gebhart/patrepeval huggingface dataset:
α4β1Integrin-dependent Cell Adhesion Is Regulated by a Low Affinity Receptor Pool That Is Conformationally Responsive to Ligand (1995)

alpha 4 beta 1 integrin (VLA-4) appears to be unique among the leukocyte integrins in that it can initiate the adhesion of circulating lymphocytes without cellular activation. It is not known how lymphocytes or other cell types maintain constitutive levels of alpha 4 beta 1 integrin activity. The current report describes a monoclonal antibody, 15/7, that recognizes a high affinity or ligand-occupied conformation of beta 1 integrin. Studies with 15/7 revealed that alpha 4 beta 1 integrin-dependent adhesion of leukocytic cell lines is mediated by a population of low affinity receptors that is conformationally responsive to ligand; the 15/7 epitope could be induced by nanomolar concentrations of soluble VCAM-1 or by micromolar concentrations of a peptide derived from the type III connecting segment domain of fibronectin (as ligands for alpha 4 beta 1 integrin). The same receptors were also responsive to adhesion activating reagents, such as Mn2+, activating anti-beta 1 integrin antibodies, and phorbol myristate acetate, which induced the 15/7 epitope directly and/or decreased the concentration of ligand required for epitope induction. In addition to the responsive receptor pool, cells expressed a second population of alpha 4 beta 1 integrin that was conformationally restrained, failing to respond to ligand or to any of the activating reagents. The relative size of the responsive and inactive receptor pools, as well as the affinity of the responsive receptors, represented a stable phenotype of different cell types and played important roles in defining the cells' adhesive capacity and ligand specificity. Similar receptor populations were measured on lymphocyte subsets in whole blood. These studies provide insight into how cells maintain different constitutive levels of alpha 4 beta 1 integrin activity, and how the activity of beta 1 integrin can be modulated by activators of cell adhesion.
Typing and molecular characterization of human papillomaviruses in genital warts from South African women (1991)

Condyloma acuminata from 12 women were examined for the presence of human papillomavirus DNA. Six of the women had HPV 6a, two had HPV 11a, one had a new HPV 6 subtype, and one a new HPV 11 subtype. The new HPV 6 subtype could be distinguished from other HPV 6 subtypes on the basis of Pst I fragments as well as Hind II fragments. The new HPV 11 subtype had a different Hpa II restriction endonuclease pattern. Restriction maps of both new subtypes were constructed. Two of the biopsies did not contain detectable HPV DNA when probed with HPV 6, HPV 11, and HPV 16. Biopsies were taken from normal tissue 1 cm away from the condyloma in 11 of the patients. Only one of these normal tissue biopsies was positive for HPV by Southern blot hybridization.
Kinetics and Mechanism of Cellobiose Hydrolysis and Retro-Aldol Condensation in Subcritical and Supercritical Water (2002)

Reactions of cellobiose in subcritical and supercritical water were studied. Kinetic study on the cellobiose decomposition clarified that the contribution of hydrolysis to the overall cellobiose decomposition rate decreased and that of retro-aldol condensation greatly increased with decreasing pressure in near-critical and supercritical water. It was found that the rate of retro-aldol condensation was expressed as a first-order reaction rate law and the kinetic parameters of this reaction were estimated. With regards to hydrolysis of cellobiose, it was indicated that the rate of hydrolysis was a second-order reaction (first-order reaction of the water concentration) and its activation energy and preexponential factor were determined. Mechanisms of these reactions were discussed based on the experimental findings. It was suggested that hydrolysis of cellobiose mainly took place by the nucleophilic attack of the oxygen atom of the water molecule or by the attack of a proton ion dissociated from supercritical water to the glycosidic carbon atom of the cellobiose molecule under the condition where the density of water was low and that the increase in the local water density around a solute promotes the hydrolysis rate at identical conditions. It was also found that retro-aldol condensation was promoted as the density of water decreased in near-critical and supercritical water. This is probably because this reaction can take place via the intermediate formed by the intramolecular hydrogen bond linkage of cellobiose, resulting in the enhancement of the intermediate formation by the increase of hydrophobic water molecules at lower water densities such as the gas-phase treatment.
On the Representation of Operators in Bases of Compactly Supported Wavelets (1992)

