gebhart/patrepeval huggingface dataset:
SHOPSMART (2008)

This paper describes a new method for providing recommendations tailored to a user's preferences using text mining techniques and online technical specifications of products. We first learn a model that can predict the price of a product given automatically-determined features describing technical specifications and users' opinions. We then use this model to rank a list of products based on individual users' preferences about various features. On a data set collected from Amazon reviews and online technical specifications, rankings produced by this model rank the best product for a user in the 87th percentile of products in its category, on average. Our approach outperforms several comparison systems by 21 percentiles or more.
MOF‐5‐Polystyrene: Direct Production from Monomer, Improved Hydrolytic Stability, and Unique Guest Adsorption (2016)

An unprecedented mode of reactivity of Zn4 O-based metal-organic frameworks (MOFs) offers a straightforward and powerful approach to polymer-hybridized porous solids. The concept is illustrated with the production of MOF-5-polystyrene wherein polystyrene is grafted and uniformly distributed throughout MOF-5 crystals after heating in pure styrene for 4-24 h. The surface area and polystyrene content of the material can be fine-tuned by controlling the duration of heating styrene in the presence of MOF-5. Polystyrene grafting significantly alters the physical and chemical properties of pristine MOF-5, which is evident from the unique guest adsorption properties (solvatochromic dye uptake and improved CO2 capacity) as well as the dramatically improved hydrolytic stability of composite. Based on the fact that MOF-5 is the best studied member of the structure class, and has been produced at scale by industry, these findings can be directly leveraged for a range of current applications.
TLR3 is an endogenous sensor of tissue necrosis during acute inflammatory events (2008)

Ligands from dying cells are a source of Toll-like receptor (TLR) activating agents. Although TLR3 is known to respond to RNA from necrotic cells, the relative importance of this response in vivo during acute inflammatory processes has not been fully explored. We observed the involvement of TLR3 activation during experimental polymicrobial septic peritonitis and ischemic gut injury in the absence of an exogenous viral stimulus. In TLR3-deficient mice, increased chemokine/cytokine levels and neutrophil recruitment characterized the initial inflammatory responses in both injury models. However, the levels of inflammatory chemokines and tumor necrosis factor alpha quickly returned to baseline in tlr3(-/-) mice, and these mice were protected from the lethal effects of sustained inflammation. Macrophages from tlr3(-/-) mice responded normally to other TLR ligands but did not respond to RNA from necrotic neutrophils. Importantly, an immunoneutralizing antibody directed against TLR3 attenuated the generation of inflammatory chemokines evoked by byproducts from necrotic neutrophils cultured with wild-type macrophages. In vivo, anti-TLR3 antibody attenuated the tissue injury associated with gut ischemia and significantly decreased sepsis-induced mortality. Collectively, these data show that TLR3 is a regulator of the amplification of immune response and serves an endogenous sensor of necrosis, independent of viral activation.
The Global File System (1996)

The Global File System (GFS) is a prototype design for a distributed file system in which cluster nodes physically share storage devices connected via a network-like Fibre Channel. Networks and network-attached storage devices have advanced to a level of performance and extensibility so that the previous disadvantages of shared disk architectures are no longer valid. This shared storage architecture attempts to exploit the sophistication of storage device technologies whereas a server architecture diminishes a device&amp;apos;s role to that of a simple component. GFS distributes the file system responsibilities across processing nodes, storage across the devices, and file system resources across the entire storage pool. GFS caches data on the storage devices instead of the main memories of the machines. Consistency is established by using a locking mechanism maintained by the storage devices to facilitate atomic read-modify-write operations. The locking mechanism is being prototyped on Seagate disk drives and Ciprico disk arrays. GFS is implemented in the Silicon Graphics IRIX operating system and is accessed using standard Unix commands and utilities.
Cortactin (2011)

