gebhart/patrepeval huggingface dataset:
Characterization of the human CD27 ligand, a novel member of the TNF gene family. (1994)

CD27 is a lymphocyte-specific member of the TNF/NGF-R family that is highly induced on T cells after TCR stimulation, primarily on lymphocytes belonging to the unprimed CD45RA+ subset. However, after prolonged activation both in vivo and in vitro, CD27 expression is gradually switched off. In search of physiologic signals that influence CD27 expression, we found that B cell lines can mediate down-regulation of CD27 surface expression on activated T cells via direct cell-to-cell contact and that preincubation of activated T cells with CD27 mAbs prevented this modulation. Based on these observations, we hypothesized that a ligand for CD27L is expressed on B cell lines and that ligand interaction would result in down-modulation of the molecule from the T cell surface. To identify this putative CD27L, mAbs were raised against the Burkitt cell line Ramos and screened for their ability to block down-modulation of CD27 on activated T cells. Using this approach, we isolated a mAb, designated 2F2, that inhibits CD27 down-regulation in a dose-dependent manner. We demonstrate that this mAb recognizes CD27L as it 1) reacted to mouse fibroblasts expressing the recently cloned CD27L, a novel surface-expressed member of the TNF gene family, and 2) prevented binding of a soluble CD27-Fc construct to a CD27L expressing cell line. Down-regulation of CD27 from the T cell surface by recombinant CD27L was shown to be at least partially caused by release of soluble CD27. The 2F2 mAb enabled us to begin to analyze the biochemical properties, tissue distribution, and function of the CD27L on human cells. From cell lysates of 125I surface-labeled Burkitt cells a complex immunoprecipitation pattern with dominant bands of 29, 55, and 122 to 127 kDa was obtained using the 2F2 mAb. Phenotypical analyses showed that freshly isolated lymphocytes lacked CD27L expression, but that expression of the molecule could be induced after in vitro stimulation of T and B cells. No expression was found on cells of the myeloid lineage or on endothelial cells. Finally, blocking of naturally expressed CD27L by the 2F2 mAb exerted a potent inhibitory effect on the proliferation of T cells in response to allogeneic B cells and PHA. The data presented in this paper identify CD27 and its ligand as potentially important structures involved in cellular interactions between T and B lymphocytes.
Innervation of the Human Vertebral Body (1998)

The histology of 69 human vertebral bodies from 23 individuals was studied by hematoxylin and eosin staining using a technique that allowed the creation of complete, large histologic sections of individual vertebral bodies. Particular attention was directed toward the documentation of intraosseous nerves. The vertebral bodies were dissected free of soft tissue, and then sectioned using a diamond wafering saw into 3-mm sagittal segments. Sections were then decalcified and whole-mounted in paraffin blocks before tissue sectioning using a very-large-format microtome. One hundred thirty-eight tissue sections were prepared for evaluation. Neurovascular bundles and intraosseous nerves were routinely identified within human vertebral bone. Nerves were noted to enter the vertebral body via the centrally located posterior vascular foramen and were found to accompany the basivertebral vessels. Branches from these nerves coursed to both central and peripheral areas of the vertebral body. Nerves were also documented that entered the vertebral body by penetrating the anterior cortex to course into the marrow. Although previous studies have documented nerves within long bones, and others have described the histology of the intervertebral disc and associated soft tissues, previous literature that documents the innervation of the human vertebral body has been very sparse. The documentation of nerve tissue within normal human vertebrae further supports the proposed role of neuronal factors in the regulation of bone physiology. Furthermore, it is possible that such intraosseous nerves may play a role in the clinical problem of back pain.
On the instability of web search engines (2000)

The output of major WWW search engines was analyzed and the results led to some surprising observations about their stability. Twenty-five queries were issued repeatedly to the engines and the results were compared. After one month, the top ten results returned by eight out of nine engines had changed by more than fifty percent. Furthermore, five out of the nine engines returned over a third of their URLs intermittently during the month.
Antibacterials. Synthesis and structure-activity studies of 3-aryl-2-oxooxazolidines. 4. Multiply-substituted aryl derivatives (1992)

