gebhart/patrepeval huggingface dataset:
Successful treatment of unresectable gallbladder cancer with low-dose paclitaxel as palliative chemotherapy after failure of gemcitabine and oral S-1: A case report (2012)

A 56-year-old female with metastatic gallbladder cancer involving the liver and stenosis of the hilar bile duct was treated with gemcitabine (1,000 mg/m(2)) plus S-1 (60 mg/m(2)). After 9 cycles of therapy, CT showed evidence of stable disease; however, the serum CEA level was increased. Therefore, the chemotherapy regimen was changed to weekly low-dose paclitaxel (60 mg/m(2)). After 12 cycles of therapy, paclitaxel was reduced to 30 mg/m(2) as the patient developed neutropenia. The patient completed 32 cycles of therapy, and the tumor was reduced in size and marked improvement in bile duct stenosis was noted without any impairment in quality of life. The patient succumbed to the disease 25 months after treatment was initiated. Thus, in this case paclitaxel was more effective than gemcitabine plus S-1. Palliative chemotherapy with paclitaxel after failure of gemcitabine and 5-FU was well-tolerated; therefore, it may be an effective treatment for biliary tract cancer (BTC). A phase I study of palliative chemotherapy with weekly low-dose paclitaxel following gemcitabine (plus cisplatin) and 5-FU is currently in progress in patients with unresectable or recurrent BTC.
Proteolytic degradation of ribonuclease A in the pretransition region of thermally and urea‐induced unfolding (2001)

The method of limited proteolysis has proven to be appropriate for the determination of unfolding rate constants (k(U)) of ribonuclease A in the transition region of thermal denaturation [Arnold, U. & Ulbrich-Hofmann, R. (1997) Biochemistry 36, 2166-2172]. The aim of the present paper was to extend this procedure to the pretransition region of thermally and urea-induced denaturation where spectroscopic methods do not allow direct measurement of k(U). The results show that the approach can be applied successfully to denaturing (free energy of unfolding Delta G < 10 kJ.mol(-1)) and to marginally native conditions (Delta G = 10-25 kJ.mol(-1)). Under moderately (Delta G = 25-30 kJ.mol(-1)) and strongly native conditions (Delta G > 30 kJ.mol(-1)), however, the determination of kU was not possible in this way as the proteolytic degradation of ribonuclease A by thermolysin or trypsin was no longer determined by global unfolding. Here, proteolysis proceeds via the native RNase A. In the presence of low concentrations of urea, the rate constants of proteolysis were, surprisingly, smaller than in the absence of urea. As the protease activity has been taken into account, this result points to a local stabilization of the RNase A molecule.
A Two-step Synthesis of the Anti-cancer Drug (R,S)-Bicalutamide (2002)

A short, efficient synthesis of the non-steroidal antiandrogen (R,S)-bicalutamide is presented. This new route generates bicalutamide in only two steps with an overall yield of 73%. The key step is a 1,2 addition of a methyl sulfone to a keto-amide.
Identification of Three N-terminal Ends of Type XVIII Collagen Chains and Tissue-specific Differences in the Expression of the Corresponding Transcripts (1995)

Transcripts for the alpha 1 chain of mouse type XVIII collagen were found to be heterogeneous at their 5'-ends and to encode three variant N-terminal sequences of the ensuing 1315-, 1527-, or 1774-residue collagen chains. The variant mRNAs appeared to originate from the use of two alternate promoters of the alpha 1(XVIII) chain gene, resulting in the synthesis of either short or long N-terminal non-collagenous NC1 domains, the latter being further subject to modification due to alternative splicing of the transcripts. As a result, the 1527- and 1774-residue polypeptides share the same signal peptide, and the lengths of their NC1 domains are 517 or 764 amino acid residues, respectively, while the 1315-residue polypeptide has a different signal peptide and a 301-residue NC1 domain. The longest NC1 domain was strikingly characterized by a 110-residue sequence with 10 cysteines, which was found to be homologous with the previously identified frizzled proteins belonging to the family of G-protein-coupled membrane receptors. Thus, it is proposed that the cysteine-rich motif, termed fz, represents a new sequence motif that can be found in otherwise unrelated proteins. Tissues containing mainly one or two NC1 domain mRNA variants or all three NC1 domains were identified, indicating that there is tissue-specific utilization of two alternate promoters and alternative splicing of alpha 1(XVIII) transcripts.
Sequence-Selective Recognition of Duplex DNA through Covalent Interstrand Cross-Linking:  Kinetic and Molecular Modeling Studies with Pyrrolobenzodiazepine Dimers (2003)

