gebhart/patrepeval huggingface dataset:
An embedded wavelet hierarchical image coder (1992)

A simple, yet remarkably effective, image compression algorithm that has the property that the bits in the bit stream are generated in order of importance, yielding fully hierarchical image compression suitable for embedded coding or progressive transmission, is described. Given an image bit stream, the decoder can cease decoding at the same image that would have been encoded at the bit rate corresponding to the truncated bit stream. The compression algorithm is based on three key concepts: (1) wavelet transform or hierarchical subband decomposition, (2) prediction of the absence of significant information across scales by exploiting the self-similarity inherent in images, and (3) hierarchical entropy-coded quantization.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Clinical Classification of Itch: a Position Paper of the International Forum for the Study of Itch (2007)

Chronic itch is a common and distressing symptom that arises from a variety of skin conditions and systemic diseases. Despite this, there is no clinically based classification of pruritic diseases to assist in the diagnosis and cost-effective medical care of patients with pruritus. The proposed classification focuses on clinical signs and distinguishes between diseases with and without primary or secondary skin lesions. Three groups of conditions are proposed: pruritus on diseased (inflamed) skin (group I), pruritus on non-diseased (non-inflamed) skin (group II), and pruritus presenting with severe chronic secondary scratch lesions, such as prurigo nodularis (group III). The next part classifies the underlying diseases according to different categories: dermatological diseases, systemic diseases including diseases of pregnancy and drug-induced pruritus, neurological and psychiatric diseases. In some patients more than one cause may account for pruritus (category "mixed") while in others no underlying disease can be identified (category "others"). This is the first version of a clinical classification worked out by the members of the International Forum for the Study of Itch. It is intended to serve as a diagnostic route for better evaluation of patients with chronic pruritus and aims to improve patients' care.
A Stochastic Grammar of Images (2007)

This exploratory paper quests for a stochastic and context sensitive grammar of images. The grammar should achieve the following four objectives and thus serves as a unified framework of representation, learning, and recognition for a large number of object categories. (i) The grammar represents both the hierarchical decompositions from scenes, to objects, parts, primitives and pixels by terminal and non-terminal nodes and the contexts for spatial and functional relations by horizontal links between the nodes. It formulates each object category as the set of all possible valid configurations produced by the grammar. (ii) The grammar is embodied in a simple And–Or graph representation where each Or-node points to alternative sub-configurations and an And-node is decomposed into a number of components. This representation supports recursive top-down/bottom-up procedures for image parsing under the Bayesian framework and make it convenient to scale up in complexity. Given an input image, the image parsing task constructs a most probable parse graph on-the-fly as the output interpretation and this parse graph is a subgraph of the And–Or graph after making choice on the Or-nodes. (iii) A probabilistic model is defined on this And–Or graph representation to account for the natural occurrence frequency of objects and parts as well as their relations. This model is learned from a relatively small training set per category and then sampled to synthesize a large number of configurations to cover novel object instances in the test set. This generalization capability is mostly missing in discriminative machine learning methods and can largely improve recognition performance in experiments. (iv) To fill the well-known semantic gap between symbols and raw signals, the grammar includes a series of visual dictionaries and organizes them through graph composition. At the bottom-level the dictionary is a set of image primitives each having a number of anchor points with open bonds to link with other primitives. These primitives can be combined to form larger and larger graph structures for parts and objects. The ambiguities in inferring local primitives shall be resolved through top-down computation using larger structures. Finally these primitives forms a primal sketch representation which will generate the input image with every pixels explained. The proposal grammar integrates three prominent representations in the literature: stochastic grammars for composition, Markov (or graphical) models for contexts, and sparse coding with primitives (wavelets). It also combines the structure-based and appearance based methods in the vision literature. Finally the paper presents three case studies to illustrate the proposed grammar.
Denaturation and Aggregation of Three α-Lactalbumin Preparations at Neutral pH (2005)

