gebhart/patrepeval huggingface dataset:
Waveguide grating coupler with subwavelength microstructures (2009)

We propose a silicon waveguide-fiber grating coupler that uses a subwavelength microstructure to achieve a continuously variable grating strength yet can be fabricated using only a single etch step. By adjusting the subwavelength microstructure at every point along the grating, the grating coupler can be optimized to give high field overlap with the optical fiber mode and also minimize backreflections along the incident waveguide path. Our design example is optimized for quasi-TM mode in a silicon photonic-wire waveguide, as required for waveguide evanescent-field-sensing applications. A field overlap of up to 94% with a standard single-mode optical fiber (SMF-28) is achieved by coupler apodization. Backreflection from the grating is reduced to ~0.1%, and the total predicted photonic wire to fiber coupling efficiency is 50%.
What Planner for Ambient Intelligence Applications? (2004)

The development of ambient intelligence (AmI) applications that effectively adapt to the needs of the users and environments requires, among other things, the presence of planning mechanisms for goal-oriented behavior. Planning is intended as the ability of an AmI system to build a course of actions that, when carried out by the devices in the environment, achieve a given goal. The problem of planning in AmI has not yet been adequately explored in literature. We propose a planning system for AmI applications, based on the hierarchical task network (HTN) approach and called distributed hierarchical task network (D- HTN), able to find courses of actions to address given goals. The plans produced by D-HTN are flexibly tailored to exploit the capabilities of the devices currently available in the environment in the best way. We discuss both the architecture and the implementation of D-HTN. Moreover, we present some of the experimental results that validated the proposed planner in a realistic application scenario in which an AmI system monitors and answers the needs of a diabetic patient.
Associations between joint space narrowing and molecular markers of collagen and proteoglycan turnover in patients with knee osteoarthritis. (2006)

Markers of type II collagen synthesis/degradation and of proteoglycan aggrecan turnover were not predictive of JSN in knee OA in this pilot study. However, serial concentrations of proteoglycan aggrecan epitope CS846 were associated with JSN during both the intervals studied.
Cetuximab in the treatment of patients with colorectal cancer (2011)

Cetuximab has modest single-agent efficacy in the treatment of patients with metastatic CRC whose tumors do not harbor a KRAS mutation. In combination with irinotecan, it is associated with an overall survival (OS) and progression-free survival (PFS) advantage in first-line therapy in patients with KRAS non mutant metastatic CRC; it can be combined with irinotecan to overcome resistance in patients with KRAS non mutant CRC who have previously progressed on prior irinotecan chemotherapy. Future studies of putative biomarkers are likely to give additional information to clearly define which patients with metastatic CRC receive therapeutic benefit from cetuximab and other monoclonal anti-EGFR therapies.
The Tat Protein of Human Immunodeficiency Virus Type 1 Is a Substrate and Inhibitor of the Interferon-induced, Virally Activated Protein Kinase, PKR (1997)

We demonstrate that the interferon-induced, double-stranded (ds) RNA-activated kinase, PKR, is able to bind to and phosphorylate the human immunodeficiency virus type 1 (HIV-1) trans-activating protein, Tat. Furthermore, Tat can inhibit the activation and activity of the kinase. Phosphorylation of Tat by PKR is dependent on the prior activation of PKR by dsRNA and occurs on serine and threonine residues adjacent to the basic region important for TAR RNA binding and Tat function. Activated PKR efficiently phosphorylates both the two-exon form of Tat (Tat-86) and the single exon form (Tat-72). Mutagenesis indicates that the interaction between PKR and Tat requires the RNA-binding region of Tat. Tat competes with eukaryotic initiation factor 2, a well-characterized substrate of PKR, for phosphorylation by activated PKR. Tat also inhibits the autophosphorylation of PKR by dsRNA. This biochemical evidence of an intimate relationship between Tat, an important regulator of HIV transcription, and PKR, a pleiotropic cellular regulator, may provide insights into HIV-1 pathogenesis and, more generally, virus/host interactions.
Expression cloning, purification and characterization of a beta-1,4-mannanase from Aspergillus aculeatus. (1994)

