gebhart/patrepeval huggingface dataset:
A Markov random field model for term dependencies (2005)

This paper develops a general, formal framework for modeling term dependencies via Markov random fields. The model allows for arbitrary text features to be incorporated as evidence. In particular, we make use of features based on occurrences of single terms, ordered phrases, and unordered phrases. We explore full independence, sequential dependence, and full dependence variants of the model. A novel approach is developed to train the model that directly maximizes the mean average precision rather than maximizing the likelihood of the training data. Ad hoc retrieval experiments are presented on several newswire and web collections, including the GOV2 collection used at the TREC 2004 Terabyte Track. The results show significant improvements are possible by modeling dependencies, especially on the larger web collections.
Polymerization Kinetics: Monitoring Monomer Conversion Using an Internal Standard and the Key Role of Sample t0 (2010)

The use of an internal standard is a conventional and convenient way to monitor the conversion of one or several monomers during a controlled radical polymerization. However, the validity of this technique relies on an accurate determination of the initial monomer-to-internal standard ratio, A0, because all subsequent calculations of the conversion are based on this value. In most kinetic studies using an internal standard for the determination of the conversion, an incorrect determination of the value of A0 will result in absurd conclusions and will thus be detected and corrected. However, an incorrect determination of A0 can be significantly misleading in the case of controlled polymerization. This article shows that deviation of the kinetic plots from their true shape because of an error in A0 will not look absurd in the case of controlled polymerization. On the contrary, the plots will fit with a possible deviation of the polymerization from a “quasi-living” to a less controlled process. As a consequence, an error on A0 may not be detected and can result in a misinterpretation of the behavior of the system.
Development of Ammonia Adsorption Filter and Its Application to LSI Manufacturing Environment (1994)

Activated carbon treated with a hydrogen salt is found to be effective in suppressing ammonia concentration in LSI cleanrooms. The hydrogen salt which contains neither phosphor nor metals is utilized. Its adsorption capacity is about 1000 mol/m 3 -carbon. This corresponds to a lifetime of about two years in an ordinary cleanroom. Compared to this, untreated activated carbon adsorbs less than 10 mol/m 3 , so it cannot be used for more than 10 days. A chemically amplified resist, known to be susceptible to degradation from alkaline gaseous substances in cleanrooms, is shown to maintain its 0.25-µm line and space patterns under hydrogen salt treated carbon filtered air, even when the developing is delayed for 60 min after excimer laser exposure.
Wisconsin physician survey on diagnosis and treatment of obesity (2014)

Robust in vitro systems are important in elucidating mechanisms regarding the heterogenetic nature of in vivo immune responses and contribute with knowledge to design good in vivo experiments. In this study, we show that initial Th1 and in particular Th2 polarization was negatively influenced by even small percentages (<5-10%) of "polluting" memory CD4+ T cells producing IL-5, IL-9, IL-10 IL-13, IL-21, IL-22, IL-31 and IFN-γ that are normally found after standard immunomagnetic bead separation of naïve CD4+ T cell. By using an alternative protocol for immunomagnetic bead separation of naïve CD4+ T cells, we found that cultures of the obtained >99% naïve CD4+ T cells resulted in better Th1 and Th2 polarization with significant reduced fractions of IL-4+ and IFN-γ+ CD4+ T cells, respectively. Moreover, the Th2 primed >99% naïve CD4+ T cells showed significantly higher ratio of IL-4+:IFN-γ+ (>4 fold) and GATA-3:+T-bet+ (>3 fold) CD4+ T cells when compared with the standard purified >90-95% naïve CD4+ T cells primed under the same culture conditions. This suggests immunomagnetic bead separation, a low cost and easy available technique, with few modifications to the manufacturer's protocol as an attractive alternative for laboratories not having a cell sorter. Taken together, we report that it is essential to use rigorously purified (>99%) naïve CD4+ T cells for optimal initial in vitro Th1 and Th2 priming.
Arabidopsis 22-Kilodalton Peroxisomal Membrane Protein. Nucleotide Sequence Analysis and Biochemical Characterization1 (1999)

