gebhart/patrepeval huggingface dataset:
Epidermal growth factor receptor as a target in cancer therapy. (2003)

Epithelial cancers have been found to overexpress the receptor to epidermal growth factor (EGFR). These include head and neck, breast, colon, lung, prostate, kidney, ovary, brain, pancreas, and bladder. A number of strategies to block EGFR have been developed to inhibit tumor proliferation and to improve overall clinical outcome because overexpression of the receptor has been associated with a poorer prognosis in cancer patients. Strategies include using monoclonal antibodies to EGFR, tyrosine kinase inhibitors, ligand-linked toxins, and antisense approaches. Antibodies such as IMC-C225 specifically target EGFRs, whereas tyrosine kinase inhibition by many small molecules is less specific but is also effective. This report focuses on EGFR and novel compounds that target it.
Signatures of cardioembolic and large‐vessel ischemic stroke (2010)

Gene expression signatures distinguish cardioembolic from large-vessel causes of ischemic stroke. These gene profiles may add valuable diagnostic information in the management of patients with stroke of unknown etiology though they need to be validated in future independent, large studies.
Molecular characterization of the pathogen-specific, 34-kilodalton membrane immunogen of Treponema pallidum (1989)

The 34-kilodalton (kDa) antigen of Treponema pallidum subsp. pallidum (T. pallidum) is a pathogen-specific integral membrane protein. DNA sequence analysis of the cloned gene revealed an open reading frame encoding a primary product of 204 residues with a molecular mass of 22,087 daltons. Sequences that correspond to a consensus Escherichia coli promoter and a ribosome-binding site were found upstream from the AUG start codon that begins the open reading frame, suggesting that the cloned gene can use its own regulatory sequences for expression. Examination of the deduced amino acid sequence revealed the presence of a typical procaryotic leader peptide 19 amino acids long; processing results in a mature molecule with a molecular mass of 20,123 daltons. Pulse-chase experiments with E. coli minicells confirmed that the 34-kDa antigen is synthesized as a higher-molecular-weight precursor that is processed to a mature form with the electrophoretic mobility that is characteristic for this protein. The presence in the leader peptide of the sequence Phe-Ser-Ala-Cys suggested that the 34-kDa antigen is a proteolipid. Although hydropathy analysis of the deduced amino acid sequence of the mature 34-kDa antigen predicted that the molecule was primarily hydrophilic, both the native and recombinant 34-kDa molecules displayed hydrophobic biochemical behavior by fractionating into the detergent phase after extraction of intact organisms with Triton X-114. Cell fractionation experiments with E. coli showed that the 34-kDa molecule was localized in both the inner and outer membranes of the recombinant host. The combined data demonstrate that the 34-kDa antigen is an integral membrane protein that behaves in a biochemically consistent manner in both T. pallidum and E. coli.
Current value of intraoperative sonography during surgery for hepatic neoplasms (2002)

Noninvasive liver imaging has developed rapidly resulting in increased accuracy for detecting primary and secondary hepatic tumors. Intraoperative ultrasonography (IOUS) was commonly considered to be the gold standard for liver staging, but the current value of IOUS is unknown in view of more sophisticated radiologic tools. The purpose of this prospective study was to evaluate the impact of IOUS on the treatment of 149 patients undergoing liver surgery for malignant disease (colorectal metastasis, 61 patients; hepatoma, 52 patients; other hepatic malignant tumors, 36 patients). The sensitivities of computed tomography (CT), helical CT, magnetic resonance imaging, and IOUS in patients with colorectal metastases were 69.2%, 82.5%, 84.9%, and 95.2% in a segment-by-segment analysis; in patients with hepatoma their sensitivities were 76.9%, 90.9%, 93.0%, and 99.3%; and in patients with other hepatic malignancies they were 66.7%, 89.6%, 93.3%, and 98.9%, respectively. Additional malignant lesions (AMLs) were first detected by inspection and palpation in 20 patients (13.4%). In another 18 patients (12.1%) IOUS revealed at least one AML. Overall, the findings obtained only by IOUS changed the surgical strategy in 34 cases (22.8%). It was concluded that IOUS, having undergone some refinement as well, still has immense diagnostic value in hepatectomy candidates. Frequently avoiding palliative liver resection and occasionally disproving unresectability as assessed by preoperative imaging, IOUS still has a significant impact on surgical decision making and should still be considered the gold standard.
Automatic Building Detection Using the Dempster-Shafer Algorithm (2006)

