gebhart/patrepeval huggingface dataset:
Forward-bias characteristics of Si bipolar junctions grown by molecular beam epitaxy at low temperatures (1993)

Forward-bias current-voltage characteristics of molecular beam epitaxy grown Si p+-i-n+ junctions have been determined at room temperature. At small widths of the i zone (Li=5 and 10 nm) band-to-band tunneling with a maximum peak-to-valley ratio of two is observed. Up to Li=30 nm (trap assisted) forward-bias tunneling is apparent with saturation tunneling current densities somewhat lower than in p-n junctions at comparable widths of the space-charge region WSCR(0). For Li≳30 nm and Tg=500 °C growth temperature surface recombination dominates the low bias range. At Li=35 nm and Tg=325 °C, both surface and bulk recombination is observed. We found evidence that Si molecular beam epitaxy layers grown at this low temperature get an increasing density of crystalline defects with growing thickness.
Characterization of Mutant Bordetella Pertussis Adenylate Cyclase Toxins with Reduced Affinity for Calmodulin (1997)

Bordetella pertussis secretes a calmodulin-stimulated adenylate cyclase toxin (CyaA) that is one of the major virulence factors of this organism. The toxin is able to enter various types of eukaryotic cells where, upon activation by calmodulin, it catalyzes the production of non-physiological amounts of cyclic AMP. The mechanism of toxin entry into target cells is unknown, although it has been shown that it does not involve receptor-mediated endocytosis. The adenylate cyclase toxin exhibits a very high affinity for calmodulin, and it has been proposed that the energy of calmodulin-binding to CyaA might be required for the entry of the toxin into the target cells [Oldenburg, D.J., Gross, M. K., Wong, C. S. & Storm, D. R. (1992) Biochemistry 31, 8884-8891]. In the present study, we have reexamined this issue by analyzing the cytotoxicity of various modified CyaA toxins that have altered calmodulin affinity. We show that despite their low affinity for calmodulin (at least 1000-times less than that of the wild type CyaA), these toxins were able to efficiently deliver their catalytic domain into the cytoplasm of the target cells, erythrocytes. These results demonstrate that high-affinity calmodulin binding is not required for the entry of B. pertussis adenylate cyclase into eukaryotic cells. However, the high-affinity of CyaA for calmodulin is crucial for an efficient synthesis of cAMP within the target cells.
Enabling XML storage from Java applets in a GUI programming course (2003)

XML, the Extensible Markup Language, is widely used in graphical user interface (GUI) programming today to both specify user interfaces and to hold the data displayed in visual components. It is relatively straightforward for Java applets to read and process XML documents over the Web, but security restrictions make it complex to store those documents back on the server after they have been modified. This paper describes a set of cooperating programs and their underlying algorithms that allow Java applets to read XML documents from - and, more importantly, to store those documents back to - a Java-enabled Web server. The author uses this approach in a GUI programming course to provide students who implement their projects as Java applets with the ability to use the full power of XML and its related technologies.
Differential Maintenance of Primitive Human SCID-Repopulating Cells, Clonogenic Progenitors, and Long-Term Culture-Initiating Cells After Incubation on Human Bone Marrow Stromal Cells (1997)

Many experimental and clinical protocols are being developed that involve ex vivo culture of human hematopoietic cells on stroma or in the presence of cytokines. However, the effect of these manipulations on primitive hematopoietic cells is not known. Our severe combined immune-deficient mouse (SCID)-repopulating cell (SRC) assay detects primitive human hematopoietic cells based on their ability to repopulate the bone marrow (BM) of immune-deficient non-obese diabetic/SCID (NOD/SCID) mice. We have examined here the maintenance of SRC, colony-forming cells (CFC), and long-term culture-initiating cells (LTC-IC) during coculture of adult human BM or umbilical cord blood (CB) cells with allogeneic human stroma. Transplantation of cultured cells in equivalent doses as fresh cells resulted in lower levels of human cell engraftment after 1 and 2 weeks of culture for BM and CB, respectively. Similar results were obtained using CD34+-enriched CB cells. By limiting dilution analysis, the frequency of SRC in BM declined sixfold after 1 week of culture. In contrast to the loss of SRC as measured by reduced repopulating capacity, the transplanted inocula of cultured cells frequently contained equal or higher numbers of CFC and LTC-IC compared with the inocula of fresh cells. The differential maintenance of CFC/LTC-IC and SRC suggests that SRC are biologically distinct from the majority of these in vitro progenitors. This report demonstrates the importance of the SRC assay in the development of ex vivo conditions that will allow maintenance of primitive human hematopoietic cells with repopulating capacity.
Characterization of β- d - N 4 -Hydroxycytidine as a Novel Inhibitor of Chikungunya Virus (2017)

