gebhart/patrepeval huggingface dataset:
State matrix kalman filter (2004)

The paper presents a general discrete-time Kalman filter for state matrix estimation using matrix measurements. The new algorithm evaluates the state matrix estimate and the estimation error covariance matrix in terms of the original system matrices. The proposed algorithm naturally fits systems which are most conveniently described by matrix process and measurement equations. Its formulation uses a compact notation for aiding both intuition and mathematical manipulation. It is a straightforward extension of the classical Kalman filter, and includes as special cases other matrix filters that were developed in the past.
Semiconductor to metal phase transition in the nucleation and growth of VO2 nanoparticles and thin films (2004)

The optical and morphological characteristics of vanadium dioxide nanoparticles and thin films during their nucleation and growth phases have been studied by correlating the temperature and sharpness of the transition with the processing parameters. Thermal annealing results in grain growth and improved crystallinity. Normally, larger crystallites show smaller hysteresis, as there is a greater probability of finding a nucleating defect in the larger volume. But at the same time, this improved crystal perfection, which accompanies the thermal annealing and grain growth, tends to a larger hysteresis, as there are fewer nucleating defects within the volume. We show that the width and shape of the hysteresis cycle are thus determined by the competing effects of crystallinity and grain size.
Mapping the Main Immunogenic Region and Toxin-Binding Site of the Nicotinic Acetylcholine Receptor (1987)

The alpha-chain of the nicotinic acetylcholine receptor carries the binding sites both for cholinergic ligands and for most experimentally induced or naturally occurring antibodies to the native receptor. By means of expression cloning in Escherichia coli, fusion proteins were derived from specific fragments of a complementary DNA encoding the mouse alpha-chain, allowing the mapping of the toxin-binding site to residues 160-216 and the main immunogenic region to residues 6-85. This approach permits the independent study of different functional domains of a complex receptor molecule and should be generally applicable to other proteins for which complementary DNA clones are available.
gp100/pmel 17 Is a Murine Tumor Rejection Antigen: Induction of “Self”-reactive, Tumoricidal T Cells Using High-affinity, Altered Peptide Ligand (1998)

Many tumor-associated antigens are nonmutated, poorly immunogenic tissue differentiation antigens. Their weak immunogenicity may be due to "self"-tolerance. To induce autoreactive T cells, we studied immune responses to gp100/pmel 17, an antigen naturally expressed by both normal melanocytes and melanoma cells. Although a recombinant vaccinia virus (rVV) encoding the mouse homologue of gp100 was nonimmunogenic, immunization of normal C57BL/6 mice with the rVV encoding the human gp100 elicited a specific CD8(+) T cell response. These lymphocytes were cross-reactive with mgp100 in vitro and treated established B16 melanoma upon adoptive transfer. To understand the mechanism of the greater immunogenicity of the human version of gp100, we characterized a 9-amino acid (AA) epitope, restricted by H-2Db, that was recognized by the T cells. The ability to induce specific T cells with human but not mouse gp100 resulted from differences within the major histocompatibility complex (MHC) class I-restricted epitope and not from differences elsewhere in the molecule, as was evidenced by experiments in which mice were immunized with rVV containing minigenes encoding these epitopes. Although the human (hgp10025-33) and mouse (mgp10025-33) epitopes were homologous, differences in the three NH2-terminal AAs resulted in a 2-log increase in the ability of the human peptide to stabilize "empty" Db on RMA-S cells and a 3-log increase in its ability to trigger interferon gamma release by T cells. Thus, the fortuitous existence of a peptide homologue with significantly greater avidity for MHC class I resulted in the generation of self-reactive T cells. High-affinity, altered peptide ligands might be useful in the rational design of recombinant and synthetic vaccines that target tissue differentiation antigens expressed by tumors.
Quantitative Mass Spectrometric Identification of Isomers Applying Coherent Laser Control (2005)