An approach and strategy for automatic detection of buildings from aerial images using combined image analysis and interpretation techniques is described in this paper. It is undertaken in several steps. A dense DSM is obtained by stereo image matching and then the results of multi-band classification, the DSM, and Normalized Difference Vegetation Index (NDVI) are used to reveal preliminary building interest areas. From these areas, a shape modeling algorithm has been used to precisely delineate their boundaries. The Dempster-Shafer data fusion technique is then applied to detect buildings from the combination of three data sources by a statistically-based classification. A number of test areas, which include buildings of different sizes, shape, and roof color have been investigated. The tests are encouraging and demonstrate that all processes in this system are important for effective building detection.
Supercontinuum generation in a photonic crystal fiber with two zero dispersion wavelengths (2004)

We demonstrate supercontinuum generation in a highly nonlinear photonic crystal fiber with two closely lying zero dispersion wavelengths. The special dispersion of the fiber has a profound influence on the supercontinuum which is generated through self-phase modulation and phasematched four-wave mixing and not soliton fission as in the initial photonic crystal fibers. The supercontinuum has high spectral density and is extremely independent of the input pulse over a wide range of input pulse parameters. Simulations show that the supercontinuum can be compressed to ultrashort pulses.
Differences in Pharmacological Activities of the Antioxidant Flavonoid MonoHER in Humans and Mice Are Caused by Variations in Its Metabolic Profile (2011)

Despite its well-known cardiotoxicity, the anthracycline doxorubicin continues to be a widely used chemotherapeutic agent. The flavonoid 7-mono-O-(β-hydroxyethyl)-rutoside (monoHER) has shown protection against doxorubicin-induced cardiotoxicity in mice. However, this protection has not been observed in humans. This prompted us to investigate monoHER metabolism in humans and compare it with that in mice. Five healthy volunteers received monoHER by intravenous infusion. After infusion, bile fluid was collected, and the monoHER metabolites were identified by liquid chromatography-diode-array detection (LC-DAD), time-of-flight mass spectrometry (TOF-MS), and (1)H-nuclear magnetic resonance (NMR). Thirteen different metabolites were identified. MonoHER was predominantly converted into inactive glucuronidated metabolites. In mice, the major metabolic route is methylation, which forms bioactive metabolites that are implicated in the cardioprotective effect of monoHER. This indicates that the different pharmacological effects of monoHER in mice and humans might be explained by a difference in monoHER metabolism. This study adds to the growing appreciation of flavonoid metabolites as bioactive compounds.
Theoretical Studies of Electronic State Localization and Wormholes in Silicon Quantum Dot Arrays (2000)

We present calculations for quantum dot (QD) arrays that are more realistic than most. They describe the arrays in atomic detail, using pseudopotentials fit to ab initio results to describe the electronic structure. Our results show that simple models, which regard QDs as (artificial) atoms, are a reasonable approximation to employ for some features of QD array electronic localization characteristics. But we also demonstrate important limitations. The need for realistic theoretical descriptions of QD arrays is highlighted.
Butyrophilin, a Milk Protein, Modulates the Encephalitogenic T Cell Response to Myelin Oligodendrocyte Glycoprotein in Experimental Autoimmune Encephalomyelitis (2000)

