gebhart/patrepeval huggingface dataset:
Fatigue characteristics of Si movable comb inserted into MEMS optical devices (2004)

Fatigue life for the moving part had been inspected at the real operation condition for the first time. The obtained fracture rate was about 0.3 indicated the MEMS devices were reliable enough for practical usage.
An epitope in human immunodeficiency virus 1 reverse transcriptase recognized by both mouse and human cytotoxic T lymphocytes. (1990)

T-cell-mediated cytotoxicity may play an important role in control of infection by the human immunodeficiency virus (HIV). In this study, we have identified and characterized a relatively conserved epitope in the HIV-1 reverse transcriptase recognized by murine and human cytotoxic T cells. This epitope was identified using a murine antigen-specific CD8+ class I major histocompatibility complex-restricted cytotoxic T-cell (CTL) line, a transfected fibroblast cell line expressing the HIV-1 pol gene, recombinant vaccinia viruses containing different truncated versions of the pol gene, and overlapping synthetic peptides. The optimal antigenic site was identified as residues 203-219 by synthesizing extended or truncated peptide analogs of the antigenic fragment. The optimal peptide was then tested for sensitization of autologous Epstein-Barr virus-transformed B-cell targets for killing by fresh human peripheral blood mononuclear cells. It was recognized by CTLs from several HIV-seropositive patients but not from any seronegative donor. Therefore, this peptide is a good candidate for inclusion in an AIDS vaccine. This study demonstrates that the same CTL epitope can be seen by murine and human CD8+ CTLs, as previously demonstrated for epitopes recognized by CD4+ helper T cells, and suggests the utility of screening for immunodominant CTL epitopes in mice prior to carrying out studies in humans.
Salient Degradation Features of a 50:50 PLA/PGA Scaffold for Tissue Engineering (1996)

An implant system that undergoes a gradual, time-dependent, nontoxic degradation process may offer an efficacious, safe, and desirable alternative to metallic materials used in the treatment of various musculoskeletal conditions. Such a scaffold may also be a suitable vehicle for growing cells and tissue in the laboratory for tissue engineering applications. We have used a scaffold of this type previously in animal studies for biological resurfacing of large articular cartilage defects.(1) This study examined important in vitro degradation characteristics of a 50:50 polylactic acid/polyglycolic acid (PLG) implant during an 8-week period. It was determined that this particular implant degraded in a biphasic fashion. The initial phase occurred during the first 2 weeks with a decrease in molecular weight and surface axial strain, coupled with an increase in percent porosity. The second phase demonstrated a decline in surface axial strain by 4 weeks and an ongoing decline in molecular weight. Loss of gross structural properties was not evident until the start of the second phase and was complete at 8 weeks. This study demonstrated the potential uses for this implant as a means of providing structural support for cells and tissue ingrowth for up to 8 weeks. Further studies need to be conducted in order to determine the biological effects of the degrading polymer byproducts on host tissues.
Engineering of coordinated up- and down-regulation of two glycosyltransferases of the o-glycosylation pathway in Chinese hamster ovary (CHO) cells (2000)

Production of O-linked oligosaccharides that interact with selectins to mediate cell–cell adhesion occurs in one segment of a branched glycan biosynthesis network. Prior efforts to direct the branched pathway towards selectin-binding oligosaccharides by amplifying enzymes in this branch of the network have had limited success, suggesting that metabolic engineering to simultaneously inhibit the competing pathway may also be required. We report here the partial cloning of the CMP-sialic acid:Galβ1,3GalNAcα2,3-sialyltransferase (ST3Gal I) gene from Chinese hamster ovary (CHO) cells and the simultaneous inhibition of expression of CHO cell ST3Gal I gene and overexpression of the human UDP-GlcNAc:Galβ1,3GalNAc-R β1,6-N-acetylglucosaminyltransferase (C2GnT) gene. A tetracycline-regulated system adjoined to tricistronic expression technology allowed “one-step” transient manipulation of multiple enzyme activities in the O-glycosylation pathway of a previously established CHO cell line already engineered to express α1,3-fucosyltransferase VI (α1,3-Fuc-TVI). Tetracycline-regulated co-expression of a ST3Gal I fragment, cloned in the antisense orientation, and of C2GnT cDNA resulted in inhibition of the ST3Gal I enzymatic activity and increase in C2GnT activity which varied depending on the extent of tetracycline reduction in the cell culture medium. This simultaneous regulated inhibition and activation of the two key enzyme activities in the O-glycosylation pathway of mammalian cells is an important addition to the metabolic engineering field. © 2000 John Wiley & Sons, Inc. Biotechnol Bioeng 68: 239–244, 2000.
BslA is a self-assembling bacterial hydrophobin that coats the Bacillus subtilis biofilm (2013)

