gebhart/patrepeval huggingface dataset:
Band structure ofAI/Si/n-type GaAs with a strained Si interfacial layer (1996)

The band structure of a coherently strained Si layer (15 \AA{}) on GaAs has been calculated using the empirical pseudopotential method. The pseudopotential from factor of the strained Si layer is derived by considering that the pseudopotential of the strained layer is slightly modified by a factor which is proportional to the volume change of the unit cell. The band-structure calculation indicates that the band gap of the strained Si layer is 0.7 eV, which is substantially smaller than that of the bulk Si. A revised band-structure model for $\mathrm{AI}/\mathrm{Si}/n$-type GaAs based on the above calculation is proposed, which agrees very well with the experimental results. This model implies that for the coherently strained Si interfacial layer, the Fermi level is unpinned not only at the Si-GaAs interface but also at the Al-Si interface.
Next-Generation Digital Information Storage in DNA (2012)

Digital information is accumulating at an astounding rate, straining our ability to store and archive it. DNA is among the most dense and stable information media known. The development of new technologies in both DNA synthesis and sequencing make DNA an increasingly feasible digital storage medium. We developed a strategy to encode arbitrary digital information in DNA, wrote a 5.27-megabit book using DNA microchips, and read the book by using next-generation DNA sequencing.
Controlling Virtual Cameras Based on a Robust Model-Free Pose Acquisition Technique (2008)

This paper presents a novel method that acquires camera position and orientation from a stereo image sequence without prior knowledge of the scene. To make the algorithm robust, the interacting multiple model probabilistic data association filter (IMMPDAF) is introduced. The interacting multiple model (IMM) technique allows the existence of more than one dynamic system in the filtering process and in return leads to improved accuracy and stability even under abrupt motion changes. The probabilistic data association (PDA) framework makes the automatic selection of measurement sets possible, resulting in enhanced robustness to occlusions and moving objects. In addition to the IMMPDAF, the trifocal tensor is employed in the computation so that the step of reconstructing the 3-D models can be eliminated. This further guarantees the precision of estimation and computation efficiency. Real stereo image sequences have been used to test the proposed method in the experiment. The recovered 3-D motions are accurate in comparison with the ground truth data and have been applied to control cameras in a virtual environment.
Optical Imaging in Breast Cancer Diagnosis: The Next Evolution (2012)

Breast cancer is one of the most common cancers among the population of the Western world. Diagnostic methods include mammography, ultrasound, and magnetic resonance; meanwhile, nuclear medicine techniques have a secondary role, being useful in regional assessment and therapy followup. Optical imaging is a very promising imaging technique that uses near-infrared light to assess optical properties of tissues and is expected to play an important role in breast cancer detection. Optical breast imaging can be performed by intrinsic breast tissue contrast alone (hemoglobin, water, and lipid content) or with the use of exogenous fluorescent probes that target specific molecules for breast cancer. Major advantages of optical imaging are that it does not use any radioactive components, very high sensitivity, relatively inexpensive, easily accessible, and the potential to be combined in a multimodal approach with other technologies such as mammography, ultrasound, MRI, and positron emission tomography. Moreover, optical imaging agents could, potentially, be used as "theranostics," combining the process of diagnosis and therapy.
The novel triterpenoid 2-cyano-3,12-dioxoolean-1,9-dien-28-oic acid induces apoptosis of human myeloid leukemia cells by a caspase-8-dependent mechanism. (2000)

The oleanane triterpenoid 2-cyano-3,12-dioxoolean-1,9-dien-28-oic acid (CDDO) is a multifunctional molecule that induces growth inhibition and differentiation of human myeloid leukemia cells. The present studies demonstrate that CDDO treatment results in apoptosis of U-937 and HL-60 myeloid leukemia cells. Similar to 1-beta-D-arabinofuranosylcytosine (ara-C), another agent that inhibits growth and induces apoptosis of these cells, CDDO induced the release of mitochondrial cytochrome c and activation of caspase-3. Overexpression of Bcl-X(L) blocked cytochrome c release, caspase-3 activation, and apoptosis in ara-C-treated cells. By contrast, CDDO-induced release of cytochrome c, and activation of caspase-3 were diminished only in part by Bcl-X(L). In concert with these findings, we demonstrate that CDDO, but not ara-C, activates caspase-8 and thereby caspase-3 by a cytochrome c-independent mechanism. The results also show that CDDO-induced cytochrome c release is mediated by caspase-8-dependent cleavage of Bid. These findings demonstrate that CDDO induces apoptosis of myeloid leukemia cells and that this novel agent activates an apoptotic signaling cascade distinct from that induced by the cytotoxic agent ara-C.
Fault diagnosis for, a gas-fired furnace using bilinear observer method (2005)