Experimental autoimmune encephalomyelitis (EAE) induced by sensitization with myelin oligodendrocyte glycoprotein (MOG) is a T cell-dependent autoimmune disease that reproduces the inflammatory demyelinating pathology of multiple sclerosis. We report that an encephalitogenic T cell response to MOG can be either induced or alternatively suppressed as a consequence of immunological cross-reactivity, or "molecular mimicry" with the extracellular IgV-like domain of the milk protein butyrophilin (BTN). In the Dark Agouti rat, active immunization with native BTN triggers an inflammatory response in the CNS characterized by the formation of scattered meningeal and perivascular infiltrates of T cells and macrophages. We demonstrate that this pathology is mediated by a MHC class II-restricted T cell response that cross-reacts with the MOG peptide sequence 76-87, I GEG KVA LRIQ N (identities underlined). Conversely, molecular mimicry with BTN can be exploited to suppress disease activity in MOG-induced EAE. We demonstrate that not only is EAE mediated by the adoptive transfer of MOG74-90 T cell lines markedly ameliorated by i.v. treatment with the homologous BTN peptide, BTN74-90, but that this protective effect is also seen in actively induced disease following transmucosal (intranasal) administration of the peptide. These results identify a mechanism by which the consumption of milk products may modulate the pathogenic autoimmune response to MOG.
Coaxial flow mixer for real‐time monitoring of cellular responses in flow cytometry (1996)

Improved time resolution of kinetic cellular events in flow cytometry is demonstrated by using a coaxial flow-mixing device integrated within a flow-injection (FI) system. The instrument is used in combination with a Becton Dickinson FACS Analyzer for on-line reagent addition, rapid sample mixing, and temperature control of cell suspensions. The coaxial flow device can instantaneously (<60 ms) mix reagent and sample streams, allowing cytometric analysis of subsecond events to be performed. Kinetic measurements can be performed on the FACS analyzer in a variable time range of from 100 ms to 3 min. The system also allows the collection of unlimited cellular events at a specific incubation time point. Because the system operates continuously and no boost in core flow is required, disturbances of flow conditions are avoided. The capabilities of the flow injection cytometer have been demonstrated by the determination of internal [Ca2+]i mobilization in Jurkat T lymphocytes per fused internally with INDO-1 and stimulated by ionomycin. © 1996 Wiley-Liss, Inc.
The purification and properties of a penicillinase whose synthesis is mediated by an R-factor in Escherichia coli (1966)

1. The penicillinase (beta-lactamase) from Escherichia coli strain TEM has been purified and its activity against a range of penicillin and cephalosporin derivatives measured. 2. The enzyme shows little resemblance to penicillinases from Bacillus cereus, Bacillus licheniformis and Staphylococcus aureus. 3. The molecular weight of the enzyme is 16700+/-5%, which is about half the value obtained for other penicillinases. 4. The enzyme is most similar in properties to a crude preparation of a penicillinase from Klebsiella (Aerobacter) aerogenes, but clearly different from crude enzyme preparations from other strains of E. coli. 5. Since penicillinase synthesis in E. coli strain TEM is mediated by an R-factor known to infect many other species of Enterobacteriaceae, the appearance of similar enzymes in other Gramnegative species is not surprising.
Adoptive transfer of pp65-specific T cells for the treatment of chemorefractory cytomegalovirus disease or reactivation after haploidentical and matched unrelated stem cell transplantation (2010)

Cytomegalovirus (CMV) disease and infection refractory to antiviral treatment after allogeneic stem cell transplantation (allo-SCT) is associated with a high mortality. Adoptive transfer of CMV-specific T cells could reconstitute viral immunity after SCT and could protect from CMV-related complications. However, logistics of producing virus-specific T-cell grafts limited the clinical application. We treated 18 patients after allo-SCT from human leukocyte antigen-mismatched/haploidentical or human leukocyte antigen-matched unrelated donors with polyclonal CMV-specific T cells generated by ex vivo stimulation with pp65, followed by isolation of interferon-γ-producing cells. Patients with CMV disease or viremia refractory to antiviral chemotherapy or both were eligible for adoptive T-cell transfer and received a mean of 21 × 10³/kg pp65-specific T cells. In 83% of cases CMV infection was cleared or viral burden was significantly reduced, even in cases of CMV encephalitis (n = 2). Viral control was associated with in vivo expansion of CMV-specific T lymphocytes in 12 of 16 evaluable cases, resulting in reconstitution of antiviral T-cell responses, without graft-versus-host disease induction or acute side effects. Our findings indicate that the infusion of low numbers of CMV-specific T cells is safe, feasible, and effective as a treatment on demand for refractory CMV infection and CMV disease after allo-SCT.
Optimization of photopolymerized bioerodible hydrogel properties for adhesion prevention (1994)