Biofilms represent the predominant mode of microbial growth in the natural environment. Bacillus subtilis is a ubiquitous Gram-positive soil bacterium that functions as an effective plant growth-promoting agent. The biofilm matrix is composed of an exopolysaccharide and an amyloid fiber-forming protein, TasA, and assembles with the aid of a small secreted protein, BslA. Here we show that natively synthesized and secreted BslA forms surface layers around the biofilm. Biophysical analysis demonstrates that BslA can self-assemble at interfaces, forming an elastic film. Molecular function is revealed from analysis of the crystal structure of BslA, which consists of an Ig-type fold with the addition of an unusual, extremely hydrophobic "cap" region. A combination of in vivo biofilm formation and in vitro biophysical analysis demonstrates that the central hydrophobic residues of the cap are essential to allow a hydrophobic, nonwetting biofilm to form as they control the surface activity of the BslA protein. The hydrophobic cap exhibits physiochemical properties remarkably similar to the hydrophobic surface found in fungal hydrophobins; thus, BslA is a structurally defined bacterial hydrophobin. We suggest that biofilms formed by other species of bacteria may have evolved similar mechanisms to provide protection to the resident bacterial community.
Design and modeling of ignition targets for the National Ignition Facility (1995)

Several targets are described that in simulations give yields of 1–30 MJ when indirectly driven by 0.9–2 MJ of 0.35 μm laser light. The article describes the targets, the modeling that was used to design them, and the modeling done to set specifications for the laser system in the proposed National Ignition Facility. Capsules with beryllium or polystyrene ablators are enclosed in gold hohlraums. All the designs utilize a cryogenic fuel layer; it is very difficult to achieve ignition at this scale with a noncryogenic capsule. It is necessary to use multiple bands of illumination in the hohlraum to achieve sufficiently uniform x-ray irradiation, and to use a low-Z gas fill in the hohlraum to reduce filling of the hohlraum with gold plasma. Critical issues are hohlraum design and optimization, Rayleigh–Taylor instability modeling, and laser–plasma interactions.
Time-Frequency Wavelet Family and its Application in Electrograstrographic Signal Analysis (1998)

This paper wavelet family, with bo:h oscillating patterns, of a regular time-frequency analysis for wavelet trar both stationary and convenient trade-off frequency and frequency given time-frequency window functions are frequency wavelet family real sine wavelets and using these four windc condition. The tim corresponding wavelet has also been investigated. cosine window sinusoid time-frequency resolution. modulated Gaussian Gaussian window complex describe our sinusoidal time-frequency analysj signals to simultaneouly activities and track low introduces a sinusoidal time-frequency real sine and complex exponential \.arious window functions. It provides analysis rather than a time-scale sform time-frequency localization of lion-stationary signals. It offers a between time resolution at low resolution at high frequency for any analysis application. Four different studied for the sinusoidal time- and it has been shown that both the the complex exponential wavelets ws satisfy the wavelet admissibility e-frequency resolution of the time-frequency localization analysis It has been show that the rising- a1 wavelet provides close to optimal It has also been shown that the w:.velet becomes a special case of the exponential wavelet. We briefly wavelet family and apply it to the s of electrogastrographic (EGG) localize high frequency spike Sequency slow waves.
Comparative logical and physical modeling in two OODBMSs (1994)

