gebhart/patrepeval huggingface dataset:
Sampling error and intraobserver variation in liver biopsy in patients with chronic HCV infection (2002)

Liver biopsy samples taken from the right and left hepatic lobes differed in histological grading and staging in a large proportion of chronic hepatitis C virus patients; however, differences of more than one stage or grade were uncommon. A sampling error may have led to underdiagnosis of cirrhosis in 14.5% of the patients. These differences could not be attributed to intraobserver variation, which appeared to be low.
A glutamic acid specific serine protease utilizes a novel histidine triad in substrate binding (1993)

Proteases specific for cleavage after acidic residues have been implicated in several disease states, including epidermolysis, inflammation, and viral processing. A serine protease with specificity toward glutamic acid substrates (Glu-SGP) has been crystallized in the presence of a tetrapeptide ligand and its structure determined and refined to an R-factor of 17% at 2.0-A resolution. This structure provides an initial description of the design of proteolytic specificity for negatively charged residues. While the overall fold of Glu-SGP closely resembles that observed in the pancreatic-type serine proteases, stabilization of the negatively charged substrate when bound to this protein appears to involve a more extensive part of the protease than previously observed. The substrate carboxylate is bound to a histidine side chain, His213, which provides the primary electrostatic compensation of the negative charge on the substrate, and to two serine hydroxyls, Ser192 and Ser216. Glu-SGP displays maximum activity at pH 8.3, and assuming normal pKa's, the glutamate side chain and His213 will be negatively charged and neutral, respectively, at this pH. In order for His213 to carry a positive charge at the optimal pH, its pKa will have to be raised by at least two units. An alternative mechanism for substrate charge compensation is suggested that involves a novel histidine triad, His213, His199, and His228, not observed in any other serine protease. The C-terminal alpha-helix, ubiquitous to all pancreatic-type proteases, is directly linked to this histidine triad and may also play a role in substrate stabilization.(ABSTRACT TRUNCATED AT 250 WORDS)
CD19 as an attractive target for antibody-based therapy (2012)

Despite progress in the treatment of B cell disorders, novel treatment approaches are still highly needed. CD19 is a pan-B cell marker that is recognized as a potential immunotherapy target for B cell disorders, including blood-borne malignancies and autoimmune diseases. Although initial attempts to target CD19 were unsuccessful, a new wave of investigational agents is currently in development. These agents are based on novel antibody-based technologies and formats that appear to better exploit CD19's therapeutic potential, and some promising clinical study data has already been reported. This review provides an overview and the rationale for the most advanced CD19-targeting programs in development.
The Energy Balance of Corn Ethanol: An Update (2002)

Studies conducted since the late 1970s have estimated the net energy value (NEV) of corn ethanol. However, variations in data and assumptions used among the studies have resulted in a wide range of estimates. This study identifies the factors causing this wide variation and develops a more consistent estimate. We conclude that the NEV of corn ethanol has been rising over time due to technological advances in ethanol conversion and increased efficiency in farm production. We show that corn ethanol is energy efficient as indicated by an energy output:input ratio of 1.34.
Candida albicans Hyr1p Confers Resistance to Neutrophil Killing and Is a Potential Vaccine Target (2010)

Candida albicans is the most common cause of invasive fungal infections in humans. It is unclear how C. albicans escapes from phagocytic attack and survives in the hostile blood environment during life-threatening systemic infections. Using a conditional overexpression or suppression genetic strategy, we discovered that HYR1 gene reduced phagocytic killing activity of C. albicans in vitro and increased tissue fungal burden in vivo. Concordant with its positive regulation by the transcription factor Bcr1p, autonomous expression of HYR1 complemented the hypersusceptibility to phagocyte-mediated killing of a bcr1 null mutant of C. albicans in vitro. As for C. albicans, heterologous expression of HYR1 in Candida glabrata rendered the organism more resistant to neutrophil killing activity. Vaccination with a recombinant Hyr1p significantly protected mice against hematogenously disseminated candidiasis (P = .001). Finally, anti-rHyr1p polyclonal antibodies enhanced mouse neutrophil killing activity by directly neutralizing rHyr1p effects in vitro. Thus, Hyr1 is an important virulence factor for C. albicans, mediating resistance to phagocyte killing. Hyr1p is a promising target for vaccine or other immunological or small molecule intervention to improve the outcomes of disseminated candidiasis.
Five different anti-prostate-specific membrane antigen (PSMA) antibodies confirm PSMA expression in tumor-associated neovasculature. (1999)