A cDNA library from the filamentous fungus Aspergillus aculeatus was constructed in the yeast expression vector pYES2.0 and used to isolate 57 full length cDNA's encoding beta-1,4-mannanase by expression in S. cerevisiae. The positive clones were identified on agar plates containing 0.2% azurine dyed cross-linked mannan by the formation of blue halos around the colonies. All clones represented transcripts of the same mannanase gene (man1). The gene was sub-cloned into an Aspergillus expression vector and transformed into Aspergillus oryzae for overexpression and purification of the enzyme. The recombinant enzyme had a molecular weight of 45 kDa, an isoelectric point of pH 4.5, a pH optimum of pH 5.0 and a temperature optimum of 60-70 degrees.
Histologic Correlation of Image-Guided Core Biopsy With Excisional Biopsy of Nonpalpable Breast Lesions (1997)

Benign disease and invasive cancer of the breast can be diagnosed with a high level of confidence using image-guided LCNB. The histologic diagnosis for patients whose LCNB specimens show ADH or DCIS may change after excision.
[Changes in the peripheral blood lymphocytes after immunization and its effect on the course of experimental inflammatory process in the lungs]. (1978)

It was shown that in the immunization of rabbits with sorbed staphylococcus toxoid and human albumin, at the height of the immune response there occurred an intensification of biosynthesis and destabilization of lysosomal membranes of blood leukocytes, with a simultaneous development of microcirculation disturbances in the lungs. Development of pneumonia against the background of immunization led to a greater destabilization of the lysosomic membranes of leukocytes and to the intensification in the lungs of infiltrative and destructive processes, in comparison with the course of inflammation in the nonimmunized animals. Peculiarities of the antigens used caused some specificity in the course of pneumonia. A relationship between the changes of blood leukocytes and disturbances in the lungs in immunization is supposed.
Chemokines, Costimulatory Molecules and Fusion Proteins for the Immunotherapy of Solid Tumors (2011)

In this article, the role of chemokines and costimulatory molecules in the immunotherapy of experimental murine solid tumors and immunotherapy used in ongoing clinical trials are presented. Chemokine networks regulate physiologic cell migration that may be disrupted to inhibit antitumor immune responses or co-opted to promote tumor growth and metastasis in cancer. Recent studies highlight the potential use of chemokines in cancer immunotherapy to improve innate and adaptive cell interactions and to recruit immune effector cells into the tumor microenvironment. Another critical component of antitumor immune responses is antigen priming and activation of effector cells. Reciprocal expression and binding of costimulatory molecules and their ligands by antigen-presenting cells and naive lymphocytes ensures robust expansion, activity and survival of tumor-specific effector cells in vivo. Immunotherapy approaches using agonist antibodies or fusion proteins of immunomodulatory molecules significantly inhibit tumor growth and boost cell-mediated immunity. To localize immune stimulation to the tumor site, a series of fusion proteins consisting of a tumor-targeting monoclonal antibody directed against tumor necrosis and chemokines or costimulatory molecules were generated and tested in tumor-bearing mice. While several of these reagents were initially shown to have therapeutic value, combination therapies with methods to delete suppressor cells had the greatest effect on tumor growth. In conclusion, a key conclusion that has emerged from these studies is that successful immunotherapy will require both advanced methods of immunostimulation and the removal of immunosuppression in the host.
Coordination of Three Signaling Enzymes by AKAP79, a Mammalian Scaffold Protein (1996)

Multivalent binding proteins, such as the yeast scaffold protein Sterile-5, coordinate the location of kinases by serving as platforms for the assembly of signaling units. Similarly, in mammalian cells the cyclic adenosine 3',5'-monophosphate-dependent protein kinase (PKA) and phosphatase 2B [calcineurin (CaN)] are complexed by an A kinase anchoring protein, AKAP79. Deletion analysis and binding studies demonstrate that a third enzyme, protein kinase C (PKC), binds AKAP79 at a site distinct from those bound by PKA or CaN. The subcellular distributions of PKC and AKAP79 were similar in neurons. Thus, AKAP79 appears to function as a scaffold protein for three multifunctional enzymes.
Sensitive chemiluminescent detection of digoxigenin-labeled nucleic acids: a fast and simple protocol and its applications. (1992)