A simulation study is undertaken on fault diagnosis for a gas-fired high temperature furnace. A single input multi output bilinear model is found to be suitable to represent the furnace. A previously proposed full-order bilinear state observer is used to generate the residual. Two actuator and two sensor faults are simulated and tested using this method.
Call admission control schemes: a review (1996)

Over the last few years, a substantial number of call admission control (CAC) schemes have been proposed for ATM networks. We review the salient features of some of these algorithms. Also, we quantitatively compare the performance of three of these schemes.
Etude structure/fonction d'une albumine entomotoxique de type A1b du pois chez le riz : application à la protection contre le ravageur des stocks Sitophilus oryzae (2006)

Une nouvelle entomotoxine, PAlb ("pea albumin 1 subunit b"), active contre des insectes de différents ordres et plus particulièrement les charançons des céréales et la teigne de la farine, a été identifiée à partir de la graine de pois par l'INSA-INRA de Lyon-Villeurbanne en association avec l'INRA de Nantes. Suite à cette découverte, l'INRA et l'INSA ont déposé un brevet concernant l'utilisation de la protéine PA1b en tant qu'insecticide (Delobel et al., 1998. 1999). Outre une très forte toxicité pour ces insectes, cette protéine de réserve de la famille des albumines contient 16% de cystéines et représente la principale réserve en acides aminés soufrés des graines de pois. PA1b (4kDa) est synthétisée à partir d'une polyprotéine PA1 (composée d'un peptide signal. des protéines PA lb et PA1 a et de leurs propeptides respectifs) dont la maturation complexe conduit aussi à la synthèse d'un autre peptide, PA la (6kDa). La synthèse conjointe de ces deux protéines est présente chez les différentes isoformes de PA1 coexistant chez le pois ainsi que chez les Fabacées. La conservation de la structure et de l'activité biologique de PA1b chez les Fabacées (Louis et al., 2004) font des isoformes de PA1b une nouvelle famille d'entomotoxines végétales. Le Cirad, en collaboration avec l'INSA-INRA et le CNRS, a entrepris une étude structure/fonction de la polyprotéine PA1 dans des riz transgéniques pour tenter d'appréhender les mécanismes aboutissant à la synthèse d'une toxine PA1b active in planta. L'analyse fonctionnelle du gène pal dans une large population de riz transgéniques a permis d'initier la compréhension du rôle de chaque domaine de la polyprotéine PA1 en terme d'expression. de régulation et d'activité entomotoxique. De plus, l'accumulation stable de l'entomotoxine PA1b dans les grains T2 et T3 de riz transgéniques a permis de protéger ces derniers contre le charançon du riz, Sitophilus oryzae, un des ravageur majeur des céréales lors de leur stockage.
Angiotensin II type I antagonist prevents pulmonary metastasis of murine renal cancer by inhibiting tumor angiogenesis. (2002)

Angiotensin II (AII) is a potent vasoconstrictor peptide from the renin-angiotensin system in the kidney. The AII type 1 receptor (AT1R) is reportedly expressed in several tumors including renal cell carcinoma, and AII is involved in tumor angiogenesis. We p.o. administered the long-acting AT1R antagonist, candesartan (10 mg/kg), to the 16 days mouse renal cancer lung metastasis model to test the preventive effects in tumor metastasis. Pulmonary metastases of renal cancer showed prominent AT1R expression in both mice and humans, and candesartan treatment dramatically prevented lung metastatic nodules (14.9 +/- 1.8; P < 0.0001; n = 12) in mice along with the inhibition of neovascularization and vascular endothelial growth factor expression, compared with control metastatic mice (123.3 +/- 8.6; n = 13). Candesartan is widely used clinically, so it seems to be a reasonable therapy for patients with lung metastases of renal cell carcinoma.
Primary Cutaneous T-Cell Lymphomas (2006)

