gebhart/patrepeval huggingface dataset:
CMOS-compatible ruggedized high-temperature Lamb wave pressure sensor (2013)

This paper describes the development of a novel ruggedized high-temperature pressure sensor operating in lateral field exited (LFE) Lamb wave mode. The comb-like structure electrodes on top of aluminum nitride (AlN) were used to generate the wave. A membrane was fabricated on SOI wafer with a 10 µm thick device layer. The sensor chip was mounted on a pressure test package and pressure was applied to the backside of the membrane, with a range of 20-100 psi. The temperature coefficient of frequency (TCF) was experimentally measured in the temperature range of -50 °C to 300 °C. By using the modified Butterworth-van Dyke model, coupling coefficients and quality factor were extracted. Temperature-dependent Young's modulus of composite structure was determined using resonance frequency and sensor interdigital transducer (IDT) wavelength which is mainly dominated by an AlN layer. Absolute sensor phase noise was measured at resonance to estimate the sensor pressure and temperature sensitivity. This paper demonstrates an AlN-based pressure sensor which can operate in harsh environment such as oil and gas exploration, automobile and aeronautic applications.
New ice‐binding face for type I antifreeze protein (1999)

Type I antifreeze protein (AFP) from winter flounder is an alanine-rich, 37 amino acid, single alpha-helix that contains three 11 amino acid repeats (Thr-X(2)-Asx-X(7)), where X is generally Ala. The regularly spaced Thr, Asx and Leu residues lie on one face of the helix and have traditionally been thought to form hydrogen bonds and van der Waals interactions with the ice surface. Recently, substitution experiments have called into question the importance of Leu and Asn for ice-binding. Sequence alignments of five type I AFP isoforms show that Leu and Asn are not well conserved, whereas Ala residues adjacent to the Thr, at right angles to the Leu/Asn-rich face, are completely conserved. To investigate the role of these Ala residues, a series of Ala to Leu steric mutations was made at various points around the helix. All the substituted peptides were fully alpha-helical and remained as monomers in solution. Wild-type activity was retained in A19L and A20L. A17L, where the substitution lies adjacent to the Thr-rich face, had no detectable antifreeze activity. The nearby A21L substitution had 10% wild-type activity and demonstrated weak interactions with the ice surface. We propose a new ice-binding face for type I AFP that encompasses the conserved Ala-rich surface and adjacent Thr.
High-Speed DNA Sequencing: An Approach Based Upon Fluorescence Detection of Single Molecules (1989)

We are developing a laser based technique for the rapid sequencing of large fragments (approximately 40 kb) of DNA based upon the detection of single, fluorescently tagged nucleotides cleaved from a single DNA fragment. We have demonstrated significant progress on several of the important steps of this technique. The projected rate of sequencing is several hundred bases per second which is orders of magnitude faster than existing methods. Once developed, this technology could be utilized by investigators for rapid sequencing of genetic material from virtually any source.
Uniform approach to risk classification and treatment assignment for children with acute lymphoblastic leukemia. (1996)

The more uniform approach to risk-based treatment assignment and to collection of specific prognostic factors should increase the efficiency of future ALL clinical research.
PerFallD: A pervasive fall detection system using mobile phones (2010)

Falls are a major health risk that diminish the quality of life among elderly people. With the elderly population surging, especially with aging “baby boomers”, fall detection becomes increasingly important. However, existing commercial products and academic solutions struggle to achieve pervasive fall detection. In this paper, we propose utilizing mobile phones as a platform for pervasive fall detection system development. To our knowledge, we are the first to do so. We design a detection algorithm based on mobile phone platforms. We propose PerFallD, a pervasive fall detection system implemented on mobile phones. We implement a prototype system on the Android G1 phone and conduct experiments to evaluate our system. In particular, we compare PerFallD's performance with that of existing work and a commercial product. Experimental results show that PerFallD achieves strong detection performance and power efficiency.
Identification of the Ligand Binding Site for the Integrin α9β1 in the Third Fibronectin Type III Repeat of Tenascin-C (1998)