An application developer's perspective is used to compare modeling and storage in two Object-Oriented Database Management Systems (OODBMSs): ODE (Object Database and Environment) and ObjectStore. Although both systems are based on the object-oriented language C++, differences exist in their OODBMS designs. Comparing the differences between these two systems provides insight into other possible designs or combinations of features that could be possible in an OODBMS. As part of this discussion, internal translations of OODBMS schemas to physical storage are shown. Such knowledge enables an application developer to create appropriate logical and physical database designs and provides a basis for understanding OODBMS software. Features compared in this paper are physical and logical clustering, iterators, sets, joins, inverse pointers, and queries. To facilitate the discussion, a simple Geographic Information System (GIS) schema is presented.
EBNA-1, a Bifunctional Transcriptional Activator (2003)

Transient-transfection assays have been used to identify transcription factors, and genetic analyses of these factors can allow a dissection of their mechanism of activation. Epstein-Barr nuclear antigen 1 (EBNA-1) has been shown to activate transcription from transfected templates, but its ability to activate transcription from nuclear templates has been controversial. We have established cells with integrated EBNA-1-responsive templates and have shown that EBNA-1 activates transcription from these chromatin-embedded templates dose dependently. A mutational analysis of EBNA-1 has identified a domain required for transcriptional activation of integrated templates, but not of transfected templates. The ability of EBNA-1 to activate transcription from both integrated and transfected templates can be inhibited by a derivative of EBNA-1 lacking the amino acids required for activation from integrated templates. EBNA-1's mode of activating transfected templates is therefore genetically distinct from that acting on integrated templates.
Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKa Values (2011)

The new empirical rules for protein pKa predictions implemented in the PROPKA3.0 software package (Olsson et al. J. Chem. Theory Comput.2010, 7, 525-537) have been extended to the prediction of pKa shifts of active site residues and ionizable ligand groups in protein-ligand complexes. We present new algorithms that allow pKa shifts due to inductive (i.e., covalently coupled) intraligand interactions, as well as noncovalently coupled interligand interactions in multiligand complexes, to be included in the prediction. The number of different ligand chemical groups that are automatically recognized has been increased to 18, and the general implementation has been changed so that new functional groups can be added easily by the user, aided by a new and more general protonation scheme. Except for a few cases, the new algorithms in PROPKA3.1 are found to yield results similar to or better than those obtained with PROPKA2.0 (Bas et al. Proteins: Struct., Funct., Bioinf.2008, 73, 765-783). Finally, we present a novel algorithm that identifies noncovalently coupled ionizable groups, where pKa prediction may be especially difficult. This is a general improvement to PROPKA and is applied to proteins with and without ligands.
Surgical treatment of peripheral small cell lung cancer. (1997)

Approximately 5% of small cell lung cancer (SCLC) patients present with an asymptomatic peripheral tumor (solitary pulmonary nodule) on "routine" chest radiography. In this setting, the diagnosis of SCLC is often made at thoracotomy. Complete resection, mediastinal lymph node sampling, and postoperative chemotherapy are indicated. If the diagnosis is made preoperatively, multiorgan scanning and mediastinoscopy are required prior to thoracotomy. Survival for pathologic stage I SCLC treated by surgery and postoperative chemotherapy is comparable to survival for surgically treated stage I non-SCLC.
Location of the disulfide bonds in human coagulation factor XI: the presence of tandem apple domains (1991)

Factor XI is a plasma glycoprotein that participates in the blood coagulation cascade. Of the 19 disulfide bonds present in each of the subunits of the human protein, 16 were determined by amino acid sequence analysis of peptide fragments produced by chemical and enzymatic digestion. Four apple domains of 90 or 91 amino acids were identified in the tandem repeats present in the amino-terminal portion of each subunit of factor XI. The disulfide bonds in the carboxyl-terminal portion of the molecule were similar to those in the catalytic region of other serine proteases. The two identical subunits of factor XI were connected by a single disulfide bond at Cys321 linking each of the fourth apple domains while each of the Cys residues at position 11 in the first apple domains forms a disulfide bond with another Cys residue.
Residential Retrofitting: Current Practice and Emerging Directions - Summary of a BEIIC Report (2010)

