gebhart/patrepeval huggingface dataset:
Excretion of a tumor‐associated trypsin inhibitor (TATI) in urine of patients with gynecological malignancy (1983)

In earlier studies we reported the finding of a tumor-associated peptide that also occurred at high concentrations in early amniotic fluid. Determination of the N-terminal sequence of this peptide revealed that it is closely related or identical to the pancreatic secretory trypsin inhibitor. Therefore, the peptide is called tumor-associated trypsin inhibitor (TATI). The concentration of TATI was determined by radioimmunoassay in the urine of 148 patients with various forms of gynecologic malignancy and in a reference population consisting of 98 patients with non-malignant gynecologic disease, and also in 40 patients with severe infections or inflammatory disease. In the reference population, the median urinary concentration of TATI was 22 micrograms/g creatinine and the central 95% reference interval was 7-50 micrograms/g creatinine. Elevated urinary levels were observed in 53% of all patients with gynecologic cancer, in 63% of those with active disease and 26% of those in clinical remission. The highest urinary TATI level (11,000 micrograms/g creatinine) was over 200 times the upper limit of the reference range. Patients with cervical cancer had the highest frequency of elevated values. Increased excretion of TATI was also observed in patients with severe bronchopulmonary infections and pancreatitis. Although increased excretion of TATI is not cancer-specific, the distinction by elevated levels of TATI between malignant and nonmalignant gynecologic disease is better than by most other putative tumor markers, and the increased excretion of TATI in patients with active disease can be important for the understanding of tumor biology.
Total synthesis of (±)-15-deoxyprostaglandin E1 (1972)

C. J. Sih, R. G. Salomon, P. Price, G. Peruzzoti and R. Sood, J. Chem. Soc., Chem. Commun., 1972, 240b DOI: 10.1039/C3972000240B
Concepts and Principles of Photodynamic Therapy as an Alternative Antifungal Discovery Platform (2012)

Opportunistic fungal pathogens may cause superficial or serious invasive infections, especially in immunocompromised and debilitated patients. Invasive mycoses represent an exponentially growing threat for human health due to a combination of slow diagnosis and the existence of relatively few classes of available and effective antifungal drugs. Therefore systemic fungal infections result in high attributable mortality. There is an urgent need to pursue and deploy novel and effective alternative antifungal countermeasures. Photodynamic therapy (PDT) was established as a successful modality for malignancies and age-related macular degeneration but photodynamic inactivation has only recently been intensively investigated as an alternative antimicrobial discovery and development platform. The concept of photodynamic inactivation requires microbial exposure to either exogenous or endogenous photosensitizer molecules, followed by visible light energy, typically wavelengths in the red/near infrared region that cause the excitation of the photosensitizers resulting in the production of singlet oxygen and other reactive oxygen species that react with intracellular components, and consequently produce cell inactivation and death. Antifungal PDT is an area of increasing interest, as research is advancing (i) to identify the photochemical and photophysical mechanisms involved in photoinactivation; (ii) to develop potent and clinically compatible photosensitizers; (iii) to understand how photoinactivation is affected by key microbial phenotypic elements multidrug resistance and efflux, virulence and pathogenesis determinants, and formation of biofilms; (iv) to explore novel photosensitizer delivery platforms; and (v) to identify photoinactivation applications beyond the clinical setting such as environmental disinfectants.
Establishment and Maintenance of a Heterochromatin Domain (2002)

The higher-order assembly of chromatin imposes structural organization on the genetic information of eukaryotes and is thought to be largely determined by posttranslational modification of histone tails. Here, we study a 20-kilobase silent domain at the mating-type region of fission yeast as a model for heterochromatin formation. We find that, although histone H3 methylated at lysine 9 (H3 Lys9) directly recruits heterochromatin protein Swi6/HP1, the critical determinant for H3 Lys9 methylation to spread in cis and to be inherited through mitosis and meiosis is Swi6 itself. We demonstrate that a centromere-homologous repeat (cenH) present at the silent mating-type region is sufficient for heterochromatin formation at an ectopic site, and that its repressive capacity is mediated by components of the RNA interference (RNAi) machinery. Moreover, cenH and the RNAi machinery cooperate to nucleate heterochromatin assembly at the endogenous mat locus but are dispensable for its subsequent inheritance. This work defines sequential requirements for the initiation and propagation of regional heterochromatic domains.
The Total Synthesis of Dynemicin A Leading to Development of a Fully Contained Bioreductively Activated Enediyne Prodrug (1996)