Branched actin assembly is critical for a variety of cellular processes that underlie cell motility and invasion, including cellular protrusion formation and membrane trafficking. Activation of branched actin assembly occurs at various subcellular locations via site-specific activation of distinct WASp family proteins and the Arp2/3 complex. A key branched actin regulator that promotes cell motility and links signaling, cytoskeletal and membrane trafficking proteins is the Src kinase substrate and Arp2/3 binding protein cortactin. Due to its frequent overexpression in advanced, invasive cancers and its general role in regulating branched actin assembly at multiple cellular locations, cortactin has been the subject of intense study. Recent studies suggest that cortactin has a complex role in cellular migration and invasion, promoting both on-site actin polymerization and modulation of autocrine secretion. Diverse cellular activities may derive from the interaction of cortactin with site-specific binding partners.
Regulation of Lymphocyte Proliferation by Uterine Serpin: Interleukin-2 mRNA Production, CD25 Expression and Responsiveness to Interleukin-2 (2000)

During pregnancy, the endometrium of the ewe secretes large amounts of a progesterone-induced protein of the serpin superfamily of serine proteinase inhibitors called ovine uterine serpin (OvUS). This protein inhibits lymphocyte proliferation in response to concanavalin A (ConA), phytohemagglutinin (PHA), or mixed lymphocyte reaction. The purpose of these experiments was to characterize the mechanism by which OvUS inhibits lymphocyte proliferation. Ovine US caused dose-dependent inhibition of lymphocyte proliferation induced by phorbol myristol acetate (PMA), an activator of protein kinase C. The PHA-induced increase in CD25 expression was inhibited in peripheral blood mononuclear leukocytes (PBML) by OvUS. However, no effect of OvUS on Con A-induced expression of CD25 was observed. Further analysis using two-color flow cytometry revealed that OvUS inhibited ConA-induced expression of CD25 in gammadelta-TCR- cells but not gammadelta-TCR+ cells. Stimulation of PBML for 14 hr with ConA resulted in an increase in steady state amounts of interleukin-2 (IL-2) mRNA that was not inhibited by OvUS. Ovine US was also inhibitory to lymphocyte proliferation induced by human IL-2. Results suggest that OvUS acts to inhibit lymphocyte proliferation by blocking the upregulation of the IL-2 receptor and inhibiting IL-2-mediated events. Lack of an effect of OvUS on ConA-stimulated CD25 expression in gammadelta-TCR+ cells may reflect a different mechanism of activation of these cells or insensitivity to inhibition by OvUS.
Tumor Immunotherapy Targeting Fibroblast Activation Protein, a Product Expressed in Tumor-Associated Fibroblasts (2005)

Murine studies have shown that immunologic targeting of the tumor vasculature, a key element of the tumor stroma, can lead to protective immunity in the absence of significant pathology. In the current study, we expand the scope of stroma-targeted immunotherapy to antigens expressed in tumor-associated fibroblasts, the predominant component of the stroma in most types of cancer. Mice were immunized against fibroblast activation protein (FAP), a product up-regulated in tumor-associated fibroblasts, using dendritic cells transfected with FAP mRNA. Using melanoma, carcinoma, and lymphoma models, we show that tumor growth was inhibited in tumor-bearing mice vaccinated against FAP and that the magnitude of the antitumor response was comparable to that of vaccination against tumor cell-expressed antigens. Both s.c. implanted tumors and lung metastases were susceptible to anti-FAP immunotherapy. The antitumor response could be further enhanced by augmenting the CD4+ T-cell arm of the anti-FAP immune response, achieved by using a lysosomal targeting sequence to redirect the translated FAP product into the class II presentation pathway, or by covaccination against FAP and a tumor cell-expressed antigen, tyrosinase-related protein 2. No morbidity or mortality was associated with anti-FAP vaccination except for a small delay in wound healing. The study suggests that FAP, a product which is preferentially expressed in tumor-associated fibroblasts, could function as a tumor rejection antigen in a broad range of cancers.
PLACE: a database of plant cis-acting regulatory DNA elements (1998)