International audience
IL-15Rα chaperones IL-15 to stable dendritic cell membrane complexes that activate NK cells via trans presentation (2008)

Natural killer (NK) cells are innate immune effectors that mediate rapid responses to viral antigens. Interleukin (IL)-15 and its high affinity IL-15 receptor, IL-15Rα, support NK cell homeostasis in resting animals via a novel trans presentation mechanism. To better understand how IL-15 and IL-15Rα support NK cell activation during immune responses, we have used sensitive assays for detecting native IL-15 and IL-15Rα proteins and developed an assay for detecting complexes of these proteins. We find that IL-15 and IL-15Rα are preassembled in complexes within the endoplasmic reticulum/Golgi of stimulated dendritic cells (DCs) before being released from cells. IL-15Rα is required for IL-15 production by DCs, and IL-15 that emerges onto the cell surface of matured DCs does not bind to neighboring cells expressing IL-15Rα. We also find that soluble IL-15–IL-15Rα complexes are induced during inflammation, but membrane-bound IL-15–IL-15Rα complexes, rather than soluble complexes, support NK cell activation in vitro and in vivo. Finally, we provide in vivo evidence that expression of IL-15Rα specifically on DCs is critical for trans presenting IL-15 and activating NK cells. These studies define an unprecedented cytokine–receptor biosynthetic pathway in which IL-15Rα serves as a chaperone for IL-15, after which membrane-bound IL-15Rα–IL-15 complexes activate NK cells via direct cell–cell contact.
Terahertz Pulsed Imaging of Human Breast Tumors (2006)

The feasibility of using terahertz pulsed imaging to map margins of exposed breast tumors was investigated by imaging 22 excised human breast tissue specimens with carcinoma excised from 22 women (mean age, 59 years; range, 39-80 years). The study was approved by the local ethics research committee, and informed consent was obtained from all patients. The size and shape of tumor regions on terahertz images were compared with those identified at histopathologic examination of the imaged section. Two image parameters were investigated: the minimum of the terahertz impulse function and the ratio of the minimum to the maximum of the terahertz impulse function. The correlation coefficient for the tumor area on images compared with that on a photomicrograph of all 22 samples was greater than 0.82 for both parameters. The shape of the tumor regions on terahertz images also correlated well with that on a photomicrograph (median Spearman rank correlation coefficient, 0.69). Findings of this study demonstrate the potential of terahertz pulsed imaging to depict both invasive breast carcinoma and ductal carcinoma in situ under controlled conditions and encourage further studies to determine the sensitivity and specificity of the technique.
A comparison of string distance metrics for name-matching tasks (2003)

Using an open-source, Java toolkit of name-matching methods, we experimentally compare string distance metrics on the task of matching entity names. We investigate a number of different metrics proposed by different communities, including edit-distance metrics, fast heuristic string comparators, token-based distance metrics, and hybrid methods. Overall, the best-performing method is a hybrid scheme combining a TFIDF weighting scheme, which is widely used in information retrieval, with the Jaro-Winkler string-distance scheme, which was developed in the probabilistic record linkage community.
A preliminary study of the effects of laser radiation on collagen metabolism in cell culture (1996)

A low power Ga-As pulse laser was used to stimulate cultured human embryonic fibroblast cells. Energy fluencies varied from 0-1 J/cm2 over a period of 1-4 days. Fibroblast procollagen production was monitored by the synthesis of [3H] hydroxyproline, and DNA replication was assessed by [3H] thymidine incorporation. Following laser treatment, controlled pepsin digestion measured the increase in cell biostimulation. Maximum increase in collagen production and cell biostimulation occurred after 4 episodes of laser treatment at 24-hour intervals. Laser doses between 0.099 and 0.522 J/cm2 had the most significant stimulatory effects on fibroblast function. Clinical efficacy of the low power Ga-As pulse laser may be related to enhanced connective tissue repair.
Logic Design of Programmable Logic Arrays (1979)