Primary cutaneous T-cell lymphomas (CTCLs) encompass a clinically and biologically heterogeneous group of non-Hodgkin lymphomas (NHLs) defined by clonal proliferation of skin-homing malignant T lymphocytes and natural killer cells. They account for up to 75% to 80% of all cutaneous lymphomas. The current WHO-EORTC classification of cutaneous lymphomas with primary cutaneous manifestations lists 13 entities. The most common subtypes-mycosis fungoides, Sézary syndrome, primary cutaneous anaplastic large cell lymphoma, and lymphomatoid papulosis-which represent approximately 95% of CTCLs, will be discussed in the following review. Each entity has unique biological characteristics and clinical course. Topical and/or systemic therapies are employed based on the stage of the disease and the tempo of progression.
Ultrafast reversible phase change in GeSb films for erasable optical storage (1992)

Amorphous-to-crystalline and crystalline-to-amorphous transformations are triggered in GeSb thin films by irradiation with femtosecond and picosecond laser pulses. Phase changes are accompanied with optical contrast and therefore the feasibility of phase-change optical recording at ultrafast rates is demonstrated for the first time. The phase reversal by ultrashort pulses seems to be related to the dependence of the degree of undercooling prior to solidification on the irradiation energy density.
Hydrolysis of the borohydride ion catalysed by metal–boron alloys (1971)

The hydrolysis of the borohydride ion according to the equation (i) is catalysed by nickel–boron and cobalt–boron, BH4–+ 3H2O → H2BO3–+ 4H2(i) alloys. The metal-catalysed hydrolysis has been studied at 22·0 °C by measurement of the hydrogen gas evolved. Analysis of the gas evolved when the reaction is carried out in deuterium oxide shows that approximately half the hydrogen evolved originates from the borohydride and half from the solvent. The deuterium content of the gas increases with reaction time. In mixtures of H2O and D2O, preferential hydrogen evolution occurs and isotope separation factors of 8·5 (for a nickel–boron catalyst) and 9·2 (for a cobalt–boron catalyst) have been derived.
A probabilistic map of the human ventral sensorimotor cortex using electrical stimulation (2015)

The authors report probabilistic maps of function in the human vSMC based on intraoperative cortical electrical stimulation. These results define the expected range of mapping outcomes in the vSMC of a single individual and shed light on the functional organization of the vSMC supporting speech motor control and nonspeech functions.
cDNA cloning and sequence of MAL, a hydrophobic protein associated with human T-cell differentiation. (1987)

We have isolated a human cDNA that is expressed in the intermediate and late stages of T-cell differentiation. The cDNA encodes a highly hydrophobic protein, termed MAL, that lacks a hydrophobic leader peptide sequence and contains four potential transmembrane domains separated by short hydrophilic segments. The predicted configuration of the MAL protein resembles the structure of integral proteins that form pores or channels in the plasma membrane and that are believed to act as transporters of water-soluble molecules and ions across the lipid bilayer. The presence of MAL mRNA in a panel of T-cell lines that express both the T-cell receptor and the T11 antigen suggests that MAL may be involved in membrane signaling in T cells activated via either T11 or T-cell receptor pathways.
Stability of Tea Polyphenol (−)-Epigallocatechin-3-gallate and Formation of Dimers and Epimers under Common Experimental Conditions (2005)

(-)-Epigallocatechin-3-gallate (EGCG), the most abundant and biologically active compound in tea, has been extensively studied for its activities related to disease prevention in animal models and in vitro. However, its stability under different experimental conditions has not been well-characterized. In the present study, the stability of EGCG in animal drinking fluid and under cell culture conditions and the factors that affect its stability under these conditions were investigated. Our results demonstrated that auto-oxidation and epimerization are the two major reactions causing the instability of EGCG. The structures of the major oxidation products, EGCG dimers, were identified. The rates of these reactions were affected by the temperature, pH, the partial pressure of oxygen, the level of antioxidants, the concentration of EGCG, and other components of tea. In future studies with EGCG, its stability should be considered in order to avoid possible artifacts.
Polyamide precursors from renewable 10-undecenenitrile and methyl acrylate via olefin cross-metathesis (2012)