Mass spectrometry (MS) is one of the oldest and most trusted analytical methods for chemical identification. Advances in biology, such as metabolic analysis and proteomics, have fueled a growing number of refinements in this method. Unfortunately, isomers, for example, o- and p-xylene, are seldom identifiable by MS because they produce identical spectra. Time-consuming and less sensitive multidimensional methods are subsequently required for structural determination. The sensitivity of MS coupled with shaped femtosecond laser pulses that control molecular fragmentation and ionization results in a new, fast, and reproducible method for molecular identification which is used here to distinguish positional and geometric isomer compounds and quantify their relative concentration in mixtures.
Generating Binding Activities from Escherichia coli by Expression of a Repertoire of Immunoglobulin Variable Domains (1989)

The immunoglobulin molecule consists of a string of domains, each consisting of about 100 amino acid residues. The antigen-binding site is fashioned by both heavy (VH) and light (VL; Vκ or Vλ) chain variable domains, as demonstrated by the solved crystallo-graphic structures of antibody in association with antigen (Amit et al. 1986; Colman et al. 1987; Sheriff et al. 1987) or hapten (Satow et al. 1986). In the crystallo-graphic structures of antibody-antigen complexes, the relative contributions of VH and VL domains to antigen binding appear to vary, although both domains make extensive interactions with the antigen. Light-chain dimers (Bence-Jones proteins) have also been crystallized, in which the two chains form a cavity that is able to bind to a single molecule of hapten (Edmundson et al. 1984).
Assembly of Liposomes Controlled by Triple Helix Formation (2013)

Attachment of DNA to the surface of different solid nanoparticles (e.g., gold and silica nanoparticles) is well established, and a number of DNA-modified solid nanoparticle systems have been applied to thermal denaturation analysis of oligonucleotides. We report herein the noncovalent immobilization of oligonucleotides on the surface of soft nanoparticles (i.e., liposomes) and the subsequent controlled assembly by DNA triple helix formation. The noncovalent approach avoids tedious surface chemistry and necessary purification procedures and can simplify and extend the available methodology for the otherwise difficult thermal denaturation analysis of complex triple helical DNA assemblies. The approach is based on lipid modified triplex forming oligonucleotides (TFOs) which control the assembly of liposomes in solution in the presence of single- or double-stranded DNA targets. The thermal denaturation analysis is monitored by ultraviolet spectroscopy at submicromolar concentrations and compared to regular thermal denaturation assays in the absence of liposomes. We report on triplex forming oligonucleotides (TFOs) based on DNA and locked nucleic acid (LNA)/DNA hybrid building blocks and different target sequences (G or C-rich) to explore the applicability of the method for different triple helical assembly modes. We demonstrate advantages and limitations of the approach and show the reversible and reproducible formation of liposome aggregates during thermal denaturation cycles. Nanoparticle tracking analysis (NTA) and dynamic light scattering (DLS) show independently from ultraviolet spectroscopy experiments the formation of liposome aggregates.
Immunotherapy for cancer: synthetic carbohydrate-based vaccines (2009)

Aberrant glycosylation of glycoproteins and glycolipids of cancer cells, which correlates with poor survival rates, is being exploited for the development of immunotherapies for cancer. In particular, advances in the knowledge of cooperation between the innate and adaptive system combined with the implementation of efficient synthetic methods for assembly of oligosaccharides and glycopeptides is providing avenues for the rationale design of vaccine candidates. In this respect, fully synthetic vaccine candidates show great promise because they incorporate only those elements requires for relevant immune responses, and hence do not suffer from immune suppression observed with classical carbohydrate-protein conjugate vaccines. Such vaccines are chemically well-defined and it is to be expected that they can be produced in a reproducible fashion. In this feature article, recent advances in the development of fully synthetic sub-unit carbohydrate-based cancer vaccines will be discussed.
Linking visual and textual data on video (2003)

The Informedia Digital Video Library Project at Carnegie Mellon University [1] combines speech, image and natural language understanding to automatically transcribe, segment and index video for intelligent search and image retrieval. Since 1995, thousands hours of video (over two terabytes of data) have been collected, with automatically generated metadata and indices for retrieving videos from the library. The distinguishing feature of the project is the integration of speech, language and image understanding technologies for efficient creation and exploration of the library.
Potentiation of a p53‐SLP vaccine by cyclophosphamide in ovarian cancer: A single‐arm phase II study (2011)