We sequenced and characterized PMP22 (22-kD peroxisomal membrane protein) from Arabidopsis, which shares 28% to 30% amino acid identity and 55% to 57% similarity to two related mammalian peroxisomal membrane proteins, PMP22 and Mpv17. Subcellular fractionation studies confirmed that the Arabidopsis PMP22 is a genuine peroxisomal membrane protein. Biochemical analyses established that the Arabidopsis PMP22 is an integral membrane protein that is completely embedded in the lipid bilayer. In vitro import assays demonstrated that the protein is inserted into the membrane posttranslationally in the absence of ATP, but that ATP stimulates the assembly into the native state. Arabidopsis PMP22 is expressed in all organs of the mature plant and in tissue-cultured cells. Expression of PMP22 is not associated with a specific peroxisome type, as it is detected in seeds and throughout postgerminative growth as cotyledon peroxisomes undergo conversion from glyoxysomes to leaf-type peroxisomes. Although PMP22 shows increased accumulation during the growth of young seedlings, its expression is not stimulated by light.
Hedgehog Fights Back: Mechanisms of Acquired Resistance against Smoothened Antagonists (2011)

Acquired resistance to targeted therapies threatens the value of these otherwise very promising agents. The recent description of resistance to the Hedgehog pathway inhibitor vismodegib (GDC-0449) in a medulloblastoma patient who had a dramatic initial response has spurred efforts to understand potential mechanisms of drug resistance. Elucidating these mechanisms will play a significant role in informing strategies to overcome this meaningful limitation.
Loss of heterozygosity at autosomal and X-linked loci during tumor progression in a patient with melanoma. (1987)

Restriction fragment length polymorphisms at 61 autosomal and 7 X-linked loci were screened for heterozygosity in cell lines derived from 6 independent metastases and autologous B-cells from a patient with melanoma. Segregations resulting in the loss of heterozygosity were detected in the tumor cells at 8 of 16 autosomes with at least 1 informative locus and at the 3 informative X-linked loci. With a single exception, karyotypic abnormalities were not detected in the region of loci where loss of heterozygosity had been detected. Three patterns of loss were identified: unique segregations in cells from a single metastasis; segregation of the same alleles in different subsets of metastases; and identical segregations in all 6 metastases. The monoclonal derivation of the 6 metastases is supported by the inactivation of the same X-chromosome and the presence of identical segregation at loci on chromosomes 9 and X. Analysis of the patterns of segregation in the metastatic tumor cells permitted the development of a genealogy of tumor progression in this patient and the development of a model of tumor progression which describes the accumulation of selectively neutral and advantageous segregations in metastatic tumor cells.
Residue 2 of TIMP-1 Is a Major Determinant of Affinity and Specificity for Matrix Metalloproteinases but Effects of Substitutions Do Not Correlate with Those of the Corresponding P1′ Residue of Substrate (1999)

The unregulated activities of matrix metalloproteinases (MMPs) are implicated in disease processes including arthritis and tumor cell invasion and metastasis. MMP activities are controlled by four homologous endogenous protein inhibitors, tissue inhibitors of metalloproteinases (TIMPs), yet different TIMPs show little specificity for individual MMPs. The large interaction interface in the TIMP-1.MMP-3 complex includes a contiguous region of TIMP-1 around the disulfide bond between Cys1 and Cys70 that inserts into the active site of MMP-3. The effects of fifteen different substitutions for threonine 2 of this region reveal that this residue makes a large contribution to the stability of complexes with MMPs and has a dominant influence on the specificity for different MMPs. The size, charge, and hydrophobicity of residue 2 are key factors in the specificity of TIMP. Threonine 2 of TIMP-1 interacts with the S1' specificity pocket of MMP-3, which is a key to substrate specificity, but the structural requirements in TIMP-1 residue 2 for MMP binding differ greatly from those for the corresponding residue of a peptide substrate. These results demonstrate that TIMP variants with substitutions for Thr2 represent suitable starting points for generating more targeted TIMPs for investigation and for intervention in MMP-related diseases.
Novel Type of ADP-Forming Acetyl Coenzyme A Synthetase in Hyperthermophilic Archaea : Heterologous Expression and Characterization of Isoenzymes from the Sulfate Reducer Archaeoglobus fulgidus and the Methanogen Methanococcus jannaschii (2002)

