gebhart/patrepeval huggingface dataset:
Expression of Avian Influenza Virus Hemagglutinin by Recombinant Fowlpox Virus (1991)

A vaccine strain of fowlpox virus (FPV) was genetically engineered to produce avian influenza virus hemagglutinin (HA). This was accomplished by inserting a cDNA copy of the avian influenza virus HA gene, which was regulated by a vaccinia virus promoter, into the FPV thymidine kinase (TK) gene. Two types of recombinant viruses, differing only in the orientation of the HA gene relative to an adjacent foreign gene (lacZ), were created. Following preliminary identification of FPV recombinants based on the generation of beta-galactosidase (lacZ gene product), correct insertion of the HA gene into the genomes of these viruses was verified by hybridization studies. Susceptible chickens vaccinated with these FPV recombinants produced specific hemagglutination-inhibiting antibodies against the HA antigen. In view of this immune response, these viruses may serve as vaccines against avian influenza virus. In this regard, they appeared to be less virulent than the parental virus.
Structure–property relationships of water adsorption in metal–organic frameworks (2014)

Among porous solids, MOFs exhibit a wealth of water adsorption behaviors.
Two interferon-induced nuclear factors bind a single promoter element in interferon-stimulated genes. (1988)

Nuclear proteins induced by interferon (IFN) treatment of human cells are capable of forming two specific complexes with DNA fragments containing the IFN-stimulated response element (ISRE). These two complexes, designated B2 and B3, are distinguished by differential migration in gel retardation assays. The factor that forms the B3 complex, termed IFN-stimulated gene factor 3 (ISGF-3), preexists in cells, is activated upon IFN treatment, and appears with kinetics paralleling those for transcriptional activation of IFN-stimulated genes. The factor that forms the B2 complex (ISGF-2) appears following a time lag after IFN treatment during which protein synthesis must occur. By extensive point mutagenesis of the ISREs from two IFN-stimulated promoters (ISG54 and ISG15), we demonstrate that the B2 and B3 complexes are formed by factors binding to the same DNA sequence. Mutations at this site decrease or eliminate transcriptional activation and impair binding of both ISGF-2 and ISGF-3. This analysis has shown that the ISGF-3 binding site is slightly broader than the ISGF-2 binding site, which is completely contained within the sequence necessary both for ISGF-3 binding and for transcriptional activation. The evidence strongly implicates ISGF-3 as the positive transcriptional regulator of IFN-stimulated genes.
High-Resolution Laser Doppler Perfusion Imaging Aids in Differentiating Between Benign and Malignant Melanocytic Skin Tumours (2002)

Malignant melanomas are characterized by heterogeneity and asymmetry as well as by a higher density of blood vessels than benign pigmented tumours. The aim of this study was to evaluate the benefit of high-resolution laser Doppler perfusion imaging (LDPI) in the differential diagnosis of pigmented skin tumours. One-hundred-and-eighty-nine patients were examined with the LDPI, 22 with malignant melanomas, 39 with clinically suspicious dysplastic melanocytic naevi and 27 with basal cell carcinomas. Following examination, the tumours were excised and examined histologically. A control group of 101 melanocytic naevi showed clinically and, with epiluminescence microscopy, definitely benign criteria. These naevi were not excised. In malignant melanomas there was a 3.6+/-1.5 times higher perfusion than in healthy skin. The corresponding figures for clinically suspicious melanocytic naevi and basal cell carcinomas were 2.2+/-1.1 and 2.0+/-0.7, respectively. The increase in flow in malignant melanomas was significantly higher than in clinically suspicious melanocytic naevi and basal cell carcinomas (p < 0.001). All malignant melanomas showed at least 1.8 times higher flow values than healthy skin. When this value is taken as the basis for the diagnosis "benign or malignant", the LDPI proved a sensitivity of 100% and a specificity of 85%. If only the distinction between malignant melanomas and clinically suspicious naevi is considered, the specificity is reduced to 48%. There was no correlation between tumour thickness and increase in the mean perfusion of malignant melanomas (r = 0.14; p = 0.5). High-resolution LDPI can be used as an additional automatic screening method.
A Unified Analysis for Coded DS-CDMA With Equal-Gain Chip Combining in the Downlink of OFDM Systems (2005)