This paper provides a summary of the 'Retrofitting Residential Housing and Precincts: Current Practice, New Strategies and Training Responses' report, which was prepared by UNSW Global Pty Ltd for the Commonwealth Department of Innovation, Industry, Science and Research (DIISR). The report was prepared with the guidance of the Built Environment Industry Innovation Council (BEIIC) and aimed to address two main research gaps: First, to identify current practice and new strategies for retrofitting residential housing and precincts in the context of climate change mitigation; Second, to provide a critical review of current upskilling and training programs for the 'green collar' construction workforce.
A phase 1/2, open-label study evaluating twice-daily administration of momelotinib in myelofibrosis (2016)

Momelotinib, a small-molecule inhibitor of Janus kinase 1 and Janus kinase 2, has demonstrated efficacy in myelofibrosis patients with 300 mg, once-daily dosing. This open-label, non-randomized, phase 1/2 study evaluated the safety and therapeutic benefit of momelotinib with twice-daily dosing. A total of 61 subjects with primary myelofibrosis or post-polycythemia vera/post-essential thrombocythemia myelofibrosis with intermediate- or high-risk disease received momelotinib. A phase 1 dose escalation identified 200 mg twice daily as the optimal dose to be expanded in phase 2. The most frequent adverse events were diarrhea (45.9%), peripheral neuropathy (44.3%), thrombocytopenia (39.3%), and dizziness (36.1%), the latter primarily due to a first-dose effect. The response assessment according to the 2006 International Working Group criteria (≥8 weeks duration at any time point) demonstrated spleen response by palpation of 72% (36/50) and anemia response of 45% (18/40). Spleen response by magnetic resonance imaging obtained at 24 weeks was 45.8% (27/59) for all subjects and 54.0% (27/50) for those with palpable splenomegaly at baseline. The symptoms of myelofibrosis were improved in most subjects. Cytokine analysis showed a rapid decline in interleukin-6 with momelotinib treatment, and a slower reduction in other inflammatory cytokines. In the subgroup of subjects with the JAK2V617F mutation at baseline (n=41), momelotinib significantly reduced the allele burden by 21.1% (median) at 24 weeks. These results provide evidence of tolerability and a potential therapeutic activity of momelotinib for subjects that support further evaluation in ongoing, phase 3 randomized trials. (clinicaltrials. gov identifier:01423058).
Endovascular Management of Intracranial Aneurysms: Current Experience and Future Advances (2006)

Long-term studies evaluating experience with aneurysm coil embolization during the past decade indicate that this is a safe and durable treatment method. The introduction of stent-assist techniques has improved the management of wide-neck aneurysms. Future technology developments will likely improve the durability of endovascular treatment further by delivering bioactive agents that promote aneurysm thrombosis beyond the coil mass alone. It is clear that endovascular therapy of both ruptured and unruptured aneurysms is becoming a mainstay of practice in this patient population. Although not replacing open surgery, the continued improvements have allowed aneurysms that previously were amenable only to open clip ligation to be treated safely with durable long-term outcomes.
Bubble nucleation in polymeric liquids. II. theoretical considerations (1990)

Abstract A theory based on classical nucleation theory is developed for bubble nucleation in polymer solutions. The theory requires information on solubility, diffusivity, concentration, surface tension, temperature, and degree of supersaturation. The effects of supersaturation and of the presence of large molecules in a liquid mixture on the free energy of bubble formation are included in the theoretical development. A semiempirical equation for the determination of bubble nucleation rate is developed, with the aid of experimental results reported in part I of this series. Using the experimental data, computer simulations of bubble nucleation in polymer solutions are performed. The consumptions of the volatile component in a liquid mixture, due to bubble nucleation and subsequent growth, and the variation of bubble nucleation rate during the expansion process are included in the simulation of the bubble nucleation process.
Surfin' the World Wide Web with Japanese (2002)

