gebhart/patrepeval huggingface dataset:
Simultaneous enumeration of cancer and immune cell types from bulk tumor gene expression data (2017)

Immune cells infiltrating tumors can have important impact on tumor progression and response to therapy. We present an efficient algorithm to simultaneously estimate the fraction of cancer and immune cell types from bulk tumor gene expression data. Our method integrates novel gene expression profiles from each major non-malignant cell type found in tumors, renormalization based on cell-type-specific mRNA content, and the ability to consider uncharacterized and possibly highly variable cell types. Feasibility is demonstrated by validation with flow cytometry, immunohistochemistry and single-cell RNA-Seq analyses of human melanoma and colorectal tumor specimens. Altogether, our work not only improves accuracy but also broadens the scope of absolute cell fraction predictions from tumor gene expression data, and provides a unique novel experimental benchmark for immunogenomics analyses in cancer research (http://epic.gfellerlab.org).
Hybrid pattern recognition using Markov networks (1993)

Markov networks are inferred automatically for different classes of learning strings. In subsequent string-to-network alignments for test samples, the networks are used to deduce structural characteristics and to provide similarity measures. By processing the similarity measures as numerical-value features, standard nonparametric decision-theoretic pattern classifiers may be applied to determine class membership. The nearest-neighbor rule and linear discriminant-function classifiers are discussed, and their performances are compared with that of a maximum-likelihood classifier. The hybrid system's ability to determine string orientation correctly is investigated. Experiments with several thousand human banded chromosomes are reported.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Biomarker Expression and Risk of Subsequent Tumors After Initial Ductal Carcinoma In Situ Diagnosis (2010)

Biomarkers can identify which women who were initially diagnosed with DCIS are at high or low risk of subsequent invasive cancer, whereas histopathology information cannot.
Dynamic Voltage and Frequency Scaling for Power-Constrained Design using Process Voltage and Temperature Sensor Circuits (2011)

In deeply scaled CMOS technologies, two major non-ideal factors are threatening the survival of the CMOS; i) PVT (process, voltage, and temperature) variations and ii) leakage power consumption. In this paper, we propose a novel post-silicon tuning methodology to scale optimum voltage and frequency "dynamically". The proposed design technique will use our PVT sensor circuits to monitor the variations and based on the monitored variation data, voltage and frequency will be compensated "automatically". During the compensation process, supply voltage is dynamically adjusted to guarantee the minimum total power consumption without violating the frequency requirement. The simulation results show that the proposed technique can reduce the total power by 85% and the static power by 53% on average for the selected ISCAS'85 benchmark circuits with 45 nm CMOS technology compared to the results of the traditional PVT compensation method.
Progressive Cyclic Nucleotide-induced Conformational Changes in the cGMP-dependent Protein Kinase Studied by Small Angle X-ray Scattering in Solution (1997)

Small angle scattering data from bovine lung type Ialpha cGMP-dependent protein kinase (PKG) in the absence of cGMP show the protein to have a highly asymmetric structure with a radius of gyration (Rg) of 45 A and a maximum linear dimension (dmax) of 165 A. The addition of cGMP induces a marked conformational change in PKG. The Rg and dmax increase 25-30%, and the protein's mass moves further away from the center of mass; this results in an even more asymmetric structure. Fourier transform infrared spectroscopy data suggest that the conformational change induced by cGMP binding is primarily due to a topographical movement of the structural domains of PKG rather than to secondary structural changes within one or more of the individual domains. Each monomer of the dimeric PKG contains one high and one low affinity cGMP-binding site. A prominent increase in the asymmetry of PKG occurs with binding to high affinity cGMP-binding sites alone, but the full domain movements require the binding to both sets of sites. These conformational changes occurring in PKG with the progressive binding of cGMP to both sets of cGMP-binding sites correlate with past data, which have indicated that cGMP binding to both sets of sites is required for the full activation of the enzyme. These results provide the first quantitative measurement of the overall PKG structure, as well as an assessment of the structural events that accompany the activation of a protein kinase upon binding a small molecular weight ligand.
The performance of direct-sequence spread spectrum with complex processing and quaternary data modulation (2000)

