gebhart/patrepeval huggingface dataset:
Geometry transformation-based adaptive in-loop filter (2016)

Recently, adaptive in-loop filter (ALF) for image/video coding has attracted increasing attention by its proven capability in improving coding performance. ALF is aiming to minimize the mean square error between original samples and decoded samples by using Wiener-based adaptive filter. Samples in a picture are classified into multiple categories and the samples in each category are then filtered with their associated adaptive filter. The filter coefficients may be signaled or inherited to optimize the tradeoff between the mean square error and the overhead. In this paper, a Geometry transformation-based ALF (GALF) scheme is proposed to further improve the performance of ALF, which introduces geometric transformations, such as rotation, diagonal and vertical flip, to be applied to the samples in filter support region depending on the orientation of the gradient of the reconstructed samples before ALF. With the introduction of geometric transformations, more spatial adaptation is supported without excessive signaling of filter coefficients. The experimental results show that GALF outperforms the existing ALF techniques and it has been adopted by the JEM reference software used as the test platform for future video coding technology exploration in JVET.
Renewable Energy Sources and the Realities of Setting an Energy Agenda (2007)

The European Commission has been devoting considerable attention to energy issues. This Perspective describes recent progress in Europe toward achieving goals for renewable energy use, and the role that technology can play, as well as the new Strategic Energy Package.
Interspecies molecular chimeras of kit help define the binding site of the stem cell factor. (1993)

The extracellular portion of the kit-encoded receptor for the stem cell factor (SCF) comprises five immunoglobulin (Ig)-like domains. To localize the ligand recognition site, we exploited the lack of binding of human SCF to the murine receptor by using human-mouse hybrids of Kit and species-specific monoclonal antibodies (MAbs) that inhibit ligand binding. Replacement of the three N-terminal Ig-like domains of the murine Kit with the corresponding portion of the human receptor conferred upon the chimeric receptor high-affinity binding of the human ligand as well as of human-specific ligand-inhibitory MAbs. By constructing five chimeric murine Kit proteins which individually contain each of these three human Ig-like units or pairs of them, we found that the second human domain confers upon the mouse Kit high-affinity binding of the human ligand and also binding of species-specific SCF-competitive MAbs. Nevertheless, the flanking Ig-like domains also affect high-affinity recognition of SCF. Moreover, it appears that the determinants that define ligand specificity of the murine and the human receptors do not structurally coincide. This observation allowed us to identify a chimeric receptor that displayed a dual specificity; namely, it bound with high affinity either the human or the murine SCF molecules and reacted with mouse- as well as human-specific ligand-inhibitory MAbs. Conversely, another chimera, which included all of the five Ig-like domains, bound neither ligand. In conclusion, interdomain packing involving the second Ig-like domain of human Kit and noncontiguous structural motifs of the receptor are involved in SCF recognition.
Security under key-dependent inputs (2007)

In this work we re-visit the question of building cryptographic primitives that remain secure even when queried on inputs that depend on the secret key. This was investigated by Black, Rogaway, and Shrimpton in the context of randomized encryption schemes and in the random oracle model. We extend the investigation to deterministic symmetric schemes (such as PRFs and block ciphers) and to the standard model. We term this notion "security against key-dependent-input attack", or KDI-security for short. Our motivation for studying KDI security is the existence of significant real-world implementations of deterministic encryption (in the context of storage encryption) that actually rely on their building blocks to be KDI secure.
FIVE-YEAR FOLLOW-UP OF MACULAR HOLE SURGERY WITH PEELING OF THE INTERNAL LIMITING MEMBRANE (2006)