The purpose of the current phase II single-arm clinical trial was to evaluate whether pretreatment with low-dose cyclophosphamide improves immunogenicity of a p53-synthetic long peptide (SLP) vaccine in patients with recurrent ovarian cancer. Patients with ovarian cancer with elevated serum levels of CA-125 after primary treatment were immunized four times with the p53-SLP vaccine. Each immunization was preceded by administration of 300 mg/m2 intravenous cyclophosphamide as a means to affect regulatory T cells (Tregs). Vaccine-induced p53-specific interferon-gamma (IFN-γ)-producing T cells evaluated by IFN-γ ELISPOT were observed in 90% (9/10) and 87.5% (7/8) of evaluable patients after two and four immunizations, respectively. Proliferative p53-specific T cells, observed in 80.0% (8/10) and 62.5% (5/8) of patients, produced both T-helper 1 and T-helper-2 cytokines. Cyclophosphamide induced neither a quantitative reduction of Tregs determined by CD4+ FoxP3+ T cell levels nor a demonstrable qualitative difference in Treg function tested in vitro. Nonetheless, the number of vaccine-induced p53-specific IFN-γ-producing T cells was higher in our study compared to a study in which a similar patient group was treated with p53-SLP monotherapy (p≤0.012). Furthermore, the strong reduction in the number of circulating p53-specific T cells observed previously after four immunizations was currently absent. Stable disease was observed in 20.0% (2/10) of patients, and the remainder of patients (80.0%) showed clinical, biochemical and/or radiographic evidence of progressive disease. The outcome of this phase II trial warrants new studies on the use of low-dose cyclophosphamide to potentiate the immunogenicity of the p53-SLP vaccine or other antitumor vaccines.
Erythropoietin Regulates theIn VitroandIn VivoProduction of Neuronal Progenitors by Mammalian Forebrain Neural Stem Cells (2001)

Recent studies have shown that neurogenesis is enhanced after hypoxia and that erythropoietin (EPO), an inducible cytokine, is produced in the brain as part of the intrinsic hypoxia response. Thus, we asked whether EPO might regulate neurogenesis by forebrain neural stem cells (NSCs). We found that EPO receptors are expressed in the embryonic germinal zone during neurogenesis as well as in the adult subventricular zone, which continues to generate neurons throughout adulthood. Cultured NSCs exposed to a modest hypoxia produced two- to threefold more neurons, which was associated with an elevation in EPO gene expression. The enhanced neuron production attributable to hypoxia was mimicked by EPO and blocked by coadministration of an EPO neutralizing antibody. EPO appears to act directly on NSCs, promoting the production of neuronal progenitors at the expense of multipotent progenitors. EPO infusion into the adult lateral ventricles resulted in a decrease in the numbers of NSCs in the subventricular zone, an increase in newly generated cells migrating to the olfactory bulb, and an increase in new olfactory bulb interneurons. Infusion of anti-EPO antibodies had the opposite effect: an increase in the number of NSCs in the subventricular zone and a decrease in the number of newly generated cells migrating to the bulb. These findings suggest that EPO is an autocrine-paracrine factor, capable of regulating the production of neuronal progenitor cells by forebrain NSCs.
The in vitro insertion of monoamine oxidase B into mitochondrial outer membranes (1988)

Bovine monoamine oxidase (MAO) B has been synthesized in vitro using a reticulocyte lysate translation system directed by bovine liver poly(A) + RNA. The newly synthesized enzyme apparently lacks a cleavable N‐terminal extension, but MAO B is readily incorporated into mitochondria or isolated mitochondrial outer membranes prepared from rat liver. ATP is not required for the binding of the newly synthesized enzyme to the outer membranes, but is necessary for the insertion of MAO B into these membrane vesicles. The ATP is not required to generate a mitochondrial membrane potential as assembly occurs under conditions that preclude either the formation or the maintenance of the potential. MAO B will bind to but not become incorporated into outer membrane vesicles which have been treated with trypsin, suggesting that the insertion of MAO B also depends on protein factors present on the outer membranes.
SmartView: Enhanced Document Viewer for Mobile Devices (2002)

