gebhart/patrepeval huggingface dataset:
Smart card applications in integrated transit fare, parking fee and automated toll payment systems-the MAPS concept (2002)

The concept for a multimodal access and payment system (MAPS) promising to provide a common mechanism for the payment of transit fares, parking fees, tolls and other transportation-related items is described. MAPS will focus on the use of smart card technology and smart cards interfaced to RF transponders on vehicles to relieve the traffic congestion and air pollution problems which are becoming increasingly severe in urban areas. MAPS smart cards will maintain logs of the actual transportation modes used on employee journeys to and from work. Trips made as passengers in ride share or high occupancy vehicles will also be recorded on the smart cards. These logs can be used for the purposes of measuring the effectiveness of corporate traffic congestion and air pollution mitigation programs and in certifying compliance with regulations in these areas. Profile information on primary and alternate travel itineraries and modes will be maintained in the smart cards. This information can be used in future extensions of MAPS to supply users with traffic and transit information, updated schedules and alternate routing specific to their trip.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Evaluation of a Novel Assay for Detection of the Fetal Marker RASSF1A: Facilitating Improved Diagnostic Reliability of Noninvasive Prenatal Diagnosis (2012)

Use of this assay for the detection of hypermethylated RASSF1A as a universal fetal marker has the potential to improve the diagnostic reliability of NIPD for fetal sex determination and single gene disorders.
Peer-to-peer information retrieval using self-organizing semantic overlay networks (2003)

Content-based full-text search is a challenging problem in Peer-to-Peer (P2P) systems. Traditional approaches have either been centralized or use flooding to ensure accuracy of the results returned.In this paper, we present pSearch, a decentralized non-flooding P2P information retrieval system. pSearch distributes document indices through the P2P network based on document semantics generated by Latent Semantic Indexing (LSI). The search cost (in terms of different nodes searched and data transmitted) for a given query is thereby reduced, since the indices of semantically related documents are likely to be co located in the network.We also describe techniques that help distribute the indices more evenly across the nodes, and further reduce the number of nodes accessed using appropriate index distribution as well as using index samples and recently processed queries to guide the search.Experiments show that pSearch can achieve performance comparable to centralized information retrieval systems by searching only a small number of nodes. For a system with 128,000 nodes and 528,543 documents (from news, magazines, etc.), pSearch searches only 19 nodes and transmits only 95.5KB data during the search, whereas the top 15 documents returned by pSearch and LSI have a 91.7% intersection.
Matching Management Of Multiple Wafer Steppers Using A Stable Standard And A Matching Simulator (1989)

Currently, wafer steppers are capable of routinely meeting a single machine overlay accuracy of 150 nm or less. However, this figure is relatively meaningless in a production environment equipped with multiple machines. The question is how to exploit single machine accuracy in a multiple stepper production environment such that production logistics will be independent of machine allocation. This paper describes the use of a matching management system supported by an overlay simulator and a reference wafer set. Every stepper is measured on a regular basis with respect to a reference wafer to determine possible deviation from the nominal grid. The reference wafers are resistant to multiple use. The simulator can be used to estimate the matching performance between non-measured machine pairs so that the need for particular adjustments can be determined. The theory is completed by an extended overlay budget justified by experimental results and a ten machine overlay experiment.
Use of Electroporation to Introduce Biologically Active Foreign Genes into Primary Rat Hepatocytes (1986)

A method is described for introducing and expressing cloned genes in isolated hepatocytes. Primary rat hepatocytes isolated by collagenase perfusion were transfected in suspension with plasmid pSV2CAT by electroporation. Forty-eight hours later, soluble extracts from transfected hepatocytes showed chloramphenicol acetyltransferase activity comparable to that obtained in rat hepatoma cell line H4AzC2 by calcium phosphate or DEAE-dextran transfection. The latter two methods could not be used successfully for primary hepatocytes because of cytotoxicity of these reagents. This indicates that electroporation is a useful method to obtain transient expression of foreign genes in primary epithelial cells, such as rat hepatocytes, which are difficult to maintain in cell culture.
Organic-Fluorous Phase Switches:  A Fluorous Amine Scavenger for Purification in Solution Phase Parallel Synthesis (1999)