Members of a homologous series of pyrrolo[2,1-c][1,4]benzodiazepine (PBD) dimers with C8-O-(CH(2))(n)-O-C8' diether linkages (n = 3-6 for 2a-d, respectively) have been studied for their ability to interact with oligonucleotide duplexes containing potential target binding sites. The results confirm earlier predictions that the n = 3 analogue (2a, DSB-120) will covalently bind to a 5'-Pu-GATC-Py sequence by cross-linking opposite-strand guanines separated by 2 bp. Preference for this DNA sequence is shown using oligonucleotides with altered bases between and/or flanking these guanines. The more extended PBD dimer 2c (n = 5) can span an extra base pair and cross-link the 5'-Pu-GA(T/A)TC-Py sequence. The ability of each homologue to cross-link linear plasmid DNA has been determined, with a rank order that correlates with the reported order of in vitro cytotoxicity: n = 3 (2a) > n = 5 (2c) > n = 6 (2d) > n = 4 (2b). The n = 3 homologue (2a) is >300-fold more efficient at cross-linking DNA than the clinically used cross-linking agent melphalan under the same conditions. Kinetic studies reveal that the n = 3 and 5 dimers achieve faster cross-linking to plasmid DNA (108 and 81% cross-linking h(-1) microM(-1) at 37 degrees C, respectively), whereas the n = 4 and 6 homologues are significantly less efficient at 10.3 and 23% cross-linking h(-1) microM(-1), respectively. Alternating activity for the odd n and even n dimers is probably due to configurational factors governed by the spatial separation of the PBD subunits and the flexible character of the tethering linkage. Molecular modeling confirms the order of cross-linking reactivity, and highlights the role of linker length in dictating sequence recognition for this class of DNA-reactive agent.
Sequestering Ability of Butylated Hydroxytoluene, Propyl Gallate, Resveratrol, and Vitamins C and E against ABTS, DPPH, and Hydroxyl Free Radicals in Chemical and Biological Systems (2003)

The antioxidant capacity of butylated hydroxytoluene (BHT; 2,6-di-tert-butyl-p-cresol), propyl gallate (3,4,5-trihydroxybenzoic acid n-propyl ester), resveratrol (trans-3,4',5-trihydroxystilbene), and vitamins C (l-ascorbic acid) and E [(+)-alpha-tocopherol] was studied in chemical and biological systems. The chemical assays evaluated the capacity of these antioxidants to sequester 2,2'-azinobis(3-ethylbenzthiazoline-6-sulfonic acid) (ABTS.) and 1,1 diphenyl-2-picrylhydrazyl (DPPH.). A new colorimetric method to determine hydroxyl radical scavenging is also described. The biological tests use the eucaryotic cells of Saccharomyces cerevisiae treated with the antioxidants in the presence of the stressing agents apomorphine, hydrogen peroxide, and paraquat dichloride (methylviologen; 1,1'-dimethyl-4,4'-bipyridinium dichloride). The results in chemical systems showed that all of the antioxidants were able to significantly inhibit the oxidation of beta-carotene by hydroxyl free radicals. The assays in yeast showed that the antioxidant activity of the tested compounds depended on the stressing agent used and the mechanism of action of the antioxidant.
Studies on biologically active nucleosides and nucleotides. 3. Synthesis of 9-(3-bromo-3-deoxy-2,5-di-O-acetyl-.beta.-D-xylofuranosyl) adenine (1977)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStudies on biologically active nucleosides and nucleotides. 3. Synthesis of 9-(3-bromo-3-deoxy-2,5-di-O-acetyl-.beta.-D-xylofuranosyl) adenineKazuhiko Kondo, Takeshi Adachi, and Ichizo InoueCite this: J. Org. Chem. 1977, 42, 24, 3967–3968Publication Date (Print):November 1, 1977Publication History Published online1 May 2002Published inissue 1 November 1977https://pubs.acs.org/doi/10.1021/jo00444a043https://doi.org/10.1021/jo00444a043research-articleACS PublicationsRequest reuse permissionsArticle Views88Altmetric-Citations5LEARN 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
Multifunctional poly(ethylene glycol) semi‐interpenetrating polymer networks as highly selective adhesive substrates for bioadhesive peptide grafting (1994)