The title compound has been synthesized as its racemate in 33 steps. An intramolecular Diels−Alder reaction (see Scheme 5, 24 → 25) was used to provide control over the eventual cis C4−C7 relationship. The installation of another cis related ethynyl group at C2 arose from transformation 40 → 42 (see Scheme 8) whose directionality is governed by a benzophenone ketal functioning as a temporary steric control unit. Closure of the enediyne unit was accomplished on a trimethylsilylethoxycarbonyl (TEOC) protected dihydroquinoline derivative. It involved use of a novel bis-iodoalkyne/distannylethylene interpolative coupling transformation (61 + 58 → 63, Scheme 12). In the terminal phase of the synthesis, a novel iminoquinone ketal 74 (Scheme 15) was condensed with homophthalic anhydride derivative 78 (Scheme 16) as indicated in Scheme 17. The final deprotection involved cleavage of a methoxymethyl ester and two methoxymethyl phenol ethers. From this work, there arose the concept and demonstration of p-quinone monoimines 82 and 93 (Scheme 18), as bioreductively activated enediyne prodrugs.
Catalytic and framework mutations in the neuraminidase active site of influenza viruses that are resistant to 4-guanidino-Neu5Ac2en (1997)

Here we report the isolation of influenza virus A/turkey/Minnesota/833/80 (H4N2) with a mutation at the catalytic residue of the neuraminidase (NA) active site, rendering it resistant to the novel NA inhibitor 4-guanidino-Neu5Ac2en (GG167). The resistance of the mutant stems from replacement of one of three invariant arginines (Arg 292-->Lys) that are conserved among all viral and bacterial NAs and participate in the conformational change of sialic acid moiety necessary for substrate catalysis. The Lys292 mutant was selected in vitro after 15 passages at increasing concentrations of GG167 (from 0.1 to 1,000 microM), conditions that earlier gave rise to GG167-resistant mutants with a substitution at the framework residue Glu119. Both types of mutants showed similar degrees of resistance in plaque reduction assays, but the Lys292 mutant was more sensitive to the inhibitor in NA inhibition tests than were mutants bearing a substitution at framework residue 119 (Asp, Ala, or Gly). Cross-resistance to other NA inhibitors (4-amino-Neu5Ac2en and Neu5Ac2en) varied among mutants resistant to GG167, being lowest for Lys292 and highest for Asp119. All GG167-resistant mutants demonstrated markedly reduced NA activity, only 3 to 50% of the parental level, depending on the particular amino acid substitution. The catalytic mutant (Lys292) showed a significant change in pH optimum of NA activity, from 5.9 to 5.3. All of the mutant NAs were less stable than the parental enzyme at low pH. Despite their impaired NA activity, the GG167-resistant mutants grew as well as parental virus in Madin-Darby canine kidney cells or in embryonated chicken eggs. However, the infectivity in mice was 500-fold lower for Lys292 than for the parental virus. These findings demonstrate that amino acid substitution in the NA active site at the catalytic or framework residues, followed by multiple passages in vitro, in the presence of increasing concentrations of the NA inhibitor GG167, generates GG167-resistant viruses with reduced NA activity and decreased infectivity in animals.
Retinal pathology of canine X-linked progressive retinal atrophy, the locus homologue of RP3. (1999)

X-linked retinal degeneration is characterized by initial degeneration of rod photoreceptors, followed by loss of cones and progressive atrophy of the inner retina. Carrier females display a phenotype consistent with random X-chromosome inactivation. Variation in genetic background may alter expression of the disease allele in affected animals, thus accounting for variation in phenotypic expression of the disease.
Biologically Active Polymers (1991)