Compared with random logic circuits, memory-type circuits are more suitable for LSI realization since their iterated structure of identical cells results in higher transistor density and higher yield. A programmable logic array (PLA) is a read only memory (ROM) with programmable addresses and it is suitable for realizing logic functions with many unspecified input combinations. For such a function, reduction of the number of input is possible in many cases. Since the cost of a PLA is mainly determined by the number of pins and the chip, both of which are affected by the number of inputs, the reduction of the number of inputs is very important in PLA design. On the other hand, the reduction of the number of product terms in a sum-of-product expression is important in conventional random logic synthesis. Since there is a tradeoff problem between the number of inputs and the number of product terms, we give a design procedure by the following preference order: 1) minimizing the number of pins, 2) minimizing the number of product terms, 3) minimizing the number of circuits used in the PLA. These factors also determine the area required for a chip.
Regulation of mevalonate synthesis in low density lipoprotein receptor knockout mice fed n‐3 or n‐6 polyunsaturated fatty acids (1999)

3-Hydroxy-3-methylglutaryl (HMG)-CoA reductase, the rate-limiting enzyme in cholesterol biosynthesis, catalyzes the formation of mevalonate which is also required for cell proliferation. Changes in HMG-CoA reductase may mediate the differential effects of n-3 and n-6 polyunsaturated fatty acids (PUFA) on experimental mammary tumorigenesis, but the mechanisms by which these fatty acids regulate HMG-CoA reductase are unclear. To determine whether the low density lipoprotein receptor (LDL-R) is required for this regulation, groups of female LDL-R knockout (-/-) and wild-type (+/+) mice were fed 7% fat diets rich in either n-3 (menhaden oil) or n-6 (safflower oil) PUFA for 1 wk. Dietary PUFA and deletion of the LDL-R had independent effects on HMG-CoA reductase and serum lipids, and a significant diet-gene interaction was observed. The effects of PUFA on HMG-CoA reductase in the mammary gland, but not the liver, were mediated by the LDL-R. We also observed that differences in HMG-CoA reductase and serum LDL-cholesterol, high density lipoprotein cholesterol, and triglycerides between -/- and +/+ mice were dependent on whether the mice were fed n-3 or n-6 PUFA. Differences between -/- and +/+ mice were much greater when animals were fed n-6 PUFA rather than n-3 PUFA. These results show that the LDL-R mediates the effects of PUFA on HMG-CoA reductase in the mammary gland but not the liver. Furthermore, the composition of dietary PUFA profoundly influences the effects of deleting the LDL-R on HMG-CoA reductase and serum lipids and suggests that diet may influence the phenotype of other knock-out or transgenic animals.
New distributional modelling approaches for gap analysis (2003)

Abstract Synthetic products based on biodiversity information such as gap analysis depend critically on accurate models of species' geographic distributions that simultaneously minimize error in both overprediction and omission. We compared current gap methodologies, as exemplified by the distributional models used in the Maine Gap Analysis project, with an alternative approach, the geographic projections of ecological niche models developed using the Genetic Algorithm for Rule‐Set Prediction (GARP). Point‐occurrence data were used to develop GARP models based on the same environmental data layers as were used in the gap project, and independent occurrence data used to test both methods. Gap models performed better in avoiding omission error, but GARP better avoided errors of overprediction. Advantages of the point‐based approach, and strategies for its incorporation into current gap efforts are discussed.
Mutual Information and Minimum Mean-Square Error in Gaussian Channels (2005)

This paper deals with arbitrarily distributed finite-power input signals observed through an additive Gaussian noise channel. It shows a new formula that connects the input-output mutual information and the minimum mean-square error (MMSE) achievable by optimal estimation of the input given the output. That is, the derivative of the mutual information (nats) with respect to the signal-to-noise ratio (SNR) is equal to half the MMSE, regardless of the input statistics. This relationship holds for both scalar and vector signals, as well as for discrete-time and continuous-time noncausal MMSE estimation. This fundamental information-theoretic result has an unexpected consequence in continuous-time nonlinear estimation: For any input signal with finite power, the causal filtering MMSE achieved at SNR is equal to the average value of the noncausal smoothing MMSE achieved with a channel whose SNR is chosen uniformly distributed between 0 and SNR.
The New I.E. Aust Accreditation: Clarification or Confusion? - an Engineering Management Perspective (1999)