The synthesis and structure-activity relationship (SAR) studies of the effect of different polysubstitution patterns in the aromatic ring of 5-(acetamidomethyl)oxazolidinone antibacterials (I) on antibacterial activity are presented. Compounds I were prepared by the six-step synthesis described previously (Gregory, W. A.; et al. J. Med. Chem. [formula: see text] 1989, 32, 1673), electrophilic aromatic substitution reactions of 3-substituted compounds, and functional-group interchange reactions of 3,4-disubstituted compounds. Antibacterial evaluation of compounds I against Staphylococcus aureus and Enterococcus faecalis gave the following results. The 2,4- and 2,5-disubstituted derivatives have weak or no antibacterial activity. Antibacterial activities of 3,4-disubstituted compounds are comparable to those of the 4-monosubstituted analogues for small 3-substituents (smaller than Br), but decline rapidly for larger 3-substituents. 3,4-Annulated derivatives are comparable in activity to their open-chain analogues. 3,5-Disubstituted and 3,4,5- and 2,4,6-trisubstituted derivatives are devoid of antibacterial activity.
Hormone-induced apoptosis by Fas-nuclear receptor fusion proteins: novel biological tools for controlling apoptosis in vivo. (1996)

We have created fusion proteins between Fas and the ligand-binding domain of the estrogen or retinoic acid receptor. Murine fibrosarcoma L929 cells and human cervical carcinoma HeLa cells expressing the fusion proteins demonstrated apoptotic phenotypes in a tightly estrogen- or retinoic acid-dependent manner in vitro. Moreover, the fusion protein-expressing L929 cells transplanted into nude mice were also killed through apoptosis after injection of an estrogen agonist. This represents a novel system, "cell targeting," that can eliminate cells not only in vitro but also in vivo through the activation of a natural suicide machinery, i.e., apoptosis, by currently used hormones. This system implies wide applications not only in developmental biology and neurobiology but also in medicine, especially for cancer gene therapy.
Robotic telemanipulator for laparoscopy (2002)

A concept of a telemanipulator for laparoscopic surgery is presented. It enables endoscopic handling of surgical effecters and cameras inside the abdominal cavity with six degrees of freedom of motion through a trocar tube 12 mm in diameter. The kinematical structure consists of fourteen axes articulated by six electrical servo drives.
PINK1-induced mitophagy promotes neuroprotection in Huntington’s disease (2015)

Huntington's disease (HD) is a fatal neurodegenerative disorder caused by aberrant expansion of CAG repeat in the huntingtin gene. Mutant Huntingtin (mHtt) alters multiple cellular processes, leading to neuronal dysfunction and death. Among those alterations, impaired mitochondrial metabolism seems to have a major role in HD pathogenesis. In this study, we used the Drosophila model system to further investigate the role of mitochondrial damages in HD. We first analyzed the impact of mHtt on mitochondrial morphology, and surprisingly, we revealed the formation of abnormal ring-shaped mitochondria in photoreceptor neurons. Because such mitochondrial spheroids were previously detected in cells where mitophagy is blocked, we analyzed the effect of PTEN-induced putative kinase 1 (PINK1), which controls Parkin-mediated mitophagy. Consistently, we found that PINK1 overexpression alleviated mitochondrial spheroid formation in HD flies. More importantly, PINK1 ameliorated ATP levels, neuronal integrity and adult fly survival, demonstrating that PINK1 counteracts the neurotoxicity of mHtt. This neuroprotection was Parkin-dependent and required mitochondrial outer membrane proteins, mitofusin and the voltage-dependent anion channel. Consistent with our observations in flies, we demonstrated that the removal of defective mitochondria was impaired in HD striatal cells derived from HdhQ111 knock-in mice, and that overexpressing PINK1 in these cells partially restored mitophagy. The presence of mHtt did not affect Parkin-mediated mitochondrial ubiquitination but decreased the targeting of mitochondria to autophagosomes. Altogether, our findings suggest that mitophagy is altered in the presence of mHtt and that increasing PINK1/Parkin mitochondrial quality control pathway may improve mitochondrial integrity and neuroprotection in HD.
Endohexosaminidase‐Catalysed Glycosylation with Oxazoline Donors: Fine Tuning of Catalytic Efficiency and Reversibility (2008)