The synthesis of the fluorous amine scavenger [(C(6)F(13)CH(2)CH(2))(3)SiCH(2)CH(2)CH(2)](2)NH and its successful application in the automated solution phase parallel synthesis of a urea library are described. Ureas were made by robotic synthesis from organic amines and excess isocyanates. The amine scavenger reacts with excess isocyanate, and the fluorous tag serves to solubilize the resulting adduct in the fluorous phase so it can be removed by fluorous-organic extraction. Organic urea products are isolated in high yields and purities after liquid-liquid extraction. Preliminary biological evaluation shows that several of the ureas have ion channel modulation abilities. In contrast to polymer and ionic quenching methods, the fluorous quench works whether the product is soluble or insoluble in the reaction medium, and ionizable functional groups are tolerated in the products.
Unique fiducial designs for CSP singulation process (2003)

This paper describes the invention of unique designs of fiducial marks on the ball pad side of substrates for different CSP (chip scale package) integrated circuit package types and sizes. These unique designs on the substrates are related to the saw singulation process in the assembly of this type of packages. The distinct, unique fiducial designs enable the PRS (pattern recognition system) of the saw singulation equipment to differentiate between different molded CSP substrates, and stop the operation when the saw program of the equipment doesn't match the expected fiducial design on the substrate. These unique fiducial marks provide an error free solution that prevents loading wrong saw programs or feeding incorrect CSP substrates/packages into the saw singulation equipment. The benefits are that different type and sizes of CSP packages will not be sawn with the wrong dimensions, and that expensive saw singulation equipment parts will not get damaged.
Mutational analysis of apolipoprotein B mRNA editing enzyme (APOBEC1): structure–function relationships of RNA editing and dimerization (1999)

APOBEC1 is the catalytic subunit of an enzyme complex that mediates apolipoprotein (apo) B mRNA editing. It dimerizes in vitro and requires complementation factor(s) for its editing activity. We have performed a systematic analysis of the structure-functional relationship of APOBEC1 by targeted mutagenesis of various sequence motifs within the protein. Using in vitro RNA editing assay, we found that basic amino acid clusters at the amino-terminal region R15R16R17 and R33K34, are essential for apoB mRNA editing. Mutation of R15R16R17 to K15K16K17 and mutation of R33K34 simultaneously to A33A34 almost completely abolished in vitro editing activity. The carboxy-terminal region of APOBEC1 contains a leucine-rich motif. Deletion analysis of this region indicates that residues 181 to 210 are important for in vitro apoB mRNA editing. Single amino acid substitutions demonstrate that L182, I185, and L189 are important residues required for normal editing function. Furthermore, the double mutant P190A/P191A also lost >90% of editing activity which suggests that a beta turn in this region of the molecule may be essential for proper functioning of APOBEC1. It was suggested that dimerization of APOBEC1 creates an active structure for deamination of apoB mRNA. When we examined the dimerization potential of truncated APOBEC1s using both amino and carboxy termini deletion mutants, we found that amino-terminal deletions up to residue A117 did not impair dimerization activity whereas carboxy-terminal deletions showed diminished dimerization. The systematic and extensive mutagenesis experiments in this study provide information on the role of various sequence motifs identified in APOBEC1 in enzyme catalysis and dimerization.
Cloning and sequence analysis of cDNA for the luminescent protein aequorin. (1985)

The luminescent jellyfish Aequorea contains a photoprotein, aequorin, which emits light by an intramolecular reaction in the presence of a trace amount of Ca2+. A cDNA library of Aequorea was constructed and clones carrying the cDNA for the Ca2+-dependent photoprotein were isolated by the method of colony hybridization using synthetic oligonucleotide probes. The primary structure of the protein deduced from the nucleotide sequence showed that the protein is composed of 189 amino acid residues and has three E-F hand structures that are characteristic for Ca2+-binding sites. The sequence also suggested that the protein has hydrophobic regions at which the protein may interact with its functional chromophore, coelenterazine.
Inactivating Variants in ANGPTL4 and Risk of Coronary Artery Disease (2016)

Carriers of E40K and other inactivating mutations in ANGPTL4 had lower levels of triglycerides and a lower risk of coronary artery disease than did noncarriers. The inhibition of Angptl4 in mice and monkeys also resulted in corresponding reductions in these values. (Funded by Regeneron Pharmaceuticals.).
P2X7 Receptor-Mediated Release of Cathepsins from Macrophages Is a Cytokine-Independent Mechanism Potentially Involved in Joint Diseases (2010)