The ruthenium-catalyzed cross-metathesis of the unsaturated fatty acid derivative 10-undecenenitrile 1 arising from castor oil with methyl acrylate produces a C12 nitrile ester with high turnover number. This product has potential as a new bio-sourced intermediate for the production of polyamides. This route competes favourably with the reverse cross-metathesis of methyl 10-undecenoate with acrylonitrile leading to the same C12 α,ω-amino ester 7 after hydrogenation of the carbon–carbon double bond and the nitrile functionality.
Maintenance of Geometric Representations Through Space Decompositions (1997)

The ability to transform between distinct geometric representations is the key to success of multiple-representation modeling systems. But the existing theory of geometric modeling does not directly address or support construction, conversion, and comparison of geometric representations. A study of classical problems of CSG ↔ b-rep conversions, CSG optimization, and other representation conversions suggests a natural relationship between a representation scheme and an appropriate decomposition of space. We show that a hierarchy of space decompositions corresponding to different representation schemes can be used to enhance the theory and to develop a systematic approach to maintenance of geometric representations.
Enhancement of Common-path Fourier-domain Optical Coherence Tomography using Active Surface Tracking Algorithm (2012)

Optical coherence tomography(OCT) can provide real-time and non-invasive subsurface imaging with ultra-high resolution of micrometer scale. However, conventional OCT systems generally have a limited imaging depth range within a depth of only 1-2 mm. To overcome the limitation, we have proposed an active surface tracking algorithm used in common-path Fourier-domain OCT system in order to extend the imaging depth range. The surface tracking algorithm based on the threshold and Savitzky-Golay filter of A-scan data was applied to real-time tracking. The algorithm has controlled a moving stage according to the sample"s surface variance in real time. An OCT image obtained by the algorithm clearly show an extended imaging depth range. Consequently, the proposed algorithm demonstrated the potential for improving the conventional OCT systems with limitary depth range.
Sequential organ failure assessment score as the determinant of outcome for patients with severe sepsis. (2004)

The SOFA scores showed high accuracy in describing the course of organ dysfunction for the patients with severe sepsis. Evolving organ dysfunction following admission to the ICU strongly affected the outcome. Cumulative SOFA scores were better in discriminating outcome compared to single organ dysfunction scores.
Progressive infertility in female lethal yellow mice ( A y / a ; strain C57BL/6J) (1986)

Obese Ay/a females of 120 days or older, when compared to age-matched a/a controls (strain C57BL/6J), exhibited abnormal oestrous cyclicity characterized by reduced frequencies of true oestrous-stage smears, decreased mating success to proven a/a males, lowered uterine weights, and depressed ovulation rates. Exogenous gonadotrophins (PMSG/hCG) partly restored ovulation in obese Ay/a females to near control levels, demonstrating the sensitivity of Ay/a ovarian tissues to FSH and LH, at least at superovulatory levels. Concentrations of endogenous gonadotrophins and/or sensitivity of ovarian target cells to gonadotrophins may therefore be impaired in obese Ay/a females. Aberrant copulatory behaviour, reduced uterine weights, and depressed conception rates strongly suggest ovarian steroid deficiencies, perhaps secondary effects of reduced endogenous gonadotrophin activity. As in other obese rodent syndromes e.g. ob/ob, db/db, and fa/fa), a possible fundamental Ay-induced hypothalamic lesion is consistent with our data.
HepDirect prodrugs for targeting nucleotide-based antiviral drugs to the liver. (2006)

HepDirect prodrugs represent a novel class of cytochrome P450-activated prodrugs capable of targeting certain drugs to the liver. In this review, the HepDirect prodrug concept and its use for the delivery of nucleotides to the liver for the treatment of viral hepatitis is summarized. Preclinical and clinical data for the most advanced HepDirect prodrug, pradefovir, highlight the liver-targeting capability of these prodrugs, and the potential benefit of liver targeting on drug efficacy, safety and viral resistance.
Purification and properties of transgelin: a transformation and shape change sensitive actin-gelling protein. (1993)