This paper presents a novel unified analysis for the bit-error rate in the downlink of convolutionally coded and single-user detected multicarrier code-division multiple access (CDMA), multicarrier direct-sequence CDMA, time and frequency-domain spreading CDMA, and orthogonal frequency-division multiple access. Performance is analyzed under the assumption of Hadamard spreading codes, equal-gain chip combining, and a highly correlated frequency-selective Rayleigh-fading channel. Closed-form expressions are presented for the cumulative distribution function, probability distribution function, and moment-generating function for the signal-to-noise plus interference ratio after despreading. The presented results assume error-free channel estimates, a perfectly synchronized receiver, and are found to reasonably well agree with simulation results.
Palladium catalyzed arylation of malonate accompanying in situ dealkoxycarbonylation (2001)

One-pot conversion of aryl halides into aryl acetates was achieved by the palladium catalyzed arylation of malonate accompanying in situ dealkoxycarbonylation of aryl malonates using Cs2CO3 as a base and as a catalyst.
Efficacy of Adoptive T-cell Therapy Is Improved by Treatment with the Antioxidant N-Acetyl Cysteine, Which Limits Activation-Induced T-cell Death (2016)

Abstract Although adoptive transfer of autologous tumor antigen–specific T-cell immunotherapy can produce remarkable clinical efficacy, most patients do not achieve durable complete responses. We hypothesized that reducing susceptibility of T cells to activation-induced cell death (AICD), which increases during the rapid in vitro expansion of therapeutic T cells before their infusion, might improve the persistence of adoptively transferred cells. Our investigations revealed that repetitive stimulation of the T-cell receptor (TCR) induced AICD, as a result of activating the DNA damage response pathway through ATM-mediated Ser15 phosphorylation of p53. Activation of this DNA damage response pathway also occurred upon antigen-specific restimulation in TCR-transduced TIL1383I T cells prepared for adoptive transfer to patients as part of a clinical trial. Notably, treatment with the antioxidant N-acetyl cysteine (NAC) significantly reduced upregulation of the DNA damage marker γH2AX, subsequent ATM activation, and cell death. In the Pmel mouse model of melanoma, the presence of NAC during ex vivo T-cell expansion improved the persistence of adoptively transferred cells, reduced tumor growth, and increased survival. Taken together, our results offer a preclinical proof of concept for the addition of NAC to current therapeutic T-cell expansion protocols, offering immediate potential to improve the quality and therapeutic efficacy of adoptive T-cell therapeutics infused into patients. Cancer Res; 76(20); 6006–16. ©2016 AACR.
Expression, Purification, and Characterization of Choline Kinase, Product of the CKI Gene from Saccharomyces cerevisiae (1998)

In the yeast Saccharomyces cerevisiae, choline kinase (ATP:choline phosphotransferase, EC 2.7.1.32) is the product of the CKI gene. Choline kinase catalyzes the committed step in the synthesis of phosphatidylcholine by the CDP-choline pathway. The yeast enzyme was overexpressed 106-fold in Sf-9 insect cells and purified 71.2-fold to homogeneity from the cytosolic fraction by chromatography with concanavalin A, Affi-Gel Blue, and Mono Q. The N-terminal amino acid sequence of purified choline kinase matched perfectly with the deduced sequence of the CKI gene. The minimum subunit molecular mass (73 kDa) of purified choline kinase was in good agreement with the predicted size (66.3 kDa) of the CKI gene product. Native choline kinase existed in oligomeric structures of dimers, tetramers, and octomers. The amounts of the tetrameric and octomeric forms increased in the presence of the substrate ATP. Antibodies were raised against the purified enzyme and were used to identify choline kinase in insect cells and in S. cerevisiae. Maximum choline kinase activity was dependent on Mg2+ ions (10 mM) at pH 9.5 and at 30 degrees C. The equilibrium constant (0.2) for the reaction indicated that the reverse reaction was favored in vitro. The activation energy for the reaction was 6.26 kcal/mol, and the enzyme was labile above 30 degrees C. Choline kinase exhibited saturation kinetics with respect to choline and positive cooperative kinetics with respect to ATP (n = 1.4-2.3). Results of the kinetic experiments indicated that the enzyme catalyzes a sequential Bi Bi reaction. The Vmax for the reaction was 138.7 micromol/min/mg, and the Km values for choline and ATP were 0.27 mM and 90 microM, respectively. The turnover number per choline kinase subunit was 153 s-1. Ethanolamine was a poor substrate for the purified choline kinase, and it was also poor inhibitor of choline kinase activity. ADP inhibited choline kinase activity (IC50 = 0.32 mM) in a positive cooperative manner (n = 1.5), and the mechanism of inhibition with respect to ATP and choline was complex. The regulation of choline kinase activity by ATP and ADP may be physiologically relevant.
Efficient Inverted Bulk-Heterojunction Polymer Solar Cells with Self-Assembled Monolayer Modified Zinc Oxide (2013)