The receiver processing that is often employed for direct-sequence spread spectrum with quaternary data modulation operates separately on in-phase and quadrature components of the spread-spectrum signal. Previous results on complex quaternary sequences, which are also referred to as four-phase sequences, provide a strong motivation to employ alternative processing methods that permit the receiver to benefit from the correlation properties of these sequences. With this goal in mind we present receiver architectures that use complex processing and are capable of demodulating the signals proposed for the third-generation mobile cellular code-division multiple-access systems. The performance of the proposed receiver architecture with complex processing is shown to be determined by the complex aperiodic correlation functions for the spreading sequences. Comparisons are made with systems in which the quaternary sequences are derived from pairs of common binary spreading sequences and the receiver employs separate in-phase and quadrature processing. We find that in spite of their superior periodic crosscorrelation properties, the previously developed quaternary sequences do not provide significantly smaller error probabilities in multiple-access systems.
Diagnostic and Therapeutic Applications of Lytic Phages (2003)

Abstract The ability of lytic phages to rapidly kill and lyse infected bacteria, the specificity of phages for particular bacteria, and the ability of phages to increase in number during the infection process make phages excellent potential diagnostic and therapeutic agents for fighting bacterial disease. However, temperate phages are of little use in phage diagnostics and therapy.
An essential gene, ESR1, is required for mitotic growth, DNA repair and meiotic recombination Saccharomyces cerevisiae (1994)

A new mutant, which was sensitive to both methyl-methanesulfonate (MMS) and ultra-violet light (UV) and defective in meiotic recombination, was isolated from Saccharomyces cerevisiae. The gene, ESR1, was cloned by complementation of the MMS sensitivity of the mutant and found to be essential for cell growth, as the deleted haploid strain was lethal. The ESR1 gene was adjacent to the CKS1 gene on chromosome II and encoded a putative 2368-amino acid protein with a molecular weight of 273 k. The ESR1 transcript was 8.0 kb long and was induced during meiosis. The predicted Esr1 protein had a mosaic structure composed of homologous regions and showed amino acid sequence similarities to Schizosaccharomyces pombe rad3+ protein, which monitors completion of DNA repair synthesis, and cut1+ protein, which is required for spindle pole body (SPB) duplication. The Esr1 protein was also similar to phosphatidylinositol (PI) 3-kinases, including Saccharomyces cerevisiae TOR2 (and DRR1), which are involved in G1 progression. These results suggest that ESR1 is multi-functional throughout mitosis and meiosis.
Reverse flux through cardiac NADP<sup>+</sup>-isocitrate dehydrogenase under normoxia and ischemia (2002)

Little is known about the role of mitochondrial NADP(+)-isocitrate dehydrogenase (NADP(+)-ICDH) in the heart, where this enzyme shows its highest expression and activity. We tested the hypothesis that in the heart, NADP(+)-ICDH operates in the reverse direction of the citric acid cycle (CAC) and thereby may contribute to the fine regulation of CAC activity (Sazanov and Jackson, FEBS Lett 344: 109-116, 1994). We documented a reverse flux through this enzyme in rat hearts perfused with the medium-chain fatty acid octanoate using [U-(13)C(5)]glutamate and mass isotopomer analysis of tissue citrate (Comte et al., J Biol Chem 272: 26117-26124, 1997). In this study, we assessed the significance of our previous finding by perfusing hearts with long-chain fatty acids and tested the effects of changes in O(2) supply. We showed that under all of these conditions citrate was enriched in an isotopomer containing five (13)C atoms. This isotopomer can only be explained by substrate flux through reversal of the NADP(+)-ICDH reaction, which is evaluated at 3-7% of flux through citrate synthase. Small variations in reversal fluxes induced by low-flow ischemia that mimicked hibernation occurred despite major changes in contractile function and O(2) consumption of the heart as well as citrate and succinate release rates and tissue levels. Our data show a reverse flux through NADP(+)-ICDH and support its hypothesized role in the fine regulation of CAC activity in the normoxic and O(2)-deprived heart.
Synthesis, polymerization and characterization of substituted dithieno[3,4-b:3′,4′-d]thiophenes (1999)