The integrin α<sub>9</sub> subunit forms a single heterodimer, α<sub>9</sub>β<sub>1</sub> that mediates cell adhesion to a site within the third fibronectin type III repeat of tenascin-C (TNfn3). In contrast to at least 3 other integrins that bind to this region of tenascin-C, α<sub>9</sub>β<sub>1</sub> does not recognize the common integrin recognition motif, Arg-Gly-Asp (RGD). In this report, we have used substitution mutagenesis to identify a unique ligand recognition sequence in TNfn3. We introduced mutations substituting alanine for each of the acidic residues in or adjacent to each of the exposed loops predicted from the solved crystal structure. Most of these mutations had little or no effect on adhesion of α<sub>9</sub>-transfected SW480 colon carcinoma cells, but mutations of either of two acidic residues in the B-C loop region markedly reduced attachment of these cells. In contrast, cells expressing the integrin α<sub>v</sub>β<sub>3</sub>, previously reported to bind to the RGD sequence in the adjacent F-G loop, attached to all mutant fragments except one in which the RGD site was mutated to RAA. The peptide, AEIDGIEL, based on the sequence of human tenascin-C in this region blocked the binding of α<sub>9</sub>-transfected cells, but not β<sub>3</sub>-transfected cells to wild type TNfn3. This sequence contains a tripeptide, IDG, homologous to the sequences LDV, IDA, and LDA in fibronectin and IDS in VCAM-1 recognized by the closely related integrin α<sub>4</sub>β<sub>1</sub>. These findings support the idea that this tripeptide motif serves as a ligand binding site for the α<sub>4</sub>/α<sub>9</sub> subfamily of integrins.
Immune system versus tumor: shifting the balance in favor of DCs and effective immunity (2004)

Despite the initial excitement over cancer vaccines, the clinical effectiveness of immunotherapy has been disappointing. The suppressive milieu present within established tumors inhibits effective immune responses, although new strategies are emerging to manipulate the local tumor microenvironment and shift the balance back to a proinflammatory environment, promote DC activation, and enhance tumor immunity .
Broadly cross-reactive antibodies dominate the human B cell response against 2009 pandemic H1N1 influenza virus infection (2011)

The 2009 pandemic H1N1 influenza pandemic demonstrated the global health threat of reassortant influenza strains. Herein, we report a detailed analysis of plasmablast and monoclonal antibody responses induced by pandemic H1N1 infection in humans. Unlike antibodies elicited by annual influenza vaccinations, most neutralizing antibodies induced by pandemic H1N1 infection were broadly cross-reactive against epitopes in the hemagglutinin (HA) stalk and head domain of multiple influenza strains. The antibodies were from cells that had undergone extensive affinity maturation. Based on these observations, we postulate that the plasmablasts producing these broadly neutralizing antibodies were predominantly derived from activated memory B cells specific for epitopes conserved in several influenza strains. Consequently, most neutralizing antibodies were broadly reactive against divergent H1N1 and H5N1 influenza strains. This suggests that a pan-influenza vaccine may be possible, given the right immunogen. Antibodies generated potently protected and rescued mice from lethal challenge with pandemic H1N1 or antigenically distinct influenza strains, making them excellent therapeutic candidates.
Fungal Autofluorescence with Ultraviolet Illumination (1983)

Fungal autofluorescence of hematoxylin and eosin (H & E)-stained tissue sections viewed under ultraviolet illumination was evaluated for diagnostic utilization. Cases examined included coccidioidomycosis, candidiasis, aspergillosis, mucormycosis, and histoplasmosis. The method was most useful in identifying Coccidioides immites, Candida spp., and Aspergillus spp. in sections from solid parenchymatous organs, loose connective tissue, granulomata, or necrotic tissue debris. The architectural detail of spherules, yeast forms, and hyphae was very well delineated. Histoplasma capsulatum was not autofluorescent in one specimen (a broncholith) and the cases of mucormycosis failed to demonstrate intrinsic hyphal autofluorescence but did show a "negative image" appearance against surrounding native tissue autofluorescence. The advantages of using fungal autofluorescence include the possibility, in some cases, of rapid organism identification without the use of special stains or where organisms may not be present on additional sections prepared for special stains, the decreased interference to fungal identification of certain background cellular components or debris, and the improved simultaneous evaluation of organism identification and architecture of the surrounding histologic milieu.
A review of selected optimal power flow literature to 1993. I. Nonlinear and quadratic programming approaches (1999)

The paper presents a review of literature on optimal power flow tracing progress in this area over from 1962-93. Part I deals with the application of nonlinear and quadratic programming.
Studies on the Effects of the N-Terminal Domain Antibodies of Calcitonin Receptor-Like Receptor and Receptor Activity–Modifying Protein 1 on Calcitonin Gene-Related Peptide-Induced Vasorelaxation in Rat Uterine Artery1 (2004)