The performance of poly(3-hexylthiophen) (P3HT) and [6, 6]phenyl C61 butyric acid methyl ester ([60]PCBM)-based inverted bulk-heterojunction (BHJ) polymer solar cells (PSCs) is enhanced by the modification of zinc oxide (ZnO)/BHJ interface with carboxylic-acid-functionalized self-assembled monolayers (SAMs). Under simulated solar illumination of AM 1.5 (100 mW/cm2), the inverted devices fabricated with SAM-modified ZnO achieved an enhanced power conversion efficiency (PCE) of 3.34% due to the increased fill factor and photocurrent density as compared to unmodified cells with PCE of 2.60%. This result provides an efficient method for interface engineering in inverted BHJ PSCs.
Mapping of Regions of Physical Deletion on Chromosome 16q in Prostate Cancer Cells by Fluorescence in Situ Hybridization (FISH) (1995)

Recent evidence suggests that a tumor suppressor gene important in the progression of prostatic carcinoma may reside on chromosome 16q. The exact location and identity of this gene are unknown. We used fluorescence in situ hybridization in a novel manner to define more clearly the location of this gene. Region-specific chromosome 16 cosmid contig probes were hybridized directly to interphase prostatic carcinoma nuclei in order to measure physical deletion of chromosomal loci. Fifteen of 30 tumors (50%) showed evidence of physical deletion of 16q24. Other probes were used to test for regions of chromosome 16 deletions in the same specimens, and a map showing a region of common deletion was created. This map showed the proximal terminus of the region of common deletion to be located distal to 16q23.1. These data correlate well with loss of heterozygosity data in the literature and provide further evidence for the presence of a prostatic carcinoma tumor suppressor gene on chromosome 16q.
Evaluation of a malarial antibody assay for use in the screening of blood and tissue products for clinical use (2004)

The assay is more sensitive than a previously implemented malarial antibody EIA (73% in acute P. falciparum and 56% in acute P. vivax infections). The sensitivity of this new EIA is comparable to that of the IFAT, and the specificity is sufficient to screen 'malaria-risk' donors.
Direct Measurement of the Anticholinergic Activity of a Series of Pharmacological Compounds on the Canine and Rabbit Urinary Bladder (1982)

Antimuscarinic therapy is used widely in the treatment of urine storage failure. Examples of antimuscarinic agents used clinically include atropine, propantheline bromide and glycopyrrolate. Other agents used in clinical urology that are believed to act at least in part by antimuscarinic activity include oxybutynin, imipramine and dicyclomine, These studies were designed to determine the relative potency of a variety of agents to compete directly for muscarinic cholinergic receptors isolated from the canine and rabbit urinary bladder. Radio-ligand binding assays for muscarinic receptors were performed with 10 nM 3H-QNB and various concentrations of the drugs under study. Of the agents tested, propantheline bromide, atropine, and glycopyrrolate were the potent muscarinic antagonists/unit of concentration. Oxybutynin and dicyclomine hydrochloride were 30 to 50 times less potent than atropine. Chlorpromazine and desmethylimipramine were approximately 500 times less potent than atropine. As expected, agents such as guanethidine, tranylcypramine and hexamethonium possessed little antimuscarinic activity.
Mannose-binding Lectin-deficient Mice Are Susceptible to Infection with Staphylococcus aureus (2004)