The denaturation and aggregation of reagent-grade (Sigmaalpha-La), ion-exchange chromatography purified (IEXalpha-La), and a commercial-grade (Calpha-La) alpha-lactalbumin were studied with differential scanning calorimetry (DSC), polyacrylamide gel electrophoresis, and turbidity measurement. All three preparations had similar thermal denaturation temperatures with an average of 63.7 degrees C. Heating pure preparations of alpha-lactalbumin produced three non-native monomer species and three distinct dimer species. This phenomenon was not observed in Calpha-La. Turbidity development at 95 degrees C (tau95 degrees C) indicated that pure preparations rapidly aggregate at pH 7.0, and evidence suggests that hydrophobic interactions drove this phenomenon. The Calpha-La required 4 times the phosphate or excess Ca2+ concentrations to develop a similar tau95 degrees C to the pure preparations and displayed a complex pH-dependent tau95 degrees C behavior. Turbidity development dramatically decreased when the heating temperature was below 95 degrees C. A mechanism is provided, and the interrelationship between specific electrostatic interactions and hydrophobic attraction, in relation to the formation of disulfide-bonded products, is discussed.
A Vertical Insulated Gate AlGaN/GaN Heterojunction Field-Effect Transistor (2007)

We fabricated a vertical insulated gate AlGaN/GaN heterojunction field-effect transistor (HFET), using a free-standing GaN substrate. This HFET has apertures through which the electron current vertically flows. These apertures were formed by dry etching the p-GaN layer below the gate electrodes and regrowing n--GaN layer without mask. The HFET exhibited a specific on-resistance of as low as 2.6 mΩ·cm2 with a threshold voltage of -16 V. This HFET would be a prototype of a GaN-based high-power switching device.
DNA recognition by lexitropsins, minor groove binding agents (1994)

Consideration is given to alternative approaches to the development of DNA sequence selective binding agents because of their potential applications in diagnosis and treatment of cancer as well as in molecular biology. The concept of lexitropsins, or information-reading molecules, is introduced within the antigene strategy as an alternative to, and complementary with, the antisense approach for cellular intervention and gene control. The chemical, physical and pharmacological factors involved in the design of effective lexitropsins are discussed and illustrated with experimental results. Among the factors contributing to the molecular recognition processes are: the presence and disposition of hydrogen bond accepting and donating groups, ligand shape, chirality, stereochemistry, flexibility and charge. For longer ligands, such as are required to target unique sequences in biological systems (14-16 base pairs), the critical feature is the phasing or spatial correspondence between repeat units in the ligand and the receptor. The recently discovered 2:1 lexitropsin-DNA binding motif provides a further refinement in molecular recognition in permitting discrimination between GC and CG base pairs. The application of these factors in the design and synthesis of novel agents which exhibit anticancer, antiviral and antiretroviral properties, and inhibition of critical cellular enzymes including topoisomerases is discussed. The emerging evidence of a relationship between sequence selectivity of the new agents and the biological responses they invoked is also described.
Acceleration techniques for progressive refinement radiosity (1990)

The progressive refinement radiosity method provides a means for computing the global illumination of an environment in time proportional to the size of the environment. Additionally, the method supplies a sequence of solutions that monotonically converge to a high-quality result, allowing it to be used for interactive applications that deliver "near real-time" updates as the computation proceeds. This paper presents two methods for accelerating the radiosity method. First, the traditional hemi-cube algorithm is modified to accelerate the expensive form-factor calculation. Second, the radiosity method is parallelized across a coarse-grain network, and the efficiency of the parallel system is discussed.
Saccharomyces cerevisiae GAL1-GAL10 Divergent Promoter Region: Location and Function of the Upstream Activating Sequence UAS G (1984)