In Brief Purpose: To report on long-term results of macular hole surgery with peeling of the internal limiting membrane (ILM) in a prospective nonrandomized study. Methods: Sixty-four consecutive patients with a follow-up of at least 36 months were included. Only idiopathic macular holes were included in the study. All patients had undergone standard pars plana vitrectomy with removal of the ILM and intraocular gas tamponade with a 15% hexafluoroethane (C2F6) gas–air mixture followed by a face-down position for at least 5 days. During each follow-up visit, complete clinical examination including determination of best-corrected visual acuity, Goldmann perimetry, and optical coherence tomography was performed. Results: Fifty-two patients were female and 12 were male, and the patients’ mean age was 72 years (range, 53–82 years) at the last visit. We observed stage 2 holes in 5 patients, stage 3 holes in 47, and stage 4 holes in 12. The median postoperative follow-up was 62 months (mean, 56 months; range, 36–75 months). Sixty-two patients (97%) were pseudophakic at the last examination: 3 patients (5%) were already pseudophakic at the time of macular hole surgery; a combined procedure was performed on 9 patients (14%); and 50 patients (78%) underwent cataract surgery later. The median follow-up for patients after cataract extraction was 61 months (mean, 56 months; range, 36–75 months). Anatomical closure was achieved in 61 (95%) of 64 patients as confirmed clinically and by optical coherence tomography. No late reopening of a macular hole or formation of epiretinal membranes was observed after successful hole closure. Best-corrected visual acuity improved in 59 (92%) of 64 patients, remained unchanged in 2, and deteriorated in 3. Best-corrected visual acuity improved from a median of 20/100 preoperatively to a median of 20/32 postoperatively (P < 0.001). There was a median gain of 5 lines (range, -6 to 12). The development of visual acuity did not depend on the duration of symptoms, the number of surgeries, or the stage of the macular hole. Conclusions: Macular hole surgery with peeling of the ILM is a very safe procedure, even in the long term. It leads to very good and stable functional and anatomical results. In this prospective, ongoing investigation we report on the stability of good functional and anatomical outcome of macular hole surgery with ILM peeling over a period of 5 years. There was no correlation between the stage of the hole or preoperative duration of symptoms and functional results.
A PCR primer bank for quantitative gene expression analysis (2003)

Although gene expression profiling by microarray analysis is a useful tool for assessing global levels of transcriptional activity, variability associated with the data sets usually requires that observed differences be validated by some other method, such as real-time quantitative polymerase chain reaction (real-time PCR). However, non-specific amplification of non-target genes is frequently observed in the latter, confounding the analysis in approximately 40% of real-time PCR attempts when primer-specific labels are not used. Here we present an experimentally validated algorithm for the identification of transcript-specific PCR primers on a genomic scale that can be applied to real-time PCR with sequence-independent detection methods. An online database, PrimerBank, has been created for researchers to retrieve primer information for their genes of interest. PrimerBank currently contains 147 404 primers encompassing most known human and mouse genes. The primer design algorithm has been tested by conventional and real-time PCR for a subset of 112 primer pairs with a success rate of 98.2%.
Predictive and Pharmacodynamic Biomarker Studies in Tumor and Skin Tissue Samples of Patients With Recurrent or Metastatic Squamous Cell Carcinoma of the Head and Neck Treated With Erlotinib (2007)

PURPOSE Pharmacodynamic tissue studies were conducted on a phase I/II trial of erlotinib and cisplatin in patients with recurrent or metastatic head and neck squamous cell carcinoma (HNSCC). Levels of epidermal growth factor receptor (EGFR), downstream signaling components, and markers of angiogenesis and apoptosis were evaluated to determine the relationship between correlative end points and clinical outcomes. PATIENTS AND METHODS Pretreatment and during-treatment tumor and skin biopsies, and archival tumor specimens were evaluated for EGFR, phosphorylated (p) -EGFR, extracellular signal-regulated kinase (ERK), p-ERK, Akt, p-Akt, Ki67, p27, p-nuclear factor kappa B (NFkappaB), p-signal transducer and activator of transcription 3 (STAT3), and EGFR gene copy number. Results On 37 archival samples, response to therapy was evident in two of four (50%) patients with high EGFR gene copy number tumors and in four of 27 (15%) patients with low gene copy number tumors. On nine paired tumor biopsies, elevated pretreatment levels of p27 and p-STAT3 predicted for prolonged time to progression (TTP) and overall survival (OS; P < or = .03). With treatment, a decrease in p-EGFR, p-NFkappaB, and p27 correlated with increased TTP, OS, or both TTP and OS, respectively (P < or = .04). Multidimensional scaling (MDS) models revealed clustering profiles of tumor markers by immunofluorescence could predict response. On 32 paired skin biopsies, suppression of p-EGFR with therapy correlated with increased OS (P = .045). CONCLUSION High EGFR gene copy in tumor specimens may predict which patients have an increased likelihood of response to erlotinib, and decreased p-EGFR level in skin biopsies during therapy may represent a potential surrogate marker for improved clinical outcome. MDS represents a novel way to evaluate the relationships between molecular markers and clinical outcome. Additional biomarker studies with larger sample sizes are required to elucidate HNSCC patients who may benefit from this targeted therapy.
Development of Effective Immunotherapy for B-Cell Non-Hodgkin’s Lymphoma with CD19-Specific Cytotoxic T Cells. (2004)

