gebhart/patrepeval huggingface dataset:
Clinical relevance of the <i>Helicobacter pylori</i> gene for blood-group antigen-binding adhesin (1999)

Infection with Helicobacter pylori is associated with different human gastric diseases. Biochemical studies, in vitro adherence assays, and in vivo animal models revealed that epithelial attachment of H. pylori can be mediated by the blood-group antigen-binding adhesin (BabA) targeting human Lewis(b) surface epitopes. Studies with transgenic mice expressing the Lewis(b) epitope have shown that such attachment can alter disease outcome. In the current study, the presence of the babA2 gene encoding the adhesin was investigated in clinical isolates from a German population by using PCR and reverse transcription-PCR. A positive genotype was correlated to allelic variations in the genes encoding VacA and CagA and also to the prevalence of duodenal ulcer, distal gastric adenocarcinoma, mucosa-associated lymphoid tissue lymphoma, and antral gastritis. The presence of babA2 was significantly associated with duodenal ulcer (P = 0.0002) and adenocarcinoma (P = 0.033). In contrast, type 1 strains (vacAs1- and cagA-positive) were associated with only duodenal ulcer (P = 0.004) but not adenocarcinoma (P = 0.235). Genotype presence of babA2, vacAs1, and cagA ("triple-positive" strains) showed a highly significant correlation to the prevalence of ulcer (P = 0.000002) and adenocarcinoma (P = 0.014) and discriminated significantly better between disease outcome than did the current type 1 classification. These results indicate that the babA2 gene is of high clinical relevance and would be a useful marker to identify patients who are at higher risk for specific H. pylori-related diseases.
No role of interleukin‐4 in CD23/IgE‐mediated enhancement of the murine antibody response <i>in vivo</i> (1995)

Antigen-specific IgE up-regulates the specific IgM, IgG1, IgG2a and IgE response in vivo when given to mice together with antigen. The enhancement is mediated by the low-affinity receptor for IgE, Fc epsilon RII or CD23, as demonstrated both in CD23-deficient mice and by blocking CD23 with anti-CD23 monoclonal antibodies. A possible mechanism behind the regulatory effects of CD23 is that the IgE/CD23/antigen complex is endocytosed by B cells, leading to increased antigen processing and presentation on major histocompatibility complex (MHC) class II molecules to T helper cells. In the present study we have found that the expression of CD23 is reduced fivefold on splenic B cells in mice genetically deficient for IL-4. When IL-4-deficient mice and normal littermates were immunized with 2,4,6-trinitrophenyl (TNP)-specific IgE followed by bovine serum albumin (BSA)-TNP or with BSA-TNP alone, the BSA-specific IgG1 and IgG2a responses were equally well augmented by IgE in all mice. In addition, a low but significant IgE response was seen even in the IL-4-deficient mice. Thus, enhancement of the antibody response through IgE and CD23 occur in the absence of IL-4 and is not dependent on CD23 up-regulation.
Rising Atmospheric Carbon Dioxide and Seed Yield of Soybean Genotypes (2001)

If intraspecific variation to rising atmospheric CO 2 exists in soybean [ Glycine max (L.) Merr.], such variation could be used to select for optimal, high‐yielding cultivars. To quantify the range and determine the basis for variation in seed‐yield with increasing CO 2 , eight ancestral and one modern soybean cultivar differing in determinacy, maturity group, and morphology were grown to reproductive maturity at two CO 2 partial pressures, 40 Pa (ambient) and 71 Pa (elevated). Experiments were replicated three times in temperature controlled glasshouses during 1998 and 1999. Although all cultivars showed a significant increase in seed yield with elevated CO 2 ,(∼40%) Mandarin, an ancestral indeterminate cultivar, showed a greater relative response of seed yield to increased CO 2 than did all other cultivars (∼80%). The observed variation in seed yield response to CO 2 was not correlated with any vegetative parameter. At maturity, significant correlations in the relative response of seed yield to CO 2 were observed for both pod weight per plant and seed weight from branches. The later observation suggests that the sensitivity of seed yield response to CO 2 was associated with plasticity in the ability to form new seed in axillary branches in a high CO 2 environment. Genotypic differences in the seed yield response among existing ancestral soybeans suggests that sufficient germplasm is available for breeders to begin selecting lines which maximize soybean yield in response to increasing atmospheric CO 2
Electrocutaneous Stimulation for Sensory Communication in Rehabilitation Engineering (1982)