The aim of this study was to optimize the properties of a lubricious bioerodible hydrogel barrier for the prevention of postoperative adhesions. Water-soluble macromers based on block copolymers of poly(ethylene glycol) (PEG) and poly(lactic acid) or poly(glycolic acid) with terminal acrylate groups were used, and these macromers were gelled in vivo by exposure to long wavelength ultraviolet light. The precursor was photopolymerized from buffered saline solution while in contact with the tissues. This resulted in the conformal coating of the tissue with an adherent hydrogel film, while forming a nonadhesive barrier at the free surface, on the treated wound site. The hydrogels were evaluated in two animal models of postsurgical adhesions, first in a rat cecum abrasion model and then in a rabbit uterine horn ischemia model. In the rat cecum model, six of seven animals treated with a hydrogel, with glycolide in the precursor as the comonomer, showed no adhesions; untreated animals and animals treated with precursor, but not gelled with light, showed consistent dense adhesions. In the rabbit uterine horn ischemia model, using hydrogels with lactide in the precursor as the comonomer, and PEG of molecular weight from 6,000 to 18,500 Da, adhesions were dramatically reduced, with occurrence in none of seven animals treated with a gel containing PEG 10,000. By contrast, the seven animals in the control group demonstrated a mean of 35% involvement of the horn length in dense, fibrous adhesions. These materials, photopolymerized in vivo in direct contact with the tissues, appear to form an adherent hydrogel barrier that is highly effective in reducing postoperative adhesions in the models used.(ABSTRACT TRUNCATED AT 250 WORDS)
The use of fuzzy relational thesauri for classificatory problem solving in information retrieval and expert systems (1993)

The problem-solving strategy applied in knowledge-based systems may often be characterized as classification. Central to classification is computation of the degree to which an object is an instance of a given class (concept, category). Two kinds of problems, namely object-querying and class-querying, as exemplified by, respectively, information retrieval systems and expert systems, are distinguished. In the first kind, the problem is to identify the objects (e.g. documents) to which a given concept (the query) applies. In the second kind, the problem is to identify the concepts (categories) that apply to a given object (the observation). A fuzzy-set-based scheme for construction of efficient problem solving systems of the two kinds is developed. The problem of vocabulary mismatch in information retrieval is considered, and the scheme is proposed as a solution to this problem. The knowledge base applies a term-centered representation form called a fuzzy relational thesaurus. To avoid recomputation of deductive information in problem-solving tasks, the deductive closure of the knowledge base is derived at the outset. This closure is computed in O(n/sup 3/) time.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Temporal Stability of Serum Concentrations of Cytokines and Soluble Receptors Measured Across Two Years in Low-Risk HIV-Seronegative Men (2013)

These findings lend support to using these serologic immune biomarkers in prospective studies investigating associations with chronic diseases.
Silicon nanomembranes for fingertip electronics (2012)

We describe the use of semiconductor nanomaterials, advanced fabrication methods and unusual device designs for a class of electronics capable of integration onto the inner and outer surfaces of thin, elastomeric sheets in closed-tube geometries, specially formed for mounting on the fingertips. Multifunctional systems of this type allow electrotactile stimulation with electrode arrays multiplexed using silicon nanomembrane (Si NM) diodes, high-sensitivity strain monitoring with Si NM gauges, and tactile sensing with elastomeric capacitors. Analytical calculations and finite element modeling of the mechanics quantitatively capture the key behaviors during fabrication/assembly, mounting and use. The results provide design guidelines that highlight the importance of the NM geometry in achieving the required mechanical properties. This type of technology could be used in applications ranging from human-machine interfaces to 'instrumented' surgical gloves and many others.
Randomized clinical studies of anti-tumor vaccination: state of the art in 2008 (2008)