Chikungunya virus (CHIKV) represents a reemerging global threat to human health. Recent outbreaks across Asia, Europe, Africa, and the Caribbean have prompted renewed scientific interest in this mosquito-borne alphavirus. There are currently no vaccines against CHIKV, and treatment has been limited to nonspecific antiviral agents, with suboptimal outcomes. Herein, we have identified β-d-<i>N</i><sup>4</sup>-hydroxycytidine (NHC) as a novel inhibitor of CHIKV. NHC behaves as a pyrimidine ribonucleoside and selectively inhibits CHIKV replication in cell culture.
Toxic effects of human and rodent variants of alpha‐synuclein in vivo (2016)

In Parkinson's disease, abnormal alpha-synuclein (asyn) accumulation leads to the formation of soluble oligomeric species thought to be toxic to cells as well as intraneuronal inclusions. To date, the precise mechanisms leading to aggregation of asyn in the brain is not well-understood. Previous studies in yeast, drosophila, and transgenic mice suggested that a non-A beta component depleted version of human asyn [h-asyn(D70-83)] or human beta-synuclein (h-bsyn), naturally lacking this centrally located hydrophobic region, are less prone to form aggregates in vitro and are expected to be less toxic compared to h-asyn in vivo, although not all experimental studies unequivocally support the latter view. To address this outstanding issue, we directly compared the neurotoxicity of human asyn against that of h-asyn(D70-83), h-bsyn as well as rat asyn using an adeno-associated viral vector to express these proteins in a dose-response study where the vector load was varied over two orders of magnitude. By quantifying the neurodegeneration of rat substantia nigra dopamine neurons here we show that h-asyn, h-bsyn, and h-asyn(D70-83) display comparable neurotoxicity across the vector doses tested. On the other hand, rat asyn and GFP control vectors displayed a different profile, where no detectable neurodegeneration was seen except at the highest vector titer. Thus, the two main conclusions of our study are that (i) deletion of the central hydrophobic region in h-asyn is not sufficient to alter its neurotoxic properties and (ii) expression of the widely used GFP control protein can cause measurable neurodegeneration at high titers.
Paneth cells directly sense gut commensals and maintain homeostasis at the intestinal host-microbial interface (2008)

The intestinal epithelium is in direct contact with a vast microbiota, yet little is known about how epithelial cells defend the host against the heavy bacterial load. To address this question we studied Paneth cells, a key small intestinal epithelial lineage. We found that Paneth cells directly sense enteric bacteria through cell-autonomous MyD88-dependent toll-like receptor (TLR) activation, triggering expression of multiple antimicrobial factors. Paneth cells were essential for controlling intestinal barrier penetration by commensal and pathogenic bacteria. Furthermore, Paneth cell-intrinsic MyD88 signaling limited bacterial penetration of host tissues, revealing a role for epithelial MyD88 in maintaining intestinal homeostasis. Our findings establish that gut epithelia actively sense enteric bacteria and play an essential role in maintaining host-microbial homeostasis at the mucosal interface.
Specificity of Bacillus thuringiensis var. colmeri insecticidal delta-endotoxin is determined by differential proteolytic processing of the protoxin by larval gut proteases (1986)