Gram-positive organisms like Staphylococcus aureus are a major cause of morbidity and mortality worldwide. Humoral response molecules together with phagocytes play a role in host responses to S. aureus. The mannose-binding lectin (MBL, also known as mannose-binding protein) is an oligomeric serum molecule that recognizes carbohydrates decorating a broad range of infectious agents including S. aureus. Circumstantial evidence in vitro and in vivo suggests that MBL plays a key role in first line host defense. We tested this contention directly in vivo by generating mice that were devoid of all MBL activity. We found that 100% of MBL-null mice died 48 h after exposure to an intravenous inoculation of S. aureus compared with 45% mortality in wild-type mice. Furthermore, we demonstrated that neutrophils and MBL are required to limit intraperitoneal infection with S. aureus. Our study provides direct evidence that MBL plays a key role in restricting the complications associated with S. aureus infection in mice and raises the idea that the MBL gene may act as a disease susceptibility gene against staphylococci infections in humans.
Lymphokines, monoclonal antibodies, and other biological response modifiers in the treatment of cancer (1984)

Biologicals and biological response modifiers (BRMs) represent a new class of agents for cancer therapy. Historically, there have been many attempts to stimulate the immune response with nonspecific immunomodulators in the form of bacterial extracts, viruses, and chemicals. Although these approaches have occasionally proven useful under defined conditions in experimental models, their extension to the clinic has been largely unsuccessful. Recent advances in molecular biology and hybridoma technology have made available genetically engineered lymphokines and cytokines, as well as monoclonal antibodies, as highly purified biologicals for cancer treatment. These agents may act directly on tumor cells and/or may act on the patient's own biological responses to induce an antitumor response. Selective defects in T-cell function have recently been identified in cancer patients and in patients with acquired immunodeficiency syndrome (AIDS). Simultaneously, the availability of gamma interferon (gamma-IF) and interleukin-2 (IL-2) may allow for the selective correction of these T-cell deficits, leading to restoration of the patient's immune responses and perhaps correction of the clinical syndromes. Preliminary data suggest that gamma-IF and IL-2 have in vitro activity on these T-cell defects, and the preliminary evidence that these agents have activity in vivo will be reviewed. Extensive trials are being conducted at the National Cancer Institute with monoclonal antibodies as anticancer agents. Animal model experiments have demonstrated considerable antitumor activity of immunoconjugates using monoclonal antibodies tied to toxins. Preliminary clinical results suggest that T-101 in leukemia and lymphoma and 9.2.27 in malignant melanoma may prove useful as specific reagents in the treatment of these disorders. While the antitumor effects with these antibodies have not been dramatic, our preliminary data in approximately 30 patients with leukemia, lymphoma, and melanoma clearly demonstrate the ability of intravenous monoclonal antibody to locate and specifically label tumor cells bearing the target antigens. It has been possible to localize antibody on the tumor cells in melanoma deposits that are barely visible in the skin. These data and radioimaging data suggest a future role for immunoconjugates as anticancer agents.
A gene inducible by serum growth factors encodes a member of the steroid and thyroid hormone receptor superfamily. (1988)

We previously identified, by cDNA cloning, a set of genes that are expressed during the G0/G1 transition (cell cycle reentry) in mouse fibroblasts. These immediate early genes are transcriptionally activated within minutes of addition of serum or purified growth factors, and their mRNAs are superinduced in the presence of protein-synthesis inhibitors. We report here that one of these genes, represented by nur/77 cDNA (originally called 3CH77), encodes a member of the superfamily of ligand-binding transcription factors that includes the steroid and thyroid hormone receptors. The nur/77 cDNA sequence encodes a protein of 601 amino acids containing two regions of sequence similarity to members of this nuclear receptor superfamily, corresponding to their DNA-binding and ligand-binding domains. These results suggest that the growth factor-inducible immediate early gene nur/77 encodes a ligand-binding protein that regulates the genomic response to growth factors.
The AtProT Family. Compatible Solute Transporters with Similar Substrate Specificity But Differential Expression Patterns (2004)