The vascular relaxation sensitivity to calcitonin gene-related peptide (CGRP) is enhanced during pregnancy, compared with nonpregnant human and rat uterine arteries. In the rat uterine artery, two types of CGRP receptors have been shown to coexist, CGRP-A receptor, which is a complex of calcitonin receptor-like receptor (CRLR), and receptor activity-modifying protein (RAMP(1)) and CGRP-B receptor, which is different from CRLR. In the present study, we hypothesized that: 1) CGRP-induced vasorelaxation in rat uterine artery is mediated through CGRP-A receptor and 2) N-terminal (Nt) domain of CRLR (Nt-CRLR) has a major contribution in ligand binding and mediating CGRP- induced relaxation effects in rat uterine artery. Polyclonal antibodies against Nt-domain of CRLR and RAMP(1) (Nt-RAMP(1)) were raised in rabbits and characterized for their specificity and were used to inhibit CGRP-induced vasorelaxation in rat uterine artery. For vascular relaxation studies, uterine arteries from Day 18 pregnant rats were isolated, and responsiveness of the vessels to CGRP was examined with a small vessel myograph. CGRP (10(-10) to 10(-7) M) produced a concentration-dependent relaxation of norepinephrine-induced contractions in Day 18 pregnant rat uterine arteries. These effects were significantly (P < 0.05) inhibited when uterine arteries were incubated with the antibody raised against Nt-CRLR (PD(2) = 6.75 +/- 0.20) and were totally abolished in presence of antibodies for both Nt-CRLR and Nt-RAMP(1) (PD(2) = 6.14 +/- 0.35). In contrast, a monoclonal antibody for CGRP-B receptor had no effect on CGRP-induced rat uterine artery relaxation. These studies suggest that CGRP effects in rat uterine artery are mediated through CGRP-A receptor and that Nt-domain of CRLR may play a predominant role in CGRP binding and thus in causing CGRP-induced uterine artery relaxation.
STRATEGIES TO ENHANCE THE COEXPRESSION OF CYTOCHROME P450 2E1 AND REDUCTASE IN BACTERIA* (1999)

Mammalian P450 cytochromes comprise a superfamily of membrane-bound hemeproteins involved in the oxidation of a wide variety of exogenous and endogenous substances. Although expression of mammalian...
Feature engineering in Context-Dependent Deep Neural Networks for conversational speech transcription (2011)

We investigate the potential of Context-Dependent Deep-Neural-Network HMMs, or CD-DNN-HMMs, from a feature-engineering perspective. Recently, we had shown that for speaker-independent transcription of phone calls (NIST RT03S Fisher data), CD-DNN-HMMs reduced the word error rate by as much as one third-from 27.4%, obtained by discriminatively trained Gaussian-mixture HMMs with HLDA features, to 18.5%-using 300+ hours of training data (Switchboard), 9000+ tied triphone states, and up to 9 hidden network layers.
Optical absorption and modulation behavior of strained InxGa1−xAs/GaAs(100)(x≤0.25) multiple quantum well structures grown via molecular beam epitaxy (1990)

We report on the optical absorption and modulation characteristics of strained InxGa1−xAs/GaAs(0.1≤x≤0.25) multiple quantum well (MQW) structures grown on GaAs (100) substrates which also included regions of prepatterned mesas. Sharp excitonic features were realized in samples optimally grown by employing reflection high-energy electron diffraction. High optical quality MQW structures as thick as 1.5 μm are realized. To date, the highest modulation per unit field at low fields (&amp;lt;50 kV/cm) in this system is achieved.
Expanding the genetic editing tool kit: ZFNs, TALENs, and CRISPR-Cas9 (2014)

The past decade has been one of rapid innovation in genome-editing technology. The opportunity now exists for investigators to manipulate virtually any gene in a diverse range of cell types and organisms with targeted nucleases designed with sequence-specific DNA-binding domains. The rapid development of the field has allowed for highly efficient, precise, and now cost-effective means by which to generate human and animal models of disease using these technologies. This review will outline the recent development of genome-editing technology, culminating with the use of CRISPR-Cas9 to generate novel mammalian models of disease. While the road to using this same technology for treatment of human disease is long, the pace of innovation over the past five years and early successes in model systems build anticipation for this prospect.
Synthesis, pH-Dependent Structural Characterization, and Solution Behavior of Aqueous Aluminum and Gallium Citrate Complexes (2001)