The native crystal delta-endotoxin produced by Bacillus thuringiensis var. colmeri, serotype 21, is toxic to both lepidopteran (Pieris brassicae) and dipteran (Aedes aegypti) larvae. Solubilization of the crystal delta-endotoxin in alkaline reducing conditions and activation with trypsin and gut extracts from susceptible insects yielded a preparation whose toxicity could be assayed in vitro against a range of insect cell lines. After activation with Aedes aegypti gut extract the preparation was toxic to all of the mosquito cell lines but only one lepidopteran line (Spodoptera frugiperda), whereas an activated preparation produced by treatment with P. brassicae gut enzymes or trypsin was toxic only to lepidopteran cell lines. These in vitro results were paralleled by the results of in vivo bioassays. Gel electrophoretic analysis of the products of these different activation regimes suggested that a 130-kDa protoxin in the native crystal is converted to a 55-kDa lepidopteran-specific toxin by trypsin or P. brassicae enzymes and to a 52-kDa dipteran toxin by A. aegypti enzymes. Two-step activation of the 130-kDa protoxin by successive treatment with trypsin and A. aegypti enzymes further suggested that the 52-kDa dipteran toxin is derived from the 55-kDa lepidopteran toxin by enzymes specific to the mosquito gut. Confirmation of this suggestion was obtained by peptide mapping of these two polypeptides. The native crystal 130 kDa delta-endotoxin and the two insect-specific toxins all cross-reacted with antiserum to B. thuringiensis var. kurstaki P1 lepidopteran toxin. Preincubation of the two activated colmeri toxins with P1 antiserum neutralized their cytotoxicity to both lepidopteran and dipteran cell lines.
Raman scattering of ytterbium intercalated C60 compounds (2000)

Experiment results on Raman spectra of YbxC60 (x = 1–6) taken at room temperature are presented and discussed. In the nominal composition Yb3C60 superconducting phase, the broadening of Raman lines was observed due to electron–phonon interaction. In high Yb concentration, YbxC60 (x ≥ 4) Raman lines are broadened severely, this behaviour indicates that the C60 molecules are distorted strongly. However, when YbxC60 samples are exposed to air, this distortion decreases considerably, although the fulleride solids have transformed into an amorphous phase. Copyright © 2000 John Wiley & Sons, Ltd.
Dicarboxy‐Starch by Sodium Hypochlorite/Bromide Oxidation and Its Calcium Binding Properties (1994)

Abstract Various aspects of the glycolic oxidation of the glucose units of starch with stoichiometric amounts of sodium hypochlorite applying sodium bromide as the catalyst have been investigated. The main objective of the study was to optimize the reaction conditions for the preparation of dicarboxy‐starch and to establish the calcium sequestering capacity of the material. The products, polycarboxylates, are obtained in high yields (90‐95%) and they have a sequestering capacity up to 1.4 mmole Ca/g, which is somewhat higher than that of the materials obtained in a non‐catalyzed oxidation. This result is attributed to the facts that the reaction with sodium bromide may be carried out at higher pH (&gt;9) than the non‐catalyzed reaction and that a relatively low concentration of hypochlorite throughout the process could be maintained. In this way the decomposition of hypochlorous acid/hypochlorite, especially occurring at high concentration of hypochlorous acid at lower pH (6‐8) is prevented. Other advantages of this procedure are the colourless appearance of the materials and the higher reaction rate. The feasibility for largescale preparation follows from the results of a few exploratory experiments, including an electrochemical preparation.
Effects of Caspase Inhibitors on Hematopoietic Engraftment after Short-Term Culture (2002)