Proline transporters (ProTs) mediate transport of the compatible solutes Pro, glycine betaine, and the stress-induced compound gamma-aminobutyric acid. A new member of this gene family, AtProT3, was isolated from Arabidopsis (Arabidopsis thaliana), and its properties were compared to AtProT1 and AtProT2. Transient expression of fusions of AtProT and the green fluorescent protein in tobacco (Nicotiana tabacum) protoplasts revealed that all three AtProTs were localized at the plasma membrane. Expression in a yeast (Saccharomyces cerevisiae) mutant demonstrated that the affinity of all three AtProTs was highest for glycine betaine (K(m) = 0.1-0.3 mM), lower for Pro (K(m) = 0.4-1 mM), and lowest for gamma-aminobutyric acid (K(m) = 4-5 mM). Relative quantification of the mRNA level using real-time PCR and analyses of transgenic plants expressing the beta-glucuronidase (uidA) gene under control of individual AtProT promoters showed that the expression pattern of AtProTs are complementary. AtProT1 expression was found in the phloem or phloem parenchyma cells throughout the whole plant, indicative of a role in long-distance transport of compatible solutes. beta-Glucuronidase activity under the control of the AtProT2 promoter was restricted to the epidermis and the cortex cells in roots, whereas in leaves, staining could be demonstrated only after wounding. In contrast, AtProT3 expression was restricted to the above-ground parts of the plant and could be localized to the epidermal cells in leaves. These results showed that, although intracellular localization, substrate specificity, and affinity are very similar, the transporters fulfill different roles in planta.
Enantioselective Cyanosilylation of Ketones by a Catalytic Double‐Activation Method with an Aluminium Complex and an N‐Oxide (2004)

Double-activation catalysis promises high catalytic efficiency in the enantioselective cyanosilylation of ketones through the combined use of a Lewis acid and a Lewis base. Catalyst systems composed of a chiral salen-Al complex and an N-oxide have high catalytic turnovers (200 for aromatic ketones, 1000 for aliphatic ones). With these catalysts, a wide range of aliphatic and aromatic ketones were converted under mild conditions into tertiary cyanohydrin O-TMS ethers in excellent yields and with high enantioselectivities (94% ee for aromatic ketones, 90% ee for aliphatic ones). Preliminary mechanistic studies revealed that the salen-Al complex played the role of a Lewis acid to activate the ketone and the N-oxide that of a Lewis base to activate TMSCN; that is, double activation.
Highly Efficient and Stable Perovskite Solar Cells by Interfacial Engineering Using Solution-Processed Polymer Layer (2017)

Solution-processed organo-lead halide perovskite solar cells with deep pinholes in the perovskite layer lead to shunt-current leakage in devices. Herein, we report a facile method for improving the performance of perovskite solar cells by inserting a solution-processed polymer layer between the perovskite layer and the hole-transporting layer. The photovoltaic conversion efficiency of the perovskite solar cell increased to 18.1% and the stability decreased by only about 5% during 20 days of exposure in moisture ambient conditions through the incorporation of a poly(methyl methacrylate) (PMMA) polymer layer. The improved photovoltaic performance of devices with a PMMA layer is attributed to the reduction of carrier recombination loss from pinholes, boundaries, and surface states of perovskite layer. The significant gain generated by this simple procedure supports the use of this strategy in further applications of thin-film optoelectronic devices.
Testing Computer Software (1988)

From the Publisher:
This book will teach you how to test computer software under real-world conditions. The authors have all been test managers and software development managers at well-known Silicon Valley software companies. Successful consumer software companies have learned how to produce high-quality products under tight time and budget constraints. The book explains the testing side of that success.
Who this book is for:*Testers and Test Managers*Project Managers-Understand the timeline, depth of investigation, and quality of communication to hold testers accountable for.*Programmers-Gain insight into the sources of errors in your code, understand what tests your work will have to pass, and why testers do the things they do.*Students-Train for an entry-level position in software development.
What you will learn:*How to find important bugs quickly*How to describe software errors clearly*How to create a testing plan with a minimum of paperwork*How to design and use a bug-tracking system*Where testing fits in the product development process*How to test products that will be translated into other languages*How to test for compatibility with devices, such as printers*What laws apply to software quality
JACK FALK consults on software quality management and software engineering management. Jack is certified in Software Quality Engineering by the American Society of Quality. He is Vice Chair of the Santa Clara Valley Software Quality Association and an active participant in the Los Altos Workshops on Software Testing. 
HUNG Q. NGUYEN is Founder, President, and CEO of softGear technology. He has worked in the computer software and hardware industries, holding management positionsinengineering, quality assurance, testing, product development, and information technology, as well as making significant contributions as a tester and programmer. He is an ASQ-Certified Quality Engineer, and a senior member and San Francisco Section Certification Chairman of the American Society for Quality.