Physiological and psychophysical functions underlying electrocutaneous stimulation are discussed, including a comparative review of stimulus parameters and coding formats. Procedures are recommended for implementing electrotactile displays and for generating reliable, painfree sensations with a useful communications bandwidth.
Blockchain: Blueprint for a New Economy (2015)

Bitcoin is starting to come into its own as a digital currency, but the blockchain technology behind it could prove to be much more significant. This book takes you beyond the currency (Blockchain 1.0) and smart contracts (Blockchain 2.0) to demonstrate how the blockchain is in position to become the fifth disruptive computing paradigm after mainframes, PCs, the Internet, and mobile/social networking. Author Melanie Swan, Founder of the Institute for Blockchain Studies, explains that the blockchain is essentially a public ledger with potential as a worldwide, decentralized record for the registration, inventory, and transfer of all assetsnot just finances, but property and intangible assets such as votes, software, health data, and ideas. Topics include:Concepts, features, and functionality of Bitcoin and the blockchain Using the blockchain for automated tracking of all digital endeavors Enabling censorship? resistant organizational modelsCreating a decentralized digital repository to verify identity Possibility of cheaper, more efficient services traditionally provided by nations Blockchain for science: making better use of the data-mining network Personal health record storage, including access to ones own genomic dataOpen access academic publishing on the blockchain This book is part of an ongoing OReilly series. Mastering Bitcoin: Unlocking Digital Crypto-Currencies introduces Bitcoin and describes the technology behind Bitcoin and the blockchain. Blockchain: Blueprint for a New Economy considers theoretical, philosophical, and societal impact of cryptocurrencies and blockchain technologies.
A note on orthogonal sets of hypercubes (1997)

Mutually orthogonal sets of hypercubes are higher dimensional generalizations of mutually orthogonal sets of Latin squares. For Latin squares, it is well known that the Cayley table of a group of order n is a Latin square, which has no orthogonal mate if n is congruent to 2 modulo 4. We will prove an analogous result for hypercubes. © 1997 John Wiley & Sons, Inc. J Combin Designs 5: 231–233, 1997
Mechanisms of Thrombospondin-1-Mediated Metastasis and Angiogenesis (2004)

The major route of tumor spread is through the bloodstream. Once in circulation, the tumor cells aggregate in clumps with platelets, which enhances the tumor cell survival. The tumor emboli will then adhere to the endothelium and by the release of proteases extravasation of the cells will occur. One of the platelet-secreted proteins is thrombospondin-1. In this article, thrombospondin-1 will be described as a modulator of angiogenesis through its role in regulating endothelial cell apoptosis, protease expression, and vascular endothelial growth factor expression. We hope to convey the idea that activity of thrombospondin-1 in tumor progression is dependent upon its interaction with several host- and tumor-associated proteins.
Phakic Intraocular Lenses: The New Focus in Refractive Surgery (2004)

Phakic intraocular lenses represent the next major stage in the ongoing refractive surgery revolution. Thin, foldable and removable, these lenses can be inserted under local anesthetic as part of an outpatient procedure that is relatively easy to perform.
Dynamic Denoising of Tracking Sequences (2008)

In this paper, we describe an approach to the problem of simultaneously enhancing image sequences and tracking the objects of interest represented by the latter. The enhancement part of the algorithm is based on Bayesian wavelet denoising, which has been chosen due to its exceptional ability to incorporate diverse a priori information into the process of image recovery. In particular, we demonstrate that, in dynamic settings, useful statistical priors can come both from some reasonable assumptions on the properties of the image to be enhanced as well as from the images that have already been observed before the current scene. Using such priors forms the main contribution of the present paper which is the proposal of the dynamic denoising as a tool for simultaneously enhancing and tracking image sequences. Within the proposed framework, the previous observations of a dynamic scene are employed to enhance its present observation. The mechanism that allows the fusion of the information within successive image frames is Bayesian estimation, while transferring the useful information between the images is governed by a Kalman filter that is used for both prediction and estimation of the dynamics of tracked objects. Therefore, in this methodology, the processes of target tracking and image enhancement "collaborate" in an interlacing manner, rather than being applied separately. The dynamic denoising is demonstrated on several examples of SAR imagery. The results demonstrated in this paper indicate a number of advantages of the proposed dynamic denoising over "static" approaches, in which the tracking images are enhanced independently of each other.
Novel Retinal Prosthesis System with Three Dimensionally Stacked LSI Chip (2006)