PLACE (http://www.dna.affrc.go.jp/htdocs/PLACE/) is a database of motifs found in plant cis -acting regulatory DNA elements, all from previously published reports. It covers vascular plants only. In addition to the motifs originally reported, their variations in other genes or in other plant species reported later are also compiled. The PLACE database also contains a brief description of each motif and relevant literature with PubMed ID numbers. This report summarizes the present status of this database and available tools.
A Phase II Study to Evaluate Recombinant Platelet-Derived Growth Factor-BB in the Treatment of Stage 3 and 4 Pressure Ulcers (1994)

Data from this small trial suggest that local application of rPDGF-BB may be of therapeutic benefit in accelerating the healing of chronic pressure ulcers.
Diagnosis of chronic myeloid and acute lymphocytic leukemias by detection of leukemia-specific mRNA sequences amplified in vitro. (1988)

The Philadelphia chromosome is present in more than 95% of chronic myeloid leukemia patients and 13% of acute lymphocytic leukemia patients. The Philadelphia translocation, t(9;22), fuses the BCR and ABL genes resulting in the expression of leukemia-specific, chimeric BCR-ABL messenger RNAs. To facilitate diagnosis of these leukemias, we have developed a method of amplifying and detecting only the unique mRNA sequences, using an extension of the polymerase chain reaction technique. Diagnosis of chronic myeloid and acute lymphocytic leukemias by this procedure is rapid, much more sensitive than existing protocols, and independent of the presence or absence of an identifiable Philadelphia chromosome.
A suggestive interface for 3D drawing (2001)

This paper introduces a new type of interface for 3D drawings that improves the usability of gestural interfaces and augments typical command-based modeling systems. In our suggestive interface, the user gives hints about a desired operation to the system by highlighting related geometric components in the scene. The system then infers possible operations based on the hints and presents the results of these operations as small thumbnails. The user completes the editing operation simply by clicking on the desired thumbnail. The hinting mechanism lets the user specify geometric relations among graphical components in the scene, and the multiple thumbnail suggestions make it possible to define many operations with relatively few distinct hint patterns. The suggestive interface system is implemented as a set of suggestion engines working in parallel, and is easily extended by adding customized engines. Our prototype 3D drawing system, Chateau, shows that a suggestive interface can effectively support construction of various 3D drawings.
Use of gene fusions to study outer membrane protein localization in Escherichia coli. (1977)

Escherichia coli strains have been isolated that produce hybrid proteins comprised of an NH2-terminal sequence from the lamB gene product (an outer membrane protein) and a major portion of the COOH-terminal sequence of beta-galactosidase (beta-D-galactoside galactohydrolase, EC 3.2.1.23; a cytoplasmic protein). These proteins exhibit beta-galactosidase activity. One such strain, pop 3105, produces a hybrid protein containing very little of the lamB gene protein; the protein is found in the cytoplasm. The protein found in a second strain, pop 3186, contains much more of the lamB gene protein; a substantial fraction of the beta-galactosidase activity is found in the outer membrane, probably facing outward. These results indicate that information necessary to direct the lamB gene product to its outer membrane location is located within the lamB gene itself. The properties of such fusion strains open up the prospect of a precise genetic analysis of the genetic components involved in protein transport.
A PREALBUMIN ACTIVATOR OF PREKALLIKREIN (1972)

Human plasma kallikrein has been shown to directly and selectively attract human neutrophils from a mixed leukocyte population. The capacity of plasma kallikrein to be chemotactic and to generate the nonapeptide bradykinin was maintained during progressive purification. While neither highly purified prekallikrein nor the prealbumin Hageman factor fragments were chemotactic alone, their interaction so as to convert prekallikrein to kallikrein yielded both chemotactic and kinin-generating activity. Both functions of kallikrein were inhibited by treatment with diisopropyl fluorophosphate, indicating an essential role for the active site of the enzyme in the expression of its chemotactic activity.
Adaptive resource allocation for prioritized call admission over an ATM-based wireless PCN (1997)