Reactions of Al(III) and Ga(III) with citric acid in aqueous solutions, yielded the complexes (NH(4))(5)[M(C(6)H(4)O(7))(2)].2H(2)O (M(III) = Al (1), Ga (2)) at alkaline pH, and the complexes (Cat)(4)[M(C(6)H(5)O(7))(C(6)H(4)O(7))].nH(2)O (M(III) = Al (3), Ga (4), Cat. = NH(4)(+), n = 3; M(III) = Al (5), Ga (6), Cat. = K(+), n = 4) at acidic pH. All compounds were characterized by spectroscopic (FT-IR, (1)H, (13)C, and (27)Al NMR, (13)C-MAS NMR) and X-ray techniques. Complex 1 crystallizes in space group P1, with a = 9.638(5) A, b = 9.715(5) A, c = 7.237(4) A, alpha = 90.96(1) degrees, beta = 105.72(1) degrees, gamma = 119.74(1) degrees, V = 557.1(3) A(3), and Z = 1. Complex 2 crystallizes in space group P1, with a = 9.659(6) A, b = 9.762(7) A, c = 7.258(5) A, alpha = 90.95(2) degrees, beta = 105.86(2) degrees, gamma = 119.28(1) degrees, V = 564.9(7) A(3), and Z = 1. Complex 3 crystallizes in space group I2/a, with a = 19.347(3) A, b = 9.857(1) A, c = 23.412(4) A, beta = 100.549(5) degrees, V = 4389(1) A(3), and Z = 8. Complex 4 crystallizes in space group I2/a, with a = 19.275(1) A, b = 9.9697(6) A, c = 23.476(1) A, beta = 100.694(2) degrees, V = 4432.8(5) A(3), and Z = 8. Complex 5 crystallizes in space group P1, with a = 7.316(1) A, b = 9.454(2) A, c = 9.569(2) A, alpha = 64.218(4) degrees, beta = 69.872(3) degrees, gamma = 69.985(4) degrees, V = 544.9(2) A(3), and Z = 1. Complex 6 crystallizes in space group P1, with a = 7.3242(2) A, b = 9.4363(5) A, c = 9.6435(5) A, alpha = 63.751(2) degrees, beta = 70.091(2) degrees, gamma = 69.941(2) degrees, V = 547.22(4) A(3), and Z = 1. The crystal structures of 1-6 reveal mononuclear octahedral complexes of Al(III) (or Ga(III)) bound to two citrates. Solution NMR, on both 4- and 5- species, reveals rapid intramolecular exchange of the bound and unbound terminal carboxylates. Upon dissolution in water, the complexes, through a complicated reaction cascade, transform to oligonuclear 1:1 species that, in agreement with previous studies, represent the thermodynamically stable state in solution. The data provide, for the first time, structural details of low MW, mononuclear complexes of Al(III) (or Ga(III)) with citrate that are dictated, among other factors, by pH. The properties of 1-6 may provide clues relevant to their biological association with humans.
DC-SIGN and L-SIGN Can Act as Attachment Receptors for Alphaviruses and Distinguish between Mosquito Cell- and Mammalian Cell-Derived Viruses (2003)

C-type lectins such as DC-SIGN and L-SIGN, which bind mannose-enriched carbohydrate modifications of host and pathogen proteins, have been shown to bind glycoproteins of several viruses and facilitate either cis or trans infection. DC-SIGN and L-SIGN are expressed in several early targets of arbovirus infection, including dendritic cells (DCs) and cells of the reticuloendothelial system. In the present study, we show that DC-SIGN and L-SIGN can function as attachment receptors for Sindbis (SB) virus, an arbovirus of the Alphavirus genus. Human monocytic THP-1 cells stably transfected with DC-SIGN or L-SIGN were permissive for SB virus replication, while untransfected controls were essentially nonpermissive. The majority of control THP-1 cells were permissive when attachment and entry steps were eliminated through electroporation of virus transcripts. Infectivity for the DC-SIGN/L-SIGN-expressing cells was largely blocked by yeast mannan, EDTA, or a DC-SIGN/L-SIGN-specific monoclonal antibody. Infection of primary human DCs by SB virus was also dependent upon SIGN expression by similar criteria. Furthermore, production of virus particles in either C6/36 mosquito cells or CHO mammalian cells under conditions that limited complex carbohydrate content greatly increased SB virus binding to and infection of THP-1 cells expressing these lectins. C6/36-derived virus also was much more infectious for primary human DCs than CHO-derived virus. These results suggest that (i) lectin molecules such as DC-SIGN and L-SIGN may represent common attachment receptor molecules for arthropod-borne viruses, (ii) arbovirus particles produced in and delivered by arthropod vectors may preferentially target vertebrate host cells bearing these or similar lectin molecules, and (iii) a cell line has been identified that can productively replicate alphaviruses but is deficient in attachment receptors.
In Situ β Cell Death Promotes Priming of Diabetogenic CD8 T Lymphocytes (2002)