The ATP-gated P2X(7) receptor (P2X(7)R) is a promising therapeutic target in chronic inflammatory diseases with highly specific antagonists currently under clinical trials for rheumatoid arthritis. Anti-inflammatory actions of P2X(7)R antagonists are considered to result from inhibition of P2X(7)R-induced release of proinflammatory cytokines from activated macrophages. However, P2X(7)Rs are also expressed in resting macrophages, suggesting that P2X(7)R may also signal via cytokine-independent mechanisms involved in joint disease. In this study, we examined P2X(7)R function in resting human lung macrophages and mouse bone marrow-derived macrophages and found that ATP induced rapid release of the lysosomal cysteine proteases cathepsin B, K, L, and S and that was independent of the presence of the proinflammatory cytokines IL-1beta and IL-18. Cathepsins released into the medium were effective to degrade collagen extracellular matrix. ATP-induced cathepsin release was abolished by P2X(7)R antagonists, absent from P2X(7)R(-/-) mouse macrophages, and not associated with cell death. Our results suggest P2X(7)R activation may play a novel and direct role in tissue damage through release of cathepsins independently of its proinflammatory actions via IL-1 cytokines.
Elicitation of High-Frequency Cytotoxic T-Lymphocyte Responses against both Dominant and Subdominant Simian-Human Immunodeficiency Virus Epitopes by DNA Vaccination of Rhesus Monkeys (2001)

Increasing evidence suggests that the generation of cytotoxic T-lymphocyte (CTL) responses specific for a diversity of viral epitopes will be needed for an effective human immunodeficiency virus type 1 (HIV-1) vaccine. Here, we determine the frequencies of CTL responses specific for the simian immunodeficiency virus Gag p11C and HIV-1 Env p41A epitopes in simian-human immunodeficiency virus (SHIV)-infected and vaccinated rhesus monkeys. The p11C-specific CTL response was high frequency and dominant and the p41A-specific CTL response was low frequency and subdominant in both SHIV-infected monkeys and in monkeys vaccinated with recombinant modified vaccinia virus Ankara vectors expressing these viral antigens. Interestingly, we found that plasmid DNA vaccination led to high-frequency CTL responses specific for both of these epitopes. These data demonstrate that plasmid DNA may be useful in eliciting a broad CTL response against multiple epitopes.
The Molecular Genetics of Cancer (1987)

The search for genetic damage in neoplastic cells now occupies a central place in cancer research. Diverse examples of such damage are in hand, and they in turn hint at biochemical explanations for neoplastic growth. The way may be open to solve the riddles of how normal cells govern their replication and why cancer cells do not.
Vi polysaccharide of Salmonella typhi targets the prohibitin family of molecules in intestinal epithelial cells and suppresses early inflammatory responses (2004)

Vi capsular polysaccharide (Vi) was first identified as a virulence antigen of Salmonella typhi, the causative agent of typhoid fever in humans; it renders S. typhi resistant to phagocytosis and the action of serum complement. However, the role of Vi during the infection of intestinal epithelium with S. typhi is not completely understood. We show here that Vi can interact with a model human intestinal epithelial cell line, Caco-2, through a cell-surface-associated molecular complex containing two major proteins of 30 and 35 kDa and a minor protein of approximately 68 kDa. The two major proteins were identified as the putative tumor suppressor molecule, prohibitin, and its closely related homolog, B cell receptor-associated protein 37. These two proteins were enriched in lipid rafts, and Vi readily associated with these membrane microdomains. Engagement of Caco-2 cells with Vi inhibited their ability to produce an inflammatory response upon infection with Vi(-) S. typhi. Consistent with this effect, infection of Caco-2 cells with Vi(+) S. typhi produced less IL-8 compared with Vi(-) S. typhi. Cells treated with Vi showed reduced extracellular signal-regulated kinase phosphorylation in response to infection with Vi(-) S. typhi or stimulation with phorbol 12-myristate 13-acetate, suggesting that the mitogen-activated protein kinase pathway might be a target for Vi-mediated inhibition of inflammatory responses. These findings reveal a crucial role for Vi in the modulation of early inflammatory responses during infection with S. typhi. This kind of a modulation could play a significant role in the establishment of infection by S. typhi.
A molecular mechanism for the effect of lithium on development. (1996)