In future personal communications networks (PCNs) supporting network-wide handoffs, new and handoff requests will compete for connection resources in both the mobile and backbone networks. Forced call terminations due to handoff call blocking are generally more objectionable than new call blocking. The previously proposed guard channel scheme for radio channel allocation in cellular networks reduces handoff call blocking probability substantially at the expense of slight increases in new call blocking probability by giving resource access priority to handoff calls over new calls in call admission control. While the effectiveness of a fixed number of guard channels has been demonstrated under stationary traffic conditions, with nonstationary call arrival rates in a practical system, the achieved handoff call blocking probability may deviate significantly from the desired objective. We propose a novel dynamic guard channel scheme which adapts the number of guard channels in each cell according to the current estimate of the handoff call arrival rate derived from the current number of ongoing calls in neighboring cells and the mobility pattern, so as to keep the handoff call blocking probability close to the targeted objective while constraining the new call blocking probability to be below a given level. The proposed scheme is applicable to channel allocation over cellular mobile networks, and is extended to bandwidth allocation over the backbone network to enable a unified approach to prioritized call admission control over the ATM-based PCN.
Pathway analysis of NAD+ metabolism (2011)

NAD(+) is well known as a crucial cofactor in the redox balance of metabolism. Moreover, NAD(+) is degraded in ADP-ribosyl transfer reactions, which are important components of multitudinous signalling reactions. These include reactions linked to DNA repair and aging. In the present study, using the concept of EFMs (elementary flux modes), we established all of the potential routes in a network describing NAD(+) biosynthesis and degradation. All known biosynthetic pathways, which include de novo synthesis starting from tryptophan as well as the classical Preiss-Handler pathway and NAD(+) synthesis from other vitamin precursors, were detected as EFMs. Moreover, several EFMs were found that degrade NAD(+), represent futile cycles or have other functionalities. The systematic analysis and comparison of the networks specific for yeast and humans document significant differences between species with regard to the use of precursors, biosynthetic routes and NAD(+)-dependent signalling.
Prognostic Impact of Coronary Vasodilator Dysfunction on Adverse Long-Term Outcome of Coronary Heart Disease (2000)

Coronary endothelial vasodilator dysfunction predicts long-term atherosclerotic disease progression and cardiovascular event rates. Thus, the assessment of coronary endothelial vasoreactivity can provide pivotal information as both a diagnostic and prognostic tool in patients at risk for coronary heart disease.
Undifferentiated carcinoma of the pancreas: analysis of intermediate filament profile and Ki‐ras mutations provides evidence of a ductal origin (1998)

Undifferentiated carcinomas and osteoclast-like giant cell tumours of the pancreas commonly contain foci of neoplastic ductal glands. To test the hypothesis that undifferentiated carcinomas and osteoclast-like giant cell tumours have a ductal origin, the immunocytochemical cytokeratin pattern and the frequency and type of Ki-ras mutations at colon 12 were studied in a series of 17 undifferentiated carcinomas and two osteoclast-like giant cell tumours. The cytokeratin features of undifferentiated carcinomas and osteoclast-like giant cell tumours were compared with those found in 10 ductal adenocarcinomas, 20 acinar cell carcinomas, 25 neuroendocrine tumours, and 15 solid-pseudopapillary tumours. All undifferentiated carcinomas and osteoclast-like giant cell tumours stained with at least one cytokeratin antibody, and 13/19 of them with antibodies against cytokeratins 7, 8, 18, and 19. The latter cytokeratins were expressed in all ductal adenocarcinomas, but only in 15/20 acinar cell carcinomas, 2/25 neuroendocrine tumours, and 1/15 solid-pseudopapillary tumours. In addition to cytokeratin, 15/19 undifferentiated carcinomas/osteoclast-like giant cell tumours were positive for vimentin. Ki-ras mutations at codon 12 were found in 10 undifferentiated carcinomas and one osteoclast-like giant cell tumour from which DNA could be successfully amplified. The Ki-ras mutation patterns were analysed in six tumours and corresponded to those typical of ductal adenocarcinomas. In tumours with ductal and anaplastic components, both components revealed identical mutation patterns. From these findings, it is concluded that both undifferentiated carcinomas and osteoclast-like giant cell tumours belong to the pancreatic tumours that show a ductal phenotype. Since undifferentiated carcinomas and osteoclast-like giant cell tumours share the same cytokeratin and Ki-ras features, they are probably derived from the same cell lineage. © 1998 John Wiley & Sons, Ltd.
Variant Arteriovenous Fistula o f the Superior Sagittal Sinus —Case Report— (1999)

