gebhart/patrepeval huggingface dataset:
Human protein metabolism: its measurement and regulation (2002)

The body's protein mass not only provides architectural support for cells but also serves vital roles in maintaining their function and survival. The whole body protein pool, as well as that of individual tissues, is determined by the balance between the processes of protein synthesis and degradation. These in turn are regulated by interactions among hormonal, nutritional, neural, inflammatory, and other influences. Prolonged changes in either the synthetic or degradative processes (or both) that cause protein wasting increase morbidity and mortality. The application of tracer kinetic methods, combined with measurements of the activity of components of the cellular signaling pathways involved in protein synthesis and degradation, affords new insights into the regulation of both protein synthesis and breakdown in vivo. These insights, including those from studies of insulin, insulin-like growth factor I, growth hormone, and amino acid-mediated regulation of muscle and whole body protein turnover, provide opportunities to develop and test therapeutic approaches with promise to minimize or prevent these adverse health consequences.
Wafer printability simulation accuracy based on UV optical inspection images of reticle defects (1999)

As semiconductor processes have moved towards lower k<SUB>1</SUB> and mask inspection equipment has moved into the UV range, more subtle reticle defects have been found to cause manufacturing problems. Lower k<SUB>1</SUB> and new lithography processes and reticle technologies, such as OPC and PSM, have made it difficult to determine the significant and these defects. This paper reports on the development of a simulation tool that will improve the yield and productivity of photomask manufacturers and wafer manufacturers by improving reticle defect assessment. This study demonstrates the accuracy of simulation software that predicts resist patterns based on sophisticated modeling software that uses optical images obtained from a state-of-the-art UV optical inspection system. A DUV 4X reduction stepper was used to print a reticle with programmed defects across an exposure/focus matrix, with the minimum feature size being 200 nm. Quantitative comparisons between predicted and measured wafer CDs were made. In summary, it was found that the simulation software based solely on aerial images predicted absolute CDs with limited accuracy, but differential CDs with limited accuracy, but differential CDs, obtained by utilizing both the reference and defect images, were predicted accurately. Comparison of simulations using both reticle SEM images and optical reticle inspection images showed good agreement, demonstrating the accuracy and high resolution of the optical reticle inspection images. Application of differential aerial images to a simple test case showed that it was possible to identify and therefore eliminate a significant number of defects that did not print, thereby improving defect assessment.
Overview of Biacore Systems and Their Applications (2006)

Surface plasmon resonance (SPR) allows for the investigation of the functional nature of binding interactions and provides detailed kinetic information across a wide range of molecular weights, including small molecules, all without the use of labels. Here the various Biacore instrument platforms and their primary uses, ranging from semi-automated systems designed for simple, flexible basic research to fully automated, high-throughput systems, and systems designed to function in regulated environments, are all highlighted. The available sensor chip surfaces and immobilization techniques are also discussed. Biacore SPR biosensors can be used for a wide variety of assays, including specificity, active concentration measurement, kinetics, and affinity and thermodynamic parameters. Biacore SPR biosensors, which measure real-time analysis of biospecific interactions without the use of labeled molecules, can be used for a wide variety of protein interaction assays. In this unit, examples and recommendations for studying protein interactions with a variety of molecules are provided. This unit also shows how the technology can be used to determine binding specificity, active concentration measurements, and the determination of kinetic and thermodynamic parameters.
Extending Attack Graph-Based Security Metrics and Aggregating Their Application (2010)

The attack graph is an abstraction that reveals the ways an attacker can leverage vulnerabilities in a network to violate a security policy. When used with attack graph-based security metrics, the attack graph may be used to quantitatively assess security-relevant aspects of a network. The Shortest Path metric, the Number of Paths metric, and the Mean of Path Lengths metric are three attack graph-based security metrics that can extract security-relevant information. However, one's usage of these metrics can lead to misleading results. The Shortest Path metric and the Mean of Path Lengths metric fail to adequately account for the number of ways an attacker may violate a security policy. The Number of Paths metric fails to adequately account for the attack effort associated with the attack paths. To overcome these shortcomings, we propose a complimentary suite of attack graph-based security metrics and specify an algorithm for combining the usage of these metrics. We present simulated results that suggest that our approach reaches a conclusion about which of two attack graphs correspond to a network that is most secure in many instances.
Cyclooxygenase-2 mediates microglial activation and secondary dopaminergic cell death in the mouse MPTP model of Parkinson's disease (2006)

These results indicate that reducing COX-2 activity can mitigate the secondary and progressive loss of dopaminergic neurons as well as the motor deficits induced by MPTP, possibly by suppression of microglial activation in the SNpc.
4 Strong-stop Strand Transfer during Reverse Transcription (1993)

