gebhart/patrepeval huggingface dataset:
Identification of an immunoreactive Brucella abortus HtrA stress response protein homolog (1994)

An 11-kb fragment of Brucella abortus genomic DNA cloned into the BamHI site of pUC9 expressed a 60-kDa protein in Escherichia coli DH5-alpha. Antibodies reactive with this 60-kDa protein were detected by Western blot (immunoblot) analysis in sera from mice, cattle, and goats experimentally infected with B. abortus, in sera from mice experimentally infected with Brucella melitensis, and in serum from a dog experimentally infected with Brucella canis. Similar results were seen with sera obtained from cattle and dogs with naturally acquired brucellosis. The gene encoding the 60-kDa Brucella protein was localized to a 2-kb EcoRI fragment which was also reactive in Southern blots with genomic DNA from other strains of B. abortus as well as with genomic DNA from B. melitensis and B. canis. Nucleotide sequence analysis of the cloned EcoRI fragment revealed an open reading frame encoding a protein with a predicted molecular mass of 51,847 Da and an isoelectric point of 5.15. Comparison of the deduced amino acid sequence of the immunoreactive Brucella protein with the SWISS-PROT protein sequence data base revealed that it shares > 40% amino acid sequence identity with the E. coli and Salmonella typhimurium HtrA stress response proteins. Computer-assisted analysis of this amino acid sequence also predicted that the putative Brucella HtrA homolog contains an export signal sequence and a serine protease active site, two structural features characteristic of previously described HtrA proteins. A potential sigma E type heat shock promoter sequence was detected upstream of the cloned Brucella htrA gene, and Northern (RNA) blot analysis demonstrated that exposure of B. abortus 2308 to heat shock conditions resulted in a transient elevation of htrA transcription. These results strongly suggest that the immunoreactive 60-kDa Brucella protein is a member of the HtrA class of stress response proteins.
Eosinophilopoiesis in A Murine Model of Allergic Airway Eosinophilia: Involvement of Bone Marrow IL-5 and IL-5 Receptor α (2000)

The airway inflammation in asthma is dominated by eosinophils. The aim of this study was to elucidate the contribution of newly produced eosinophils in airway allergic inflammation and to determine mechanisms of any enhanced eosinophilopoiesis. OVA-sensitized BALB/c mice were repeatedly exposed to allergen via airway route. Newly produced cells were identified using a thymidine analog, 5-bromo-2'-deoxyuridine, which is incorporated into DNA during mitosis. Identification of IL-5-producing cells in the bone marrow was performed using FACS. Bone marrow CD3+ cells were enriched to evaluate IL-5-protein release in vitro. Anti-IL-5-treatment (TRFK-5) was given either systemically or directly to the airways. IL-5R-bearing cells were localized by immunocytochemistry. Repeated airway allergen exposure caused prominent airway eosinophilia after three to five exposures, and increased the number of immature eosinophils in the bone marrow. Up to 78% of bronchoalveolar lavage (BAL) granulocytes were 5-bromo-2'-deoxyuridine positive. After three allergen exposures, both CD3+ and non-CD3 cells acquired from the bone marrow expressed and released IL-5-protein. Anti-IL-5 given i.p. inhibited both bone marrow and airway eosinophilia. Intranasal administration of anti-IL-5 also reduced BAL eosinophilia, partly via local effects in the airways. Bone marrow cells, but not BAL eosinophils, displayed stainable amounts of the IL-5R alpha-chain. We conclude that the bone marrow is activated by airway allergen exposure, and that newly produced eosinophils contribute to a substantial degree to the airway eosinophilia induced by allergen. Airway allergen exposure increases the number of cells expressing IL-5-protein in the bone marrow. The bone marrow, as well as the lung, are possible targets for anti-IL-5-treatment.
Efficient state preparation for a register of quantum bits (2006)

We describe a quantum algorithm to prepare an arbitrary pure state of a register of a quantum computer with fidelity arbitrarily close to 1. Our algorithm is based on Grover's quantum search algorithm. For sequences of states with suitably bounded amplitudes, the algorithm requires resources that are polynomial in the number of qubits. Such sequences of states occur naturally in the problem of encoding a classical probability distribution in a quantum register.
Cannabinoids for Cancer Treatment: Progress and Promise (2008)