The GAL1 and GAL10 genes, separated by 680 base pairs and divergently transcribed on chromosome 2 of Saccharomyces cerevisiae, were separately fused to the lacZ gene of Escherichia coli so that beta-galactosidase synthesis in S. cerevisiae reflected GAL1 and GAL10 promoter function. Analysis of two sets of deletions defined a 75-base-pair sequence, located ca. midway between the transcription initiation regions of GAL1 and GAL10, that mediates GAL4-dependent induction of both genes. Deletion of various parts of this sequence (called the GAL upstream activating sequence or UASG) reduced GAL1 and GAL10 induction about equally. Sequences in the GAL10-proximal half of UASG in some sequence contexts functioned independently of sequences in the GAL1-proximal half of UASG. A 33-base-pair deletion of the GAL10-proximal half of UASG drastically reduced induction. Deletions between UASG and the GAL1 TATA box caused beta-galactosidase to be synthesized at an unexpectedly high basal level, that is, in the absence of galactose and GAL4 product. Some of these mutations also reduced the repression caused by glucose.
A RETROSPECTIVE COHORT STUDY OF SEATBELT USE AND PREGNANCY OUTCOME AFTER A MOTOR VEHICLE CRASH (1993)

To determine the effect of seatbelt use on pregnancy outcome we conducted a population-based retrospective cohort study of pregnant women (20 weeks' gestation or more) involved in motor vehicle collisions. Birth and fetal death certificates were obtained for 1243 restrained and 1349 unrestrained pregnant women involved in police-investigated motor vehicle crashes from 1980 through 1988. Unrestrained pregnant women drivers were 1.9 times more likely to have a low birth weight baby (95% confidence intervals = 1.2, 2.9) and 2.3 times more likely to give birth within 48 hours after the motor vehicle crash (95% confidence intervals = 1.1, 4.8) than restrained pregnant women drivers after adjusting for age and gestational age at crash. Although a trend for an increased risk of fetal deaths was observed among unrestrained women, too few fetal deaths occurred to accurately describe any association with restraint status. This study provides reassurance that the current recommendations on use of seatbelts by pregnant women are appropriate and should be continued.
Objective laparoscopic skills assessments of surgical residents using Hidden Markov Models based on haptic information and tool/tissue interactions. (2001)

Comparison of HMM's between groups showed significant differences between all skill levels, supporting the objective definition of a learning curve. The major differences between skill levels were: (i) magnitudes of F/T applied (ii) types of tool/tissue interactions used and the transition between them and (iii) time intervals spent in each tool/tissue interaction and the overall completion time. The objective HMM analysis showed that the greatest difference in performance was between R1 and R3 groups and then decreased as the level of expertise increased, suggesting that significant laparoscopic surgical capability develops between the first and the third years of their residency training. The power of the methodology using HMM for objective surgical skill assessment arises from the fact that it compiles enormous amount of data regarding different aspects of surgical skill into a very compact model that can be translated into a single number representing the distance from expert performance. Moreover, the methodology is not limited to in-vivo condition as demonstrated in the current study. It can be extended to other modalities such as measuring performance in surgical simulators and robotic systems.
SLICOT—A Subroutine Library in Systems and Control Theory (1999)

computations in systems and control theory. OP****.
Hull Fouling of Maritime Vessels as a Pathway for Marine Species Invasions to the Hawaiian Islands (2003)

The natural barriers to species invasions that exist in isolated marine environments such as Hawaii are overcome by anthropogenic influences on the dispersal patterns of marine organisms. This creates a situation where the marine habitats of the Hawaiian Archipelago are more readily exposed to marine non-indigenous species. A case study of a particular anthropogenic dispersal mode, maritime vessel hull fouling, is reviewed. This mode has effects on altered environments, such as harbors, as well as unaltered coastal habitats. Hull fouling of commercial maritime vessels is documented as a transport vector, and an inter-island dispersal mechanism for marine non-indigenous species to the main Hawaiian Islands.
A phase I trial of subcutaneously administered recombination tumor necrosis factor to patients with advanced malignancy. (1989)