A complete series of oxazoline di-, tri-, tetra-, and hexasaccharides, corresponding to the core sections of N-linked glycoprotein high mannose glycans, together with the corresponding oligosaccharides containing a central glucose unit, were synthesised and tested as glycosyl donors for glycosylation of a GlcNAcAsn glycosyl amino acid catalysed by the endohexosaminidases M (Endo M), A (Endo A) and H (Endo H). Whilst Endo H did not catalyse any glycosylation reactions, both Endo M and Endo A efficiently catalysed glycosylations that were not limited to donors containing the Manbeta(1-->4)GlcNAc linkage. Precise structure activity relationships and time course studies have revealed fine-tuning of the efficiency of the synthetic processes which correlated both with the enzyme used and the precise oxazoline structure. Efficient irreversible glycosylation was achievable with both Endo M and Endo A, further demonstrating the use of structurally modified oxazoline donors as transition state mimics in order to promote enzyme-catalysed synthesis, whilst precluding product hydrolysis; enzymes in these cases display "glycoligase" activity.
Expression of ERCC1, TYMS, RRM1, TUBB3, non-muscle myosin II, myoglobin and MyoD1 in lung adenocarcinoma pleural effusions predicts survival in patients receiving platinum-based chemotherapy (2014)

The association between the expression of excision repair cross‑complementing gene 1 (ERCC1), thymidylate synthase (TYMS), ribonuleotide reductase M1 (RRM1), βIII‑tubulin (TUBB3), non‑muscle myosin II, myoglobin and MyoD1 in metastatic lung adenocarcinoma, and clinical outcomes with platinum‑based chemotherapy treatment is not well‑established. Recently, increasing attention has been focused on the involvement of ERCC1, TYMS, RRM1 and TUBB3 in the development of drug resistance. There has been less research into the role of muscle myosin II, myoglobin and MyoD1 in the pathogenesis of lung cancer, although these genes are known to have important functions within tumor cells. In the current study, malignant pleural effusion from 116 patients with untreated lung adenocarcinoma diagnosed between 2011 and 2012, were collected. The protein expression levels of ERCC1, TYMS, RRM1 and TUBB3 were evaluated with immunocytochemistry and western blot analysis. The expression levels of non‑muscle myosin II, myoglobin and MyoD1 were measured in a subset of 50 patients, treated with platinum‑based chemotherapy. The association of each of these seven factors with one another, as well as with patient survival were analyzed. Immunohistochemistry demonstrated that the percentage of pleural fluid samples from patients with lung adenocarcinoma expressing ERCC1, TYMS, RRM1 and TUBB3 was 37, 36.2, 82.7 and 69.8%, respectively. In the subset of 50 patients in whom the remaining factors were analyzed, the percentage expressing non‑muscle myosin II was 48%, for myoglobin the figure was 40% and for MyoD1 it was 38%. There was a positive correlation between each pair of the above seven molecules with the exception of TYMS and RRM1. Expression of ERCC1, TYMS, TUBB3, non‑muscle myosin II, myoglobin and MyoD1 genes was associated with decreased survival in patients with metastatic lung adenocarcinoma. Expression of ERCC1, TYMS, TUBB3, non‑muscle myosin II, myoglobin and MyoD1 was also associated with decreased survival rates of patients with lung adenocarcinoma treated with platinum‑based chemotherapy. These factors may be used as clinical biomarkers to predict the biological behavior and chemoresistance of tumor cells, and the survival of patients with lung carcinoma.
Determining the user intent of web search engine queries (2007)