Lithium, one of the most effective drugs for the treatment of bipolar (manic-depressive) disorder, also has dramatic effects on morphogenesis in the early development of numerous organisms. How lithium exerts these diverse effects is unclear, but the favored hypothesis is that lithium acts through inhibition of inositol monophosphatase (IMPase). We show here that complete inhibition of IMPase has no effect on the morphogenesis of Xenopus embryos and present a different hypothesis to explain the broad action of lithium. Our results suggest that lithium acts through inhibition of glycogen synthase kinase-3 beta (GSK-3 beta), which regulates cell fate determination in diverse organisms including Dictyostelium, Drosophila, and Xenopus. Lithium potently inhibits GSK-3 beta activity (Ki = 2 mM), but is not a general inhibitor of other protein kinases. In support of this hypothesis, lithium treatment phenocopies loss of GSK-3 beta function in Xenopus and Dictyostelium. These observations help explain the effect of lithium on cell-fate determination and could provide insights into the pathogenesis and treatment of bipolar disorder.
PERCEIVED EFFECTS OF TESTOSTERONE REPLACEMENT THERAPY IN PERIMENOPAUSAL AND POSTMENOPAUSAL WOMEN: AN INTERNET PILOT STUDY (2003)

Women experience somatic, mood, energy, and libido changes during menopause. Testosterone replacement therapy is being prescribed in conjunction with estrogen replacement therapy (ERT) for these symptoms. Little is known about women's perceptions of the benefits and risks of testosterone, so an Internet survey was conducted to elicit women's perceptions of the effects on mood, energy, sexuality, and somatic symptoms. A sample of 61 women primarily from the United States and Canada participated in the survey; one woman from Germany and one from Sweden also took part in the survey. Participants reported significantly improved sexuality and improved mood and vigor, with a decline in fatigue. Of the 7 somatic complaints assessed, improvements were noted in 5 (sleep disturbances, hot flashes, night sweats, vaginal dryness, and appetite). A prospective clinical trial is needed to confirm these results.
Direct association of presenilin‐1 with β‐catenin (1998)

Families bearing mutations in the presenilin-1 (PSI) gene develop Alzheimer's disease (AD). However, the mechanism through which PS1 causes AD is unclear. The co-immunoprecipitation with PS1 in transfected COS-7 cells indicates that PSI directly interacts with endogenous beta-catenin, and the interaction requires residues 322450 of PSI and 445-676 of beta-catenin. Both proteins are co-localized in the endoplasmic reticulum. Over-expression of PS1 reduces the level of cytoplasmic beta-catenin, and inhibits beta-catenin-T cell factor-regulated transcription. These results indicate that PSI plays a role as inhibitor of the beta-catenin signal, which may be connected with the AD dysfunction.
Impaired mechanical stability, migration and contractile capacity in vimentin deficient fibroblasts (1998)

Loss of a vimentin network due to gene disruption created viable mice that did not differ overtly from wild-type littermates. Here, primary fibroblasts derived from vimentin-deficient (-/-) and wild-type (+/+) mouse embryos were cultured, and biological functions were studied in in vitro systems resembling stress situations. Stiffness of -/- fibroblasts was reduced by 40% in comparison to wild-type cells. Vimentin-deficient cells also displayed reduced mechanical stability, motility and directional migration towards different chemo-attractive stimuli. Reorganization of collagen fibrils and contraction of collagen lattices were severely impaired. The spatial organization of focal contact proteins, as well as actin microfilament organization was disturbed. Thus, absence of a vimentin filament network does not impair basic cellular functions needed for growth in culture, but cells are mechanically less stable, and we propose that therefore they are impaired in all functions depending upon mechanical stability.
Monoclonal Antibody A7 Tumor Localization Enhancement by Its F(ab′)2 Fragments to Colon Carcinoma Xenografts in Nude Mice (1990)