Nineteen patients with advanced cancer for which there was no effective standard therapy or whose disease was refractory to standard therapy were treated with recombinant tumor necrosis factor (rTNF). The rTNF was administered subcutaneously for 5 consecutive days every other week for 3 treatment weeks. The doses administered ranged from 5 micrograms/m2/day to 150 micrograms/m2/day. There was no intrapatient dose escalation. Systemic side effects of chills, fever, hypotension, nausea, vomiting, and headache were mild and self-limiting. At the maximum tolerated dose of 150 micrograms/m2/day, five of seven patients experienced moderate to severe thrombocytopenia. Mild rapid declines in total leukocyte count occurred within 60-90 min of administration of the drug, followed by a rise in the total leukocyte count by 120 min. When the total daily dose was administered in a single subcutaneous site, skin ulceration and necrosis occurred at the 100 micrograms/m2/day dose. By giving the total daily dose in two subcutaneous sites, the maximum tolerated dose increased to 150 micrograms/m2/day, and there was no further skin ulceration or necrosis. Skin necrosis occurred in the abdomen and thigh but not on the upper extremity at the 100 micrograms/m2/day dose given in a single site. There was no other significant organ toxicity. No rTNF was detectable in the serum even at the highest doses. No antibodies to TNF developed in any of the patients. The recommended dose of rTNF for Phase II trials given for 5 days subcutaneously is 150 micrograms/m2/day divided into two or more sites.
Immune Regulation of Cancer (2010)

Innate and adaptive immune system cells play a major role in regulating the growth of cancer. Although it is commonly thought that an immune response localized to the tumor will inhibit cancer growth, it is clear that some types of inflammation induced in a tumor may also lead to cancer proliferation, invasion, and dissemination. Recent evidence suggests, however, that some patients with cancer can mount an antitumor immune response that has the potential to control or eliminate cancer. Indeed, a so-called "immune response" signature has been described in malignancy that is associated with improved outcomes in several tumor types. Moreover, the presence of specific subsets of T cells, which have the capability to penetrate tumor stroma and infiltrate deep into the parenchyma, identifies patients with an improved prognosis. Immune-based therapies have the potential to modulate the tumor microenvironment by eliciting immune system cells that will initiate acute inflammation that leads to tissue destruction.
Characterization of the L gene and 5' trailer region of Ebola virus. (1999)

The nucleotide sequences of the L gene and 5' trailer region of Ebola virus strain Mayinga (subtype Zaire) have been determined, thus completing the sequence of the Ebola virus genome. The putative transcription start signal of the L gene was identical to the determined 5' terminus of the L mRNA (5' GAGGAAGAUUAA) and showed a high degree of similarity to the corresponding regions of other Ebola virus genes. The 3' end of the L mRNA terminated with 5' AUUAUAAAAAA, a sequence which is distinct from the proposed transcription termination signals of other genes. The 5' trailer sequence of the Ebola virus genomic RNA consisted of 676 nt and revealed a self-complementary sequence at the extreme end which may play an important role in virus replication. The L gene contained a single ORF encoding a polypeptide of 2212 aa. The deduced amino acid sequence showed identities of about 73 and 44% to the L proteins of Ebola virus strain Maleo (subtype Sudan) and Marburg virus, respectively. Sequence comparison studies of the Ebola virus L proteins with several corresponding proteins of other non-segmented, negative-strand RNA viruses, including Marburg viruses, confirmed a close relationship between filoviruses and members of the Paramyxovirinae. The presence of several conserved linear domains commonly found within L proteins of other members of the order Mononegavirales identified this protein as the RNA-dependent RNA polymerase of Ebola virus.
Drug discovery and design : medical aspects (2002)

This volume is a potpourri of review articles and research articles related to the Bioactive Drugs in Drug Discovery and Design. It can be regarded as a continuation volume of the Vol. 22 published by IOS Press in the series of Biomedical and Health Research. Most of the articles are part of the lectures given in the course of Medicinal Chemistry for graduate students. This book, as the first volume, is divided into four different topics in order to help the reader locate easily the manuscript of his interest. The topics which are covered in this book are the synthesis and properties of bioactive molecules and enzymes, the role of membranes in drug activity and formulation, the conformational analysis of bioactive drugs and the molecular targets and drug design.
Acoustic separation of circulating tumor cells (2015)