Chemical or electrochemical oxidation of substituted dithieno[3,4-b:3′,4′-d]thiophenes provides polymers with defined regiochemical structures. These materials have lower bandgaps (0.7-0.9 eV) than the unsubstituted fused heteroarene. Potential cycling of the 1,3-dimethyl substituted polymer film shows repetitive p- and n-dopability. The chemically-prepared dioctyl analog is soluble in common solvents such as chloroform, dichloromethane and THF. However, overoxidation of the polymers at an electrode surface presents a limitation to the polymerization of substituted analogs of the parent fused heteroarene.
Human T‐Cell Epitopes on the <i>Mycobacterium tuberculosis</i> Secreted Protein MPT64 (1996)

Mycobacterium tuberculosis secretes a number of proteins into the extracellular environment, some of which are restricted to the M. tuberculosis complex. These proteins are targets for T- and B-cell immune responses in tuberculosis (TB) patients and their contacts. The authors have mapped the immunogenic regions of the MPT64 protein of M. tuberculosis using peripheral blood mononuclear cells (PBMC) from TB patients and a set of overlapping peptides encompassing the complete sequence of the protein. T-cell epitopes which induced proliferation or interferon-gamma (IFN-gamma) release were distributed over the full length of the protein. A C-terminal region of the protein, however, contains sequences recognized in the context of multiple HLA-DR phenotypes by more than 80% of the subjects tested. The nature of the T-cell response was further investigated by generating MPT64-specific T-cell lines. These lines also identified the T-cell epitopes in the C-terminal region of the protein. On stimulation with antigen the lines secreted IFN-gamma, but not interleukin 4 (IL-4). A minority of TB patients (6/32) mounted an antibody response to MPT64. Sera from half (3/6) of these identified two linear antibody binding sites. These results confirm the significance of this protein in the immune response to tuberculosis infection.
Bone structure: from ångstroms to microns (1992)

Bone has a complex hierarchical structure, which despite much investigation, is still not well understood. Here we bring together pieces of this complicated puzzle, albeit from different sources, to present a tentative overview of bone structure. The basic building blocks are the extremely small plate-shaped crystals of carbonate apatite, just hundreds of angstroms long and wide and some 20-30 A thick. They are arranged in parallel layers within the collagenous framework. At the next hierarchical level these mineral-filled collagen fibrils are ordered into arrays in which the fibril axes and the crystal layers are all organized into a 3-dimensional structure that makes up a single layer or lamella of bone a few microns thick. The orientations of the collagen fibrils and the crystal layers in alternating lamellae of rat bone differ such that in the thinner lamellae, the fibrils and the crystal layers are parallel to the lamellar boundaries. In the thicker lamellae the fibrils are parallel to the boundary, but the crystal layers are rotated out of the plane of the boundary. In many bones these alternating lamellae are organized into even larger ordered structures to produce what is truly a remarkably ordered material, all the way from the molecular scale to the macroscopic product.
Specificity of the hepatitis C virus NS3 serine protease: effects of substitutions at the 3/4A, 4A/4B, 4B/5A, and 5A/5B cleavage sites on polyprotein processing (1994)

Cleavage at four sites (3/4A, 4A/4B, 4B/5A, and 5A/5B) in the hepatitis C virus polyprotein requires a viral serine protease activity residing in the N-terminal one-third of the NS3 protein. Sequence comparison of the residues flanking these cleavage sites reveals conserved features including an acidic residue (Asp or Glu) at the P6 position, a Cys or Thr residue at the P1 position, and a Ser or Ala residue at the P1' position. In this study, we used site-directed mutagenesis to assess the importance of these and other residues for NS3 protease-dependent cleavages. Substitutions at the P7 to P2' positions of the 4A/4B site had varied effects on cleavage efficiency. Only Arg at the P1 position or Pro at P1' substantially blocked processing at this site. Leu was tolerated at the P1 position, whereas five other substitutions allowed various degrees of cleavage. Substitutions with positively charged or other hydrophilic residues at the P7, P3, P2, and P2' positions did not reduce cleavage efficiency. Five substitutions examined at the P6 position allowed complete cleavage, demonstrating that an acidic residue at this position is not essential. Parallel results were obtained with substrates containing an active NS3 protease domain in cis or when the protease domain was supplied in trans. Selected substitutions blocking or inhibiting cleavage at the 4A/4B site were also examined at the 3/4A, 4B/5A, and 5A/5B sites. For a given substitution, a site-dependent gradient in the degree of inhibition was observed, with a 3/4A site being least sensitive to mutagenesis, followed by the 4A/4B, 4B/5A, and 5A/5B sites. In most cases, mutations abolishing cleavage at one site did not affect processing at the other serine protease-dependent sites. However, mutations at the 3/4A site which inhibited cleavage also interfered with processing at the 4B/5A site. Finally, during the course of these studies an additional NS3 protease-dependent cleavage site has been identified in the NS4B region.
Human Immunodeficiency Viruses (1986)

