gebhart/patrepeval huggingface dataset:
Fetuin-A/Albumin-Mineral Complexes Resembling Serum Calcium Granules and Putative Nanobacteria: Demonstration of a Dual Inhibition-Seeding Concept (2009)

Serum-derived granulations and purported nanobacteria (NB) are pleomorphic apatite structures shown to resemble calcium granules widely distributed in nature. They appear to be assembled through a dual inhibitory-seeding mechanism involving proteinaceous factors, as determined by protease (trypsin and chymotrypsin) and heat inactivation studies. When inoculated into cell culture medium, the purified proteins fetuin-A and albumin fail to induce mineralization, but they will readily combine with exogenously added calcium and phosphate, even in submillimolar amounts, to form complexes that will undergo morphological transitions from nanoparticles to spindles, films, and aggregates. As a mineralization inhibitor, fetuin-A is much more potent than albumin, and it will only seed particles at higher mineral-to-protein concentrations. Both proteins display a bell-shaped, dose-dependent relationship, indicative of the same dual inhibitory-seeding mechanism seen with whole serum. As ascertained by both seeding experiments and gel electrophoresis, fetuin-A is not only more dominant but it appears to compete avidly for nanoparticle binding at the expense of albumin. The nanoparticles formed in the presence of fetuin-A are smaller than their albumin counterparts, and they have a greater tendency to display a multi-layered ring morphology. In comparison, the particles seeded by albumin appear mostly incomplete, with single walls. Chemically, spectroscopically, and morphologically, the protein-mineral particles resemble closely serum granules and NB. These particles are thus seen to undergo an amorphous to crystalline transformation, the kinetics and completeness of which depend on the protein-to-mineral ratios, with low ratios favoring faster conversion to crystals. Our results point to a dual inhibitory-seeding, de-repression model for the assembly of particles in supersaturated solutions like serum. The presence of proteins and other inhibitory factors tend to block apatite nuclei formation or to stabilize the nascent nuclei as amorphous or semi-crystalline spherical nanoparticles, until the same inhibitory influences are overwhelmed or de-repressed, whereby the apatite nuclei grow in size to coalesce into crystalline spindles and films-a mechanism that may explain not only the formation of calcium granules in nature but also normal or ectopic calcification in the body.
Inhibition of an ecto‐ATP‐diphosphohydrolase by azide (1999)

Cell surface ATPases (ecto-ATPases or E-ATPases) hydrolyze extracellular ATP and other nucleotides. Regulation of extracellular nucleotide concentration is one of their major proposed functions. Based on enzymatic characterization, the E-ATPases have been divided into two subfamilies, ecto-ATPases and ecto-ATP-diphosphohydrolases (ecto-ATPDases). In the presence of either Mg2+ or Ca2+, ecto-ATPDases, including proteins closely related to CD39, hydrolyze nucleoside diphosphates in addition to nucleoside triphosphates and are inhibited by millimolar concentrations of azide, whereas ecto-ATPases appear to lack these two properties. This report presents the first systematic kinetic study of a purified ecto-ATPDase, the chicken oviduct ecto-ATPDase (Strobel, R.S., Nagy, A.K., Knowles, A.F., Buegel, J. & Rosenberg, M.O. (1996) J. Biol. Chem. 271, 16323-16331), with respect to ATP and ADP, and azide inhibition. Km values for ATP obtained at pH 6.4 and 7.4 are 10-30 times lower than for ADP and the catalytic efficiency is greater with ATP as the substrate. The enzyme also exhibits complicated behavior toward azide. Variable inhibition by azide is observed depending on nucleotide substrate, divalent ion, and pH. Nearly complete inhibition by 5 mm azide is obtained when MgADP is the substrate and when assays are conducted at pH 6-6.4. Azide inhibition diminishes when ATP is the substrate, Ca2+ as the activating ion, and at higher pH. The greater efficacy of azide in inhibiting ADP hydrolysis compared to ATP hydrolysis may be related to the different modes of inhibition with the two nucleotide substrates. While azide decreases both Vmax and Km for ADP, it does not alter the Km for ATP. These results suggest that the apparent affinity of azide for the E.ADP complex is significantly greater than that for the free enzyme or E.ATP. The response of the enzyme to three other inhibitors, fluoride, vanadate, and pyrophosphate, is also dependent on substrate and pH. Taken together, these results are indicative of a discrimination between ADP and ATP by the enzyme. A mechanism of azide inhibition is proposed.
Mechanism of in vitro collagen fibril assembly. Kinetic and morphological studies. (1986)

