gebhart/patrepeval huggingface dataset:
Detection of disseminated tumor cells in peripheral blood of colorectal cancer patients (1997)

All cancer staging systems seek to identify clinical and pathological features that can predict outcome or guide therapy. In particular, a non-invasive method for the early detection of disseminating disease would be of great interest. We investigated the use of cytokeratin genes expression to detect blood metastases from colorectal tumors. Epithelial tumor cells were isolated from whole blood using the monoclonal antibody (MAb) BerEP4 and magnetic beads, and detected by reverse transcription-polymerase chain reaction using oligonucleotides derived from the cDNA sequences of cytokeratins 8, 19 and 20. The sensitivity of this assay was determined by spiking SW620 colon carcinoma cells in normal blood. Using cytokeratin 19 expression we were able to detect 1 epithelial tumor cell in 1 ml of whole blood. The clinical applicability of this technique was explored by evaluating patients with a colorectal carcinoma. Epithelial cells were detected in the blood of 12 out of 23 patients, 2 (20%) of 10 with Astler-Coller stage A or B, and 10 (77%) of 13 with stage C or D cancer. In conclusion, this test is a non-invasive, sensitive, and specific assay for detecting circulating epithelial cells in blood. It may be useful for the early diagnosis of disseminating disease, to determine whether the presence of micrometastatic cells at the time of surgery is correlated with an early relapse and for monitoring adjuvant therapeutic trials.
Efficient and nontoxic biomolecule delivery to primary human hematopoietic stem cells using nanostraws (2020)

Introduction of exogenous genetic material into primary stem cells is essential for studying biological function and for clinical applications. Traditional delivery methods for nucleic acids, such as electroporation, have advanced the field, but have negative effects on stem cell function and viability. We introduce nanostraw-assisted transfection as an alternative method for RNA delivery to human hematopoietic stem and progenitor cells (HSPCs). Nanostraws are hollow alumina nanotubes that can be used to deliver biomolecules to living cells. We use nanostraws to target human primary HSPCs and show efficient delivery of mRNA, short interfering RNAs (siRNAs), DNA oligonucleotides, and dextrans of sizes ranging from 6 kDa to 2,000 kDa. Nanostraw-treated cells were fully functional and viable, with no impairment in their proliferative or colony-forming capacity, and showed similar long-term engraftment potential in vivo as untreated cells. Additionally, we found that gene expression of the cells was not perturbed by nanostraw treatment, while conventional electroporation changed the expression of more than 2,000 genes. Our results show that nanostraw-mediated transfection is a gentle alternative to established gene delivery methods, and uniquely suited for nonperturbative treatment of sensitive primary stem cells.
Depletion of Tumor-Infiltrating Macrophages Is Associated with Amphoterin Expression in Colon Cancer (2004)

Macrophage infiltration into colon cancer and amphoterin expression in cancer cells was examined in 42 human colon cancers invading the subserosa. The mean number of infiltrating macrophages was significantly higher in Dukes' B cases than in Dukes' C cases (p = 0.0065). Tumors with few infiltrating macrophages (macrophage depletion) were significantly more frequent in Dukes' C cases than in Dukes' B cases (p = 0.0014). No Dukes' C cases with relevant macrophage infiltration showed macrophage-cancer cell contact, whereas 5 Dukes' B cases showed such contact (p < 0.0001). In human colon cancer cells implanted in the cecum of nude mice, KM12SM (highly metastatic) tumors yielded less macrophage infiltration and more liver metastases than KM12C (low risk of metastasis) tumors (14 +/- 3 vs. 78 +/- 32 and 24 +/- 6 vs. 5 +/- 3 per liver, respectively). Amphoterin expression was detected at high frequency in both Dukes' B and C cases (p = 0.0684). In macrophage-depleted cases, amphoterin expression was significantly higher than that in non-depleted cases (p = 0.0015). To confirm biological effects of amphoterin on macrophages, an infiltration assay using the cell-layered Boyden chamber was done. Infiltration of PMA-treated U937 monocytes through the KM12SM cell layer was increased by pretreatment of KM12SM cells with amphoterin antisense S-oligodeoxynucleotide exposure. Moreover, extracted amphoterin inhibited PMA-U937 monocyte infiltration in a dose-dependent manner. Thus, amphoterin may play an important role in the inhibition of macrophage infiltration into colon cancer.
Reduced susceptibility to collagen-induced arthritis in mice deficient in IFN-gamma receptor. (1998)