Cannabinoids are a class of pharmacologic compounds that offer potential applications as antitumor drugs, based on the ability of some members of this class to limit inflammation, cell proliferation, and cell survival. In particular, emerging evidence suggests that agonists of cannabinoid receptors expressed by tumor cells may offer a novel strategy to treat cancer. Here, we review recent work that raises interest in the development and exploration of potent, nontoxic, and nonhabit forming cannabinoids for cancer therapy.
Effect of Ionic Strength on Surface-Selective Patch Binding-Induced Phase Separation and Coacervation in Similarly Charged Gelatin−Agar Molecular Systems (2010)

Coacervate is defined as a polymer-rich dense phase, which remains in thermodynamic equilibrium with its low concentrated phase called the supernatant. The effect of ionic strength (I = 0-0.1 M NaCl) on the mechanism of surface patch binding-induced protein-polysaccharide interaction leading to complex coacervation, between agar (a polyanionic polysaccharide) and gelatin B (a polyampholyte protein), both having similar net charge, at a particular mixing ratio, [gelatin]/[agar] = 1, was studied at various temperatures (20-40 °C). The coacervation transition was probed by turbidity and zeta-potential measurements. The intermolecular association had the signature of surface-selective binding, and a model calculation could explain the potential energy of interactions operative in such processes. The thermo-mechanical features of the coacervates were found to be strongly dependent on ionic strength, which has been interpreted as originating from formation of salt-bridges between the biopolymers. The microstructure of the coacervate materials was analyzed using rheology and small angle neutron scattering (SANS) techniques, which probed the heterogeneity prevailing in the system that had characteristic length in the range 1.3-2.0 nm, and the same data yielded the correlation length of concentration fluctuations, which was estimated to lay in the range 2.4-4 nm. It is concluded that the coacervation transition driven by surface-selective binding is not influenced by the ionic strength of the solution, but the mobile ions participate in the structural organization of the interacting polyions in the coacervate.
Improved prenatal detection of a fetal point mutation for achondroplasia by the use of size‐fractionated circulatory DNA in maternal plasma—case report (2004)

The enrichment of circulatory fetal DNA in maternal plasma by size-fractionation facilitates the detection of subtle feto-maternal genetic differences, such as those involving point mutations. This approach can easily be extended for the non-invasive prenatal determination of other fetal loci.
Simultaneous detection of different mRNA sequences coding for neuropeptide hormones by double in situ hybridization using FITC- and biotin-labeled oligonucleotides. (1990)

Oligonucleotides labeled with FITC or biotin were applied for detection of specific mRNAs in microscopic preparations by in situ hybridization. The oligonucleotides were labeled with one FITC or biotin molecule at the 5' end or with a tail of biotin molecules at the 3' end. The target sequences were mRNAs coding for an ovulation hormone (CDCH) in the caudodorsal cells (CDC) of the pond snail Lymnaea stagnalis and a molluscan insulin-like peptide (MIP) in the light green cells (LGC) of the same organism. The hybridized oligonucleotides were detected either directly after the hybridization procedure by fluorescence microscopy or indirectly after an immunocytochemical procedure to visualize the biotin or FITC moiety. The results indicate that the detectability of the mRNA sequences is at least partially dependent on the accessibility of the target sequences for the immunocytochemical detection systems. The positive hybridization results obtained with oligonucleotides containing different labels enabled us to perform double hybridization experiments for simultaneous detection of CDCH and MIP mRNAs in one tissue section. Using FITC- and biotin-labeled oligonucleotides, we also demonstrated simultaneously different sequences on the same mRNA molecule.
Reduction of crystal violet by diphenylketyl radicals (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReduction of crystal violet by diphenylketyl radicalsYousry M. A. Naguib, Saul G. Cohen, and Colin. SteelCite this: J. Am. Chem. Soc. 1986, 108, 1, 128–133Publication Date (Print):January 1, 1986Publication History Published online1 May 2002Published inissue 1 January 1986https://pubs.acs.org/doi/10.1021/ja00261a021https://doi.org/10.1021/ja00261a021research-articleACS PublicationsRequest reuse permissionsArticle Views402Altmetric-Citations33LEARN 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
Tumor-targeting, Systemically Delivered Antisense HER-2 Chemosensitizes Human Breast Cancer Xenografts Irrespective of HER-2 Levels (2002)