Novel artificial extracellular matrices were synthesized in the form of semi-interpenetrating polymer networks containing copolymers of poly(ethylene glycol) and acrylic acid (PEG-co-AA) grafted with synthetic bioadhesive peptides onto exposed carboxylic acid moieties. These substrates were very resistant to cell adhesion, but when they were grafted with adhesive peptides they were highly biospecific in their ability to support cell adhesion. Extensive preadsorption of adhesive proteins or peptides did not render these materials cell adhesive; yet covalent grafting of adhesive peptides did render these materials highly cell adhesive even in the absence of serum proteins. Polymer networks containing immobilized PEG-co-AA were grafted with peptides at densities of 475 +/- 40 pmol/cm(2). Polymer networks containing immobilized PEG-co-AA N-terminally grafted with GRGDS supported cell adhesion efficiencies of 42 +/- 4% 4 h after seeding and became confluent after 12 h. These cells displayed cell spreading and cytoskeletal grafted with inactive control peptides (GRDGS, GRGES, or no peptide) supported cell adhesion efficiencies of 0 +/- 0%, even when challenged with high seeding densities (to 100,000 cell/cm(2)) over 14 days. These polymer networks are suitable substrates to investigate in vitro cell-surface interactions in the presence of serum proteins without nonspecific protein adsorption adhesion signals other than those immobilized for study.
Effect of SOCl2 Treatment on Electrical and Mechanical Properties of Single-Wall Carbon Nanotube Networks (2005)

Chemical modification by SOCl2 of an entangled network of purified single-wall carbon nanotubes, also known as 'bucky paper', is reported to profoundly change the electrical and mechanical properties of this system. Four-probe measurements indicate a conductivity increase by up to a factor of 5 at room temperature and an even more pronounced increase at lower temperatures. This chemical modification also improves the mechanical properties of SWNT networks. Whereas the pristine sample shows an overall semiconducting character, the modified material behaves as a metal. The effect of SOCl2 is studied in terms of chemical doping of the nanotube network. We identified the microscopic origin of these changes using SEM, XPS, NEXAFS, EDX, and Raman spectroscopy measurements and ab initio calculations. We interpret the SOCl2-induced conductivity increase by p-type doping of the pristine material. This conclusion is reached by electronic structure calculations, which indicate a Fermi level shift into the valence band, and is consistent with the temperature dependence of the thermopower.
Hybridoma Antibody to Breast Cancer Immune Complexes (1982)

Hybridoma clones were established by fusing spleen cells from mice immunized with purified breast cancer-related immune complexes to drug-resistant nonproducing myelomas. Hybridoma cultures were evaluated for antibody production using immunofluorescence, radioimmunoassay and immunoperoxidase techniques. One antibody demonstrated strong reactivity against breast tumor cells (BT-20) in culture and also was found to bind ductal epithelial cells within sections of human mammary tissue. Antigen was detected within the soluble fraction of breast tumors with molecular weight greater than 500 K. The possible relationship between antigen detected in breast tumor cells and in immune-complexed form is discussed.
Using the Microcyte Flow Cytometer To Monitor Cell Number, Viability, and Apoptosis in Mammalian Cell Culture (2000)

The Microcyte is a novel, portable flow cytometer based on diode laser technology whose use has been established for yeast and bacterial analysis. We present data that demonstrate its suitability for routine mammalian cell counting and viability determination. To extend its range of applications in the field of animal cell culture biotechnology, a test to determine the number of apoptotic cells present has been developed for use with the instrument. Apoptosis was induced in hybridoma cell cultures by treatment with camptothecin. Apoptotic cells were labeled with biotinylated Annexin V and then visualized using a streptavidin-allophycocyanin conjugate. Their numbers were counted, and the cell size of the apoptotic cell population was determined using the Microcyte.
Evolution of the Molecular Machines for Protein Import into Mitochondria (2006)