Acetyl coenzyme A (CoA) synthetase (ADP forming) (ACD) represents a novel enzyme of acetate formation and energy conservation (acetyl-CoA + ADP + P(i) right harpoon over left harpoon acetate + ATP + CoA) in Archaea and eukaryotic protists. The only characterized ACD in archaea, two isoenzymes from the hyperthermophile Pyrococcus furiosus, constitute 145-kDa heterotetramers (alpha(2), beta(2)). The coding genes for the alpha and beta subunits are located at different sites in the P. furiosus chromosome. Based on significant sequence similarity of the P. furiosus genes, five open reading frames (ORFs) encoding putative ACD were identified in the genome of the hyperthermophilic sulfate-reducing archaeon Archaeoglobus fulgidus and one ORF was identified in the hyperthermophilic methanogen Methanococcus jannaschii. The ORFs constitute fusions of the homologous P. furiosus genes encoding the alpha and beta subunits. Two ORFs, AF1211 and AF1938, of A. fulgidus and ORF MJ0590 of M. jannaschii were cloned and functionally overexpressed in Escherichia coli. The purified recombinant proteins were characterized as distinctive isoenzymes of ACD with different substrate specificities. In contrast to the Pyrococcus ACD, the ACDs of Archaeoglobus and Methanococcus constitute homodimers of about 140 kDa composed of two identical 70-kDa subunits, which represent fusions of the homologous P. furiosus alpha and beta subunits in an alphabeta (AF1211 and MJ0590) or betaalpha (AF1938) orientation. The data indicate that A. fulgidus and M. jannaschii contains a novel type of ADP-forming acetyl-CoA synthetase in Archaea, in which the subunit polypeptides and their coding genes are fused.
Function and glycosylation of plant-derived antiviral monoclonal antibody (2003)

Plant genetic engineering led to the production of plant-derived mAb (mAb P ), which provides a safe and economically feasible alternative to the current methods of antibody production in animal systems. In this study, the heavy and light chains of human anti-rabies mAb were expressed and assembled in planta under the control of two strong constitutive promoters. An alfalfa mosaic virus untranslated leader sequence and Lys-Asp-Glu-Leu (KDEL) endoplasmic reticulum retention signal were linked at the N and C terminus of the heavy chain, respectively. mAb P was as effective at neutralizing the activity of the rabies virus as the mammalian-derived antibody (mAb M ) or human rabies Ig (HRIG). The mAb P contained mainly oligomannose type N-glycans (90%) and had no potentially antigenic α(1,3)-linked fucose residues. mAb P had a shorter half-life than mAb M . The mAb P was as efficient as HRIG for post-exposure prophylaxis against rabies virus in hamsters, indicating that differences in N-glycosylation do not affect the efficacy of the antibody in this model.
Highly Conformal Deposition of Pure Co Films by MOCVD Using Co[sub 2](CO)[sub 8] as a Precursor (2006)

Highly conformal Co thin films were deposited on trenches with an aspect ratio of 13 by metallorganic chemical vapor deposition (MOCVD) using as a precursor in a low-temperature regime of where the growth rate was . Lowering the pressure of the process reduces the number of collisions in the gas phase and, thus, widens the temperature regime in which the surface reaction controls the growth rate. A processing pressure of allows for conformal deposition only at , whereas deposition at a reduced pressure of widens the temperature regime in which excellent conformality can be obtained. The conformal Co thin film, produced at and , showed a resistivity of and contained 1.0 atom % oxygen and less than 1.0 atom % carbon. After annealing this film at , its resistivity was reduced to , which is close to the bulk resistivity of Co. Therefore, this low-temperature process, which allows for the excellent conformal deposition of pure Co films, can be utilized to produce silicided contacts for advanced devices which require a low contact resistance and good electrical performance.
Expression of the Proto-Oncogene Axl in Renal Cell Carcinoma (2003)