Although there are other reports of liposomal delivery of AS ODNs, this is the first report of in vivo efficacy against human cancer cells using a tumor-targeting liposome delivery system for systemic AS therapy. Moreover, the increased stability in circulation and anti-tumor efficacy observed were obtained without the need for continuous intravenous infusion. HER-2 is an integral component within a network of cell growth pathways that can affect many different types of tumors where HER-2 may be a contributing factor, such as ovarian, esophageal, and GI malignancies including colon and pancreatic cancers. Therefore, the effectiveness of this therapy with xenograft tumors that do not overexpress HER-2 has the potential to expand the clinical usefulness of this efficacious form of therapy.
Psychiatric disorders in America: the epidemiologic catchment area study (1991)

The book review section of the Journal of Psychiatry and Neuroscience provides critical synopses of relevant literature in three review categories, i.e., brief or extended reviews of books recently published, and reviews of books of historical interest.This format is intended to provide variety of subject matter and quality of content, giving reviewers the opportunity to be creative and imaginative in expressing their opinions and ideas.
Nitrile- and Amide-converting Microbial Enzymes: Stereo-, Regio- and Chemoselectivity (2002)

AbstractBiotransformations using microbial nitrile- and amide-converting enzymes have developed considerably in the recent years. Most processes profited from the stereo-, regio- and chemoselectivity of nitrile hydratases, nitrilases and amidases specific for primary or secondary amides. The aim of this review is to discuss the developments in this branch of biotransformations in the last ca. 5 years by taking highlights from research journals, patents and industrial applications.KeywordsNitrile HydrataseNitrilaseAmidaseAminoacylaseCarbamoylaseDeacetylase
Detection of hepatocellular carcinoma with a new alpha-fetoprotein antibody imaging kit. (1997)

AFP-Scan appears to be a promising new antibody imaging kit for the disclosure of sites of HCC and should aid in the management of these patients by revealing primary, recurrent, and metastatic disease with a single imaging modality.
Rectification of two Escherichia coli heat-stable enterotoxin allele sequences and lack of biological effect of changing the carboxy-terminal tyrosine to histidine (1989)

Resequencing estA3, an allele of the methanol-soluble heat-stable enterotoxin of Escherichia coli showed that the proline triplet 19 is in fact an alanine codon; thus, estA alleles 3 and 4 were shown to be identical. Resequencing has also shown that the carboxy terminus of another allele, estA2, is not the previously inferred histidine triplet but the same tyrosine codon reported for all other estA alleles. The improperly inferred histidine codon was used in constructions to fuse estA2 to the B subunit of the heat-labile enterotoxin gene, and the fused gene products as well as three amino acid insertional mutants containing histidine-72 were not efficiently secreted. We show that the defective secretion is not due to histidine as a carboxy-terminal residue, since site-directed mutagenesis of wild-type tyrosine-72 to histidine did not influence the localization of the activity of the methanol-soluble heat-stable enterotoxin.
Long-Range PCR with a DNA Polymerase Fusion (2010)

Proofreading DNA polymerase fusions offer several advantages for long-range PCR, including faster run times and higher fidelity compared with Taq-based enzymes. However, their use so far has been limited to amplification of small to mid-range targets. In this article, we present a modified protocol for using a DNA polymerase fusion to amplify genomic targets exceeding 20 kb in length. This procedure overcomes several limitations of Taq blends, which up until recently, were the only option for long-range PCR. With a proofreading DNA polymerase fusion, high-molecular-weight amplicon can be generated and analyzed in a single day, and a significant proportion is expected to be error-free.
Evidence for direct inhibition of de novo purine synthesis in human MCF-7 breast cells as a principal mode of metabolic inhibition by methotrexate. (1987)