A fast and simple protocol for the chemiluminescent detection of digoxigenin-labeled nucleic acids with anti-digoxigenin antibody Fab fragments coupled to alkaline phosphatase and 3-(4-methoxyspiro[1,2-dioxetane-3,2'-tricyclo-[3.3.1.1 (3,7)]decan]-4- yl)phenyl phosphate as substrate is described. The washing and blocking procedure was optimized to yield low background even on positively charged nylon membranes. The sensitivity of the system is equal or better than radioactive methods. Exposure to x-ray or Polaroid film for up to 30 minutes is sufficient for the detection of 70 femtograms of homologous DNA. Human single-copy genes are detected in Southern blots of as low as 0.3 microgram total placental DNA. Blots can be reprobed multiple times very easily. The advantages of the digoxigenin system are high sensitivity, absence of background and ease of reprobing and are illustrated by applications for single-copy gene detection in genomic blots of human DNA, Northern hybridizations to rare mRNA, detection of E. coli genes on blots of genomic digests after pulse field gel electrophoresis, as well as for nonradioactive DNA sequencing blots with digoxigenin-labeled primers.
Immunohistochemical characterization of inflammatory cells associated with advanced atherosclerosis (1990)

During repair of 12 atherosclerotic abdominal aortic aneurysms, fresh samples of aneurysm wall were obtained. Histology confirmed the presence of advanced atherosclerosis associated with medial thinning and a variable aortic adventitial chronic inflammatory cell infiltrate. Monoclonal antibodies were used to identify the inflammatory cells throughout the aortic wall. The majority of lymphocytes in the aortic adventitia were B-cells. B-cells were not present in atheromatous plaques. T-cells, predominantly T-helper cells, were found in atheromatous plaques and in aortic adventitia. The majority of lymphocytes and macrophages in aortic adventitia and most vascular endothelial cells were HLA-DR positive. Ki-67 staining was found in B-cells and T-helper cells, indicating that these cells were proliferating. Occasional lymphocytes were BerH2 positive, indicating that some lymphocytes were activated. These findings suggest that chronic periaortitis is an active, immunologically mediated, local complication of advanced human atherosclerosis.
A new technique of optical ranging by a frequency-shifted feedback laser (1998)

We report an application of the frequency-shifted feedback (FSF) laser to optical ranging. The FSF laser output consists of periodically generated chirped frequency components whose chirp rate is faster than 100 PHz/s (P=10/sup 15/). By taking advantage of the spectral features of the FSF laser, the conventional limits on operating range and spatial resolution are removed. In the experiment, a distance of 3.7 km was measured with a resolution of 9.4 mm.
Bypass of Senescence, Immortalization, and Transformation of Human Hematopoietic Progenitor Cells (2005)

We attempted to extend the lifespan of CD34+ stem/progenitor cells in human cord blood (CB) by transduction with lentiviral vectors carrying the human telomerase catalytic subunit (hTERT) and/or the human papillomavirus type 16 (HPV16) E6 and E7 oncogenes. We found that hTERT was incapable of prolonging the replicative capacity of CB cells maintained under serum-free conditions in the presence of stem cell factor, Flt3 ligand, thrombopoietin, and interleukin-3 beyond 4 months (n=3). However, transduced CB cells cultured in the same cytokine cocktail constitutively expressing HPV16 E6/E7 alone (n=2) or in concert with hTERT (n=9) continued to proliferate, giving rise to permanent (>2 years) cell lines with a CD45+ CD34- CD133+/- CD44+ CD235a+ CD71+ CD203+ CD33+ CD13+ myeloerythroid/mast cell progenitor phenotype. Notably, CB cell cultures expressing only HPV16 E6/E7 went through a crisis period, and the resulting oligoclonal cell lines were highly aneuploid. By comparison, the CB cell lines obtained by coexpression of HPV16 E6/E7 plus hTERT exhibited near-diploid karyotypes with minimal chromosomal aberrations, concomitant with stabilization of telomere length, yet were clonally derived. The immortalized E6/E7 plus hTERT-expressing CB cells were not tumorigenic when injected intravenously or subcutaneously into sublethally irradiated immunodeficient nonobese diabetic/severe combined immunodeficient mice but could be converted to a malignant state by ectopic expression of a v-H-ras or BCR-ABL oncogene. These findings provide new insights into the mechanisms governing the senescence checkpoint of primitive human hematopoietic precursors and establish a paradigm for studies of the multistep process of human leukemogenesis.
Effects of platelet derived growth factor, epidermal growth factor and transforming growth factor‐β on the growth of human marrow fibroblasts (1988)