The kinetics of in vitro fibril assembly of Type I collagen preparations that contain different amounts of covalently cross-linked oligomers was studied with turbidimetry. Fibril formation showed a lag phase with no solution turbidity and a growth phase with a sigmoidal increase in the solution turbidity. The length of the lag phase was inversely related to both the total collagen concentration and the amount of covalently cross-linked oligomers in the solution. Double logarithmic plots of t1/4, the amount of time it takes for 1/4 of the collagen to assemble into fibrils, versus the total collagen concentration were linear but the slope decreased from -0.84 to -2.3 with decreasing amounts of covalently cross-linked oligomers in the samples. Electron microscopy showed the formation of unbanded microfibrils with diameters in the range of 3-15 nm early in the lag phase and larger diameter banded fibrils coexisting with the microfibrils near the end of the lag phase. Centrifugation of the solution at the lag phase prolonged the lag time, presumably by removal of microfibrils, but subsequent growth of the fibrils was unaffected. The results suggest a cooperative nucleation-growth mechanism for the in vitro assembly of collagen fibrils which is consistent with the results of an equilibrium study of the fibril assembly reaction we reported earlier (Na, G. C., Butz, L. J., Bailey, D. G., and Carroll, R. J. (1986) Biochemistry 25, 958-966).
MPEG Unified Speech and Audio Coding - The ISO/MPEG Standard for High-Efficiency Audio Coding of All Content Types (2012)

In early 2012 the ISO/IEC JTC1/SC29/WG11 (MPEG) finalized the new MPEG-D Unified Speech and Audio Coding standard. The new codec brings together the previously separated worlds of general audio coding and speech coding. It does so by integrating elements from audio coding and speech coding into a unified system. The present publication outlines all aspects of this standardization effort, starting with the history and motivation of the MPEG work item, describing all technical features of the final system, and further discussing listening test results and performance numbers which show the advantages of the new system over current state-of-the-art codecs.
Selection and characterisation of a phage-displayed human antibody (Fab) reactive to the lung resistance-related major vault protein (2002)

The major vault protein is the main component on multimeric vault particles, that are likely to play an essential role in normal cell physiology and to be associated with multidrug resistance of tumour cells. In order to unravel the function of vaults and their putative contribution to multidrug resistance, specific antibodies are invaluable tools. Until now, only conventional major vault protein-reactive murine monoclonal antibodies have been generated, that are most suitable for immunohistochemical analyses. The phage display method allows for selection of human antibody fragments with potential use in clinical applications. Furthermore, cDNA sequences encoding selected antibody fragments are readily identified, facilitating various molecular targeting approaches. In order to obtain such human Fab fragments recognising major vault protein we used a large non-immunized human Fab fragment phage library. Phages displaying major vault protein-reactive Fabs were obtained through several rounds of selection on major vault protein-coated immunotubes and subsequent amplification in TG1 E coli bacteria. Eventually, one major vault protein-reactive clone was selected and further examined. The anti-major vault protein Fab was found suitable for immunohistochemical and Western blot analysis of tumour cell lines and human tissues. BIAcore analysis showed that the binding affinity of the major vault protein-reactive clone almost equalled that of the murine anti-major vault protein Mabs. The cDNA sequence of this human Fab may be exploited to generate an intrabody for major vault protein-knock out studies. Thus, this human Fab fragment should provide a valuable tool in elucidating the contribution(s) of major vault protein/vaults to normal physiology and cellular drug resistance mechanisms.
The purification and properties of deoxyguanosine triphosphate triphosphohydrolase from Escherichia coli. (1988)