Collagen-induced arthritis (CIA) is an arthritic model that was developed after immunization with type II collagen (CII). Apparently, contradictory results have been reported regarding the role of IFN-gamma in the development of CIA. Therefore, we employed IFN-gamma R-deficient mice to study the role of IFN-gamma. To introduce the CIA susceptibility gene (H-2q), IFN-gamma R-deficient (H-2b/b/IFN-gamma R-/-) mice were mated with DBA/1 (H-2q/q/IFN-gamma R+/+) mice; next, the F1 mice were interbred to yield F2 offspring bearing different combinations of H-2 (H-2q/q, H-2q/b, and H-2b/b) and IFN-gamma R (IFN-gamma R+/+, IFN-gamma R+/-, and IFN-gamma R-/-) genes. Although the H-2q allele appeared to confer susceptibility to CIA, mice that were homozygous for the IFN-gamma R mutation showed a substantially decreased incidence and severity of CIA. The CII-specific IgG levels of serum samples, which are known to be involved in the development of CIA, were remarkably reduced in IFN-gamma R-/- mice. Furthermore, the anti-CII IgG2a levels controlled by IFN-gamma R were significantly reduced in IFN-gamma R-/- F2 mice compared with those seen in IFN-gamma R+/+ and IFN-gamma R+/- mice, although the levels of all IgG subclass Abs examined were lower in IFN-gamma R-/- mice than in IFN-gamma R+/+ mice. No clear evidence of the imbalance of Th1/Th2 cytokines was observed in CII-immunized, IFN-gamma R-deficient mice. Taken together, these results suggest that IFN-gamma exacerbates CIA by affecting, at least, levels of CII-specific IgG Ab rather than the imbalance of Th1/Th2 cells.
Validation of the Functional Assessment of Chronic Illness Therapy Fatigue Scale relative to other instrumentation in patients with rheumatoid arthritis. (2005)

The FACIT Fatigue is a brief, valid measure for monitoring this important symptom and its effects on patients with RA.
Impact of External Pressure and Electrolyte Transport Properties on Lithium Dendrite Growth (2018)

Practical implementation of metal anodes in commercial lithium-ion batteries has been limited by the growth of dendritic protrusions, which can cause short-circuits and adversely affect battery safety. The impacts of the physical (such as external pressure and electrolyte shear modulus) and electrochemical (for example, conductivity, diffusivity and transference number) properties of a solid electrolyte on the propensity of lithium dendrite growth are investigated here. It is found that over a range of conditions, there are critical pressures above which growth of lithium dendritic protrusions can be prevented. The magnitude of this critical pressure depends on the elastic modulus of the electrolyte. Plastic deformation of lithium at high pressure results in reduced protrusion growth, which helps in obtaining stable deposition. For the first time, phase maps have been developed based on mechanical and transport properties of electrolytes, indicating conditions under which stable deposition of lithium is possible during long-term operation. Suppression of dendrites by individually altering conductivity, or diffusivity, or transference number, or elastic modulus of the electrolyte appears to be a relatively difficult task. Finally, minor tailoring of the transference number and elastic modulus of present-day polymer electrolytes, in a combined fashion, can lead to dendrite-free deposition of lithium.
Effects of buffer layers in epitaxial growth of SrTiO3 thin film on Si(100) (1995)

SrTiO3 thin film has been formed on Si(100) substrates with various single buffer layers such as SrO, CeO2, CaF2, CoSi2 and a multibuffer layer, YSZ/Y2O3/YBa2Cu3O7 by ArF excimer laser ablation. The relation of lattice orientation of buffer layers with SrTiO3 layer has been elucidated. The orientation of SrTiO3 film is influenced not only by lattice matching but by crystal structure and chemical bonding of the buffer layers. As well, the multibuffer layer more effectively forms preferential c-axis oriented SrTiO3 film on Si(100), while CoSi2 buffer is more effective for improving the dielectric constant of SrTiO3 than other buffer layers.
Novel Nicotine Oxidoreductase-Encoding Gene Involved in Nicotine Degradation by Pseudomonas putida Strain S16 (2008)