Prostate-specific membrane antigen (PSMA) is a type II integral membrane glycoprotein that was initially characterized by the monoclonal antibody (mAb) 7E11. PSMA is highly expressed in prostate secretory-acinar epithelium and prostate cancer as well as in several extraprostatic tissues. Recent evidence suggests that PSMA is also expressed in tumor-associated neovasculature. We examined the immunohistochemical characteristics of 7E11 and those of four recently developed anti-PSMA mAbs (J591, J415, and Hybritech PEQ226.5 and PM2J004.5), each of which binds a distinct epitope of PSMA. Using the streptavidin-biotin method, we evaluated these mAbs in viable prostate cancer cell lines and various fresh-frozen benign and malignant tissue specimens. In the latter, we compared the localization of the anti-PSMA mAbs to that of the anti-endothelial cell mAb CD34. With rare exceptions, all five anti-PSMA mAbs reacted strongly with the neovasculature of a wide spectrum of malignant neoplasms: conventional (clear cell) renal carcinoma (11 of 11 cases), transitional cell carcinoma of the urinary bladder (6 of 6 cases), testicular embryonal carcinoma (1 of 1 case), colonic adenocarcinoma (5 of 5 cases), neuroendocrine carcinoma (5 of 5 cases), glioblastoma multiforme (1 of 1 cases), malignant melanoma (5 of 5 cases), pancreatic duct carcinoma (4 of 4 cases), non-small cell lung carcinoma (5 of 5 cases), soft tissue sarcoma (5 of 6 cases), breast carcinoma (5 of 6 cases), and prostatic adenocarcinoma (2 of 12 cases). Localization of the anti-PSMA mAbs to tumor-associated neovasculature was confirmed by CD34 immunohistochemistry in sequential tissue sections. Normal vascular endothelium in non-cancer-bearing tissue was consistently PSMA negative. The anti-PSMA mAbs reacted with the neoplastic cells of prostatic adenocarcinoma (12 of 12 cases) but not with the neoplastic cells of any other tumor type, including those of benign and malignant vascular tumors (0 of 3 hemangiomas, 0 of 1 hemangioendothelioma, and 0 of 1 angiosarcoma). The mAbs to the extracellular PSMA domain (J591, J415, and Hybritech PEQ226.5) bound viable prostate cancer cells (LNCaP and PC3-PIP), whereas the mAbs to the intracellular domain (7E11 and Hybritech PM2J004.5) did not. All five anti-PSMA mAbs reacted with fresh-frozen benign prostate secretory-acinar epithelium (28 of 28 cases), duodenal columnar (brush border) epithelium (11 of 11 cases), proximal renal tubular epithelium (5 of 5 cases), colonic ganglion cells (1 of 12 cases), and benign breast epithelium (8 of 8 cases). A subset of skeletal muscle cells was positive with 7E11 (7 of 7 cases) and negative with the other four anti-PSMA mAbs. PSMA was consistently expressed in the neovasculature of a wide variety of malignant neoplasms and may be an effective target for mAb-based antineovasculature therapy.
Future directions in silicon ICs for RF personal communications (2002)

This paper presents an overview of technical challenges in achieving higher integration levels, lower power dissipation, smaller form factor, and lower cost in portable battery-powered RF transceivers for personal communications applications. Specific emphasis is placed on silicon integrated circuits for transceivers in the 800 MHz-2.5 GHz range of frequencies.
Comprehensive transposon mutant library of Pseudomonas aeruginosa (2003)