Abstract Less than 60% of patients with B-cell non-Hodgkin’s lymphoma (B-NHL) can be cured with contemporary therapy. Using artificial receptors it is possible to redirect the specificity of immune cells to tumor-associated antigens, a strategy that holds great potential as a novel cancer therapy. Since B-NHL cells invariably express CD19, we transduced human peripheral blood T lymphocytes with a recently developed receptor (anti-CD19-BB-ζ), which consists of the single-chain variable domain (scFv) of an anti-CD19 monoclonal antibody, the hinge and transmembrane domains of CD8α, and the signaling domains of CD3ζ and 4-1BB. CD3ζ delivers the primary stimulus upon receptor engagement, while 4-1BB delivers co-stimulatory signals that are crucial for T-cell cytotoxicity. It has been shown that elicitation of 4-1BB signaling enhances the immune response to tumors in vivo, even when an immune response cannot be induced by CD28 stimulation. Retroviral transduction led to anti-CD19-BB-ζ expression in T cells with high efficiency: median percent of transduced cells was 60.3% (range, 25.7%–83.4%; n = 9). T lymphocytes expressing anti-CD19-BB-ζ expanded more vigorously that T cells transduced with receptors lacking 4-1BB and exerted powerful cytotoxicity against the CD19+ B-NHL cell lines Raji, Daudi, RL, and HT in vitro: at a 0.5: 1 effector: target ratio, mean (± SD) cell specific lymphoma cell killing was 96.6% ± 4.6% after 5–7 days of culture (4 experiments in each cell line). Transduced T cells were also effective against freshly isolated cells from patients with diffuse large, follicular large, Burkitt, and mantle cell lymphoma cultured on bone marrow-derived mesenchymal cells: in 10 samples, cell killing was 93.6% ± 5.7% at a 0.5: 1 ratio after 5–7 days of culture. Sensitivity to anti-CD19-BB-ζ-mediated killing was observed regardless of high Bcl-2 expression. T cells expressing anti-CD19-BB-ζ were also effective in a xenograft model of NHL, in which NOD/SCID mice were inoculated subcutaneously with lymphoma cells (1 x 107). Subsequent inoculation of T cells (2 x 106) transduced with anti-CD19-BB-ζ receptors significantly suppressed tumor growth, whereas inoculation of T cells transduced with empty control vector had no effect (3 mice for each treatment). These results provide a rationale for clinical testing of autologous T cells modified with anti-CD19-BB-ζ receptors in patients with aggressive or relapsed B-NHLs refractory to conventional therapy.
Laser induced fluorescence spectroscopy from native cancerous and normal tissue (1984)

The visible fluorescence spectra have been measured from cancerous and normal rat kidney and prostate tissues, and from cancerous rat and mouse bladder tissues. The spectral profiles from the cancerous and normal tissues are substantially different; showing characteristic principal and secondary maxima. These peaks are assigned to fluorphors such as flavins and porphyrins in different environments in the two types of cell media.
Rhodopsin Arginine-135 Mutants Are Phosphorylated by Rhodopsin Kinase and Bind Arrestin in the Absence of 11-cis-Retinal (1998)