There are quite a few ongoing biochemical investigations of nicotine degradation in different organisms. In this work, we identified and sequenced a gene (designated nicA) involved in nicotine degradation by Pseudomonas putida strain S16. The gene product, NicA, was heterologously expressed and characterized as a nicotine oxidoreductase catalyzing the initial steps of nicotine metabolism. Biochemical analyses using resting cells and the purified enzyme suggested that nicA encodes an oxidoreductase, which converts nicotine to 3-succinoylpyridine through pseudooxynicotine. Based on enzymatic reactions and direct evidence obtained using H(2)(18)O labeling, the process may consist of enzyme-catalyzed dehydrogenation, followed by spontaneous hydrolysis and then repetition of the dehydrogenation and hydrolysis steps. Sequence comparisons revealed that the gene showed 40% similarity to genes encoding NADH dehydrogenase subunit I and cytochrome c oxidase subunit I in eukaryotes. Our findings demonstrate that the molecular mechanism for nicotine degradation in strain S16 involves the pyrrolidine pathway and is similar to the mechanism in mammals, in which pseudooxynicotine, the direct precursor of a potent tobacco-specific lung carcinogen, is produced.
Sites and Mechanisms of Aconitase Inactivation by Peroxynitrite:  Modulation by Citrate and Glutathione (2005)

Aconitases are iron-sulfur cluster-containing proteins present both in mitochondria and cytosol of cells; the cubane iron-sulfur (Fe-S) cluster in the active site is essential for catalytic activity, but it also renders aconitase highly vulnerable to reactive oxygen and nitrogen species. This study examined the sites and mechanisms of aconitase inactivation by peroxynitrite (ONOO-), a strong oxidant and nitrating agent readily formed from superoxide anion and nitric oxide generated by mitochondria. ONOO- inactivated aconitase in a dose-dependent manner (half-maximal inhibition was observed with approximately 3 microM ONOO-). Low levels of ONOO- caused the conversion of the Fe-S cluster from the [4Fe-4S]2+ form to the inactive [3Fe-4S]1+ form with the loss of labile iron, as confirmed by low-temperature EPR analysis. In the presence of the substrate, citrate, 66-fold higher concentrations of ONOO- were required for half-maximal inhibition. The protective effects of citrate corresponded to its binding to the active site. The inactivation of aconitase in the presence of citrate was due to ONOO--mediated cysteine thiol loss and tyrosine nitration in the enzyme as shown by Western blot analyses. LC/MS/MS analyses revealed that ONOO- treatment to aconitase resulted in nitration of tyrosines 151 and 472 and oxidation to sulfonic acid of cysteines 126 and 385. The latter is one of the three cysteine residues in aconitase that binds to the Fe-S cluster. All other modified tyrosine and cysteine residues were adjacent to the binding site, thus suggesting that these modifications caused conformational changes leading to active-site disruption. Aconitase cysteine thiol modifications other than oxidation to sulfonic acid, such as S-glutathionylation, also decreased aconitase activity, thus indicating that glutathionylation may be an important means of modulating aconitase activity under oxidative and nitrative stress. Taken together, these results demonstrate that the Fe-S cluster in the active site, cysteine 385 bound to the Fe-S cluster, and tyrosine and cysteine residues in the vicinity of the active site are important targets of oxidative and/or nitrative attack, which is selectively controlled by the mitochondrial matrix citrate levels. The mechanisms inherent in aconitase inactivation by ONOO- are discussed in terms of the mitochondrial matrix metabolic and thiol redox state.
EFFECT OF GERMINATION ON NUTRITIVE VALUE AND BAKING PROPERTIES OF DRY PEAS, LENTILS, AND FABA BEANS (1980)

ABSTRACT Dry yellow peas, lentils, and faba beans were germinated under laboratory conditions. Periodic rinsing with water at 2‐hr intervals was effective in controlling microbial growth. Marked increase in ascorbic acid of the legumes was observed during germination. Amino acid contents did not change appreciably after 4day germination. Wheat flour blends containing ungerminated and germinated legume flours at 5, 10, and 15% levels were used in baking studies. Addition of 15% legume flours to bread resulted in only small deleterious effects on loaf volume, crumb grain, and flavor. Germination adversely affected the baking properties of peas and lentils, but not faba beans. Blanching of the germinated peas further impaired its baking properties.
Docosahexaenoic Acid Modulates the Interactions of the Interphotoreceptor Retinoid-binding Protein with 11-cis-Retinal (1996)