We have developed technologies for creating saturating libraries of sequence-defined transposon insertion mutants in which each strain is maintained. Phenotypic analysis of such libraries should provide a virtually complete identification of nonessential genes required for any process for which a suitable screen can be devised. The approach was applied to Pseudomonas aeruginosa, an opportunistic pathogen with a 6.3-Mbp genome. The library that was generated consists of 30,100 sequence-defined mutants, corresponding to an average of five insertions per gene. About 12% of the predicted genes of this organism lacked insertions; many of these genes are likely to be essential for growth on rich media. Based on statistical analyses and bioinformatic comparison to known essential genes in E. coli, we estimate that the actual number of essential genes is 300-400. Screening the collection for strains defective in two defined multigenic processes (twitching motility and prototrophic growth) identified mutants corresponding to nearly all genes expected from earlier studies. Thus, phenotypic analysis of the collection may produce essentially complete lists of genes required for diverse biological activities. The transposons used to generate the mutant collection have added features that should facilitate downstream studies of gene expression, protein localization, epistasis, and chromosome engineering.
Femtojoule electro-optic modulation using a silicon–organic hybrid device (2015)

Energy-efficient electro-optic modulators are at the heart of short-reach optical interconnects, and silicon photonics is considered the leading technology for realizing such devices. However, the performance of all-silicon devices is limited by intrinsic material properties. In particular, the absence of linear electro-optic effects in silicon renders the integration of energy-efficient photonic–electronic interfaces challenging. Silicon–organic hybrid (SOH) integration can overcome these limitations by combining nanophotonic silicon waveguides with organic cladding materials, thereby offering the prospect of designing optical properties by molecular engineering. In this paper, we demonstrate an SOH Mach–Zehnder modulator with unprecedented efficiency: the 1-mm-long device consumes only 0.7 fJ bit−1 to generate a 12.5 Gbit s−1 data stream with a bit-error ratio below the threshold for hard-decision forward-error correction. This power consumption represents the lowest value demonstrated for a non-resonant Mach–Zehnder modulator in any material system. It is enabled by a novel class of organic electro-optic materials that are designed for high chromophore density and enhanced molecular orientation. The device features an electro-optic coefficient of r33≈180 pm V−1 and can be operated at data rates of up to 40 Gbit s−1. Scientists have demonstrated a hybrid silicon–organic electro-optic modulator that consumes just 0.7 fJ of energy per processed data bit. Such highly energy efficient optical modulators are needed for the short-reach, high-density data interconnects of the future. The 1-mm-long device is based on a Mach–Zehnder interferometer design and is compatible with data rates of up to 40 Gbit s−1. The modulator realizes a subfemtojoule efficiency by employing silicon slot waveguides filled with a highly nonlinear organic material called DLD164, which has a very large electro-optic coefficient of 180 pm V−1. The researchers, who are from Europe, the USA and China, claim that the modulator has the lowest power consumption demonstrated to date for a non-resonant Mach–Zehnder modulator realized in any material system.
Paclitaxel Plus Carboplatin Versus Gemcitabine Plus Paclitaxel in Advanced Non–Small-Cell Lung Cancer: A Phase III Randomized Trial (2002)

The PG combination is as equally active and well tolerated as the PC combination in patients with advanced NSCLC.
Inheritance of Three Stearic Acid Mutants of Soybean1 (1985)

Three mutant lines of soybean [ Glycine max (L.) Merrill] were identified that had three‐ to six‐fold increases in stearic acid content in the seed oil compared with their parents. Our objective was to determine the inheritance of high stearic acid in the three mutants. Reciprocal crosses were made between each mutant and its parent and among the three mutants. Fatty acid analysis of the seed oil of the parents and the F 1 , F 2 , and F 3 generations indicated that high stearic acid in the mutants was controlled by a single locus. The Fas allele for low stearic acid in each parent was partially dominant to the allele for high stearic acid in the mutant derived from it. Crosses among the mutants indicated that each possessed a different allele at the same locus. The allele fas a , in the mutant A6, and fas 6 , in the mutant FA41545, were not dominant to each other. Both fas a and fas b were completely dominant to thefas allele in the mutant A81‐606085. None of the segregates from the mutant ✕ mutant crosses had a stearic acid content outside the range of the parents. Maternal and cytoplasmic effects were not important in the control of stearic acid content in these mutants.
Regioselective Labeling of Antibodies through N-Terminal Transamination (2007)