In this investigation, we examined the role of the Axl proto-oncogene in renal cell carcinoma (RCC). Axl is a tyrosine kinase receptor implicated in myeloid leukogenesis, and has been found to be overexpressed in lung cancers and breast cancers. Axl has been described to act as a mitogenic factor along with its ligand Gas-6. Axl has also shown to have a role in apoptosis, cell adhesion, and chemotaxis. The differential expression of the Axl RNA transcript was examined in 20 pairs of matched normal kidney and clear cell RCC patient samples. We found that there was a significant increase in the steady-state levels of Axl mRNA in the RCC compared with the normal kidney pair (Student's paired t-test P < 0.001). There was also a significant increase in Axl expression overall in RCC compared to normal kidney (P < 0.03). Western blotting was utilized to determine Axl protein levels in six out of the 20 pairs of the normal/RCC matched pairs. Overall, the level of expression was not significantly different between the paired normal kidneys and kidney tumors, but the detected Axl protein appeared to be at slightly different molecular weights. Primers were constructed for the two known Axl variant, RT-PCR performed, but no differences were observed in the expression of each variant. Next, we performed a gene silencing experiment utilizing double-stranded RNA constructed to silence the Axl gene in the 293 transformed kidney cell line. There was a 50% decrease in Axl gene expression in the RNAi transfected over control cells. In addition, flow cytometry performed to determine DNA content showed a 30% increase in G1/G0 cells, which were transfected with axl RNAi compared to control. Altogether, these findings suggest an overexpression of Axl as part of a proliferative phenotype in RCC.
Thermoluminescent and Exoemission Properties of New High-Sensitivity TLD a-Al2O3:C Crystals (1990)

Abstract To determine the mechanisms of the electron-hole processes in a-Al2O3:C crystals, characteristics of their thermo- and photo-stimulated exoelectron emission (TSEE, PSEE) and luminescence have been studied. It is shown that the emission of F+ centres takes place with the temperature shift relative to the emission of F centres, and the hole-induced TSEE takes place synchronously with the emission of F centres. The electron energy distribution parameters at PSEE do not depend on the energy of stimulating light photons, which testifies to thermalisation of the released holes before their recombination. Parameters determined for doped anion-deficient corundum crystals are considered within the framework of the two-stage Auger process model.
Topical Retapamulin Ointment, 1%, versus Sodium Fusidate Ointment, 2%, for Impetigo: A Randomized, Observer-Blinded, Noninferiority Study (2007)

Retapamulin is a highly effective and convenient new treatment option for impetigo, with efficacy against isolates resistant to existing therapies.
Regulation of tau phosphorylation in microtubule fractions by apolipoprotein E (1999)

In Alzheimer's disease (AD), a family of proteins collectively named tau are displaced from their normal association with microtubules and are found in in a hyperphosphorylated state deposited into paired helical filaments (PHFs). PHFs are the hallmark cytoskeletal pathology of the disease, and the degree of PHF pathology correlates with the clinical severity of AD. Certain apolipoprotein E (apoE) isoforms have been identified as either risk or protective factors for AD, and one of the proposed mechanisms involves an interaction and potentially modulatory effects on tau hyperphosphorylation by the different apoE isoforms. In these studies, we directly tested the effects of apoE, E2 ,E3, and E4 on AD-like phosphorylation of tau in brain microtubule fractions. We found that apoE attenuates tau hyperphosphorylation in the fractions, but the pattern was indistinguishable for the different isoforms. J. Neurosci. Res. 56:271–274, 1999. © 1999 Wiley-Liss, Inc.
Characterization and Biologic Activities of Recombinant Rat Soluble Interleukin-6 Receptor (1996)

The soluble interleukin-6 receptor (sIL-6R) consists of the extracellular domain of the membrane-bound IL-6 receptor (gp80) found on many types of cells. Contrary to most other soluble cytokine receptors, it possesses in vitro agonistic properties, yet its physiologic role remains unknown. We have generated a cDNA encoding the rat sIL-6R and have expressed and purified the protein using Escherichia coli and baculovirus systems. Analysis of purified protein by electrophoresis and silver staining showed a single band migrating at 35 kDa for E. coli (nonglycosylated) and at 47 kDa for baculovirus-derived material. The purified protein is biologically active, as determined by the ability to convert human hepatoma cells (HepG2) from nonresponsive to responsive to rat IL-6 and induce acute-phase protein synthesis. Most important, we show that rat sIL-6R directly induces proliferation of the IL-6-dependent murine hybridoma cell line (B9) in an IL-6-like manner, with 50% proliferation induced by 100 ng/ml of baculovirus-derived receptor protein. Physiologic concentrations of sIL-6R dramatically enhance the sensitivity of B9 cells to IL-6, indicating that the bioassay for IL-6 is susceptible to modulation by the presence of sIL-6R in rodent serum samples. This sIL-6R-dependent B9 cell proliferation is fully abrogated by antibodies directed against rodent IL-6 and indicates autocrine production of low amounts of IL-6 by the B9 cell line.
Deep Learning Assessment of Tumor Proliferation in Breast Cancer Histological Images (2016)