In creating mitochondria some 2 billion years ago, the first eukaryotes needed to establish protein import machinery in the membranes of what was a bacterial endosymbiont. Some of the preexisting protein translocation apparatus of the endosymbiont appears to have been commandeered, including molecular chaperones, the signal peptidase, and some components of the protein-targeting machinery. However, the protein translocases that drive protein import into mitochondria have no obvious counterparts in bacteria, making it likely that these machines were created de novo. The presence of similar translocase subunits in all eukaryotic genomes sequenced to date suggests that all eukaryotes can be considered descendants of a single ancestor species that carried an ancestral "protomitochondria."
Processing queries by linear constraints (1997)

Article Processing queries by linear constraints Share on Authors: Jonathan Goldstein Computer Sciences Department, University of Wisconsin-Madison, 1210 W. Dayton St., Madison, WI Computer Sciences Department, University of Wisconsin-Madison, 1210 W. Dayton St., Madison, WIView Profile , Raghu Ramakrishnan Computer Sciences Department, University of Wisconsin-Madison, 1210 W. Dayton St., Madison, WI Computer Sciences Department, University of Wisconsin-Madison, 1210 W. Dayton St., Madison, WIView Profile , Uri Shaft Computer Sciences Department, University of Wisconsin-Madison, 1210 W. Dayton St., Madison, WI Computer Sciences Department, University of Wisconsin-Madison, 1210 W. Dayton St., Madison, WIView Profile , Jie-Bing Yu Computer Sciences Department, University of Wisconsin-Madison, 1210 W. Dayton St., Madison, WI Computer Sciences Department, University of Wisconsin-Madison, 1210 W. Dayton St., Madison, WIView Profile Authors Info & Claims PODS '97: Proceedings of the sixteenth ACM SIGACT-SIGMOD-SIGART symposium on Principles of database systemsMay 1997 Pages 257–267https://doi.org/10.1145/263661.263689Online:01 May 1997Publication History 36citation455DownloadsMetricsTotal Citations36Total Downloads455Last 12 Months8Last 6 weeks0 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Human Ebola virus infection results in substantial immune activation (2015)

Four Ebola patients received care at Emory University Hospital, presenting a unique opportunity to examine the cellular immune responses during acute Ebola virus infection. We found striking activation of both B and T cells in all four patients. Plasmablast frequencies were 10-50% of B cells, compared with less than 1% in healthy individuals. Many of these proliferating plasmablasts were IgG-positive, and this finding coincided with the presence of Ebola virus-specific IgG in the serum. Activated CD4 T cells ranged from 5 to 30%, compared with 1-2% in healthy controls. The most pronounced responses were seen in CD8 T cells, with over 50% of the CD8 T cells expressing markers of activation and proliferation. Taken together, these results suggest that all four patients developed robust immune responses during the acute phase of Ebola virus infection, a finding that would not have been predicted based on our current assumptions about the highly immunosuppressive nature of Ebola virus. Also, quite surprisingly, we found sustained immune activation after the virus was cleared from the plasma, observed most strikingly in the persistence of activated CD8 T cells, even 1 mo after the patients' discharge from the hospital. These results suggest continued antigen stimulation after resolution of the disease. From these convalescent time points, we identified CD4 and CD8 T-cell responses to several Ebola virus proteins, most notably the viral nucleoprotein. Knowledge of the viral proteins targeted by T cells during natural infection should be useful in designing vaccines against Ebola virus.
Reprogramming of Somatic Cell Identity (2008)

All mammalian somatic cells originate from a single fertilized cell, the zygote, and share identical genetic information despite the dramatic changes in cell structure and function that accompany organismal development. The genome is subjected to a wide array of epigenetic modifications during lineage specification, a process that contributes to the implementation and maintenance of specific gene expression programs in somatic cells. Nuclear transfer and cell-fusion experiments demonstrate that the epigenetic signature directing a cell identity can be erased and modified into that of another cell type. Furthermore, in the case of cloning, differentiated cells can be reprogrammed back to pluripotency to support the reexpression of all developmental programs. Recent breakthroughs highlight the importance of transcription factors as well as epigenetic modifiers in the establishment, maintenance, and rewiring of cell identity. By focusing on reprogramming of terminally differentiated lymphocytes, we review and highlight recent insights into the molecular mechanisms and cellular events potentially underlying programming and reprogramming of somatic cell identity in mammals.
Two genes required for cell fusion during yeast conjugation: evidence for a pheromone-induced surface protein. (1987)