A convenient new method is described for the introduction of ketone groups at the N-termini of antibodies. The reaction occurs in the presence of pyridoxal-5'-phosphate under conditions mild enough to maintain antigen binding function, as confirmed by enzyme-linked immunosorbent assay. Further derivatization of these functional sites was accomplished through oxime formation, yielding well-defined antibody conjugates for a wide range of applications. The ability of the modified antibodies to bind their targets was confirmed via immunodot blot analysis. The generality of this method has been demonstrated on a number of monoclonal and polyclonal antibodies, all with different binding specificities.
Behavioral Testing After Spinal Cord Injury: Congruities, Complexities, and Controversies (2004)

Selection and implementation of behavioral tests in spinal cord injury research is an important process, and yet few papers have focused on these issues. The critical component of any behavioral experiment is the ability to produce reliable, reproducible, and worthwhile data. Unfortunately, the difference between worthwhile and worthless data is often subtle. This paper describes factors that must be considered in order to select the most sensitive behavioral tests to match the hypothesis of the experiment and apply any test in a standardized, consistent manner. Classifications of behavioral tests, their strengths and limitations, as well as methods to overcome these limitations are discussed. Recent work in translating behavioral tests from rats to mice is also provided. The purpose of this article is to provide a framework by which behavioral testing can be standardized within and across spinal cord injury labs.
CELL ADHESION MOLECULES: Implications for a Molecular Histology (1991)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
CD4 monoclonal antibody pairs for immunosuppression and tolerance induction (1987)

A pair of rat anti-mouse CD4 monoclonal antibodies (mAb) have been selected which bind to different epitopes of the molecule. Both the mAb are rat IgG2b and show clear synergistic activity in complement lysis in vitro. When injected together in vivo, they exhibit an improved immunosuppressive effect, compared to each antibody alone, on allogeneic graft rejection, humoral responses and on tolerance induction. Limiting dilution analysis indicates that the in vivo depletion of interleukin 2-producing cells is improved using both mAb by 2-3-fold over that obtained with the individual antibodies. As little as 60 ng per mouse of the CD4 antibody pair was sufficient to allow the induction of tolerance to human gamma-globulin, even without elimination of the CD4+ cells. The results suggest that appropriate antibody pairs may be good candidates for effective immunosuppressive serotherapy in man.
Radical Polymerization Initiated from a Solid Substrate. 3. Grafting from the Surface of an Ultrafine Powder (1999)

Kinetics of grafting radical polymerization of styrene and methyl methacrylate from the surface of titanium dioxide powder has been studied. Polymerization was initiated by hydroperoxide macroinitiator attached to the surface of the TiO2 particles. The rate of grafting is linearly proportional to the rate of the initiation reaction from the surface. The fraction of the grafted polymer in the total polymer yield depends on the chain transfer reaction and on the mechanism of chain termination (combination or disproportionation). A mathematical model of the process has been used to explain the kinetics. The Trommsdorff effect has been found for the case of methyl methacrylate graft polymerization when the grafting amount approached high values. The regime of the multilayer coating formation has been studied in model experiments in the presence of macroinhibitor with the powder before coating by PMMA.
Synthesis and reactions of functionalised gold nanoparticles (1995)

Stable functionalised gold nanoparticles are prepared by simultaneous reduction of tetrachloroaurate ions and attachment of bifunctional organic thiol molecules to the growing gold nuclei leading to a material whose chemical behaviour is characterised by the vacant functionality of the bifunctional thiol ligand.
Sila-haloperidol:  A Silicon Analogue of the Dopamine (D2) Receptor Antagonist Haloperidol (2004)