CTLs are important mediators of pancreatic beta cell destruction in the nonobese diabetic mouse model of type 1 diabetes. Cross-presentation of Ag is one means of priming CTLs. The death of Ag-bearing cells has been implicated in facilitating this mode of priming. The role of beta cell death in facilitating the onset of spontaneous autoimmune diabetes is unknown. Here, we used an adoptive transfer system to determine the time course of islet-derived Ag presentation to naive beta cell-specific CD8 T cells in nonobese diabetic mice and to test the hypothesis that beta cell death enhances the presentation of beta cell autoantigen. We have determined that beta cell death enhances autoantigen presentation. Priming of diabetogenic CD8 T cells in the pancreatic lymph nodes was negligible before 4 wk, progressively increased until 8 wk of age, and was not influenced by gender. Administration of multiple low doses of the beta cell toxin streptozotocin augmented in situ beta cell apoptosis and accelerated the onset and magnitude of autoantigen presentation to naive CD8 T cells. Increasing doses of streptozotocin resulted in both increased pancreatic beta cell death and significantly enhanced T cell priming. These results indicate that in situ beta cell death facilitates autoantigen-specific CD8 T cell priming and can contribute to both the initiation and the ongoing amplification of an autoimmune response.
Mecillinam resistance in Escherichia coli is conferred by loss of a second activity of the AroK protein (1996)

Mecillinam, a beta-lactam antibiotic specific to penicillin-binding protein 2 (PBP 2) in Escherichia coli, blocks cell wall elongation and, indirectly, cell division, but its lethality can be overcome by increased levels of ppGpp, the nucleotide effector of the stringent response. We have subjected an E. coli K-12 strain to random insertional mutagenesis with a mini-Tn10 element. One insertion, which was found to confer resistance to mecillinam in relA+ and relA strains, was mapped at 75.5 min on the E. coli map and was located between the promoters and the coding sequence of the aroK gene, which codes for shikimate kinase 1, one of two E. coli shikimate kinases, both of which are involved in aromatic amino acid biosynthesis. The mecillinam resistance conferred by the insertion was abolished in a delta relA delta spoT strain completely lacking ppGpp, and it thus depends on the presence of ppGpp. Furthermore, the insertion increased the ppGpp pool approximately twofold in a relA+ strain. However, this increase was not observed in relA strains, although the insertion still conferred mecillinam resistance in these backgrounds, showing that mecillinam resistance is not due to an increased ppGpp pool. The resistance was also abolished in an ftsZ84(Ts) strain under semipermissive conditions, and the aroK::mini-Tn10 allele partially suppressed ftsZ84(Ts); however, it did not increase the concentration of the FtsZ cell division protein. The insertion greatly decreased or abolished the shikimate kinase activity of AroK in vivo and in vitro. The two shikimate kinases of E. coli are not equivalent; the loss of AroK confers mecillinam resistance, whereas the loss of Arol, does not. Furthermore, the ability of the aroK mutation to confer mecillinam resistance is shown to be independent of polar effects on operon expression and of effects on the availability of aromatic amino acids or shikimic acid. Instead, we conclude that the AroK protein has a second activity, possibly related to cell division regulation, which confers mecillinam sensitivity. We were able to separate the AroK activities mutationally with an aroK mutant allele lacking shikimate kinase activity but still able to confer mecillinam sensitivity.
Learning from the immune system: laboratory methods for creating and refining molecular diversity in polypeptides (1991)

Journal Article Learning from the immune system: laboratory methods for creating and refining molecular diversity in polypeptides Get access Ronald Wetzel Ronald Wetzel Macromolecular Sciences, Department Smith Kline Beecham PharmaceuticalsPO Box 1539, King of Prussia, PA 19406, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Protein Engineering, Design and Selection, Volume 4, Issue 4, April 1991, Pages 371–374, https://doi.org/10.1093/protein/4.4.371 Published: 01 April 1991 Article history Received: 28 January 1991 Published: 01 April 1991