The effects of three growth factors contained in platelets on human bone marrow fibroblasts as well as fibroblast colony-forming cells were investigated to clarify the pathogenesis of marrow fibrosis frequently associated with myeloproliferative disorders. Two growth factors, platelet derived growth factor (PDGF) and epidermal growth factor (EGF), cooperatively stimulated the growth of passaged fibroblasts as well as fibroblast colony-forming cells. Transforming growth factor-beta augmented the growth of fibroblasts at low concentrations in the presence of EGF and/or PDGF, but inhibited that of colony-forming cells in the presence of PDGF or EGF. These results suggest that the growth of fibroblasts causing marrow fibrosis might be finely regulated, depending on the concentrations of growth factors released or leaked from platelets or megakaryocytes into marrow environment.
Expression of CEACAM1 in Adenocarcinoma of the Lung: A Factor of Independent Prognostic Significance (2002)

Expression of CEACAM1 was an independent prognostic factor in our patient population and can be used to stratify patients with adenocarcinomas of the lung into low-risk and high-risk groups. In contrast, the expression of sialyl Lewis X was of no prognostic relevance because it was expressed in 97% of all investigated tumors, and most likely has no influence on the function of CEACAM1 in this tumor entity.
Heterochronic parabiosis: historical perspective and methodological considerations for studies of aging and longevity (2013)

Pairing two animals in parabiosis to test for systemic or circulatory factors from one animal affecting the other animal has been used in scientific studies for at least 150 years. These studies have led to advances in fields as diverse as endocrinology, immunology, and oncology. A variation on the technique, heterochronic parabiosis, whereby two animals of different ages are joined to test for systemic regulators of aspects of aging or age-related diseases also has almost a century-long scientific history. In this review, we focus on the history of heterochronic parabiosis, methodological considerations and caveats, and the major advances that have emerged from those studies, including recent advances in our understanding of stem cell aging.
Diffuse reflectance spectroscopy with a self-calibrating fiber optic probe (2008)

Calibration of the diffuse reflectance spectrum for instrument response and time-dependent fluctuation as well as interdevice variations is complicated, time consuming, and potentially inaccurate. We describe a novel fiber optic probe with a real-time self-calibration capability that can be used for tissue optical spectroscopy. The probe was tested in a number of liquid phantoms over a relevant range of tissue optical properties. Absorption and scattering coefficients are extracted with an average absolute error and standard deviation of 6.9%+/-7.2% and 3.5%+/-1.5%, respectively.
Synthesis and hypoglycemic activity of 7,8-dihydro-6H-thiopyrano(3,2-d)pyrimidine derivatives and related compounds. (1986)

A series of 2-amino-7, 8-dihydro-4-piperazinyl- and 4-amino-7, 8-dihydro-2-piperazinyl-6H-thiopyrano[3, 2-d]pyrimidines and related compounds were synthesized and evaluated for hypoglycemic activity. Several compounds exhibited excellent activity, and 7, 8-dihydro-2-(4-methyl-piperazinyl)-4-(1-pyrrolidinyl)- (8c, dimaleate : MTP-1307) and 2-amino-7, 8-dihydro-4-piperazinyl-6H-thiopyrano[3, 2-d]pyrimidine (18a, dimaleate : MTP-1403) were selected for further investigation.Oral administration of 8c and 18a at 50 mg/kg markedly improved oral glucose tolerance in ob/ob mice. In this test, buformin also showed activity, whereas tolbutamide produced no significant improvement.
Indications for fibrinolytic therapy in suspected acute myocardial infarction : collaborative overview of early mortality and major morbidity results from all randomised trials of more than 1000 patients (1994)