The human immunodeficiency virus (HIV) is the etiologic agent of AIDS. HIVs are enveloped plus-stranded RNA viruses. The HIV genome is organized similarly to other retroviruses. It contains the gag, pol, and env genes which encode structural proteins, viral enzymes, and envelope glycoproteins, respectively. The major structural proteins which are encoded by the gag gene include p17, p24, p7, and p9. Replication begins with the attachment of virus to the target cell via the interaction of gp120 and the cellular receptor CD4. Both HIV-1 and HIV-2 have the same modes of transmission. The most common mode of HIV infection is sexual transmission at the genital mucosa through direct contact with infected blood fluids, including blood, semen, and vaginal secretions. Serological testing for HIV antibody is used for various purposes, including primary diagnosis, screening of blood products, management of untested persons in labor and delivery, evaluation of occupational exposures to blood/body fluid, and epidemiological surveillance. The first generation of HIV antibody assays relied on the detection of antibody to HIV viral protein lysates. A test using a sandwich-capture format and significantly more blood than other methods was more sensitive in early seroconversion. HIV-1 RNA load testing is sometimes requested to resolve equivocal serologic findings or to facilitate the diagnosis of HIV-1 infection during the acute phase or in a pediatric setting.
Catalytic hydride vapour phase epitaxy growth of GaN nanowires (2005)

Catalytic growth of GaN nanowires by hydride vapour phase epitaxy is demonstrated. Nickel-gold was used as a catalyst. Nanowire growth was limited to areas patterned with catalyst. Characterization of the nanowires with transmission electron microscopy, x-ray diffraction, and low temperature photoluminescence shows that the nanowires are stoichiometric 2H-GaN single crystals growing in the [0001] orientation when grown on sapphire, with occasional stacking faults along the c-axis as the only defect type observed in most of the wires. A red shift observed in the photoluminescence was too large to be explained by the minor strain observed alone, and was only marginally affected by temperature, suggesting a superposition of several factors.
Bacterial Communities Constructed in Artificial Consortia of Bacteria and Chlorella vulgaris (2010)

We established artificial consortia of bacteria inoculated from soil and a green alga, Chlorella vulgaris NIES-227. The bacteria and the alga were mixed in a tube or partitioned in a dialysing culture vessel, and the bacterial composition was examined after cultivation. The community of bacteria formed in the consortia included those phylogenetically closely related to the genera Phenylobacterium, Brevundimonas, Phyllobacterium, Afipia, Sphingomonas, Sandaracinobacter, Ramlibacter, Ralstonia, Cellvibrio, and so on. The community also included bacteria belonging to unknown genera within the phyla Bacteroidetes, Verrucomicrobia, and Acidobacteria. It was indicated that Ralstonia sp. and Cellvibrio sp. were attached to the algal cells and Phenylobacterium sp. Ramlibacter sp., Methylophilus sp., and Rhizobiaceae bacterium were not. It was suggested that bacteria belonging to the phylum Bacteroidetes and the class Alphaproteobacteria could be hemi-selectively enriched by the alga.
The electrical and defect properties of erbium-implanted silicon (1991)