Determining the user intent of Web searches is a difficult problem due to the sparse data available concerning the searcher. In this paper, we examine a method to determine the user intent underlying Web search engine queries. We qualitatively analyze samples of queries from seven transaction logs from three different Web search engines containing more than five million queries. From this analysis, we identified characteristics of user queries based on three broad classifications of user intent. The classifications of informational, navigational, and transactional represent the type of content destination the searcher desired as expressed by their query. We implemented our classification algorithm and automatically classified a separate Web search engine transaction log of over a million queries submitted by several hundred thousand users. Our findings show that more than 80% of Web queries are informational in nature, with about 10% each being navigational and transactional. In order to validate the accuracy of our algorithm, we manually coded 400 queries and compared the classification to the results from our algorithm. This comparison showed that our automatic classification has an accuracy of 74%. Of the remaining 25% of the queries, the user intent is generally vague or multi-faceted, pointing to the need to for probabilistic classification. We illustrate how knowledge of searcher intent might be used to enhance future Web search engines.
Frequent item set mining (2012)

Abstract Frequent item set mining is one of the best known and most popular data mining methods. Originally developed for market basket analysis, it is used nowadays for almost any task that requires discovering regularities between (nominal) variables. This paper provides an overview of the foundations of frequent item set mining, starting from a definition of the basic notions and the core task. It continues by discussing how the search space is structured to avoid redundant search, how it is pruned with the a priori property, and how the output is reduced by confining it to closed or maximal item sets or generators. In addition, it reviews some of the most important algorithmic techniques and data structures that were developed to make the search for frequent item sets as efficient as possible. © 2012 Wiley Periodicals, Inc. This article is categorized under: Algorithmic Development &gt; Association Rules Application Areas &gt; Data Mining Software Tools Technologies &gt; Association Rules
Role of Adhesion Molecules in the Homing and Mobilization of Murine Hematopoietic Stem and Progenitor Cells (1998)

Bone marrow (BM) transplantation still must overcome multiple difficulties and should benefit from better understanding of stem-cell homing and mobilization. Here, we analyzed the involvement of several adhesion molecules in the two processes by treating mice with monoclonal antibodies against these molecules. Treatment of lethally irradiated mice grafted with isogeneic BM cells showed that at least two migration pathways are important for stem-cell homing to the BM, whereas only one of them is involved in lodging of colony-forming unit–spleen (CFU-S) in the spleen. We confirm that the VLA-4/VCAM-1 adhesion pathway is important for stem-cell homing to the BM only and show that CD44 is involved in CFU-S lodging in both BM and spleen. These results show that entry of CFU-S into the spleen is regulated. The observation that when one migration pathway is altered, CFU-S do not enter the BM via the other pathway may indicate that the two mechanisms involved in CFU-S homing into the BM are linked. The adhesion molecules VLA-4 and CD44 are also implied in the mobilization of stem cells into the blood stream of mice injected once with anti–VLA-4 or anti-CD44. Anti–VLA-4 administration led to a significant increase in circulating stem cells as early as 8 hours after treatment. Stem cells mobilized by anti–VLA-4 comprise cells with high self-renewal potential and thus may be used for long-term reconstitution of the hematopoietic tissue. © 1998 by The American Society of Hematology.
The thermal, aliphatic Claisen rearrangement (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe thermal, aliphatic Claisen rearrangementFrederick E. ZieglerCite this: Chem. Rev. 1988, 88, 8, 1423–1452Publication Date (Print):December 1, 1988Publication History Published online1 May 2002Published inissue 1 December 1988https://pubs.acs.org/doi/10.1021/cr00090a001https://doi.org/10.1021/cr00090a001research-articleACS PublicationsRequest reuse permissionsArticle Views3895Altmetric-Citations473LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
“pH Swing” in Frozen Solutions—Consequence of Sequential Crystallization of Buffer Components (2009)