Rapid transport of retinoids across the interphotoreceptor matrix is a critical part of the visual cycle, since it serves to replenish bleached rhodopsin with its chromophore 11-cis-retinal. The transport of retinoids in the interphotoreceptor matrix is believed to be mediated by the interphotoreceptor retinoid-binding protein (IRBP), a protein that, in addition to possessing two retinoid-binding sites, associates in vivo with long chain fatty acids. Here, the interrelationships between binding of the two types of ligands to IRBP were studied. The composition of fatty acids associated with IRBP in bovine retina was determined, and it was found that polyunsaturated fatty acids constitute a significant fraction of those. It was further found that docosahexaenoic acid, but not palmitic acid, induced a rapid and specific release of 11-cis-retinal from one of the protein's retinoid-binding sites. Based on these results and on the additional observation that a steep concentration gradient of docosahexaenoic acid exists between photoreceptor and pigment epithelium cells, a model for the mechanism by which IRBP may target 11-cis-retinal to photoreceptor cells is proposed.
Neural and Adaptive Systems: Fundamentals through Simulations with CD-ROM (1999)

From the Publisher:
Neural networks have become one of the most sophisticated applications in use today by engineers and others in a myriad of applications such as cellular networks, financial analysis, stock market analysis, traffic coordination, etc. In this new approach, the authors blend neurocomputing theory with the power of a software simulator to underscore synergisms between the conceptual equations and their behavior in practical neural systems.
Reaction of 1,4-Dibromo-2,3-dihydroxynaphthalene with 2-Naphthoxide Ion. Solvent and Cation Control in the Formation of the Conformationally Locked Stereoisomers of 2,2‘,3‘,2‘‘-Tetrahydroxy-1,1‘:4‘,1‘‘-ternaphthyl and 2,2‘,3‘,2‘‘,3‘‘,2‘‘‘-Hexahydroxy-1,1‘:4‘,1‘‘:4‘‘,1‘‘‘-quaternaphthyl (1996)

The reaction of the dibromide 1 with the 2-naphthoxide ion 2 proceeds under remarkably mild conditions (25−50 °C), yielding all possible stereoisomers of ternaphthol 3 and quaternaphthol 4. An unambiguous structure assignment has been made for the individual stereoisomers and conditions for their thermal interconversion have been established. In contrast to a nonselective distribution of stereoisomers found in the thermodynamic equilibrium mixture, a high stereoselectivity can be induced in the coupling reaction under kinetic control. The coordinating ability of the alkali metal counterion (M+) of the participating 2-naphthoxide ion 2 has been found to play a key role in the stereocontrol, supporting strongly the formation of the cis stereoisomers of 3 and 4. When the coordinating ability of M+ is suppressed by an efficient solvation and/or by complexation with 18-crown-6, formation of the trans stereoisomers prevails in the reaction.
New concepts of the pathogenesis of cystic fibrosis lung disease (2003)

Although there has been impressive progress in the elucidation of the genetic and molecular basis of cystic fibrosis (CF), the pathogenesis of CF lung disease remains obscure. The elucidation of the pathogenesis of CF lung disease requires both a full description of normal innate airway defence and how absent function of the cystic fibrosis transmembrane regulator protein (CFTR) adversely perturbs this activity. Recent data have linked the abnormal ion transport properties of CF airway epithelia to depleted airway surface liquid (ASL) volume, reflecting the combined defects of accelerated Na+ transport and the failure to secrete Cl-. Depletion of a specific compartment of the ASL, i.e. the periciliary liquid (PCL), appears to abrogate both cilia-dependent and cough clearance. Subsequent to PCL depletion, mucus adheres to airway surfaces and persistent mucin secretion generates the formation of "thickened" mucus plaques and plugs, which become the nidus for bacterial infection. The paucity of liquid in these plaques/plugs, and the hypoxia in this environment, appear to promote biofilm bacterial infection. Therapeutic agents that restore airway surface liquid volume, i.e. blockers of Na+ transport, initiators of Cl- transport and osmolytes, are reviewed, as are strategies that may be required to use volume-restoring agents safely in patients with cystic fibrosis.
Epidemiology, Clinical Aspects, and Biology of IDDM Patients Under Age 40 Years: Comparison of data from Antwerp with complete ascertainment with data from Belgium with 40% ascertainment. The Belgian Diabetes Registry (1997)

