. IgG Abs are known to feedback-enhance Ab responses to soluble Ags, and this effect requires activating Fc gamma Rs. To test proliferation of Th cells, mice were adoptively transferred with CD4(+) T cells expressing a transgenic OVA-specific TCR before immunization with IgG2a anti-2,4,6-trinitrophenyl (TNP) plus OVA-TNP or with OVA-TNP alone. IgG2a induced a significant increase in OVA-specific T cell numbers, which preceded the OVA-specific Ab response and was dependent on the Fc gamma chain. The role of the inhibitory Fc gamma RIIB in Ab responses was studied in mice lacking this receptor. Although IgG2a enhanced primary Ab responses, development of germinal centers, and immunological memory in wild-type mice, enhancement was markedly stronger in Fc gamma RIIB(-/-) mice. The presented data are compatible with the hypothesis that the mechanism behind IgG2a-mediated up-regulation of Ab responses involves increased Ag presentation to CD4(+) T cells by Fc gamma R(+) APCs. Our observations also illustrate the intricate immunoregulatory role of IgG Abs. On the one hand, they enhance Ab responses via activating Fc gamma Rs, and on the other hand, they set an upper limit for the same Ab response via Fc gamma RIIB.
High-Power Blue-Violet Semipolar ($20\bar{2}\bar{1}$) InGaN/GaN Light-Emitting Diodes with Low Efficiency Droop at 200 A/cm$^{2}$ (2011)

We report a high-power blue light-emitting diode (LED) with a high external quantum efficiency and low droop on a free-standing (20) GaN substrate. At a forward current of 20 mA, the LED showed a peak external quantum efficiency of 52% and an output power of 30.6 mW. In higher current density regions, the LED also showed outstanding performance, with droop ratios of 0.7% at 35 A/cm2, 4.3% at 50 A/cm2, 8.5% at 100 A/cm2, and 14.3% at 200 A/cm2. The output power and external quantum efficiency at 200 A/cm2 were 266.5 mW and 45.3%, respectively.
Evaluation of Conservation Voltage Reduction (CVR) on a National Level (2010)

Conservation Voltage Reduction (CVR) is a reduction of energy consumption resulting from a reduction of feeder voltage. While there have been numerous CVR systems deployed in North America there has been little substantive analytic analysis of the effect; the majority of the published results are based on empirical field measurements. Since these results are based on empirical measurements it is difficult to extrapolate how this technology will behave on the various types of distribution feeders found throughout the nation. This report has utilized the Taxonomy of Prototypical feeder developed under the Modern Grid Initiative (MGI), now the Modern Grid Strategy (MGS), in order to estimate the benefits of CVR on multiple distribution feeder types. This information will then be used to determine an estimate of the national benefits of a wide scale deployment of CVR.
Spotlight on Anti‐CGRP Monoclonal Antibodies in Migraine: The Clinical Evidence to Date (2017)

Migraine, a common neurovascular brain disorder, represents a severe and widespread health problem; along with medication-induced (medication-overuse) headache, it is the third-leading cause of disability worldwide. Currently, its therapeutic management remains unsatisfactory for several reasons; up to 40% of migraineurs are eligible for prophylactic treatment, but there are issues of efficacy, safety, and adherence. In recent years the evidence on the role of calcitonin gene-related peptide (CGRP) in migraine pathophysiology has been consolidated, so new and promising treatments for migraine pain and its possible prevention have been developed. The following review reports the results of the clinical trials conducted so far with each of the new monoclonal antibodies targeting CGRP or its receptor, with particular reference to safety, tolerance, and efficacy in migraine prevention. Moreover, the pharmacological characterization and further developments of each monoclonal antibody are reported, based on current knowledge.
Heparin-dependent and -independent anti-platelet factor 4 autoantibodies in patients with systemic lupus erythematosus (2012)

PF4 is an autoimmune target in SLE patients. Heparin-dependent and -independent anti-PF4 autoantibodies may be involved in different aspects of pathophysiology of SLE.
Guidelines for the diagnosis and treatment of hepatocellular carcinoma (HCC) in adults (2003)

This document, on the diagnosis and treatment of patients with hepatocellular carcinoma (HCC), was commissioned by the British Society of Gastroenterology as part of a wider initiative to develop guidelines for clinicians in several areas of clinical practice.
Cytotoxic Pyridone Alkaloids from the Leaves of Piper aborescens (1990)

Bioactivity-guided fractionation of a CHCl3 extract of the leaves of Piper aborescens afforded a new cytotoxic pyridone alkaloid, N-(3-methoxy-4,5-methylenedioxydihydrocinnamoyl)-delta 3-pyridin-2-one [1], as well as three known cytotoxic pyridone alkaloids, N-(3-methoxy-4,5-methylenedioxycinnamoyl)-delta 3-pyridin-2-one [2], piplartine [3], and piplartine dimer A [4].
Cross-resistance to fluoroquinolones in multiple-antibiotic-resistant (Mar) Escherichia coli selected by tetracycline or chloramphenicol: decreased drug accumulation associated with membrane changes in addition to OmpF reduction (1989)