Previously, we have developed Speech-Aware Multimedia (SAM) which controls a WWW browser using English speech. We have extended its capability to use Japanese speech to browse Japanese pages, and developed a prototype using speaker-independent, continuous speech recognition with Japanese context-dependent phonetic models. Some challenges not seen in English include: segregation of Japanese text into word units for optional silence insertion, Japanese text to phone conversion and accommodation of English link names embedded in Japanese pages. In order to accomplish the first two, we modified a public-domain dictionary look-up tool for segmentation and to accommodate the heuristics required for improved text-to-phone conversion accuracy. Preliminary tests show that the conversion result contains the correct phone sequence over 97% of the time, and the prototype correctly understands the input speech 91.5% of the time.
Expression, identification and subcellular localization of the proteins encoded by the hepatitis C viral genome (1993)

We have expressed the full-length coding region and selected domains of the hepatitis C virus (HCV) cDNA in mammalian cells by transfection. Using HCV antibody-positive human sera and monospecific antibodies the proteins encoded by the putative structural and non-structural regions of the open reading frame of HCV were identified as core (p22), E1 (gp32-35), E2 (gp68-72), NS2 (p23), NS3 (p72), NS4a and b (p10 and p27) and NS5a and b (p56 and p70). We have also defined the subcellular localizations of the HCV proteins using indirect immunofluorescence assays.
Functionalization of Single-Walled Carbon Nanotubes via the Bingel Reaction (2003)

Single-walled carbon nanotubes have been cyclopropanated under Bingel reaction conditions, and the functionalized nanotubes have been characterized by atomic force microscopy using "chemical tagging" techniques.
Dual-mode ultrasound phased arrays for noninvasive surgery: post-beamforming image compounding algorithms for enhanced visualization of thermal lesions (2003)

A post-beamforming nonlinear compounding algorithm for ultrasonic imaging is presented. Fundamental and harmonic image components from beamformed radio frequency (RF) data are extracted, envelope detected and compounded using a spatial compounding functions (SCFs) derived from the transmit/receive beamforming topology used in obtaining the RF data. This is specially useful for applications where single-transmit focus (STF) imaging is used. In this paper, we present results from STF imaging experiments using a novel dual-mode phased array system for image-guided surgery. In particular, we address the enhancement of the echogenicity of thermal lesions formed in ex vivo tissue. It is shown that new nonlinear image compounding algorithm produces 25-30 dB enhancement in lesion echogenicity without loss in spatial resolution. This is to be compared with a typical enhancement of 5 dB achieved by standard echographic imaging and 20 dB achieved by second harmonic imaging alone. In addition, images resulting from the new algorithm are virtually free of beamforming artifacts that can severely degrade the performance of 2nd harmonic imaging.
The Steap proteins are metalloreductases (2006)

Iron and copper are essential for all organisms, assuming critical roles as cofactors in many enzymes. In eukaryotes, the transmembrane transport of these elements is a highly regulated process facilitated by the single electron reduction of each metal. Previously, we identified a mammalian ferrireductase, Steap3, critical for erythroid iron homeostasis. Now, through homology, expression, and functional studies, we characterize all 4 members of this protein family and demonstrate that 3 of them, Steap2, Steap3, and Steap4, are not only ferrireductases but also cupric reductases that stimulate cellular uptake of both iron and copper in vitro. Finally, the pattern of tissue expression and subcellular localization of these proteins suggest they are physiologically relevant cupric reductases and ferrireductases in vivo.
Microbial community profiling for human microbiome projects: Tools, techniques, and challenges (2009)

High-throughput sequencing studies and new software tools are revolutionizing microbial community analyses, yet the variety of experimental and computational methods can be daunting. In this review, we discuss some of the different approaches to community profiling, highlighting strengths and weaknesses of various experimental approaches, sequencing methodologies, and analytical methods. We also address one key question emerging from various Human Microbiome Projects: Is there a substantial core of abundant organisms or lineages that we all share? It appears that in some human body habitats, such as the hand and the gut, the diversity among individuals is so great that we can rule out the possibility that any species is at high abundance in all individuals: It is possible that the focus should instead be on higher-level taxa or on functional genes instead.