Interest continues to grow in polymers that have inherent biological activity or polymers which are covalently attached to well known drugs. This paper provides an introduction to these types of materials and a general review of the different types of polymeric drugs, polymeric drug conjugates, polymeric prodrugs, and targeted polymeric drugs which can be classified as biologically active polymers.
Multiple mechanisms of p16INK4A inactivation in non-small cell lung cancer cell lines. (1995)

p16INK4A, a specific inhibitor of cyclin-dependent kinase (cdk)4 and cdk6, is a candidate tumor suppressor in malignancies with wild-type retinoblastoma (Rb). Loss of p16INK4A frees these cdks from inhibition, permitting constitutive phosphorylation of Rb and inactivation of its growth suppressive properties. Consistent with this model, Rb-positive non-small cell lung cancers (NSCLCs) have little or no detectable p16INK4A protein, whereas Rb-negative lung cancers have abundant p16INK4A. However, only some NSCLCs have homozygous deletions or nonsense mutations in a remaining p16INK4A allele, suggesting that other mechanisms must account for absent or low levels of p16INK4A protein. Here, we analyzed 9 Rb-positive NSCLC cell lines for the controls governing p16INK4A activity. Four lines had homozygous deletions of p16INK4A (SK-LU-1, SK-MES-1, A-427, and SW900), and three had a point mutation in a single allele. First, in H520 cells, the previously reported deletion at codon 45 results in a frameshift that produces no detectable protein. Second, in Calu-3 cells, a His to Tyr substitution at codon 83 produced a variant with a shortened half-life that was unable to form complexes with cdk4 or cdk6. Third, in H661 cells, the previously reported point mutation in the second intron splice donor site resulted in a smaller p16INK4A protein. Although this variant formed complexes with cdk4 and cdk6, it had a profoundly reduced half-life, producing low steady-state levels of p16INK4A and abundant levels of free cdks. Finally, Calu-1 and Calu-6 cells transcribed no detectable mRNA encoding authentic p16INK4A. These cell lines displayed methylation of the CpG island surrounding the first exon of p16INK4A and expressed abundant levels of a nontranslated mRNA containing an alternative first exon (E1 beta), as did all other cell lines in which the p16INK4A locus was not deleted. These data indicate that Rb-positive NSCLC cells have evolved a variety of pathways to suppress p16INK4A expression. Reintroduction of p16INK4A into these cell lines by retroviral transfer resulted in a reduced growth rate, increased abundance of hypophosphorylated Rb, accumulation of cells in G1, and a less transformed morphology in Rb-positive, but not Rb-negative cells, suggesting that loss of p16INK4A is essential for maintenance of the transformed phenotype.
The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line (2011)

Chinese hamster ovary (CHO)-derived cell lines are the preferred host cells for the production of therapeutic proteins. Here we present a draft genomic sequence of the CHO-K1 ancestral cell line. The assembly comprises 2.45 Gb of genomic sequence, with 24,383 predicted genes. We associate most of the assembled scaffolds with 21 chromosomes isolated by microfluidics to identify chromosomal locations of genes. Furthermore, we investigate genes involved in glycosylation, which affect therapeutic protein quality, and viral susceptibility genes, which are relevant to cell engineering and regulatory concerns. Homologs of most human glycosylation-associated genes are present in the CHO-K1 genome, although 141 of these homologs are not expressed under exponential growth conditions. Many important viral entry genes are also present in the genome but not expressed, which may explain the unusual viral resistance property of CHO cell lines. We discuss how the availability of this genome sequence may facilitate genome-scale science for the optimization of biopharmaceutical protein production.
Transformation of guinea pig leukocytes by coinfection with human T-cell lymphotropic virus types I and II. (1999)

Guinea pigs and their CBMCs can be infected with HTLV-I and HTLV-II. This animal system may be useful as an experimental model of HTLV-I and HTLV-II infection.
Targeted Delivery of Gemcitabine to Pancreatic Adenocarcinoma Using Cetuximab as a Targeting Agent (2008)