Reverse transcription of retroviral genomic RNA is, in a sense, a discontinuous process. The production of each strand of integration-competent retroviral DNA begins with the synthesis of short, discrete DNA products that can be elongated only after they are moved to secondary template locations in a process called strand transfer. Both strand transfers during reverse transcription involve the translocation of short DNA products from their sites of synthesis at one end of the genome to acceptor template regions at the other end of the genome, where DNA synthesis resumes. Because of the strand-transfer reactions, the final product of reverse transcription is a linear double-stranded DNA molecule that is longer at each end than the RNA from which it was duplicated. The termini of the completed viral DNA consist of identical sequences termed long terminal repeats (LTRs), which are formed when information present near the ends of the genomic RNA is duplicated at the tips of the preintegrative DNA. The conservation of the two-LTR structure in all retroviruses and among other retroelements whose life cycles involve an integrated DNA form, such as yeast Tys and Drosophila copia elements, suggests that the process of strand transfer is as conserved a feature of these elements’ replication as the process of reverse transcription itself. Strand transfer, as a specialized form of template switching, is mechanistically related to some models for recombination during reverse transcription. Thus, the mechanisms for strong-stop strand transfer and for the generation of retroviral genetic diversity through recombination and transduction of...
Effect of RyhB Small RNA on Global Iron Use in Escherichia coli (2005)

RyhB is a noncoding RNA regulated by the Fur repressor. It has previously been shown to cause the rapid degradation of a number of mRNAs that encode proteins that utilize iron. Here we examine the effect of ectopic RyhB production on global gene expression by microarray analysis. Many of the previously identified targets were found, as well as other mRNAs encoding iron-binding proteins, bringing the total number of regulated operons to at least 18, encoding 56 genes. The two major operons involved in Fe-S cluster assembly showed different behavior; the isc operon appears to be a direct target of RyhB action, while the suf operon does not. This is consistent with previous findings suggesting that the suf genes but not the isc genes are important for Fe-S cluster synthesis under iron-limiting conditions, presumably for essential iron-binding proteins. In addition, we observed repression of Fur-regulated genes upon RyhB expression, interpreted as due to intracellular iron sparing resulting from reduced synthesis of iron-binding proteins. Our results demonstrate the broad effects of a single noncoding RNA on iron homeostasis.
Stability engineering of anti-EGFR scFv antibodies by rational design of a lambda-to-kappa swap of the VLframework using a structure-guided approach (2015)

Phage-display technology facilitates rapid selection of antigen-specific single-chain variable fragment (scFv) antibodies from large recombinant libraries. ScFv antibodies, composed of a VH and VL domain, are readily engineered into multimeric formats for the development of diagnostics and targeted therapies. However, the recombinant nature of the selection strategy can result in VH and VL domains with sub-optimal biophysical properties, such as reduced thermodynamic stability and enhanced aggregation propensity, which lead to poor production and limited application. We found that the C10 anti-epidermal growth factor receptor (EGFR) scFv, and its affinity mutant, P2224, exhibit weak production from E. coli. Interestingly, these scFv contain a fusion of lambda3 and lambda1 V-region (LV3 and LV1) genes, most likely the result of a PCR aberration during library construction. To enhance the biophysical properties of these scFvs, we utilized a structure-based approach to replace and redesign the pre-existing framework of the VL domain to one that best pairs with the existing VH. We describe a method to exchange lambda sequences with a more stable kappa3 framework (KV3) within the VL domain that incorporates the original lambda DE-loop. The resulting scFvs, C10KV3_LV1DE and P2224KV3_LV1DE, are more thermodynamically stable and easier to produce from bacterial culture. Additionally, C10KV3_LV1DE and P2224KV3_LV1DE retain binding affinity to EGFR, suggesting that such a dramatic framework swap does not significantly affect scFv binding. We provide here a novel strategy for redesigning the light chain of problematic scFvs to enhance their stability and therapeutic applicability.
Copy number control of the streptococcal plasmio plP501 occurs at three levels (1992)

Transcriptional analysis of the replication region of plasmid pIP501 has revealed three active promoters. The repR gene which is essential for pIP501 replication was transcribed from promoter pII. A small antisense RNA (136 nt, RNAIII) generated from promoter pIII was complementary to the leader region of the repR mRNA. Introduction of either point mutations or deletions into promoter pIII or RNAIII resulted in a 5-20fold increased plasmid copy number suggesting a negative regulatory function for RNAIII. The copR gene, the complete DNA and amino acid sequence of which is reported, was dispensable for pIP501 replication. However, deletion of the copR promoter pI and/or the copR coding sequence led to a 10-20fold increase in plasmid copy number. This effect was also observed when a -1 frameshift mutation was introduced into the CopR coding region. Mutations in copR and pIII/RNAIII were not additive. It is, therefore, proposed that both components act at the same level of copy number control most likely in a sequential way. A second level of copy number control was found to involve an inverted repeat structure upstream of and overlapping with promoter pII. Destruction of this repeat sequence by deletion caused an increase in copy number 2-3fold higher than that observed for either RNAIII or copR mutations. A working model is proposed how different components of pIP501 interact to regulate its copy number.
A novel method for synthetic vaccine construction based on protein assembly (2014)