A 57-year-old male presented with a rare variant of dural arteriovenous fistula, located in the wall of an unobstructed superior sagittal sinus. Drainage occurred through a cortical vein no longer connected to its parent sinus, which filled up a cluster of transmedullary running veins, one of which was the presumed site of hemorrhage. Arterial blood was supplied via the external carotid artery branches. This type of fistula seriously increases the risk of hemorrhage in the patient and therefore requires complete obliteration. Attempts to embolize the fistula failed. The draining vein was isolated and coagulated resulting in permanent occlusion of the fistula. The fistula probably developed through a process of thrombophlebitis and revascularization via arterioles of the vein rather than previous occlusion of the sinus.
Studies of mucus in mouse stomach, small intestine, and colon. II. Gastrointestinal mucus proteome reveals Muc2 and Muc5ac accompanied by a set of core proteins (2013)

The mucus that protects the surface of the gastrointestinal tract is rich in specialized O-glycoproteins called mucins, but little is known about other mucus proteins or their variability along the gastrointestinal tract. To ensure that only mucus was analyzed, we combined collection from explant tissues mounted in perfusion chambers, liquid sample preparation, single-shot mass spectrometry, and specific bioinformatics tools, to characterize the proteome of the murine mucus from stomach to distal colon. With our approach, we identified ∼1,300 proteins in the mucus. We found no differences in the protein composition or abundance between sexes, but there were clear differences in mucus along the tract. Noticeably, mucus from duodenum showed similarities to the stomach, probably reflecting the normal distal transport. Qualitatively, there were, however, fewer differences than might had been anticipated, suggesting a relatively stable core proteome (∼80% of the total proteins identified). Quantitatively, we found significant differences (∼40% of the proteins) that could reflect mucus specialization throughout the gastrointestinal tract. Hierarchical clustering pinpointed a number of such proteins that correlated with Muc2 (e.g., Clca1, Zg16, Klk1). This study provides a deeper knowledge of the gastrointestinal mucus proteome that will be important in further understanding this poorly studied mucosal protection system.
Controlled potential enzymology of methyl transfer reactions involved in acetyl-CoA synthesis by CO dehydrogenase and the corrinoid/iron-sulfur protein from Clostridium thermoaceticum. (1990)

Many anaerobic bacteria fix CO2 via the Wood pathway of acetyl-CoA synthesis. Carbon monoxide dehydrogenase (CODH), also called acetyl-CoA synthase, accepts the methyl group from the methylated corrinoid/iron-sulfur protein (C/Fe-SP), binds a carbonyl group from CO, CO2, or the carboxyl of pyruvate, and binds coenzyme A. Then CODH catalyzes the synthesis of acetyl-CoA from these enzyme-bound groups. Here, we have characterized the methyl transfer steps involved in acetyl-CoA synthesis. We have studied the reactions leading to methylation of CODH by methyl iodide and shown an absolute requirement of the C/Fe-SP in this reaction. In addition, we have discovered and partly characterized two previously unknown exchange reactions catalyzed by CODH: between the methylated C/Fe-SP and methylated CODH and between methylated CODH and the methyl moiety of acetyl-CoA. We have performed these two exchange reactions, methylation of the C/Fe-SP, and methylation of CODH at controlled potentials. The rates of all these reactions except the exchange between methylated C/Fe-SP and methylated CODH are accelerated (from 1 to 2 orders of magnitude) when run at low potentials. Our results provide strong evidence for a nucleophilic redox-active metal center on CODH as the initial acceptor of the methyl group from the methylated C/Fe-SP. This metal center also is proposed to be involved in the cleavage of acetyl-CoA in the reverse reaction.