Deoxyguanosine triphosphate (dGTP) triphosphohydrolase (EC 3.1.5.1) has been purified approximately 16,000-fold to apparent homogeneity from extracts of Escherichia coli. The enzyme has a native molecular weight of 230,000 and a sedimentation coefficient of 9.3 S. Its subunit molecular weight derived from electrophoresis in denaturing polyacrylamide gels is 58,900, and it has a unique N-terminal sequence for the first 25 amino acids, which indicate that the native enzyme is composed of 4 homologous subunits. It is insensitive to sulfhydryl reagents and EDTA and can be heated to 60 degrees C for 60 min without loss of activity. The enzyme requires Mg2+ for activity, is highly specific for dGTP among the canonical deoxynucleoside triphosphates, and has a unique activity among nucleoside triphosphatases in that the products of the reaction are deoxyguanosine and inorganic tripolyphosphate. Preliminary evidence suggest that this enzyme is responsible for the optA mutant phenotype first described by Saito and Richardson (Saito, H., and Richardson, C.C. (1981) J. Virol. 37, 343-351).
Partial Nephrectomy Versus Radical Nephrectomy in Patients With Small Renal Tumors—Is There a Difference in Mortality and Cardiovascular Outcomes? (2008)

Radical nephrectomy, which is currently the most common treatment for small renal tumors, may be associated with significant, adverse treatment effects compared with partial nephrectomy. Partial nephrectomy should be considered in most patients with small renal tumors.
Tumor-associated glycolipid antigens defined by monoclonal antibodies. (1983)

Four types of glycolipid changes have been observed associated with oncogenic transformation: 1) incomplete synthesis, 2) neosynthesis, 3) a shifting a glycolipid synthesis from one series to another, and 4) the change of glycolipid organization in membranes. Both incomplete synthesis and neosynthesis result in the accumulation of glycolipid markers which are distinctive to tumor cells and can be defined by monoclonal antibodies. Glycolipids with X determinant, particularly those with di- or poly-fucosylated structure in a large variety of human adenocarcinoma, GD3 ganglioside in human melanoma, and ceramide trihexoside in Burkitt lymphoma are among these glycolipid markers which have been well characterized. These glycolipid markers can be useful targets for diagnosis and therapy of human cancer.
Recent Kinase and Kinase Inhibitor X-ray Structures: Mechanisms of Inhibition and Selectivity Insights (2004)

Recent years have seen an explosion in the number of publicly available x-ray crystal structures of protein kinases. These structures have provided a wealth of information on the regulatory mechanisms, conformational plasticity and drugability of this important family of enzymes. Drawing upon structural information, new insights into the development of protein kinase inhibitors are discussed including de-novo design, molecular templates for ATP competitive inhibitors and alternative mechanisms of inhibition. The highly conserved nature of the ATP binding site is of central concern to drug development and the concept of a selectivity profile has arisen with structure-based design emerging as a key tool for addressing the challenges of specificity. In addition, protein-ligand complexes, where the enzyme is in an inactive conformation, signify an alternate approach to protein kinase inhibition. The belief that an inactive kinase presents a less conserved target is reviewed using observations on the structural changes occurring during protein kinase regulation.
Successful Multifold Dose Escalation of Anti-GD2 Monoclonal Antibody 3F8 in Patients With Neuroblastoma: A Phase I Study (2011)

Multifold dose escalation of 3F8 is feasible. The findings can be interpreted as compatible with the possibility that HM3F8 can modify toxicity without blunting anti-NB activity. This pain control strategy may help achieve dose escalation with other anti-G(D2) MoAbs.
Steric and Electronic Effects in the Aryl Phosphate to Arylphosphonate Rearrangement (1991)