In the history of vaccine development, the synthetic vaccine is a milestone that is in stark contrast with traditional vaccines based on live-attenuated or inactivated microorganisms. Synthetic vaccines not only are safer than attenuated or inactivated microorganisms but also provide the opportunity for vaccine design for specific purposes. The first generation of synthetic vaccines has been largely based on DNA recombination technology and genetic manipulation. This de novo generation is occasionally time consuming and costly, especially in the era of genomics and when facing pandemic outbreaks of infectious diseases. To accelerate and simplify the R&D process for vaccines, we developed an improved method of synthetic vaccine construction based on protein assembly. We optimized and employed the recently developed SpyTag/SpyCatcher technique to establish a protein assembly system for vaccine generation from pre-prepared subunit proteins. As proof of principle, we chose a dendritic cell (DC)-targeting molecule and specific model antigens to generate desired vaccines. The results demonstrated that a new vaccine generated in this way does not hamper the individual function of different vaccine components and is efficient in inducing both T and B cell responses. This protein assembly strategy may be especially useful for high-throughput antigen screening or rapid vaccine generation.
“First Generation” Automated DNA Sequencing Technology (2011)

Beginning in the 1980s, automation of DNA sequencing has greatly increased throughput, reduced costs, and enabled large projects to be completed more easily. The development of automation technology paralleled the development of other aspects of DNA sequencing: better enzymes and chemistry, separation and imaging technology, sequencing protocols, robotics, and computational advancements (including base-calling algorithms with quality scores, database developments, and sequence analysis programs). Despite the emergence of high-throughput sequencing platforms, automated Sanger sequencing technology remains useful for many applications. This unit provides background and a description of the "First-Generation" automated DNA sequencing technology. It also includes protocols for using the current Applied Biosystems (ABI) automated DNA sequencing machines.
Expression of an oncogenic mutant EGF receptor markedly increases the sensitivity of cells to an EGF‐receptor‐specific antibody‐toxin (1998)

EGFRvIII is a ligand-independent, constitutively active variant of the epidermal growth factor receptor (EGFR) that is specifically expressed in gliomas and various other human malignancies and has been proposed as a target for directed tumor therapy. We have recently constructed a highly potent single-chain antibody-toxin, scFv(14E1)-ETA, which consists of the variable domains of the antibody 14E1 specific for human full-length EGFR genetically fused to a truncated form of Pseudomonas exotoxin A. We demonstrate here binding of 14E1 antibody to both full-length and variant EGFR. In contrast to a recombinant toxin containing transforming growth factor-α (TGF-α) as a cell targeting domain, scFv(14E1)-ETA was highly active on cells expressing EGFRvIII. Surprisingly, scFv(14E1)-ETA displayed cell killing activity on EGFRvIII-expressing cells that was up to 100-fold higher than on control cells expressing full-length EGFR. No differences in the binding affinities of scFv(14E1)-ETA to full-length EGFR or EGFRvIII were observed, suggesting that events downstream of immunotoxin binding are responsible for the increased sensitivity of EGFRvIII-expressing cells. This might have implications for the development of therapeutic reagents simultaneously targeting different forms of the EGFR. Int. J. Cancer 75:878–884, 1998. © 1998 Wiley-Liss, Inc.
Instantaneous chemical profiles of banknotes by ambient mass spectrometry (2010)

Using two desorption/ionization techniques (DESI and EASI) and Brazilian real, US$ dollar, and euro bills as proof-of-principle techniques and samples, direct analysis by ambient mass spectrometry is shown to function as an instantaneous, reproducible, and non-destructive method for chemical analysis of banknotes. Characteristic chemical profiles were observed for the authentic bills and for the counterfeit bills made using different printing processes (inkjet, laserjet, phaser and off-set printers). Detection of real-world counterfeit bills and identification of the counterfeiting method has also been demonstrated. Chemically selective 2D imaging of banknotes has also been used to confirm counterfeiting. The nature of some key diagnostic ions has also been investigated via high accuracy FTMS measurements. The general applicability of ambient MS analysis for anti-counterfeiting strategies particularly via the use of "invisible ink" markers is discussed.
HIF-1α regulates function and differentiation of myeloid-derived suppressor cells in the tumor microenvironment (2010)