Current analysis of tumor proliferation, the most salient prognostic biomarker for invasive breast cancer, is limited to subjective mitosis counting by pathologists in localized regions of tissue images. This study presents the first data-driven integrative approach to characterize the severity of tumor growth and spread on a categorical and molecular level, utilizing multiple biologically salient deep learning classifiers to develop a comprehensive prognostic model. Our approach achieves pathologist-level performance on three-class categorical tumor severity prediction. It additionally pioneers prediction of molecular expression data from a tissue image, obtaining a Spearman's rank correlation coefficient of 0.60 with ex vivo mean calculated RNA expression. Furthermore, our framework is applied to identify over two hundred unprecedented biomarkers critical to the accurate assessment of tumor proliferation, validating our proposed integrative pipeline as the first to holistically and objectively analyze histopathological images.
VAX vector architecture (1990)

The VAX Architecture has been extended to include an integrated, register-based vector processor. This extension allows both high-end and low-end implementations and can be supported with only small changes by VAX/VMS and VAX/ULTRIX operating systems. The extension is effectively exploited by the new vectorizing capabilities of VAX FORTRAN. Features of the VAX Vector Architecture and the design decisions which make it a consistent extension of the VAX Architecture are discussed.
PEG–Peptide Conjugates (2014)

The remarkable diversity of the self-assembly behavior of PEG-peptides is reviewed, including self-assemblies formed by PEG-peptides with β-sheet and α-helical (coiled-coil) peptide sequences. The modes of self-assembly in solution and in the solid state are discussed. Additionally, applications in bionanotechnology and synthetic materials science are summarized.
HKI-272 in Non–Small Cell Lung Cancer (2007)

Somatic mutations in the kinase domain of the epidermal growth factor receptor (EGFR) gene are found in approximately 10% of lung adenocarcinomas sequenced in the United States and in approximately 30% sequenced in Asia. These mutations are associated with sensitivity to the EGFR inhibitors gefitinib and erlotinib. Many patients who initially respond to erlotinib or gefitinib subsequently relapse. Studies have identified EGFR T790M mutations in tumors from patients who initially responded and then relapsed. The T790M mutation, when combined in vitro with treatment-sensitizing EGFR mutations, permits the continued growth of tumor cells in the presence of erlotinib and gefitinib. HKI-272 is an irreversible EGFR/HER/ErbB inhibitor that has been shown to inhibit the growth of T790M mutant cells in vitro in human lung cancer cell lines and in murine cells transfected with sensitizing EGFR mutations. A phase I HKI-272 monotherapy trial in patients with solid tumors is close to completion. Preliminary analyses of the trial, presented at the 2006 annual meeting of American Society of Clinical Oncology, showed that HKI-272 can achieve stable disease control for over 6 months in some patients with non-small cell lung cancer that has progressed after treatment with gefitinib or erlotinib. A phase II trial of HKI-272 in non-small cell lung cancer patients has been initiated. HKI-272 might offer benefits to non-small cell lung cancer patients who have relapsed after an initial response to erlotinib.
Amyloid Deposits and Amyloidosis (1980)

SINCE Cohen's review of amyloidosis was published in the Journal in 1967, there have been major advances in our understanding of what was less than a decade ago an untreatable, usually lethal disease complex of unknown nature, cause, and pathogenesis. Much of the mystery about the character of the "waxy, eosinophilic" tissue deposits, which Virchow believed in 1853 to be of polysaccharide composition and consequently designated as "amyloid" (starch-like or cellulose-like) has now yielded to investigations employing a wide variety of chemical and physical techniques. Once it was demonstrated that unique fibrillar components comprised over 90 per cent of amyloid . . .