A number of carboxy substituted aryl phosphates have been prepared and subjected to anionic rearrangement conditions to provide the corresponding phenolic phosphonates. Steric effects of the phosphate ester group and the electronic effects of the aryl carboxy group can limit the scope of the rearrangement.
Prostate-Regenerating Capacity of Cultured Human Adult Prostate Epithelial Cells (2009)

Experimentation with the progenitor/stem cells in adult prostate epithelium can be inconvenient due to a tight time line from tissue acquisition to cell isolation and to downstream experiments. To circumvent this inconvenience, we developed a simple technical procedure for culturing epithelial cells derived from human prostate tissue. In this study, benign prostate tissue was enzymatically digested and fractionated into epithelium and stroma, which were then cultured in the medium designed for prostate epithelial and stromal cells, respectively. The cultured cells were analyzed by immunocytochemical staining and flow cytometry. Prostate tissue-regenerating capacity of cultured cells in vitro was determined by co-culturing epithelial and stromal cells in dihydrotestosterone-containing RPMI. Cell lineages in formed acini-like structures were determined by immunohistochemistry. The culture of epithelial cells mainly consisted of basal cells. A minor population was negative for known lineage markers and positive for CD133. The culture also contained cells with high activity of aldehyde dehydrogenase. After co-culturing with stromal cells, the epithelial cells were able to form acini-like structures containing multiple cell lineages. Thus, the established culture of prostate epithelial cells provides an alternative source for studying progenitor/stem cells of prostate epithelium.
MP4, a new nonvasoactive PEG‐Hb conjugate (2003)

MP4 appears to be free of a pressor effect, a major limitation to the development of a safe and effective RBC substitutes in the past.
Engine Oil Development for Preventing Pre-Ignition in Turbocharged Gasoline Engine (2014)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;Gasoline engine downsizing combined with a turbocharger is one of the more effective approaches to improve fuel efficiency without sacrificing power performance. The benefit comes from lower pumping loss, lower mechanical friction due to ‘downsizing’ of the engine displacement and ‘down-speeding’ of the engine by using higher transmission gear ratios which is allowed by the higher engine torque at lower engine speeds. However abnormal combustion referred to as Low-Speed Pre-ignition (LSPI) is known to be able to occur in low-speed and high-torque conditions. It is a potential restriction to maximize the engine performance and its benefit, therefore prevention of LSPI is strongly desired for long-term durability of engine performance.&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;According to recent technical reports, auto-ignition of an engine oil droplet in a combustion chamber is believed to be one of major contributing factors of LSPI and its formulations have a significant effect on LSPI frequency. Toyota has reported that the oxidation stability of engine oil can be a dominant factor of its auto-ignition, which is a function of its base oil and additive components, of which an example was found that calcium-based detergents significantly increase LSPI frequency.&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;Based on these findings, we have developed a new engine oil product which can reduce LSPI frequency to less than 10% of that of conventional ILSAC certified gasoline engine oils. High quality base oils (Group III, Group IV) and optimized additive components were formulated in which the amount of calcium-based detergent was reduced to levels lower than general ILSAC oils, and a sufficient amount of anti-oxidants were added. This newly developed engine oil is scheduled to be introduced for Toyota's new turbocharged gasoline engine vehicles. The new engine was released in July 2014 in the Japanese market. Toyota plans to subsequently launch the engine in Europe and the rest of the world.&lt;/div&gt;&lt;/div&gt;
Schizophrenia: susceptibility genes and oligodendroglial and myelin related abnormalities (2014)