In Antwerp, the incidence rate of IDDM under age 15 years is intermediately high compared with the rates in other European regions. It is similar in the 15-39 years age-group, but with a marked male predominance. Demographic, clinical, and biological data show the same age-dependent heterogeneity as the data collected nationwide, with 40% ascertainment indicating the representativeness of the latter.
ChemInform Abstract: Synthesis of Benzoquinolinoisoxazoles and Benzoquinolinopyrazoles. (1987)

Abstract The title compounds (VII) are synthesized starting from 2‐naphthylamine (I) as shown in the scheme.
Sterilization of skin allografts by ionizing radiation. (2002)

The skin has a fundamental role in the viability of human body. In the case of extensive wounds, skin allografts provide an alternative to cover temporarily the damaged areas. After donor screening and preservation in glycerol 85%, the skin can be stored in a Skin Bank. Glycerol at this concentration has a bacteriostatic effect after certain time of preservation. On the other hand, skin sterilization by ionizing radiation may reduce the quarentine period for transplantation in patients. The objective of this work was to evaluate allograft sterilization using two sources of ionizing radiation. Through the analysis of stress-strain, it was intended to verify possible effects of the radiation on the structure of preserved grafts. Three groups of skin samples were selected. The first group was maintained in the initial conditions, not irradiated. The second was exposed to cobalt-60, while the third one was irradiated using an Dynamitron Accelerator JOB188 electron beam. The irradiation dose was 25 kGy for both tests. Both irradiation sources, and the Instron Universal Machine used for biomechanical experiments, are installed at the Centro de Tecnologia das Radiações/Instituto de Pesquisas Energéticas e Nucleares (São Paulo, Brazil). According to the preliminary results, biomechanical characteristics of the samples irradiated seem to be maintained with regard to the non irradiated group.
Automated microscopy for high-content RNAi screening (2010)

Fluorescence microscopy is one of the most powerful tools to investigate complex cellular processes such as cell division, cell motility, or intracellular trafficking. The availability of RNA interference (RNAi) technology and automated microscopy has opened the possibility to perform cellular imaging in functional genomics and other large-scale applications. Although imaging often dramatically increases the content of a screening assay, it poses new challenges to achieve accurate quantitative annotation and therefore needs to be carefully adjusted to the specific needs of individual screening applications. In this review, we discuss principles of assay design, large-scale RNAi, microscope automation, and computational data analysis. We highlight strategies for imaging-based RNAi screening adapted to different library and assay designs.
Attenuated Listeria monocytogenes as a live vector for induction of CD8+ T cells in vivo: a study with the nucleoprotein of the lymphocytic choriomeningitis virus (1995)

Listeria monocytogenes spends most of its intracellular life cycle in the cytosol of the infected eucaryotic cells. Within this cellular compartment originates the endogenous pathway of antigen processing and presentation. We thus assumed that recombinant L. monocytogenes expressing an heterologous protein, the nucleoprotein of the lymphocytic choriomeningitis virus (LCMV), should be able to induce antigen-specific CD8+ T cells in vivo. The LCMV nucleoprotein gene was inserted in phase with the sequence coding for the putative signal sequence of the hemolysin of L. monocytogenes in order to target its secretion into the cytosol of the infected cell. The ability of this recombinant bacterium to induce LCMV-reactive CD8+ T cells was then monitored in BALB/c mice. The immune status of the immunized BALB/c mice was studied on the seventh day after a single i.v. injection of a sublethal dose of the recombinant bacteria: (i) cytotoxic CD8+ T cells were detected in liver; (ii) using in vitro re-stimulation with PMA and ionomycin, secondary cytotoxic CD8+ T cells were detected in spleen; (iii) an early inflammatory reaction dependent on the presence of CD8+ T cells occurred in the footpad after intraplantar inoculation of live LCMV; and (iv) mice were protected against an otherwise lethal intracerebral LCMV challenge; the protection was accompanied by elimination of the virus. When the immune status of the immunized hosts was monitored for a longer period post-immunization, the balance between immune protection and immunopathology described for the anti-LCMV immune responses was observed; two phases of protection were detected, flanking a transitory phase of exacerbation of the lymphocytic choriomeningitis disease (weeks 2-5).(ABSTRACT TRUNCATED AT 250 WORDS)