One of the key challenges in anticancer therapy is the toxicity and poor bioavailability of the anticancer drugs. Nanotechnology can play a pivotal role by delivering drugs in a targeted fashion to the malignant cells that will reduce the systemic toxicity of the anticancer drug. In this report, we show a stepwise development of a nanoparticle-based targeted delivery system for in vitro and in vivo therapeutic application in pancreatic cancer. In the first part of the study, we have shown the fabrication and characterization of the delivery system containing gold nanoparticle as a delivery vehicle, cetuximab as a targeting agent, and gemcitabine as an anticancer drug for in vitro application. Nanoconjugate was first characterized physico-chemically. In vitro targeting efficacy, tested against three pancreatic cancer cell lines (PANC-1, AsPC-1, and MIA Paca2) with variable epidermal growth factor receptor (EGFR) expression, showed that gold uptake correlated with EGFR expression. In the second part, we showed the in vivo therapeutic efficacy of the targeted delivery system. Administration of this targeted delivery system resulted in significant inhibition of pancreatic tumor cell proliferation in vitro and orthotopic pancreatic tumor growth in vivo. Tumor progression was monitored noninvasively by measuring bioluminescence of the implanted tumor cells. Pharmacokinetic experiments along with the quantitation of gold both in vitro and in vivo further confirmed that the inhibition of tumor growth was due to targeted delivery. This strategy could be used as a generalized approach for the treatment of a variety of cancers characterized by overexpression of EGFR.
Estrogen Prevents the Lipopolysaccharide-Induced Inflammatory Response in Microglia (2001)

After neuronal injury and in several neurodegenerative diseases, activated microglia secrete proinflammatory molecules that can contribute to the progressive neural damage. The recent demonstration of a protective role of estrogen in neurodegenerative disorders in humans and experimental animal models led us to investigate whether this hormone regulates the inflammatory response in the CNS. We here show that estrogen exerts an anti-inflammatory activity on primary cultures of rat microglia, as suggested by the blockage of the phenotypic conversion associated with activation and by the prevention of lipopolysaccharide-induced production of inflammatory mediators: inducible form of NO synthase (iNOS), prostaglandin-E(2) (PGE(2)), and metalloproteinase-9 (MMP-9). These effects are dose-dependent, maximal at 1 nm 17beta-estradiol, and can be blocked by the estrogen receptor (ER) antagonist ICI 182,780. The demonstration of ERalpha and ERbeta expression in microglia and macrophages and the observation of estrogen blockade of MMP-9 mRNA accumulation and MMP-9 promoter induction further support the hypothesis of a genomic activity of estrogen via intracellular receptors. This is the first report showing an anti-inflammatory activity of estrogen in microglia. Our study proposes a novel explanation for the protective effects of estrogen in neurodegenerative and inflammatory diseases and provides new molecular and cellular targets for the screening of ER ligands acting in the CNS.
Stabilization of an Immunoglobulin Fold Domain by an Engineered Disulfide Bond at the Buried Hydrophobic Region (2007)

We report for the first time the stabilization of an immunoglobulin fold domain by an engineered disulfide bond. In the llama single-domain antibody, which has human chorionic gonadotropin as its specific antigen, Ala49 and Ile70 are buried in the structure. A mutant with an artificial disulfide bond at this position showed a 10 degrees C higher midpoint temperature of thermal unfolding than that without the extra disulfide bond. The modified domains exhibited an antigen binding affinity comparable with that of the wild-type domain. Ala49 and Ile70 are conserved in camel and llama single-domain antibody frameworks. Therefore, domains against different antigens are expected to be stabilized by the engineered disulfide bond examined here. In addition to the effect of the loop constraints in the unfolded state, thermodynamic analysis indicated that internal interaction and hydration also control the stability of domains with disulfide bonds. The change in physical properties resulting from mutation often causes unpredictable and destabilizing effects on these interactions. The introduction of a hydrophobic cystine into the hydrophobic region maintains the hydrophobicity of the protein and is expected to minimize the unfavorable mutational effects.
Analysis of the human tonsil B cell repertoire by somatic hybridization: occurrence of both “monospecific” and “multispecific” (auto)antibody‐secreting cells (1987)