We have proposed a novel retinal prosthesis system with three-dimensionally stacked retinal prosthesis chip. The retinal prosthesis chip consists of several LSI chips that are vertically stacked and electrically connected using three-dimensional integration technology. We fabricated retinal prosthesis chip including photodetectors and stimulus current generators. We confirmed that current waveform parameters can be varied by bias voltages. Implantable stimulus electrode array was also fabricated for the electrical stimulation of the retina. To evaluate optimal retinal stimulus current, electrically evoked potential (EEP) was recorded in animal experiments. The recorded waveform shows a similar behavior to the visually evoked potential (VEP) waveform, indicating possibilities that the electrical stimulation of the retina can restore visual sensation for the blind patients
Secure Cloud Assisted Smart Cars Using Dynamic Groups and Attribute Based Access Control (2019)

Future smart cities and intelligent world will have connected vehicles and smart cars as its indispensable and most essential components. The communication and interaction among such connected entities in this vehicular internet of things (IoT) domain, which also involves smart traffic infrastructure, road-side sensors, restaurant with beacons, autonomous emergency vehicles, etc., offer innumerable real-time user applications and provide safer and pleasant driving experience to consumers. Having more than 100 million lines of code and hundreds of sensors, these connected vehicles (CVs) expose a large attack surface, which can be remotely compromised and exploited by malicious attackers. Security and privacy are serious concerns that impede the adoption of smart connected cars, which if not properly addressed will have grave implications with risk to human life and limb. In this research, we present a formalized dynamic groups and attribute-based access control (ABAC) model (referred as \cvac) for smart cars ecosystem, where the proposed model not only considers system wide attributes-based security policies but also takes into account the individual user privacy preferences for allowing or denying service notifications, alerts and operations to on-board resources. Further, we introduce a novel notion of groups in vehicular IoT, which are dynamically assigned to moving entities like connected cars, based on their current GPS coordinates, speed or other attributes, to ensure relevance of location and time sensitive notification services to the consumers, to provide administrative benefits to manage large numbers of smart entities, and to enable attributes and alerts inheritance for fine-grained security authorization policies. We present proof of concept implementation of our model in AWS cloud platform demonstrating real-world uses cases along with performance metrics.
Recent Advances in the Synthesis of Carboxylic Acid Esters (2018)

In this chapter, recent advances in the synthesis of carboxylic acid esters are summarized based on the utilization of carboxylic acids as electrophiles or nucleophiles in reactions. Condensation reagents or catalysts connect the carboxylic acids with the alcohols to afford the corresponding esters, together with the formation of 1 equiv. of H2O, in which the carboxylic acids can be regarded as the electrophile. In contrast, the carboxylate ion intermediates derived from the carboxylic acids react with alkyl halides, carbocations, or their equivalents to produce the esters, in which the carboxylate ions from the carboxylic acids can be regarded as the nucleophile. This chapter mainly introduces the recent progress in this field of the formation of esters, based on the classification of the role of carboxylic acids in reactions.
Phase III Study of Letrozole Versus Tamoxifen as First-Line Therapy of Advanced Breast Cancer in Postmenopausal Women: Analysis of Survival and Update of Efficacy From the International Letrozole Breast Cancer Group (2003)

This study documents the superiority of letrozole over tamoxifen in first-line endocrine therapy in postmenopausal women with advanced breast cancer.
A computational approach to distinguish somatic vs. germline origin of genomic alterations from deep sequencing of cancer specimens without a matched normal (2018)