We characterized two genes, FUS1 and FUS2, which are required for fusion of Saccharomyces cerevisiae cells during conjugation. Mutations in these genes lead to an interruption of the mating process at a point just before cytoplasmic fusion; the partition dividing the mating pair remains undissolved several hours after the cells have initially formed a stable "prezygote." Fusion is only moderately impaired when the two parents together harbor one or two mutant fus genes, and it is severely compromised only when three or all four fus genes are inactivated. Cloning of FUS1 and FUS2 revealed that they share some functional homology; FUS1 on a high-copy number plasmid can partially suppress a fus2 mutant, and vice versa. FUS1 remains essentially unexpressed in vegetative cells, but is strongly induced by incubation of haploid cells with the appropriate mating pheromone. Immunofluorescence microscopy of alpha factor-induced a cells harboring a fus1-LACZ fusion showed the fusion protein to be localized at the cell surface, concentrated at one end of the cell (the shmoo tip). FUS1 maps near HIS4, and the intervening region (including BIK1, a gene required for nuclear fusion) was sequenced along with FUS1. The sequence of FUS1 revealed the presence of three copies of a hexamer (TGAAAC) conserved in the 5' noncoding regions of other pheromone-inducible genes. The deduced FUS1 protein sequence exhibits a striking concentration of serines and threonines at the amino terminus (46%; 33 of 71), followed by a 25-amino acid hydrophobic stretch and a predominantly hydrophilic carboxy terminus, which contains several potential N-glycosylation sites (Asn-X-Ser/Thr). This sequence suggests that FUS1 encodes a membrane-anchored glycoprotein with both N- and O-linked sugars.
Cetuximab-Induced MET Activation Acts as a Novel Resistance Mechanism in Colon Cancer Cells (2014)

Aberrant MET expression and hepatocyte growth factor (HGF) signaling are implicated in promoting resistance to targeted agents; however, the induced MET activation by epidermal growth factor receptor (EGFR) inhibitors mediating resistance to targeted therapy remains elusive. In this study, we identified that cetuximab-induced MET activation contributed to cetuximab resistance in Caco-2 colon cancer cells. MET inhibition or knockdown sensitized Caco-2 cells to cetuximab-mediated growth inhibition. Additionally, SRC activation promoted cetuximab resistance by interacting with MET. Pretreatment with SRC inhibitors abolished cetuximab-mediated MET activation and rendered Caco-2 cells sensitive to cetuximab. Notably, cetuximab induced MET/SRC/EGFR complex formation. MET inhibitor or SRC inhibitor suppressed phosphorylation of MET and SRC in the complex, and MET inhibitor singly led to disruption of complex formation. These results implicate alternative targeting of MET or SRC as rational strategies for reversing cetuximab resistance in colon cancer.
Characterization of methoxy adsorption on some transition metals: A first principles density functional theory study (2005)

Based on the gradient-density functional theory, calculation results of methoxy adsorption on Au(111), Ag(111), Cu(111), Pt(111), Pd(111), Ni(111), Rh(111), and Fe(100) surfaces are presented, and a consistent picture for some key physical properties determining the reactivity of metals appears. These eight metals belong to two groups: either with filled d electrons (group IB) or with unfilled but more than half filled d electrons (group VIII). The calculated adsorption energies are quite in agreement with the experimental data as well as the previous theoretical calculation results. Importantly, using the analysis of B. Hammer and J. K. Norskov, Nature (London) 376, 232 (1995) and in Chemisorption and Reactivity on Supported Clusters and Thin Films, edited by R. M. Lambert and G. Pacchioni (Kluwer Academic, Dordrecht, 1997), pp. 285-351, the binding energies have selectively been linearly correlated to the d-band center and to the size of the metal d-band orbital overlapping with the adsorbate (coupling matrix element) for these two groups of metals. And by analyzing the nature of the adsorption bonding, the possible reason of this difference is suggested.