Chromosomal multiple-antibiotic-resistant (Mar) mutants of Escherichia coli, selected on agar containing low concentrations of tetracycline or chloramphenicol, were 6- to 18-fold less susceptible to the fluoroquinolones than were their wild-type E. coli K-12 or E. coli C parental strains. The frequency of emergence of such mutants was at least 1,000-fold higher than that of those selected by the fluoroquinolone norfloxacin directly. When Mar mutants, but not wild-type cells, were plated on norfloxacin, mutants resistant to high levels of norfloxacin (2 micrograms/ml) appeared at a relatively high (approximately 10(-7] frequency. In addition to decreased amounts of OmpF, Mar mutants had other outer membrane protein changes and were four- to eightfold less susceptible to fluoroquinolones than was an ompF::Tn5 mutant lacking only OmpF. Accumulation of [3H]norfloxacin was more than threefold lower in the Mar mutants than in wild-type cells and twofold lower than in the OmpF-deficient derivative. These differences were not attributable to a change in the endogenous active efflux system for norfloxacin in E. coli. Norfloxacin-induced inhibition of DNA synthesis was threefold lower in intact cells of a Mar mutant than in susceptible cells, but this difference was not seen in toluene-permeabilized cells. Insertion of Tn5 into marA (min 34.05 on the chromosome) led to a return of the wild-type patterns of norfloxacin accumulation, fluoroquinolone and other antimicrobial agent susceptibilities, and outer membrane protein profile, including partial restoration of OmpF. These findings together suggest that marA-dependent fluoroquinolone resistance is linked to decreased cell permeability, only part of which can be accounted for by the reduction in OmpF. Once mutated to marA, cells can achieve high levels of quinolone resistance at a relatively high frequency.
Comparative cytotoxicity of CI‐973, cisplatin, carboplatin and tetraplatin in human ovarian carcinoma cell lines (1991)

The clinical efficacy of cisplatin-based chemotherapy for ovarian cancer is frequently compromised by drug resistance or dose-limiting renal and neurologic toxicities. CI-973 (NK-121), a 2-methyl-1,4-butanediamine analogue of carboplatin, has shown little nephro- and neuro-toxicity in pre-clinical model systems and in phase-I trials. Its in vitro spectrum of activity against ovarian cancer cell lines has not been previously characterized. The in vitro activities of CI-973, cisplatin, carboplatin and tetraplatin were compared in several platinum-sensitive and -resistant human ovarian carcinoma cell lines. Cytotoxicity was assessed by inhibition of clonogenic survival in soft agar with continuous drug exposure. On a molar basis, cisplatin and tetraplatin were the most potent analogues, while carboplatin was consistently less potent. Cisplatin, carboplatin and CI-973 elicited a very similar response pattern by Spearman rank correlation, distinct from that seen with tetraplatin. The magnitude of resistance to CI-973 was comparable to cisplatin in 5 cell lines but was substantially lower in the highly cisplatin-resistant 2780-CP70 and OVCAR-10 cell lines. These results suggest that CI-973 and tetraplatin may have potential utility in some cases of cisplatin-resistant ovarian cancer. In addition, our data are consistent with the existence of at least 2 platinum-resistance phenotypes--one with moderate levels of resistance to cisplatin, carboplatin and CI-973 but highly resistant to tetraplatin, the other highly resistant to cisplatin and carboplatin but only partially cross-resistant with tetraplatin and CI-973. The recognition of different resistance phenotypes may facilitate the study of cellular resistance mechanisms to cisplatin and newer platinum analogues.
Intestinal immunity ofEscherichia coliNISSLE 1917: a safe carrier for therapeutic molecules (2004)

The development of novel approaches that allow accurate targeting of therapeutics to the intestinal mucosa is a major task in the research on intestinal inflammation. For the first time, a live genetically modified bacterial strain has been approved by Dutch authorities as a therapeutic agent for experimental therapy of intestinal bowel disease (IBD) in humans. Genetically modified probiotics can very well be used as carriers for localized antigen delivery into the intestine. Therapeutic safety, however, of such a carrier organism, is crucial, especially when a specific probiotic strain has to be used under diseased conditions. In this study, we tested the potential of Escherichia coli NISSLE 1917 to serve as a safe carrier for targeted delivery of recombinant proteins to the intestinal mucosa. In a well-defined and very sensitive immunological system, we demonstrate that intestinal recombinant E. coli NISSLE 1917 has no effect on migration, clonal expansion and activation status of specific CD4+ T cells, neither in healthy mice nor in animals with acute colitis. Furthermore, recombinant E. coli NISSLE 1917 has no effect on the induction or breakdown of peripheral T-cell tolerance in an autoimmune environment. The excellent colonization properties of E. coli NISSLE 1917 render this strain an ideal candidate as carrier organism for gut-focused in situ synthesis of therapeutic molecules.
Triplex-forming molecules for modulation of DNA information processing. (2000)