Given that the genetic risk for schizophrenia is highly polygenic and the effect sizes, even for rare or de novo events, are modest at best, it has been suggested that multiple biological pathways are likely to be involved in the etiopathogenesis of the disease. Most efforts in understanding the cellular basis of schizophrenia have followed a "neuron-centric" approach, focusing on alterations in neurotransmitter systems and synapse cytoarchitecture. However, multiple lines of evidence coming from genetics and systems biology approaches suggest that apart from neurons, oligodendrocytes and potentially other glia are affected from schizophrenia risk loci. Neurobiological abnormalities linked with genetic association signal could identify abnormalities that are more likely to be primary, versus environmentally induced changes or downstream events. Here, we summarize genetic data that support the involvement of oligodendrocytes in schizophrenia, providing additional evidence for a causal role with the disease. Given the undeniable evidence of both neuronal and glial abnormalities in schizophrenia, we propose a neuro-glial model that invokes abnormalities at the node of Ranvier as a functional unit in the etiopathogenesis of the disease.
The Challenge of Research into Religion and Spirituality (Keynote 1) (2014)

There are many claims that religious and spiritual belief and practice lead to better physical and mental health. What is the evidence underlying these claims and how good is the research? This paper argues that although published research shows that there is a positive statistical relationship between religion and health, the size of that health gain is extremely small. Furthermore, it would seem that spirituality divorced from religious practice may be associated with worse mental health. Much of the research is poorly conducted and some researchers hold strong personal beliefs that may influence its interpretation. Differences between research findings in the USA and Europe may help us to understand why some findings conflict.This article was first delivered as a keynote speech at the Third International Conference of the British Association for the Study of Spirituality, Spirituality in a Challenging World.
Evidence for Good Recovery of Lengths of Real Objects Seen with Natural Stereo Viewing (1996)

Six experiments are described in which good performance of the task of matching the lengths of two stationary real objects, gnarled wooden sticks, under a variety of binocular viewing conditions, including variations in viewing distances was demonstrated. Relatively poor matching performance was observed when the sticks were viewed monocularly in oscillatory motion, or monocularly and stationary. The results suggest that stereo can support good representations of metric scene structure when length judgments of natural objects are required under (quasi-)natural viewing. The implications of these results for theories of structure from stereo and structure from motion are discussed.
High expression of MAGE-A9 in tumor and stromal cells of non-small cell lung cancer was correlated with patient poor survival. (2015)

Melanoma associated antigen-A (MAGE-A) is an oncogene and correlated with tumor initiation and development. However the roles of MAGE-A9 in non-small cell lung cancer (NSCLC) are still unknown. We investigated MAGE-A9 mRNA expression in 18 tumor tissues of NSCLC by qRT-PCR and MAGE-A9 protein expression in 213 NSCLC samples of tissue arrays by immunohistochemical staining. We assessed the relationship between MAGE-A9 expression and clinical parameters. The results showed that the high expression of MAGE-A9 protein in NSCLC tumor cells were commonly present in squamous cell carcinomas (P = 0.030). It was also related to larger tumor diameter, lymph node metastasis and later stage grouping with TNM classification (all P < 0.05). Whereas the expression of MAGE-A9 in stromal cells was higher in squamous cell carcinomas as well. Cox regression univariate and multivariable analysis revealed that MAGE-A9 expression in tumor cells of NSCLC (P < 0.001) is an independent prognostic factor in five-year overall survival rate. We concluded that the molecular assessment of MAGEA9 could be considered to improve prognostic evaluation and to identify eligible patients for potential target therapy.
The LIMSI continuous speech dictation system: evaluation on the ARPA Wall Street Journal task (2002)

We report progress made at LIMSI in speaker-independent large vocabulary speech dictation using the ARPA Wall Street Journal-based CSR corpus. The recognizer makes use of continuous density HMM with Gaussian mixture for acoustic modeling and n-gram statistics estimated on the newspaper texts for language modeling. The recognizer uses a time-synchronous graph-search strategy which is shown to still be viable with vocabularies of up to 20 K words when used with bigram back-off language models. A second forward pass, which makes use of a word graph generated with the bigram, incorporates a trigram language model. Acoustic modeling uses cepstrum-based features, context-dependent phone models (intra and interword), phone duration models, and sex-dependent models. The recognizer has been evaluated in the Nov92 and Nov93 ARPA tests for vocabularies of up to 20,000 words.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>