A detailed study of the electrical and defect properties of ion-implanted erbium in silicon shows that erbium doping introduces donor states. The concentration of erbium related donors as a function of implant dose saturates at 4×1016 cm−3 at a peak implanted Er-ion concentration of (4–7)×1017 cm−3. The defect levels related to erbium in silicon are characterized by deep level transient spectroscopy and identified as E(0.09), E(0.06), E(0.14), E(0.18), E(0.27), E(0.31), E(0.32), and E(0.48). The dependence of the photoluminescence on annealing temperature for float zone and for Czochralski-grown silicon show that oxygen and lattice defects can enhance the luminescence at 1.54 μm from the erbium. Temperature-dependent capacitance-voltage profiling shows donor emission steps when the Fermi level crosses EC − ET = 0.06 eV and EC − ET = 0.16 eV.
Automatic construction of frame representations for spontaneous speech in unrestricted domains (1998)

This paper presents a system which automatically generates shallow semantic frame structures for conversational speech in unrestricted domains.We argue that such shallow semantic representations can indeed be generated with a minimum amount of linguistic knowledge engineering and without having to explicitly construct a semantic knowledge base. The system is designed to be robust to deal with the problems of speech dysfluencies, ungrammaticalities, and imperfect speech recognition.Initial results on speech transcripts are promising in that correct mappings could be identified in 21% of the clauses of a test set (resp. 44% of this test set where ungrammatical or verb-less clauses were removed).
Transmission of Retroviruses by Transfusion of Screened Blood in Patients Undergoing Cardiac Surgery (1989)

We determined the rates of seroconversion to human immunodeficiency virus type 1 (HIV-1) and human T-cell leukemia virus Type I (HTLV-I) in a cohort of patients receiving transfusions of blood components screened for antibody to HIV-1. Preoperative and postoperative serum samples were collected from 4163 adults undergoing cardiac surgery who received 36,282 transfusions of blood components. The postoperative samples from all patients were tested for serologic evidence of HIV-1 infection, and those that were positive were compared with the corresponding preoperative samples. One case of HIV-1 transmission by transfusion of screened blood components was identified; two preexisting HIV-1 infections were found. Samples from 2749 patients were tested similarly for serologic evidence of HTLV-I infection; these patients received 20,963 units of blood components. Five new cases and two preexisting cases of HTLV-I infection were detected. The observed risk of HIV-1 transmission by transfusion was 0.003 percent per unit; the risk of HTLV-I transmission was 0.024 percent per unit. We conclude that there is a very small risk of HTLV-I infection from transfused blood products that have been screened for antibodies to HIV-1, but that it is nearly 10-fold higher than the risk of HIV-1 infection.
Fabrication of GaAlAs ‘window-stripe’ multi-quantum-well heterostructure lasers utilising Zn diffusion-induced alloying (1984)

By utilising Zn-diffusion induced alloying, a window-stripe GaAs-AlGaAs multi-quantum-well (MQW) laser was fabricated, and an increase by three times in the ultimate output power was achieved as compared with an MQW laser without window.
Secure the image-based simulated telesurgery system (2003)

Telemedicine services involve transmission of patient data over open computer network, and thus confront serious security challenges when the consequences are a matter of life and death. In this paper, we introduce an image-based simulated system for kyphoplasty telesurgery, wherein special attention is given to the fine-grained security implementation issues. Various security requirements are formalized and corresponding solutions are presented. Consequently, we implement the system to work in a secure way, while taking efficiency as a premier consideration.
Lead Optimization toward Proof-of-Concept Tools for Huntington’s Disease within a 4-(1<i>H</i>-Pyrazol-4-yl)pyrimidine Class of Pan-JNK Inhibitors (2015)

Through medicinal chemistry lead optimization studies focused on calculated properties and guided by X-ray crystallography and computational modeling, potent pan-JNK inhibitors were identified that showed submicromolar activity in a cellular assay. Using in vitro ADME profiling data, 9t was identified as possessing favorable permeability and a low potential for efflux, but it was rapidly cleared in liver microsomal incubations. In a mouse pharmacokinetics study, compound 9t was brain-penetrant after oral dosing, but exposure was limited by high plasma clearance. Brain exposure at a level expected to support modulation of a pharmacodynamic marker in mouse was achieved when the compound was coadministered with the pan-cytochrome P450 inhibitor 1-aminobenzotriazole.