The purpose of our study was to investigate the (auto)antibody repertoire of human tonsil B cells. To this end, unseparated tonsil B cells and "large" and "small" tonsil B cells, obtained after fractionation on a discontinuous Percoll gradient, were fused with the (human X mouse) heterohybridoma K6H6/B5. The IgM antibodies secreted by individual clones were analyzed in spot-enzyme-linked immunosorbent assay for reactivity against a panel of 5 autoantigens and 1 xenoantigen. The results show that both "mono-" and "multispecific" (auto)antibody-secreting clones can be obtained by somatic hybridization of unseparated, "small" and "large" tonsil B cells. The patterns of IgM reactivities in these three collections of hybridomas did not differ significantly. Inhibition experiments revealed that "multispecific" antibodies can bind with high affinity to more than one (auto)antigen. The results of these experiments are discussed in relation to the state of activation of tonsil B lymphocytes.
Atrial natriuretic peptide, brain natriuretic peptide and c‐type natriuretic peptide: effects on testicular microcirculation and immunohistochemical localization (1997)

The effect of local injection of atrial (ANP), brain (BNP) and C-type (CNP) natriuretic peptides and an ANP antagonist (HS-142-1) on testicular microcirculation and vasomotion was studied using laser Doppler flowmetry. The natriuretic peptides were also localized immunohistochemically within the testis. ANP, BNP-32, CNP-22 and CNP-53 all caused a dose-related increase in testicular blood flow. The effect of ANP was blocked by concomitant injection of the ANP antagonist. Immunoreactive (ir) CNP and ir BNP were found in Leydig cells whereas in ANP was observed in the seminiferous tubules. It is suggested that the natriuretic peptides could play a role in local regulation of the testicular microcirculation.
Investigating the Activity Spectrum for Ring-Substituted 8-Hydroxyquinolines (2010)

In this study, a series of fourteen ring-substituted 8-hydroxyquinoline derivatives were prepared. The synthesis procedures are presented. The compounds were analyzed using RP-HPLC to determine lipophilicity. They were tested for their activity related to inhibition of photosynthetic electron transport (PET) in spinach (Spinacia oleracea L.) chloroplasts. Primary in vitro screening of the synthesized compounds was also performed against four mycobacterial strains and against eight fungal strains. Several compounds showed biological activity comparable with or higher than the standards isoniazid or fluconazole. For all the compounds, the relationships between the lipophilicity and the chemical structure of the studied compounds are discussed.
Insensitivity to Metalaxyl in California Populations ofBremia lactucaeand Resistance of California Lettuce Cultivars to Downy Mildew (1991)

Ninety-seven California isolates of Bremia lactucae were characterized for virulence phenotype, metalaxyl insensitivity, and sexual compability type from 1987 to 1989. Seventy-eight lettuce cultivars and 85 lettuce accessions were screened for resistance to lettuce downy mildew caused by the three major California pathotypes of B. lactucae. Of the 97 B. lactucae isolates, two were California pathotype IA, four were pathotype II, 30 were pathotype III, and 61 seemed to be pathotype IV. Several pathotype IV isolates were separated easily into derivatives having virulence phenotypes identical to either pathotype II or pathotype III (...)
Cooperative Regenerating Codes (2013)

One of the design objectives in distributed storage system is the minimization of the data traffic during the repair of failed storage nodes. By repairing multiple failures simultaneously and cooperatively rather than successively and independently, further reduction of repair traffic is made possible. A closed-form expression of the optimal tradeoff between the repair traffic and the amount of storage in each node for cooperative repair is given. We show that the points on the tradeoff curve can be achieved by linear cooperative regenerating codes, with an explicit bound on the required finite-field size. The proof relies on a max-flow-min-cut-type theorem from combinatorial optimization for submodular flows. Two families of explicit constructions are given.
Biocompatible Luminescent Silicon Quantum Dots for Imaging of Cancer Cells (2008)

Luminescent silicon quantum dots (Si QDs) have great potential for use in biological imaging and diagnostic applications. To exploit this potential, they must remain luminescent and stably dispersed in water and biological fluids over a wide range of pH and salt concentration. There have been many challenges in creating such stable water-dispersible Si QDs, including instability of photoluminescence due their fast oxidation in aqueous environments and the difficulty of attaching hydrophilic molecules to Si QD surfaces. In this paper, we report the preparation of highly stable aqueous suspensions of Si QDs using phospholipid micelles, in which the optical properties of Si nanocrystals are retained. These luminescent micelle-encapsulated Si QDs were used as luminescent labels for pancreatic cancer cells. This paves the way for silicon quantum dots to be a valuable optical probe in biomedical diagnostics.