Large randomised trials have demonstrated that fibrinolytic therapy can reduce mortality in patients with suspected acute myocardial infarction (AMI). The indications for, and contraindications to, this treatment in some categories of patient are disputed, examples being late presentation, elderly patients, and those in cardiogenic shock. This overview aims to help resolve some of the remaining uncertainties. From all trials of fibrinolytic therapy versus control that randomised more than 1000 patients with suspected AMI, information was sought and checked on deaths during the first 5 weeks and on major adverse events occurring during hospitalisation. The nine trials included 58,600 patients, among whom 6177 (10.5%) deaths, 564 (1.0%) strokes, and 436 (0.7%) major non-cerebral bleeds were reported. Fibrinolytic therapy was associated with an excess of deaths during days 0-1 (especially among patients presenting more than 12 h after symptom onset, and in the elderly) but this was outweighed by a much larger benefit during days 2-35. This "early hazard" should not obscure the very clear overall survival advantage that is produced by fibrinolytic therapy. Benefit was observed among patients presenting with ST elevation or bundle-branch block (BBB)--irrespective of age, sex, blood pressure, heart rate, or previous history of myocardial infarction or diabetes--and was greater the earlier treatment began. Among the 45,000 patients presenting with ST elevation or BBB the relation between benefit and delay from symptom onset indicated highly significant absolute mortality reductions of about 30 per 1000 for those presenting within 0-6 h and of about 20 per 1000 for those presenting 7-12 h from onset, and a statistically uncertain benefit of about 10 per 1000 for those presenting at 13-18 h (with more randomised evidence needed in this latter group to assess reliably the net effects of treatment). Fibrinolytic therapy was associated with about 4 extra strokes per 1000 during days 0-1: of these, 2 were associated with early death and so were already accounted for in the overall mortality reduction, 1 was moderately or severely disabling, and 1 was not. This overview indicates that fibrinolytic therapy is beneficial in a much wider range of patients than is currently given such treatment routinely.
The effect of anti-α4 integrin antibody on brain lesion activity in MS (1999)

Short-term treatment with monoclonal antibody against alpha4 integrin results in a significant reduction in the number of new active lesions on MRI. Further studies will be required to determine the longer term effect of this treatment on MRI and clinical outcomes.
Dependence of photoetching rates of polymers at 193 nm on optical absorption depth (1986)

Mixtures of poly(methyl methacrylate) and poly(α-methyl styrene) were prepared and their optical absorption coefficients at 193 nm were measured. A study of photoetching rate of these polymeric materials using an ArF excimer laser at 193 nm shows two regions of distinctly different etching characteristics. At relatively high fluences (&amp;gt;300 mJ/cm2) the photoetch rate decreased with increasing absorption in the polymer films, while at lower fluences, an optimum range of absorption coefficients was found to give the maximum photoetching rate.
Genotyping of the Apolipoprotein B R3500Q Mutation Using Immobilized Locked Nucleic Acid Capture Probes (2002)

Hyperlipidemia and coronary heart disease (CHD) are associated with genetic variation in the apolipoprotein B (apoB) gene (1). Nonexchangeable apolipoprotein B-100 (ApoB-100) is an important determinant of LDL-cholesterol in plasma; it plays a central role in cholesterol transport by its association to LDL particles as a ligand for the LDL receptor (2). One of the first mutations in the apoB gene to be discovered was the ApoB-100 R3500Q (apoBR3500Q) mutation (3), a single nucleotide transition, CGG to CAG, in exon 26. This mutation reduces the affinity to the LDL receptor by at least 95% (4) and is the major cause of familial defective ApoB-100 (FDB). The frequency of the mutation is 1:500 to 1:700 in Caucasians (5)(6). Because the cholesterol concentration is often within the reference interval in FDB patients, the only reliable way of detecting FDB is by genotyping. At present, genotyping of the apoBR3500Q mutation is based on PCR (7)(8)(9), but other methods, such as heteroduplex analysis and real-time PCR, have also been applied (10)(11)(12). In general, these methods are time-consuming and need to be optimized. Here we describe a simple, rapid, and sensitive assay for genotyping the apoBR3500Q mutation that is suitable for the 96-well microtiter plate format and relies on hybridization of PCR amplicons to allele-specific locked nucleic acid (LNA) capture probes (13)(14).

The microtiter plates were prepared by covalent photoimmobilization of 10 pmol/well of either wild-type (wt)-LNA8 [AQ-CONH-(CH2)3-TACATGTTATGCTGA-GLALMeCLMeCLGLTLGLTLG] or mutant (m)-LNA8 [AQ-CONH-(CH2)3-TACATGTTATGCTGA-GLALMeCLTLGLTLGLTLG] capture probes using an …