This review elucidates state-of-the-art clinical studies on active specific immunotherapy with tumor vaccines. It refers solely to randomized studies and has a special focus on patient's survival, the most important parameter for any therapy. Of special interest, from a tumor immunological point of view, is a comparison between the results obtained with allogeneic tumor cell-derived vaccines and those obtained with autologous tumor cell-derived vaccines. Overall, autologous vaccines have given better results than allogeneic vaccines. Random mutations in cancer generate unique antigens in each individual case. The superiority of autologous vaccines suggests that unique tumor-associated antigens are particularly important in generating responsive T cells for a therapeutic effect.
Regioselective Cyclizations of Delocalized 1,3‐Amide Dianions with Oxalic Acid Dielectrophiles (1997)

Abstract A novel strategy for the synthesis of nitrogen‐rich heterocycles by regioselective C,N‐cyclization of ambident dianions with oxalimidoyl dichlorides is reported. One ‐ pot reactions provide γ‐iminotetramic acid amides 1 , radialenes 2 and tetraimino‐diazaspiro[4.4]nonenones 3 . Chemical properties and structural features of the new heterocyclic systems, including the tautomerism of 2 , were investigated.
Prophylactic and Therapeutic Effects of Small Interfering Rna Targeting Sars-Coronavirus (2004)

Chemically synthesized siRNA duplexes targeting SARS-CoV genomic RNA are potent agents for inhibition of the viral infection and replication. The location effects of siRNAs were revealed at both genome sequence and open-reading frame levels. The rapid development of siRNA-based SARS-CoV inhibitors marked a novel approach for combating newly emergent infectious diseases.
Hierarchy concepts: classification and preparation strategies for zeolite containing materials with hierarchical porosity (2015)

'Hierarchy' is a property which can be attributed to a manifold of different immaterial systems, such as ideas, items and organisations or material ones like biological systems within living organisms or artificial, man-made constructions. The property 'hierarchy' is mainly characterised by a certain ordering of individual elements relative to each other, often in combination with a certain degree of branching. Especially mass-flow related systems in the natural environment feature special hierarchically branched patterns. This review is a survey into the world of hierarchical systems with special focus on hierarchically porous zeolite materials. A classification of hierarchical porosity is proposed based on the flow distribution pattern within the respective pore systems. In addition, this review might serve as a toolbox providing several synthetic and post-synthetic strategies to prepare zeolitic or zeolite containing material with tailored hierarchical porosity. Very often, such strategies with their underlying principles were developed for improving the performance of the final materials in different technical applications like adsorptive or catalytic processes. In the present review, besides on the hierarchically porous all-zeolite material, special focus is laid on the preparation of zeolitic composite materials with hierarchical porosity capable to face the demands of industrial application.
Robust principal component analysis? (2011)

This article is about a curious phenomenon. Suppose we have a data matrix, which is the superposition of a low-rank component and a sparse component. Can we recover each component individually? We prove that under some suitable assumptions, it is possible to recover both the low-rank and the sparse components exactly by solving a very convenient convex program called Principal Component Pursuit ; among all feasible decompositions, simply minimize a weighted combination of the nuclear norm and of the ℓ 1 norm. This suggests the possibility of a principled approach to robust principal component analysis since our methodology and results assert that one can recover the principal components of a data matrix even though a positive fraction of its entries are arbitrarily corrupted. This extends to the situation where a fraction of the entries are missing as well. We discuss an algorithm for solving this optimization problem, and present applications in the area of video surveillance, where our methodology allows for the detection of objects in a cluttered background, and in the area of face recognition, where it offers a principled way of removing shadows and specularities in images of faces.
Entanglement of Formation of an Arbitrary State of Two Qubits (1998)

The entanglement of a pure state of a pair of quantum systems is defined as the entropy of either member of the pair. The entanglement of formation of a mixed state $\ensuremath{\rho}$ is the minimum average entanglement of an ensemble of pure states that represents \ensuremath{\rho}. An earlier paper conjectured an explicit formula for the entanglement of formation of a pair of binary quantum objects (qubits) as a function of their density matrix, and proved the formula for special states. The present paper extends the proof to arbitrary states of this system and shows how to construct entanglement-minimizing decompositions.