Circulating tumor cells (CTCs) are important targets for cancer biology studies. To further elucidate the role of CTCs in cancer metastasis and prognosis, effective methods for isolating extremely rare tumor cells from peripheral blood must be developed. Acoustic-based methods, which are known to preserve the integrity, functionality, and viability of biological cells using label-free and contact-free sorting, have thus far not been successfully developed to isolate rare CTCs using clinical samples from cancer patients owing to technical constraints, insufficient throughput, and lack of long-term device stability. In this work, we demonstrate the development of an acoustic-based microfluidic device that is capable of high-throughput separation of CTCs from peripheral blood samples obtained from cancer patients. Our method uses tilted-angle standing surface acoustic waves. Parametric numerical simulations were performed to design optimum device geometry, tilt angle, and cell throughput that is more than 20 times higher than previously possible for such devices. We first validated the capability of this device by successfully separating low concentrations (∼100 cells/mL) of a variety of cancer cells from cell culture lines from WBCs with a recovery rate better than 83%. We then demonstrated the isolation of CTCs in blood samples obtained from patients with breast cancer. Our acoustic-based separation method thus offers the potential to serve as an invaluable supplemental tool in cancer research, diagnostics, drug efficacy assessment, and therapeutics owing to its excellent biocompatibility, simple design, and label-free automated operation while offering the capability to isolate rare CTCs in a viable state.
Induction of NKG2D Ligands and Increased Sensitivity of Tumor Cells to NK Cell-mediated Cytotoxicity by Hematoporphyrin-based Photodynamic Therapy (2011)

Natural killer (NK) cells are important innate effector cells which can irradicate tumor cells through specific interactions between activating receptors on NK cells and their cognate ligands on cancer cells. Recently, it has been known that induction of activating NKG2D ligands including MHC class I chain-related (MIC) and UL16-binding protein (ULBP) families on tumor cells by various stresses makes them more susceptible to NK cell-mediated cytotoxicity. Therefore, it was investigated whether sublethal dose of hematoporphyrin-based photodynamic therapy (PDT) could up-regulate NKG2D ligands on tumor cells and increase the susceptibility of cancer cells against NK cells. Treatment with sublethal dose of hematoporphyrin-based PDT increased mRNA transcription and surface expression of ULBP1 and ULBP2 genes in SNU-1 human gastric tumor cell line and MICA/B, ULBP1, ULBP2 and ULBP3 genes in SW-900 human lung cancer cell line. These results were followed by increased susceptibility of cancer cells to NK cell-mediated cytotoxicity after sublethal PDT, which was abolished by addition of a blocking NKG2D mAb. Therefore, it could be suggested that the effect of hematoporphyrin-based PDT might be mediated in part by the increased susceptibility to NK cells via induction of NKG2D ligands on tumor cells, which survived after treatment with PDT.
Cleavage of carbon–carbon sigma bonds by Ru3(CO)12 (1973)

T. H. Whitesides and R. A. Budnik, J. Chem. Soc., Chem. Commun., 1973, 87 DOI: 10.1039/C39730000087
In silico Analysis of Genes Nucleoprotein, Neuraminidase and Hemagglutinin: A Comparative Study on Different Strains of Influenza A (Bird Flu) Virus Sub-Type H5N1 (2006)

The avian influenza (bird flu) is an infectious disease of birds, ranging from a mild to a severe form of illness. Influenza viruses pose significant challenges to both human and animal health. The proteins, nucleoprotein (NP), neuraminidase (NA) and hemagglutinin (HA) of influenza A virus (Bird flu virus) sub-type A/Hatay/2004/(H5N1) from chicken were selected for this study. Our in silico analysis predicted that HA of influenza A virus is highly sensitive to mutations and hence it is significant for its pathogenic nature. None of the mutations was detected as an important change except in NA where K332R was at a PKC phosphorylation site. Analysis of the sequence comparison showed that the maximum number of mutations were observed in HA. These mutations are significant as they are involved in change in polarity or hydrophobicity as well as in propensity of each amino acid residue to stabilize the secondary structure. The program MAPMUTATION can be used to monitor the mutations, and predict the trend of mutations.