We have purified the transformation and shape change sensitive isoform of an actin associated polypeptide doublet previously described by us (Shapland, C., P. Lowings, and D. Lawson. 1988. J. Cell Biol. 107:153-161) and have shown that it is evolutionarily conserved as far back as yeast. The purified protein: (a) binds directly to actin filaments at a ratio of 1:6 actin monomers, with a binding constant (Ka) of approximately 7.5 x 10(5) M-1; and (b) causes actin filament gelation within 2 min. Although these activities are controlled by ionic strength (and may be mediated by positively charged amino acid residues) the molecule remains as a monomer irrespective of ionic conditions. EM reveals that the addition of this protein to actin filaments converts them from a loose, random distribution into a tangled, cross-linked meshwork within 1 min, and discrete tightly aggregated foci after 10 min. By use of an "add-back" cell permeabilization system we can rebind this molecule specifically to actin filaments in cells from which it has previously been removed. Since the protein is transformation sensitive and gels actin, we have named it transgelin.
Activation-induced expression of CD137 permits detection, isolation, and expansion of the full repertoire of CD8+ T cells responding to antigen without requiring knowledge of epitope specificities (2007)

CD137 is a member of the TNFR-family with costimulatory function. Here we show that it also has many favorable characteristics as a surrogate marker for antigen-specific activation of human CD8(+) T cells. Although undetectable on unstimulated CD8(+) T cells, it is uniformly up-regulated 24 hours after stimulation on virtually all responding cells regardless of differentiation stage or profile of cytokine secretion, which circumvents limitations of current surrogate markers for defining the repertoire of responding cells based on only individual functions. Antibody-labeled responding CD137(+) cells can be easily and efficiently isolated by flow sorting or magnetic beads to substantially enrich antigen-specific T cells. To test this approach for epitope discovery, we examined in vitro priming of naive T cells from healthy donors to Wilms tumor antigen 1 (WT1), a protein overexpressed in various malignancies. Two overlapping pentadecamers were identified as immunogenic, and further analysis defined WT1((286-293)) as the minimal amino acid sequence and HLA-Cw07 as the HLA restriction element. In conclusion, this approach appears to be an efficient and sensitive in vitro technique to rapidly identify and isolate antigen-specific CD8(+) T cells present at low frequencies and displaying heterogeneous functional profiles, and does not require prior knowledge of the specific epitopes recognized or the HLA-restricting elements.
Gene Therapy Using Hematopoietic Stem Cells: Sisyphus Approaches the Crest (2000)

Gene transfer targeting cells of the blood and immune system was one of the first areas of investigation in the field of gene therapy. Despite the encouraging results achieved in early studies using murine bone marrow, the task of gene transfer into human hematopoietic stem cells proved to be far more difficult. As a result, progress has been disappointingly slow and initial clinical trials generally failed to achieve significant levels of gene marking. The continued application of new advances in vectorology and hematopoietic stem cell biology has now led to improvements in preclinical models that are being translated into clinical trials. The progress and remaining problems are discussed in this review article.
Insertion signal sequence fused to minimal peptides elicits specific CD8+ T-cell responses and prolongs survival of thymoma-bearing mice. (1994)

CD8+ T-lymphocytes (TCD8+) recognize minimal peptides of 8-10 residues which are the products of intracellularly processed proteins and are presented at the cell surface by major histocompatibility complex class I molecules. An important step in this process is the translocation of processed proteins from the cytosol across the endoplasmic reticulum membrane, mediated by transporter associated with antigen-processing proteins or alternatively by endoplasmic reticulum-insertion signal sequences located at the NH2-terminus of the precursor molecules. We report here that the addition of an endoplasmic reticulum-insertion signal sequence at the NH2-terminus of TCD8+ epitopes from chicken ovalbumin (amino acids 257-264) or a naturally occurring tumor antigen expressed by the murine mastocytoma P815 (P1A amino acids 35-43) significantly enhanced the priming of specific TCD8+ in vivo. The signal sequence did not enhance peptide immunogenicity by merely increasing the hydrophobicity of the peptide, since ovalbumin amino acids 257-264 peptide with the signal sequence at its COOH-terminus did not demonstrate enhanced efficacy. The signal sequence did not act as a helper epitope, since TCD8+ responses were not diminished in class II-deficient transgenic mice or in mice depleted of CD4+ T-cells in vivo. Importantly, a single immunization with the fusion peptide significantly prolonged survival of mice challenged with E.G7OVA, a thymoma transfected with the complementary DNA of chicken ovalbumin.