Succinate buffer solutions of different initial pH values and concentrations were cooled. The solution pH and the phases crystallizing from solution were monitored as a function of temperature. In a solution buffered to pH 4.0 (200 mM), the freeze-concentrate pH initially increased to 8.0 and then decreased to 2.2. On the basis of X-ray diffractometry (synchrotron source), the “pH swing” was attributed to the sequential crystallization of succinic acid, monosodium succinate, and disodium succinate. A similar swing, but in the opposite direction, was seen when a solution with an initial pH of 6.0 was cooled. In this case, crystallization of the basic buffer component occurred first. The direction and magnitude of the pH shift depended on both the initial pH and the buffer concentration. In light of the pH-sensitive nature of a significant fraction of pharmaceuticals (especially proteins), extreme care is needed, both in the buffer selection and in its concentration.
Method for determining whether a gene of Escherichia coli is essential: application to the polA gene (1984)

We have developed a general method for determining whether a gene of Escherichia coli is essential for viability. The method requires cloned DNA spanning the gene in question and a reasonably detailed genetic and physical map of the cloned segment. Using this information, one constructs a deletion of the target gene in vitro. For convenience, the deletion can be marked by an antibiotic resistance gene. A DNA segment containing the deletion is then cloned onto an att delta phage lambda vector. Integration of this phage, by homologous recombination at the target locus, and subsequent excision provide an efficient route for crossing the marked deletion onto the bacterial chromosome. Failure to delete the target gene indicates either that the resulting deletion was not viable or that the desired recombinational event did not take place. The use of prophage excision to generate the deletion allows one to estimate the fraction of deletion-producing events by analysis of the other product of the excision, the phage produced on induction of the prophage. In this way one can determine whether failure to recover a particular chromosomal deletion was due to its never having been formed, or, once formed, to its failure to survive. Applying this method to the polA gene, we found that polA is required for growth on rich medium but not on minimal medium. We repeated the experiment in the presence of plasmids carrying functional fragments of the polA gene, corresponding to the 5'-3' exonuclease and the polymerase-3'-5' exonuclease portions of DNA polymerase I. Surprisingly, either of these fragments, in the absence of the other, was sufficient to allow growth on rich medium.
Smart Certi cates: Extending X.509 for Secure Attribute Services on the Web (1999)

An attribute is a particular property of an entity, such as a role, access identity, group, or clearance. If attributes are provided integrity, authentication, and con dentiality, Web servers can then trust these secure attributes and use them for many purposes, such as access control, authorization, authentication, and electronic transactions. In this paper, we present a comprehensive approach to secure attribute services on the Web. We identify the user-pull and server-pull models and analyze their advantages and disadvantages. To support these models on the Web, we extend X.509 certi cates, which are already in widespread current use. We name these extended X.509 certi cates smart certi cates. Smart certi cates have several sophisticated features: they support short-lived lifetime and multiple CAs, contain attributes, provide postdated and renewable certi cates, and provide con dentiality. This paper also discusses possible applications of smart certi cates on the Web.
Myocardial Restoration and Tissue Engineering of Heart Structures (2007)

The restoration or de novo engineering of heart structures poses a challenge because of the unique structure and physical properties of the heart. The heart is a heterogeneous, complex helical structure with asymmetric and anisotropic features. Hence, it is variably built and consists of spiraling muscle bands (first described by Torrent-Guasp), valves, coronary vessels, and a conduction system. Therefore, successful construction of muscular or valvular grafts needs to meet specific prerequisites, such as mechanical stability, optimal porosity, and contractile function. A series of studies have reported on various mixtures of scaffolds and (stem) cells and subsequent production of spontaneously contractile cardiac grafts in vitro. In vivo studies have provided evidence of engraftment of such bioartificial myocardial grafts and of improved heart function of the host. Two fundamental types of bioartificial/engineered valves have been reported: decellularized xenogeneic valves and recellularized valves with the recipient's own cells. Large-scale clinical results are awaited. Finally, bioartificial vessels are being produced, either through de novo construction from collagens and cells or from previously harvested recipient's own fibroblasts and endothelial cells. The main goal envisioned here is long-term patency following implantation in vivo. This review surveys upon recent developments and indicates caveats in the field of tissue engineering of cardiac, valvular, and vascular structures.
Carbonic Anhydrase: New Insights for an Ancient Enzyme (2001)

Carbonic anhydrase catalyzes the reversible hydration of CO 2 (Equation