A key constraint in genomic testing in oncology is that matched normal specimens are not commonly obtained in clinical practice. Thus, while well-characterized genomic alterations do not require normal tissue for interpretation, a significant number of alterations will be unknown in whether they are germline or somatic, in the absence of a matched normal control. We introduce SGZ (somatic-germline-zygosity), a computational method for predicting somatic vs. germline origin and homozygous vs. heterozygous or sub-clonal state of variants identified from deep massively parallel sequencing (MPS) of cancer specimens. The method does not require a patient matched normal control, enabling broad application in clinical research. SGZ predicts the somatic vs. germline status of each alteration identified by modeling the alteration's allele frequency (AF), taking into account the tumor content, tumor ploidy, and the local copy number. Accuracy of the prediction depends on the depth of sequencing and copy number model fit, which are achieved in our clinical assay by sequencing to high depth (>500x) using MPS, covering 394 cancer-related genes and over 3,500 genome-wide single nucleotide polymorphisms (SNPs). Calls are made using a statistic based on read depth and local variability of SNP AF. To validate the method, we first evaluated performance on samples from 30 lung and colon cancer patients, where we sequenced tumors and matched normal tissue. We examined predictions for 17 somatic hotspot mutations and 20 common germline SNPs in 20,182 clinical cancer specimens. To assess the impact of stromal admixture, we examined three cell lines, which were titrated with their matched normal to six levels (10-75%). Overall, predictions were made in 85% of cases, with 95-99% of variants predicted correctly, a significantly superior performance compared to a basic approach based on AF alone. We then applied the SGZ method to the COSMIC database of known somatic variants in cancer and found >50 that are in fact more likely to be germline.
Purification and structural characterization of placental NAD+-linked 15-hydroxyprostaglandin dehydrogenase. The primary structure reveals the enzyme to belong to the short-chain alcohol dehydrogenase family (1990)

Human placental NAD(+)-linked 15-hydroxyprostaglandin dehydrogenase was purified to homogeneity according to a five-step method, with chromatography on DEAE-Sepharose, Blue Sepharose, and Mono-Q FPLC as principal steps. Final yield was 23% and purification about 13,000-fold, with a specific activity of 24,000 milliunits/mg. The subunit molecular weight is about 29,000 as determined by sodium dodecyl sulfate/polyacrylamide gel electrophoresis, and the native protein molecular weight is about 54,000 as estimated by Sephadex G-100 chromatography, establishing the enzyme to be a dimer of similar-sized protein chains. The subunit N-terminal residue is methionine, and the alpha-amino group is free. The complete primary structure was determined by peptide analysis, based essentially on four different proteolytic treatments (Lys-specific protease, Glu-specific protease, Asp-specific protease, and CNBr). The protein chain is composed of 266 residues, with C-terminal glutamine. A microheterogeneity was detected at position 217, with both Cys and Tyr, in about equal amounts, from a preparation starting with a single placenta. No other subunit heterogeneities were detected. The protein is clearly but distantly related to insect alcohol dehydrogenases, characterized bacterial dehydrogenases of sugar metabolism, and bacterial and eukaryotic steroid dehydrogenases. Together, these results establish that placental 15-hydroxyprostaglandin dehydrogenase is a member of the short-chain nonmetalloenzyme alcohol dehydrogenase protein family. The protein has four cysteine residues (five with the positional microheterogeneity), but there is no evidence for functional importance of any of these residues.(ABSTRACT TRUNCATED AT 250 WORDS)
The effects of social resources on recovery and perceived sense of control among the disahled* (1980)

Abstract This study examines the effects of social resources on recovery and perceived sense of control among the physically disabled. Data were obtained from personal interviews with 770 non‐institutionalized disabled adults. Two types of social resources are distinguished: those derived from primary group affiliations and those derived from secondary (formal) group relationships. Secondary group sources of supportive services for the disabled may be necessary but not sufficient elements in the recovery process and in determining the disabled's perceived control over the situation. It is hypothesized that recovery and sense of control will be enhanced for those disabled who tend to utilize their social resources. The results are equivocal. An absence of any marked effect of primary group resources and an observed negative effect of secondary group resources appears to enhance recovery. Use of these social resources has little effect on one's perceived sense of control at the time of recovery. The implications of these limited findings are discussed in terms of conceptual and methodological issues involved in delineating and measuring key factors in the process of rehabilitation and recovery.
Germ cell transplantation from large domestic animals into mouse testes (2000)