Web pages with complex layout do not display well on small screens. They are difficult to read on mobile devices such as PDAs or Web enabled phones because they require extensive horizontal scrolling. SmartView is a browser feature that performs partitioning of an HTML document content into logical sections. Individual sections can be selected by the user for viewing independently from the rest of the document. The selected portion of the document is presented in a detailed view with modified layout for optimal reading or meeting other user’s or device requirements. The SmartView interface enforces the concept of a document by allowing the user to view both the document overview (e.g., a zoomed-out version of the document, a document thumbnail, etc.), indicating the logical decomposition of the document, and a detailed view of the selected section of the document. SmartView further enhances the user’s browsing experience by providing additional information on the document content. This information annotates logical sections and is derived from the document itself or supplied by external services. For example, SmartView assists the user in searching and browsing by providing feedback on the relevance of the page and its constituent parts with respect to a previously issued query to a search engine. The feedback is provided in two forms: as indicators of the number of hits on the overview presentation of the page and as term highlights within detailed view of a selected portion of the page. SmartView can be implemented on the device as an integral feature of the browser or as a (local or remote) service that provides the decomposition of a page and query processing on the client’s behalf.
Analogues of the frog skin peptide alyteserin‐2a with enhanced antimicrobial activities against Gram‐negative bacteria (2012)

The emergence of strains of multidrug-resistant Gram-negative bacteria mandates a search for new types of antimicrobial agents. Alyteserin-2a (ILGKLLSTAAGLLSNL.NH₂) is a cationic, α-helical peptide, first isolated from skin secretions of the midwife toad, Alytes obstetricans, which displays relatively weak antimicrobial and haemolytic activities. Increasing the cationicity of alyteserin-2a while maintaining amphipathicity by the substitution Gly¹¹ → Lys enhanced the potency against both Gram-negative and Gram-positive bacteria by between fourfold and 16-fold but concomitantly increased cytotoxic activity against human erythrocytes by sixfold (mean concentration of peptide producing 50% cell death; LC₅₀=24 µM). Antimicrobial potency was increased further by the additional substitution Ser⁷ →Lys, but the resulting analogue remained cytotoxic to erythrocytes (LC₅₀=38 µM). However, the peptide containing D-lysine at positions 7 and 11 showed high potency against a range of Gram-negative bacteria, including multidrug-resistant strains of Acinetobacter baumannii and Stenotrophomonas maltophilia (minimum inhibitory concentration = 8 µM) but appreciably lower haemolytic activity (LC₅₀=185 µM) and cytotoxicity against A549 human alveolar basal epithelial cells (LC₅₀=65 µM). The analogue shows potential for treatment of nosocomial pulmonary infections caused by bacteria that have developed resistance to commonly used antibiotics.
High power X-band (8.4 GHz) SiGe/Si heterojunctionbipolar transistor (2001)

A high-performance double-mesa type Si/SiGe/Si power HBT at X-band (8.4 GHz) frequency is demonstrated. Under continuous wave operation, a single 20-finger common-base Si/Si0.75Ge0.25/Si (2 × 10 µm2 of each emitter finger) HBT has an output power of 27.4 dBm and an associated power gain of 7 dB at peak PAE of 32.3%. These parametric values represent the state-of-the-art power performance of SiGe-based HBTs.
A comprehensive two-hybrid analysis to explore the yeast protein interactome (2001)