The induction of apoptosis during cytokine-induced proliferation of hematopoietic stem and progenitor cells (HSPC) may result in the loss of hematopoietic function. We tested the ability of several caspase inhibitors to maintain transplantation potential of mouse HSPC during in vitro culture. HSPC were isolated from mouse bone marrow by cell sorting and cultured in the presence of steel factor (STL) with or without various caspase inhibitors. After incubation, cells were harvested and tested for in vitro colony-forming cell (CFC) potential and transplantation activity in both short- and long-term in vivo assays. HSPC required STL to retain CFC activity during a 24-h culture at 37 degrees C, and none of three caspase inhibitors could substitute for STL in this respect. In transplant assays, a twofold higher frequency of animals showed donor-derived blood cells 12 weeks after competitive transplantation of 50 HSPC cultured for 4 h in the presence of STL plus n-acetyl-Tyr-Val-Ala-Asp-chloromethyl ketone (ac-YVAD) compared with 50 cells cultured in STL alone. To evaluate the effect of ac-YVAD on short-term engraftment, 500 cultured HSPC were transplanted into lethally irradiated mice. Animals transplanted with cells cultured in the presence of ac-YVAD showed a higher survival rate and a faster recovery of platelets and hematocrit compared with animals transplanted with cells cultured in STL alone. We conclude that both the short-term and the long-term engraftment potentials of HSPC cultured in the presence of STL + ac-YVAD were superior to that obtained from cells cultured in STL alone.
A Test of the Stability of the Cetscale, A Measure of Consumers’ Ethnocentric Tendencies (1997)

The consumers’ ethnocentric tendencies scale (CETSCALE) is a multi-item measure that reflects a proclivity to prefer products made domestically over those of foreign origin. For such a scale to be used properly the stability of the measure over time must be understood. This study investigates the stability of the CETSCALE over an eight week period during the summer of 1992, a period that included two patriotic events which were expected to affect mean scores. A random sample of 426 adults in South Carolina were surveyed by phone. Findings indicate that when the population is viewed as a whole, mean scores appear stable over time; however, they are not when viewed by specific sub-groups. For those who have not served in the military, CETSCALE scores increase during patriotic events; the reverse is true for military personnel. In light of the tendency for those with high CETSCALE scores to purchase domestic products, e.g., American automobiles, gaining insight into factors that cause systematic differences in scores both within and between groups offers clear practical import.
Purification and mapping of specific mRNAs by hybridization-selection and cell-free translation. (1979)

We describe a simple procedure for isolating specific mRNAs and for mapping them to the regions of the DNA from which they originate. The method involves hybridization of total cytoplasmic RNA to restriction fragments of DNA that have been fractionated in agarose gels and immobilized on nitrocellulose filters. The hybridization-selected RNAs are eluted and translated in a cell-free system in order to identify their encoded polypeptides. Optimal hybridization and filter washing conditions are given for selection of mRNAs from adenovirus 2-infected cells and transformed cells.
Postulated Physiological Roles of the Seven-carbon Sugars, Mannoheptulose, and Perseitol in Avocado (2002)

Avocado ( Persea americana Mill.) tissues contain high levels of the seven-carbon (C7) ketosugar mannoheptulose and its polyol form, perseitol. Radiolabeling of intact leaves of `Hass' avocado on `Duke 7' rootstock indicated that both perseitol and mannoheptulose are not only primary products of photosynthetic CO 2 fixation but are also exported in the phloem. In cell-free extracts from mature source leaves, formation of the C7 backbone occurred by condensation of a three-carbon metabolite (dihydroxyacetone-P) with a four-carbon metabolite (erythrose-4-P) to form sedoheptulose-1,7-bis-P, followed by isomerization to a phosphorylated d -mannoheptulose derivative. A transketolase reaction was also observed which converted five-carbon metabolites (ribose-5-P and xylulose-5-P) to form the C7 metabolite, sedoheptulose-7-P, but this compound was not metabolized further to mannoheptulose. This suggests that C7 sugars are formed from the Calvin Cycle, not oxidative pentose phosphate pathway, reactions in avocado leaves. In avocado fruit, C7 sugars were present in substantial quantities and the normal ripening processes (fruit softening, ethylene production, and climacteric respiration rise), which occurs several days after the fruit is picked, did not occur until levels of C7 sugars dropped below an apparent threshold concentration of ≈20 mg·g -1 fresh weight. The effect of picking could be mimicked by girdling the fruit stalks, which resulted in ripening on the tree. Again, ripening followed a decline in C7 sugars to below an apparent threshold level. Taken together, these data indicate that the C7 sugars play important roles in carbon allocation processes in the avocado tree, including a possible novel role as phloem-mobile ripening inhibitors.
Collateral sensitivity to azidothymidine in methotrexate resistant human leukemia cells. (1992)