Myeloid-derived suppressor cells (MDSCs) are a major component of the immune-suppressive network described in cancer and many other pathological conditions. We demonstrate that although MDSCs from peripheral lymphoid organs and the tumor site share similar phenotype and morphology, these cells display profound functional differences. MDSC from peripheral lymphoid organs suppressed antigen-specific CD8(+) T cells but failed to inhibit nonspecific T cell function. In sharp contrast, tumor MDSC suppressed both antigen-specific and nonspecific T cell activity. The tumor microenvironment caused rapid and dramatic up-regulation of arginase I and inducible nitric oxide synthase in MDSC, which was accompanied by down-regulation of nicotinamide adenine dinucleotide phosphate-oxidase and reactive oxygen species in these cells. In contrast to MDSC from the spleen, MDSC from the tumor site rapidly differentiated into macrophages. Exposure of spleen MDSC to hypoxia resulted in the conversion of these cells to nonspecific suppressors and their preferential differentiation to macrophages. Hypoxia-inducible factor (HIF) 1α was found to be primarily responsible for the observed effects of the tumor microenvironment on MDSC differentiation and function. Thus, hypoxia via HIF-1α dramatically alters the function of MDSC in the tumor microenvironment and redirects their differentiation toward tumor-associated macrophages, hence providing a mechanistic link between different myeloid suppressive cells in the tumor microenvironment.
Complete Covalent Structure of a Human IgA1 Immunoglobulin (1976)

The complete covalent structure has been determined for a human myeloma IgA1 immunoglobulin. This protein has unique features in the amino acid sequence and disulfide bridge structure of the variable (V) and constant (C) regions of both the alpha heavy and the lambda light chains, and in the number and loci of oligosaccharides. Whereas C region domains of heavy chains have evolved independently over eons, recent isotypic variations have occured in lambda light chains and possibly in alpha heavy chains.
Computational design of receptors for an organophosphate surrogate of the nerve agent soman (2004)

We report the computational design of soluble protein receptors for pinacolyl methyl phosphonic acid (PMPA), the predominant hydrolytic product of the nerve agent soman. Using recently developed computational protein design techniques, the ligand-binding pockets of two periplasmic binding proteins, glucose-binding protein and ribose-binding protein, were converted to bind PMPA instead of their cognate sugars. The designs introduce 9-12 mutations in the parent proteins. Twelve of 20 designs tested exhibited PMPA-dependent changes in emission intensity of a fluorescent reporter with affinities between 45 nM and 10 microM. The contributions to ligand binding by individual residues were determined in two designs by alanine-scanning mutagenesis, and are consistent with the molecular models. These results demonstrate that designed receptors with radically altered binding specificities and affinities that rival or exceed those of the parent proteins can be successfully predicted. The designs vary in parent scaffold, sequence diversity, and orientation of docked ligand, suggesting that the number of possible solutions to the design problem is large and degenerate. This observation has implications for the genesis of biological function by random processes. The designed receptors reported here may have utility in the development of fluorescent biosensors for monitoring nerve agents.
Genes encoding the NAD-reducing hydrogenase ofRhodococcus opacus MR11 (1997)

The dissociation of the soluble NAD-reducing hydrogenase of Rhodococcus opacus MR11 into two dimeric proteins with different catalytic activities and cofactor composition is unique among the NAD-reducing hydrogenases studied so far. The genes of the soluble hydrogenase were localized on a 7.4 kbp Asnl fragment of the linear plasmid pHG201 via heterologous hybridization. Analysis of the nucleotide sequence of this fragment revealed the seven open reading frames ORF1, hoxF, -U, -Y, -H, -W and ORF7. The six latter ORFs belong to the gene cluster of the soluble hydrogenase. Their gene products are highly homologous to those of the NAD-reducing enzyme of Alcaligenes eutrophus H16. The genes hoxF, -U, -Y and -H encode the subunits alpha, gamma, delta and beta, respectively. The gene hoxW encodes a putative protease, which may be essential for C-terminal processing of the beta subunit. Finally, ORF7 encodes a protein which has similarities to cAMP- and cGMP-binding protein kinases, but its function is not known. ORF1, which lies upstream of the hydrogenase gene cluster, encodes a putative transposase found in IS elements of other bacteria. Northern hybridizations and primer extensions using total RNA of autotrophically and heterotrophically grown cells of R. opacus MR11 indicated that the hydrogenase genes are under control of a delta 70-like promoter located at the right end of ORF1 and are even transcribed under heterotrophic conditions at a low level. Furthermore, this promoter was shown to be active in the recombinant Escherichia coli strain LHY1 harbouring the 7.4 kbp Asnl fragment, resulting in overexpression of the hydrogenase genes. Although all four subunits of the soluble hydrogenase were shown via Western immunoblots to be synthesized in E. coli, no active enzyme was detectable.