This paper analyses the new I.E. Aust Accreditation Manual from an engineering management perspective. Whilst it is clear the new accreditation policy and procedures mark a new change of direction and increased I.E. Aust participation in the accreditation of engineering curricula process, and attempt to clarify the new requirements for accreditation, in relation to management studies in engineering they have added more confusion rather than clarification. The latest I.E. Aust. survey revealed engineers involved in management outnumber technical specialist engineers by three to one. Yet engineering management is treated so superficially and lacks clarification that the new manual has set the clock back in management studies, whilst supposedly to be more flexible and dependent on outcomes rather than policies and processes, they may range from 'soft options' to Mickey Mouse courses, much dependent on engineering academics' interpretations of 'professional practice.' Without clearer guidelines and definitions, first aid, stress and conflict management, waste management, figure management, pain and anger management, and environmental management can be passed off as 'management studies,' without any relevance to engineering .
EXTRACTION OF LEAD AND STRONTIUM FROM HAZARDOUS WASTE STREAMS BY SOLVENT EXTRACTION WITH 4',4',(5')-DI-(T-BUTYLDICYCLOHEXO)-18-CROWN-6 (1997)

ABSTRACT Extraction of Pb from nitric acid solutions and simulated acidic hazardous waste streams has been demonstrated with 0.15 M 4',4',(5')-di-(t-butyldicyclohexo) 18-crown-6 and 1,2 M tributyl phosphate in a commercial isoparaffinic hydrocarbon called Isopar L∗. The extraction has been shown to be dependent upon extractant concentration, aqueous nitrate concentration, and the identity of the predominant anion in the aqueous phase. It has been shown that Pb and Sr can be extracted simultaneously and stripped efficiently from the loaded organic phase. The quantitative (>99%) removal of Pb and Sr can be achieved in 3 to 4 batch contact extractions. Batch contact flowsheets have been utilized to demonstrate the potential for the simultaneous removal of Sr and Pb from simulated radioactive waste followed by partitioning of the extracted Sr fraction from the Pb fraction.
Opioid use in chronic pain (1997)

Many of the important questions for those who prescribe opioids in chronic pain, and important for those who take the drugs, still have to be answered with inadequate evidence, because we lack randomised trials on these topics. Two of the principal reasons for "failure' of opioids to relieve pain, incident pain and neuropathic pain, are discussed. Some specific adverse effect problems are addressed, and the paper concludes with a section on the vexed issue of opioid prescription in non-cancer pain.
Mechanism of interaction of Dictyostelium severin with actin filaments. (1982)

Severin, a 40,000-dalton protein from Dictyostelium that disassembles actin filaments in a Ca2+ -dependent manner, was purified 500-fold to greater than 99% homogeneity by modifications of the procedure reported by Brown, Yamamoto, and Spudich (1982. J. Cell Biol. 93:205-210). Severin has a Stokes radius of 29 A and consists of a single polypeptide chain. It contains a single methionyl and five cysteinyl residues. We studied the action of severin on actin filaments by electron microscopy, viscometry, sedimentation, nanosecond emission anisotropy, and fluorescence energy transfer spectroscopy. Nanosecond emission anisotropy of fluoresence-labeled severin shows that this protein changes its conformation on binding Ca2+. Actin filaments are rapidly fragmented on addition of severin and Ca2+, but severin does not interact with actin filaments in the absence of Ca2+. Fluorescence energy transfer measurements indicate that fragmentation of actin filaments by severin leads to a partial depolymerization (t1/2 approximately equal to 30 s). Depolymerization is followed by exchange of a limited number of subunits in the filament fragments with the disassembled actin pool (t1/2 approximately equal to 5 min). Disassembly and exchange are probably restricted to the ends of the filament fragments since only a few subunits in each fragment participate in the disassembly or exchange process. Steady state hydrolysis of ATP by actin in the presence of Ca2+-severin is maximal at an actin: severin molar ratio of approximately 10:1, which further supports the inference that subunit exchange is limited to the ends of actin filaments. The observation of sequential depolymerization and subunit exchange following the fragmentation of actin by severin suggests that severin may regulate site-specific disassembly and turnover of actin filament arrays in vivo.
New somatic mutations andWNK1-B4GALNT3gene fusion in papillary thyroid carcinoma (2015)