Donor-derived spermatogenesis after spermatogonial transplantation to recipient animals could serve as a novel approach to manipulate the male germ line in species where current methods of genetic modification are still inefficient. The objective of the present study was to investigate germ cell transplantation from boars, bulls, and stallions, which are economically important domestic animals, to mouse recipients. Donor testis cells (fresh, cryopreserved, or cultured for 1 month) were transplanted into testes of immunodeficient recipient mice in which endogenous spermatogenesis had been destroyed. Recipient testes were analyzed from 1 to > 12 months after transplantation for the presence of donor germ cells by donor-specific immunohistochemistry. Donor cells were present in most recipient testes with species-dependent differences in pattern and extent of colonization. Porcine donor germ cells formed chains and networks of round cells connected by intercellular bridges but later stages of donor-derived spermatogenesis were not observed. Transplanted bovine testis cells initially appeared similar but then developed predominantly into fibrous tissue within recipient seminiferous tubules. Few equine germ cells proliferated in mouse testes with no obvious difference between cells recovered from a scrotal or a cryptorchid donor testis. The pattern of colonization after transplantation of cultured cells did not resemble spermatogonial proliferation. These results indicate that fresh or cryopreserved germ cells from large animals can colonize the mouse testis but do not differentiate beyond the stage of spermatogonial expansion. Species-specific differences in the compatibility of large animal donors and mouse recipients were detected which cannot be predicted solely on the basis of phylogenetic distance between donor and recipient species.
Squalene synthetase. Solubilization and partial purification of squalene synthetase, copurification of presqualene pyrophosphate and squalene synthetase activities. (1987)

Squalene synthetase (farnesyldiphosphate:farnesyldiphosphate farnesyltransferase, EC 2.5.1.21) is an intrinsic microsomal protein that catalyzes the synthesis of squalene from farnesyl pyrophosphate via the intermediate presqualene pyrophosphate. We have solubilized this enzyme from yeast with a mixture of the detergents N-octyl beta-D-glucopyranoside and Lubrol PX. Approximately 50-fold purification of the solubilized activities has been achieved by chromatography on DEAE-cellulose and hydroxylapatite and by isoelectric focusing. The most highly purified preparation has one major band of protein with a molecular weight of 53,000 as estimated by electrophoresis under denaturing conditions. The enzyme may also have been modified by proteolysis during isolation since a 47,000 molecular weight species was also found. The two activities, presqualene pyrophosphate synthetase and squalene synthetase, copurified during isolation.
Determination of mevalonate in blood plasma in man and rat. Mevalonate “tolerance” tests in man. (1979)

A method is described for the determination of mevalonate in ultrafiltrates of blood plasma. The method depends on the phosphorylation of mevalonate with [gamma-32P]ATP and mevalonate kinase to 5-[32P]phosphomevalonate, and the subsequent isolation of the 5-[32P]phosphomevalonate together with known amounts of added 5-phospho[14C]mevalonate by ion-exchange chromatography. The 32P/14C ratio in the isolated 5-phosphomevalonate is a linear function of the mevalonate content of the samples. The smallest amount that can be determined is 1--2 pmol. The fasting level in human plasma varied between 20 and 75 pmol/ml. Human red blood cells absorb mevalonate from plasma relatively slowly; their maximum storage capacity is about 1.3 pmol/10(6) red cells. An oral and intravenous "mevalonate tolerance test" in man is described that can be carried out with 200 and 30 mumol. respectively, of the unlabeled (RS)-mevalonate in a 70-kg man. Beer and wine contain mevalonate at a concentration of 3--8 microns, too low to provide a significant amount of mevalonate even for heavy drinkers. The mevalonate content of the plasma from the blood of the vena cava inferior of male rats varied between 81 and 502 pmol/ml and is positively related to the levels of liver 3-hydroxy-3-methylgultaryl-CoA reductase, suggesting that the liver is probably the main source of mevalonate circulating in blood. The plasma of renal venous blood contained only 33--85% as much mevalonate as the arterial plasma.