We have investigated the role of dihydrofolate (H2PteGlu) accumulation in the inhibition of de novo purine synthesis by methotrexate (MTX) in human MCF-7 breast cancer cells. Previous studies have shown that cytotoxic concentrations of MTX that inhibit dihydrofolate reductase produce only minimal depletion of the reduced folate cofactor, 10-formyltetrahydrofolate, required for purine synthesis. At the same time, de novo purine synthesis is totally inhibited. In these studies, we show that 10 microM MTX causes inhibition of purine synthesis at the step of phosphoribosylaminoimidazolecarboxamide (AICAR) transformylase, as reflected in a 2-3-fold expansion of the intracellular AICAR pool. The inhibition of purine synthesis coincides with the rapid intracellular accumulation of H2PteGlu, a known inhibitor of AICAR transformylase. When the generation of H2PteGlu is blocked by pretreatment with 50 microM 5-fluorodeoxyuridine (FdUrd), an inhibitor of thymidylate synthase, MTX no longer causes inhibition of purine synthesis. Intermediate levels of H2PteGlu produced in the presence of lower (0.1-10 microM) concentrations of FdUrd led to proportional inhibition of purine biosynthesis, and the exogenous addition of H2PteGlu to breast cells in culture re-established the block in purine synthesis in the presence of FdUrd and MTX. The early phases of inhibition of purine biosynthesis could be ascribed only to H2PteGlu accumulation. MTX polyglutamates, also known to inhibit AICAR transformylase, were present in breast cells only after 6 h of incubation with the parent compounds and were not formed in cells preincubated with FdUrd. The lipid-soluble antifolate trimetrexate, which does not form polyglutamates, produced modest 10-formyltetrahydrofolate depletion, but caused marked H2PteGlu accumulation and a parallel inhibition of purine biosynthesis. This evidence leads to the conclusion that MTX and the lipid-soluble analog trimetrexate cause inhibition of purine biosynthesis through the accumulation of H2PteGlu behind the blocked dihydrofolate reductase reaction.
Secreted PCSK9 decreases the number of LDL receptors in hepatocytes and inlivers of parabiotic mice (2006)

Proprotein convertase subtilisin/kexin type 9 (PCSK9) is a member of the proteinase K subfamily of subtilases that reduces the number of LDL receptors (LDLRs) in liver through an undefined posttranscriptional mechanism. We show that purified PCSK9 added to the medium of HepG2 cells reduces the number of cell-surface LDLRs in a dose- and time-dependent manner. This activity was approximately 10-fold greater for a gain-of-function mutant, PCSK9(D374Y), that causes hypercholesterolemia. Binding and uptake of PCSK9 were largely dependent on the presence of LDLRs. Coimmunoprecipitation and ligand blotting studies indicated that PCSK9 and LDLR directly associate; both proteins colocalized to late endocytic compartments. Purified PCSK9 had no effect on cell-surface LDLRs in hepatocytes lacking autosomal recessive hypercholesterolemia (ARH), an adaptor protein required for endocytosis of the receptor. Transgenic mice overexpressing human PCSK9 in liver secreted large amounts of the protein into plasma, which increased plasma LDL cholesterol concentrations to levels similar to those of LDLR-knockout mice. To determine whether PCSK9 was active in plasma, transgenic PCSK9 mice were parabiosed with wild-type littermates. After parabiosis, secreted PCSK9 was transferred to the circulation of wild-type mice and reduced the number of hepatic LDLRs to nearly undetectable levels. We conclude that secreted PCSK9 associates with the LDLR and reduces hepatic LDLR protein levels.
Effect of Hydroxyurea on the Frequency of Painful Crises in Sickle Cell Anemia (1995)

Hydroxyurea therapy can ameliorate the clinical course of sickle cell anemia in some adults with three or more painful crises per year. Maximal tolerated doses of hydroxyurea may not be necessary to achieve a therapeutic effect. The beneficial effects of hydroxyurea do not become manifest for several months, and its use must be carefully monitored. The long-term safety of hydroxyurea in patients with sickle cell anemia is uncertain.
A simple and expressive semantic framework for policy composition in access control (2007)