Arginine-135, located at the border between the third transmembrane domain and the second cytoplasmic loop of rhodopsin, is one of the most highly conserved amino acids in the family of G protein-coupled receptors. The effect of mutation at Arg-135 on the ability of rhodopsin to undergo desensitization was investigated. Four mutants, R135K, R135Q, R135A, and R135L, were examined for their ability to be phosphorylated by rhodopsin kinase, to bind arrestin, and to activate the rod cell G protein, transducin (Gt). All of the mutants were phosphorylated, bound arrestin, and were able to activate Gt when reconstituted with 11-cis-retinal. Surprisingly, several of the mutants could be phosphorylated by rhodopsin kinase and could bind arrestin in the absence of 11-cis-retinal but were not able to activate Gt. These observations represent the first demonstration of a mutant G protein-coupled receptor that assumes a conformation able to interact with its G protein-coupled receptor kinase and arrestin, but not with its G protein, in the absence of ligand.
Simulation of Nonlinear Circuits in the Frequency Domain (1986)

Simulation in the frequency domain avoids many of the severe problems experienced when trying to use traditional time-domain simulators such as SPICE to find the steady-state behavior of analog and microwave circuits. In particular, frequency-domain simulation eliminates problems from distributed components and high-Q circuits by foregoing a nonlinear differential equation representation of the circuit in favor of a complex algebraic representation. This paper reviews the method of harmonic balance as a general approach to converting a set of differential equations into a nonlinear algebraic system of equations that can be solved for the periodic steady-state solution of the original differential equations. Three different techniques are applied to solve the algebraic system of equations: optimization, relaxation, and Newton's method. The implementation of the algorithm resulting from the combination of Newton's method with harmonic balance is described. Several new ways of exploiting both the structure of the formulation and the characteristics of the circuits that would typically be seen by this type of simulator are presented. These techniques dramatically reduce the time required for a simulation, and allow harmonic balance to be applied to much larger circuits than were previously attempted, making it suitable for use on monolithic microwave integrated circuits (MMIC's).
Competitive and noncompetitive inhibition of the DNA-dependent protein kinase. (1999)

The DNA-dependent protein kinase (DNA-PK) is a serine/threonine protein kinase that is involved in mammalian DNA double-strand break repair. The catalytic subunit of DNA-PK (DNA-PKcs) shares sequence homology in its kinase domain with phosphatidylinositol (PI) 3-kinase. Here, we provide a detailed kinetic analysis of DNA-PK inhibition by the PI 3-kinase inhibitor wortmannin and demonstrate this inhibition to be of a noncompetitive nature, with a Ki of 120 nM. Another inhibitor of PI 3-kinase. LY294002, its parent compound, quercetin, and other derivatives have also been studied. These chemicals are competitive inhibitors of DNA-PK, with LY294002 having a Ki of 6.0 microM. Using an antibody to wortmannin, we found that this compound binds covalently to the kinase domain of DNA-PKcs both in vitro and in vivo. Binding of wortmannin to the active site of DNA-PKcs is inhibited by ATP but not by a peptide substrate. Furthermore, wortmannin is able to bind to DNA-PKcs independently of Ku, and it is not stimulated by the presence of DNA. This suggests that the ATP binding site of DNA-PKcs is open constitutively and that DNA activation of the kinase is mediated via another mechanism.
Genetic engineering of the multicellular green algaVolvox: a modified and multiplied bacterial antibiotic resistance gene as a dominant selectable marker (1999)

The green alga Volvox represents the simplest multicellular organism: Volvax is composed of only two cell types, somatic and reproductive. Volvox, therefore, is an attractive model system for studying various aspects of multicellularity. With the biolistic nuclear transformation of Volvox carteri, the powerful molecular genetic manipulation of this organism has been established, but applications have been restricted to an auxotrophic mutant serving as the DNA recipient. Therefore, a dominant selectable marker working in all strains and mutants of this organism is required. Among several gene constructs tested, the most advantageous results were obtained with a chimeric gene composed of the coding sequence of the bacterial ble gene, conferring resistance to the antibiotic zeocin, modified with insertions of two endogenous introns from the Volvox arylsulfatase gene and fused to 5' and 3' untranslated regions from the Volvox beta 2-tubulin gene. In the most suitable plasmid used, the gene dosage was increased 16-fold by a technique that allows exponential multiplication of a DNA fragment. Co-transformation of this plasmid and a non-selectable plasmid allowed the identification of zeocin resistant transformants with nuclear integration of both selectable and non-selectable plasmids. Stable expression of the ble gene and of genes from several non-selectable plasmids is demonstrated. The modified ble gene provides the first dominant marker for transformation of both wild-type and mutant strains of Volvox.
Hypocarotenemia in Patients Fed Enterally with Commercial Liquid Diets (1988)