Protein-protein interactions play crucial roles in the execution of various biological functions. Accordingly, their comprehensive description would contribute considerably to the functional interpretation of fully sequenced genomes, which are flooded with novel genes of unpredictable functions. We previously developed a system to examine two-hybrid interactions in all possible combinations between the approximately 6,000 proteins of the budding yeast Saccharomyces cerevisiae. Here we have completed the comprehensive analysis using this system to identify 4,549 two-hybrid interactions among 3,278 proteins. Unexpectedly, these data do not largely overlap with those obtained by the other project [Uetz, P., et al. (2000) Nature (London) 403, 623-627] and hence have substantially expanded our knowledge on the protein interaction space or interactome of the yeast. Cumulative connection of these binary interactions generates a single huge network linking the vast majority of the proteins. Bioinformatics-aided selection of biologically relevant interactions highlights various intriguing subnetworks. They include, for instance, the one that had successfully foreseen the involvement of a novel protein in spindle pole body function as well as the one that may uncover a hitherto unidentified multiprotein complex potentially participating in the process of vesicular transport. Our data would thus significantly expand and improve the protein interaction map for the exploration of genome functions that eventually leads to thorough understanding of the cell as a molecular system.
Should imporvement in rheumatoid arthritis clinical trials be defined as fifty percent or seventy percent improvement in core set measures, rather than twenty percent? (1998)

Adopting a definition of efficacy in RA trials that requires 50% or 70% improvement in core set parameters would likely compromise statistical power and make it more difficult to distinguish between 2 treatments with different efficacy. ACR 20 should continue to be the primary measure of efficacy in RA trials, with higher thresholds for improvement being determined and reported as secondary efficacy measures.
Carbonylative Sonogashira coupling of terminal alkynes with aryl iodides under atmospheric pressure of CO using Pd(ii)@MOF as the catalyst (2014)

A novel, highly efficient, and phosphine-free heterogeneous palladium-MOF catalytic system for the carbonylative Sonogashira coupling of terminal alkynes with aryl iodides was developed. The catalyst could efficiently promote the carbonylative coupling reaction under atmospheric pressure of CO, affording the corresponding aryl α,β-alkynyl ketones in good to excellent yields. Besides high activity and selectivity, the proposed catalytic system features a broad substrate scope for both alkynes and aryl iodides. Moreover, the heterogeneous catalyst was recyclable, showed negligible metal leaching, and could be reused at least five times without significant loss in catalytic efficiency under the investigated conditions.
Migration and division of progenitor cell populations in periodontal ligament after wounding (1980)

Connective tissue cells responding to wounding of the periodontal ligament of the lower first molar in mice were studied using the techniques of radioautography and grain counting. Animals were given an intraperitoneal injection of 2 uCi 1g 3 H‐Tdr 1 hr before being killed at either 30, 72 or 120 hr after wounding. The ligament in 1 um plastic sections was divided into compartments on the basis of distance from the wound, and the relative number of labelled cells in each compartment was assessed at 30, 72 and 120 hours after wounding. The distance of each labelled cell from the closest blood vessel was also measured at each time to detect relative movement of labelled cells away from blood vessels. In a Parallel experiment, haematogenous progenitors of macrophages were depleted by irradiating the animals with 800rads prior to woundilng to determine if mistakes in identification between fibroblasts and marophages could significantly affect the results. The ultrastructural characteristics of 150 of the 3 H‐Tdr labelled cells was examined in thin sections of wounded periodontal ligament prepared for elctron microcope radioautography, The majority of cells lebelled 30 hours after wounding were confirmed to be paravascular, and most of them were found to be located within 200 μ of the wound margin. Some of these cells appreared to have divided a number of times between 30 and 72 hours after wounding, and to have migrated into the wound between 70 and 120 hours after wounding. Examination of the irradiated material and the electron microscope radio‐autographs suggested that significant numbers of macrophages had not been included in the counts of labelled cells. The elctron microscope radioautographs also suggested that cells which exhibited different degrees of cytodifferentiation had incorporated 3 H‐Tdr.
Protein Design is NP-hard (2002)

Biologists working in the area of computational protein design have never doubted the seriousness of the algorithmic challenges that face them in attempting in silico sequence selection. It turns out that in the language of the computer science community, this discrete optimization problem is NP-hard. The purpose of this paper is to explain the context of this observation, to provide a simple illustrative proof and to discuss the implications for future progress on algorithms for computational protein design.