Haloperidol (1a), a dopamine (D2) receptor antagonist, is in clinical use as an antipsychotic agent. Carbon/silicon exchange (sila-substitution) at the 4-position of the piperidine ring of 1a (R3COH → R3SiOH) leads to sila-haloperidol (1b). Sila-haloperidol was synthesized in a multistep synthesis, starting from tetramethoxysilane, and was isolated as the hydrochloride 1b·HCl. ESI-MS studies of aqueous solutions of the silanol 1b and the corresponding disiloxane 10 at different pH values revealed a remarkable stability of 1b. The C/Si analogues 1a·HCl and 1b·HCl were structurally characterized by single-crystal X-ray diffraction and solution ([D6]DMSO) NMR spectroscopy. Analogous chair conformations of the piperidinium (1a·HCl) and 4-silapiperidinium (1b·HCl) skeleton were observed in the crystal, and two analogous chair conformations of the cations were detected in solution, the molar ratios of these two conformers differing substantially (1a·HCl, 13:1; 1b·HCl, 2:1). In radioligand binding studies, the C/Si analogues 1a and 1b displayed similar potencies at recombinant human dopamine hD1, hD4, and hD5 receptors, whereas the silicon compound 1b was 4.7-fold more potent at hD2 receptors than its carbon analogue 1a; i.e., sila-substitution of haloperidol has changed the receptor selectivity profile.
Jitter Analysis and a Benchmarking Figure-of-Merit for Phase-Locked Loops (2009)

This brief analyzes the jitter as well as the power dissipation of phase-locked loops (PLLs). It aims at defining a benchmark figure-of-merit (FOM) that is compatible with the well-known FOM for oscillators but now extended to an entire PLL. The phase noise that is generated by the thermal noise in the oscillator and loop components is calculated. The power dissipation is estimated, focusing on the required dynamic power. The absolute PLL output jitter is calculated, and the optimum PLL bandwidth that gives minimum jitter is derived. It is shown that, with a steep enough input reference clock, this minimum jitter is <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">independent</i> of the reference frequency and output frequency <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">for</i> <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">a</i> <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">given</i> <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">PLL</i> <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">power</i> <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">budget</i> . Based on these insights, a benchmark FOM for PLL designs is proposed.
Role of immunosuppression in the development of quinolone‐resistant Escherichia coli spontaneous bacterial peritonitis and in the mortality of E. coli spontaneous bacterial peritonitis (2003)

Associated immunosuppression is an important co-factor for the development of quinolone-resistant E. coli spontaneous bacterial peritonitis and for E. coli spontaneous bacterial peritonitis-related mortality.
Access to a Messenger RNA Sequence or Its Protein Product Is Not Limited by Tissue or Species Specificity (1989)

RNA amplification with transcript sequencing (RAWTS) is a rapid and sensitive method of direct sequencing that involves complementary DNA synthesis, polymerase chain reaction (PCR) with a primer or primers containing a phage promoter, transcription from the phage promoter, and reverse transcriptase-mediated sequencing. By means of RAWTS, it was possible to sequence each of four tissue-specific human messenger RNAs (blue pigment, factor IX, phenylalanine hydroxylase, and tyrosine hydroxylase) in four cell types examined (white blood cells, liver, K562 erythroleukemia cells, and chorionic villus cells). These results indicate that there is a basal rate of transcription, splicing, and polyadenylation of tissue-specific mRNAs in adult and embryonic tissues. In addition to revealing sequence information, it is possible to generate a desired in vitro translation product by incorporating a translation initiation signal into the appropriate PCR primer. RAWTS can be used to obtain novel mRNA sequence information from other species as illustrated with a segment of the catalytic domain of factor IX. In general, the ability to obtain mRNA sequences rapidly across species boundaries should aid both the study of protein evolution and the identification of sequences crucial for protein structure and function.