We have found that 12 patients requiring permanent enteral feeding secondary to cerebrovascular accident with adequate Vitamin A nutritional status had serum concentrations of various carotenoids which were only 8–17% of sex‐and age‐matched healthy controls. Their serum retinol levels were normal, but only 61% of their controls despite receiving two to three times the recommended daily allowance (RDA) in retinol equivalents. Commercial enteral formulas were found to contain only negligible quantities of the carotenoids and were the cause of the hypocarotenemia. To assess the ability of these patients to absorb beta‐carotene, nine tube‐fed patients were given 15 mg of beta‐carotene (2.5 times the RDA) in a single dose. Serum concentration time curves showed that only four patients absorbed significant quantities of the beta‐carotene and absorption was delayed compared to previously studied subjects taking enteral formulas as meals. These studies suggest that the efficiency of absorption of the fat soluble vitamins may be lower in tube‐fed patients and that patients receiving long‐term tube feeding are denied the possible protective effects of the carotenoids normally contained in the American diet. ( Journal of Parenteral and Enteral Nutrition 12: 484–489, 1988)
Design, Synthesis, and Evaluation of a Mechanism-Based Inhibitor for Gelatinase A (2005)

[structure: see text] Matrix metalloproteinases (MMPs), of which 26 are known, have been implicated in a number of pathological conditions, including tumor metastasis. We have previously described the first mechanism-based inhibitor for MMPs (J. Am. Chem. Soc. 2000, 122, 6799-6800), which in chemistry mediated by the active site zinc ion selectively and covalently inhibits MMP-2, -3, and -9. Computational analyses indicated that this selectivity in inhibition of MMPs could be improved by design of new variants of the inhibitor class. We report herein the syntheses of methyl 2-(4-{4-[(2-thiiranylpropyl)sulfonyl]phenoxy}phenyl)acetate (3) and 2-(4-{4-[(2-thiiranylpropyl)sulfonyl]phenoxy}phenyl)acetic acid (4), and show that compound 3 serves as a mechanism-based inhibitor exclusively for MMP-2. This molecule should prove useful in delineating the functions of MMP-2 in biological systems.
The role of vascular endothelial growth factor SNPs as predictive and prognostic markers for major solid tumors (2009)

Angiogenesis is crucial for development and metastasis of tumors, and vascular endothelial growth factor (VEGF) is a key mediator of this process. The importance of VEGF in tumorigenesis and tumor progression makes it an attractive target for the development of anticancer therapies. Inhibition of angiogenesis has shown promising clinical efficacy; however, not all patients treated with antiangiogenic agents derive benefit from them. Some patients are predisposed to refractory disease, whereas others develop resistance after initial response. Patients may also have different severity of drug-related adverse events. Optimization of drug administration based on disease status and individual responsiveness is important in limiting the treatment failure and minimization of side-effects. Single nucleotide polymorphisms (SNP) in VEGF may alter VEGF protein concentrations, influence the process of angiogenesis, and may relate to interindividual variation in the risk and progression of selected tumors, and their resistance to treatments. This review examines the role of SNPs in the VEGF gene as predictive and prognostic markers for major solid tumors, including the breast, non-small cell lung, colorectal, and prostate cancers. Selected VEGF SNPs seem to be associated with risk of these cancers; however, there is lack of unanimity in findings, in part influenced by differences in study design and analysis.
The role of nonsteroidal anti-inflammatory drugs in colorectal cancer prevention (1995)

Colorectal cancer is the second leading cause of cancer death in the U.S.A. Recent research suggests that nonsteroidal anti-inflammatory drugs (NSAIDs) are effective in the prevention of colorectal neoplasia. This review summarises the results of research in animals and humans of these compounds in preventing tumours of the colorectum.