The design of specific DNA ligands is an important challenge in biological and biomedical sciences. Targeting the source of genetic information may allow highly efficient gene-directed modulation of cell function. Triplex-forming molecules specifically recognize oligopyrimidine/oligopurine sequences by hydrogen bonding interactions. In cell cultures they have been used successfully to downregulate or upregulate transcription in a gene-specific manner or to induce site-directed mutagenesis and recombination. For biotechnological applications, triplex-forming molecules are powerful tools for gene-specific chemistry.
REDD2 Gene Is Upregulated by Modified LDL or Hypoxia and Mediates Human Macrophage Cell Death (2004)

We showed that stimulation of REDD2 expression in macrophages increases oxLDL-induced cell death, suggesting that REDD2 gene might play an important role in arterial pathology.
Using the genetic algorithm to build optimal neural networks for fault-prone module detection (2002)

The genetic algorithm is applied to developing optimal or near optimal backpropagation neural networks for fault-prone/not-fault-prone classification of software modules. The algorithm considers each network in a population of neural networks as a potential solution to the optimal classification problem. Variables governing the learning and other parameters and network architecture are represented as substrings (genes) in a machine-level bit string (chromosome). When the population undergoes simulated evolution using genetic operators-selection based on a fitness function, crossover, and mutation-the average performance increases in successive generations. We found that, on the same data, compared with the best manually developed networks, evolved networks produced improved classifications in considerably less time, with no human effort, and with greater confidence in their optimality or near optimality. Strategies for devising a fitness function specific to the problem are explored and discussed.
Minimalistic, dynamic, tube climbing robot (2010)

This video shows the investigation of a novel minimalistic, dynamic climbing robot which can climb up tubes of different shapes using a simple dc motor. The motor moves an eccentric mass in a constant velocity. The location of the eccentric mass relative to the contact point determines the stability and the direction of the climbing motion. We present the analysis of this mechanism, simulation and experimental results.
Control and evaluation of a 7-axis surgical robot for laparoscopy (2002)

This paper describes the control and ergonomic evaluation of a ceiling mounted (or support frame suspended) 7-axis surgical robot (HISAR) for laparoscopic camera navigation. A key feature of the robot is that it incorporates a passive wrist for natural compliance with the port of entry into the patient. The use of a previously reported constrained Cartesian controller is motivated and demonstrated, and the results of successfully applying this control methodology to the manipulator are presented. The significance of the control strategy is the ease with which control of passive axes, the fulcrum constraint, and the motion inversion effect created by the fulcrum are accommodated. We also report on the results of laboratory evaluations of the arm in terms of its work volume, ergonomic factors, ease of control, and overall design within the context of laparoscopic camera control.
Toll-like receptor signal transduction (2007)

Toll-like receptors (TLRs) are the archetypal pattern recognition receptors in sensing exogenous pathogens. Activation of TLRs is a first line of defense of the immune system, leading to the activation and recruitment of neutrophils and macrophages to sites of infection and enhances antimicrobial activity. The TLR signaling through different intracellular molecules, such as MAP kinases and IkappaB kinases which are conserved signaling elements for many receptors, leads to a distinct set of proinflammatory gene expressions. However, how these pathways differentially and precisely control the transcription of identical genes remains largely unknown. Our review focuses on the details of up-to-date signaling molecules including negative regulators and their role in controlling innate immune response. We also stress the importance of developing systemic approaches for the global understanding of TLR signaling so that appropriate drug therapeutic targets can be identified for regulating inflammatory diseases.
Infectious Bronchitis Virus in the Chicken Harderian Gland and Lachrymal Fluid: Viral Load, Infectivity, Immune Cell Responses, and Effects of Viral Immunodeficiency (2008)

We compared detection of infectious bronchitis virus (IBV) by quantitative RT-PCR (qRT-PCR) in tears and trachea of IBV-infected chickens and found that quantitative detection of IBV RNA in tears is more sensitive than in tracheal homogenates. Furthermore, we demonstrated that IBV contained in chicken lachrymal fluid is infectious and that tears of IBV-infected chickens can be used to infect naive chickens. We compared the immune responses to IBV in the Harderian gland and cecal tonsils of immunocompetent chickens and chickens infected with chicken anemia virus (CAV) and/or infectious bursal disease virus (IBDV). Flow cytometry analyses of lymphocytes in Harderian glands and cecal tonsils indicated that the relative abundance of IgM+ B cells in the Harderian glands and cecal tonsils following exposure to IBV in combination with immunosuppressive viruses was reduced compared to chickens infected with IBV alone. CAV, but not IBDV, reduced the CD4+/CD8+ T cell ratios compared to chickens infected with IBV alone. Enzyme-linked immuno-spot forming assays on cells in the Harderian glands and cecal tonsils of IBV-infected chickens indicated that maximum IBV-specific IgA-secreting cell responses were reduced in chickens infected with CAV. IBDV co-infected chickens displayed a delayed IgA response to IBV. Thus immunosuppressive viruses reduced B cells and T helper cells in the Harderian glands and cecal tonsils in response to IBV, and slowed the kinetics and/or reduced the magnitude of the mucosal immune response against IBV. We have shown for the first time that CAV affects pathogen-specific B cell responses in a mucosal effector site.