Papillary thyroid carcinoma (PTC) is the most frequent thyroid malignant neoplasia. Oncogene activation occurs in more than 70% of the cases. Indeed, about 40% of PTCs harbor mutations in BRAF gene, whereas RET rearrangements (RET/PTC oncogenes) are present in about 20% of cases. Finally, RAS mutations and TRK rearrangements account for about 5% each of these malignancies. We used RNA-Sequencing to identify fusion transcripts and mutations in cancer driver genes in a cohort of 18 PTC patients. Furthermore, we used targeted DNA sequencing to validate identified mutations. We extended the screening to 50 PTC patients and 30 healthy individuals. Using this approach we identified new missense mutations in CBL, NOTCH1, PIK3R4 and SMARCA4 genes. We found somatic mutations in DICER1, MET and VHL genes, previously found mutated in other tumors, but not described in PTC. We identified a new chimeric transcript generated by the fusion of WNK1 and B4GALNT3 genes, correlated with B4GALNT3 overexpression. Our data confirmed PTC genetic heterogeneity, revealing that gene expression correlates more with the mutation pattern than with tumor staging. Overall, this study provides new data about mutational landscape of this neoplasia, suggesting potential pharmacological adjuvant therapies against Notch signaling and chromatin remodeling enzymes.
OpenStreetMap: User-Generated Street Maps (2008)

The OpenStreetMap project is a knowledge collective that provides user-generated street maps. OSM follows the peer production model that created Wikipedia; its aim is to create a set of map data that's free to use, editable, and licensed under new copyright schemes. A considerable number of contributors edit the world map collaboratively using the OSM technical infrastructure, and a core group, estimated at approximately 40 volunteers, dedicate their time to creating and improving OSM's infrastructure, including maintaining the server, writing the core software that handles the transactions with the server, and creating cartographical outputs. There's also a growing community of software developers who develop software tools to make OSM data available for further use across different application domains, software platforms, and hardware devices. The OSM project's hub is the main OSM Web site.
Metabolism and anti-human immunodeficiency virus-1 activity of 2-halo-2‘,3‘-dideoxyadenosine derivatives. (1988)

Both 2',3'-dideoxyadenosine and 2',3'-dideoxyinosine have been shown (Mitsuya, H., and Broder, S. (1987) Nature 325, 773-778) to have in vitro activity against the human immunodeficiency virus-1 (HIV). However, these dideoxynucleosides may be catabolized by human T cells, even when adenosine deaminase is inhibited by deoxycoformycin. To overcome this problem, we have synthesized the 2-fluoro-, 2-chloro-, and 2-bromo-derivatives of 2',3'-dideoxyadenosine. The metabolism and anti-HIV activity of the 2-halo-2',3'-dideoxyadenosine derivatives and of 2',3'-dideoxyadenosine were compared. The 2-halo-2',3'-dideoxyadenosine derivatives were not deaminated significantly by cultured CEM T lymphoblasts. Experiments with 2-chloro-2',3'-dideoxyadenosine showed that the T cells converted the dideoxynucleoside to the 5'-monophosphate, 5'-diphosphate, and 5'-triphosphate metabolites. At concentrations lower than those producing cytotoxicity in uninfected cells (3-10 microM), the 2-halo-2',3-dideoxyadenosine derivatives inhibited the cytopathic effects of HIV toward MT-2 T lymphoblasts, and retarded viral replication in CEM T lymphoblasts. Experiments with a deoxycytidine kinase-deficient mutant CEM T cell line showed that this enzyme was necessary for the phosphorylation and anti-HIV activity of the 2-chloro-2',3'-dideoxyadenosine. In contrast, 2',3'-dideoxyadenosine was phosphorylated by the deoxycytidine kinase-deficient mutant and retained anti-HIV activity in this cell line. Thus, the 2-halo derivatives of 2',3'-dideoxyadenosine, in contrast to 2',3'-dideoxyadenosine itself, are not catabolized by T cells. Their anti-HIV and anti-proliferative activities are manifest only in cells expressing deoxycytidine kinase. The in vivo implications of these results for anti-HIV chemotherapy are discussed.