In defining large, complex access control policies, one would like to compose sub-policies, perhaps authored by different organizations, into a single global policy. Existing policy composition approaches tend to be ad-hoc, and do not explain whether too many or too few policy combinators have been defined. We define an access controlpolicy as a four-valued predicate that maps accesses to either grant, deny, conflict, or unspecified. These correspond to the four elements of the Belnap bilattice. Functions on this bilattice are then extended to policies to serve as policy combinators. We argue that this approach provides a simple andnatural semantic framework for policy composition, with a minimal but functionally complete set of policy combinators. We define derived, higher-level operators that are convenient for the specification of access control policies, and enable the decoupling of conflict resolution from policy composition. Finally, we propose a basic query language and show that it can reduce important analyses (e.g., conflict analysis) to checks of policy refinement. Copyright 2007 ACM.
Introduction of Fluorine and Fluorine‐Containing Functional Groups (2013)

Over the past decade, the most significant, conceptual advances in the field of fluorination were enabled most prominently by organo- and transition-metal catalysis. The most challenging transformation remains the formation of the parent C-F bond, primarily as a consequence of the high hydration energy of fluoride, strong metal-fluorine bonds, and highly polarized bonds to fluorine. Most fluorination reactions still lack generality, predictability, and cost-efficiency. Despite all current limitations, modern fluorination methods have made fluorinated molecules more readily available than ever before and have begun to have an impact on research areas that do not require large amounts of material, such as drug discovery and positron emission tomography. This Review gives a brief summary of conventional fluorination reactions, including those reactions that introduce fluorinated functional groups, and focuses on modern developments in the field.
KinectFusion (2011)

We present KinectFusion, a system that takes live depth data from a moving Kinect camera and in real-time creates high-quality, geometrically accurate, 3D models. Our system allows a user holding a Kinect camera to move quickly within any indoor space, and rapidly scan and create a fused 3D model of the whole room and its contents within seconds. Even small motions, caused for example by camera shake, lead to new viewpoints of the scene and thus refinements of the 3D model, similar to the effect of image super-resolution. As the camera is moved closer to objects in the scene more detail can be added to the acquired 3D model.
A phase I trial of monoclonal antibody M195 in acute myelogenous leukemia: specific bone marrow targeting and internalization of radionuclide. (1991)

Ten patients with myeloid leukemias were treated in a phase I trial with escalating doses of mouse monoclonal antibody (mAb) M195, reactive with CD33, a glycoprotein found on myeloid leukemia blasts and early hematopoietic progenitor cells but not on normal stem cells. M195 was trace-labeled with iodine-131 (131I) to allow detailed pharmacokinetic and dosimetric studies by serial sampling of blood and bone marrow and whole-body gamma-camera imaging. Total doses up to 76 mg were administered safely without immediate adverse effects. Absorption of M195 onto targets in vivo was demonstrated by biopsy, pharmacology, flow cytometry, and imaging; saturation of available sites occurred at doses greater than or equal to 5 mg/m2. The entire bone marrow was specifically and clearly imaged beginning within hours after injection; optimal imaging occurred at the lowest dose. Bone marrow biopsies demonstrated significant dose-related uptake of M195 as early as 1 hour after infusion in all patients, with the majority of the dose found in the marrow. Tumor regressions were not observed. An estimated 0.33 to 1.0 rad/mCi 131I was delivered to the whole body, 1.1 to 6.1 rad/mCi was delivered to the plasma, and up to 34 rad/mCi was delivered to the red marrow compartment. 131I-M195 was rapidly modulated, with a majority of the bound immunoglobulin G (IgG) being internalized into target cells in vivo. These data indicate that whole bone marrow ablative doses of 131I-M195 can be expected. The rapid, specific, and quantitative delivery to the bone marrow and the efficient internalization of M195 into target cells in vivo also suggest that the delivery of other isotopes such as auger or alpha emitters, toxins, or other biologically important molecules into either leukemia cells or normal hematopoietic progenitor cells may be feasible.