The monoclonal antibody A7 (MoAb A7), which belongs to IgG1, was digested with pepsin to yield F(ab')2 fragments. The maximum binding to the human colon cancer cell line, SW1116, was 27% with 125-I labeled whole MoAb A7 and 24% with 125-I labeled F(ab')2 fragments using an in vitro binding assay. The results showed that the binding activity of F(ab')2 to SW1116 was practically the same as that of whole MoAb A7. The preferred localization of the fragments to tumor tissue, compared with normal mouse tissue, was demonstrated in mice carrying SW1116 xenografts. The tumor:blood ratio three days after injection was 2.64:18.5 for whole MoAb A7:F(ab')2, respectively. The tissue:blood ratios for the F(ab')2 fragments showed a value of 18.5 in tumors, whereas its was a value less than 1.0 in normal organs. The tumor accumulation of F(ab')2 fragments was also dependent on the antigenic expression of each tumor among xenografts of colon carcinoma SW1116 and WiDr, and squamous cell carcinoma KB. In kinetic experiments with whole MoAb A7 and its F(ab')2 fragments, whole MoAb A7 was lost, with a half-life of 4 days, in both blood and tumors, whereas F(ab')2 fragments were rapidly lost with a half-life of 1.5 days. These results suggested that the F(ab')2 fragments were cleared from the blood faster than was whole MoAb A7.
Isolation and structural analysis of microsomal membrane proteins (1998)

Investigation of the endoplasmic reticulum requires a methodological background in the solubilization, purification, and structural analysis of membrane proteins. The experience of one laboratory with microsomal proteins over 30 years is summarized in this review. We focus on the isolation and structure of the major proteins of rabbit liver microsomes. The special pitfalls encountered with fragile protein complexes, hydrophobic peptides, and post-translational modifications are emphasized.
Modeling and performance analysis of file transfer in a satellite wide area network (1992)

The authors consider the network modeling and performance analysis of multimedia file transfer between workstations connected to remotely located local area networks (LANs). The LANs are linked by a satellite wide-area network (SWAN) with a high bandwidth and high path delay. Four areas are addressed: (1) development of a fairly accurate interconnection network model using measured delay values for different network elements; (2) derivation of tight upper and lower bounds for the network throughput for both error-free and error-prone channels using mean value analysis; (3) validation of the model using computer simulation; and (4) analysis of the SWAN performance using numerical results for a wide range of parameters (file sizes, window size, link speed, number of workstations, etc.) for the case of a multimedia SWAN. Based on the analyses, performance bottlenecks for different operating conditions that could be used to evolve design criteria for better overall system performance are identified.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Cytotoxicity of activated monocytes on endothelial cells. (1990)

Unstimulated human monocytes did not express appreciable levels of cytotoxicity on normal human umbilical vein endothelial cells (EC) in a 24-48 hr TdR release assay. On activation with IFN-gamma and LPS, monocytes had appreciable cytotoxicity on EC. Monocyte cytotoxicity on EC was not dependent on the presence of contaminating lymphoid cells. Recombinant TNF, IL-1, and IL-6 as well as monocyte supernatants did not exert a cytotoxic effect on EC. Moreover, anti-TNF, anti-IL-1, and anti-IL-6 antibodies, as well as scavengers of reactive oxygen intermediates, did not affect the cytotoxicity of activated monocytes on EC. Antibodies against the beta-chain (CD18) of leukocyte integrins inhibited the adhesion and cytotoxicity of activated monocytes on EC. Pretreatment of EC with IL-1 augmented the adhesion of monocytes on EC. Normal monocytes were not cytotoxic on IL-1-pretreated EC and IL-1 treatment did not increase the susceptibility of EC to activated monocytes. Thus adhesion is necessary but not sufficient for monocyte killing of EC. Anti-alpha L (LFA-1) antibodies markedly reduced monocyte cytotoxicity on EC, although anti-alpha X (p150) antibodies had only a modest effect. Anti-alpha M (Mac-1/CR3) antibodies were intermediate inhibitors of EC killing by activated monocytes. Thus, alpha L, beta 2 (LFA-1), and, to a lesser extent, alpha M, beta 2 (Mac-1/CR3) and alpha X, beta 2 (p 150, 95) integrins are the main adhesive structures involved in the cytotoxic interaction of activated monocytes with EC. Monocyte-mediated damage of EC could play a role as a mechanism of tissue injury under conditions of local or systemic activation of mononuclear phagocytes.
The number of people with glaucoma worldwide in 2010 and 2020 (2006)

Glaucoma is the second leading cause of blindness worldwide, disproportionately affecting women and Asians.