Resistance to methotrexate (MTX) is a well established clinical problem and strategies to circumvent this would obviously be beneficial. The human leukemia cell line, CCRF-CEM, was grown in folinic acid to study MTX resistance-reflecting more in vivo conditions. A 15.8-fold resistant subline, CEM/MTX, was evolved by stepwise increases in MTX exposure. The MTX resistant cell line exhibited both increased dihydrofolate reductase (DHFR) activity due to gene amplification as well as impaired MTX uptake. An additional mechanism of resistance to MTX was a 2-fold increase in thymidine kinase (TK). As a result of this increased TK activity, the CEM/MTX cells were collaterally sensitive to the nucleoside analogue, azidothymidine (AZT). CEM cells resistant to MTX possess properties that can be exploited by AZT and these studies may have clinical implications.
Ecto-5’-nucleotidase: Structure function relationships (2006)

Ecto-5'-nucleotidase (ecto-5'-NT) is attached via a GPI anchor to the extracellular membrane, where it hydrolyses AMP to adenosine and phosphate. Related 5'-nucleotidases exist in bacteria, where they are exported into the periplasmic space. X-ray structures of the 5'-nucleotidase from E. coli showed that the enzyme consists of two domains. The N-terminal domain coordinates two catalytic divalent metal ions, whereas the C-terminal domain provides the substrate specificity pocket for the nucleotides. Thus, the substrate binds at the interface of the two domains. Here, the currently available structural information on ecto-5'-NT is reviewed in relation to the catalytic properties and enzyme function.
Conjunctival inflammation in the chronic phase of Stevens-Johnson syndrome (2000)

The infiltrating cell population in the Stevens-Johnson syndrome samples includes macrophages, CD4 positive T cells, and CD8 positive T cells. The cytokine expression pattern suggests CD4 positive T cells are Th1 cells. The infiltrating cell population is similar in Stevens-Johnson syndrome and chemical injury conjunctivalised corneas.
Ubiquitin-conjugating enzyme Ubc13 controls breast cancer metastasis through a TAK1-p38 MAP kinase cascade (2014)

Metastatic spread is the leading cause of cancer mortality. Breast cancer (BCa) metastatic recurrence can happen years after removal of the primary tumor. Here we show that Ubc13, an E2 enzyme that catalyzes K63-linked protein polyubiquitination, is largely dispensable for primary mammary tumor growth but is required for metastatic spread and lung colonization by BCa cells. Loss of Ubc13 inhibited BCa growth and survival only at metastatic sites. Ubc13 was dispensable for transforming growth factor β (TGFβ)-induced SMAD activation but was required for activation of non-SMAD signaling via TGFβ-activating kinase 1 (TAK1) and p38, whose activity controls expression of numerous metastasis promoting genes. p38 activation restored metastatic activity to Ubc13-deficient cells, and its pharmacological inhibition attenuated BCa metastasis in mice, suggesting it is a therapeutic option for metastatic BCa.
Prophylaxis for Tuberculosis in Europe—Ongoing Research (1996)

The incidence of tuberculosis (TB) in patients with human immunodeficiency virus (HIV) infection has increased in recent years, raising issues regarding preventive therapy for TB in this high-risk patient population. To determine if an HIV-positive individual is at risk for reactivation of latent infection, testing with purified protein derivative (PPD) is recommended; however, many people with impaired cell-mediated immunity due to HIV are anergic. Strategies regarding PPD testing and criteria for HIV-positive patients are presented. Isoniazid has been the accepted drug for use as prophylaxis for TB in immunocompetent patients, and there is evidence that isoniazid is also effective in HIV-positive, PPD-positive patients. Data from efficacy and feasibility trials and the risks and benefits of preventive therapy with isoniazid are discussed. Because of toxicity and compliance problems with isoniazid, there is a continuing need for development of alternative therapies. The results of some preliminary studies of newer therapies are presented here.
beta-Adrenergic receptors, transgenic mice, and pharmacological model systems. (2001)

Several important issues are raised in the current article by [Engelhardt et al. (2001)][1] (see pp. 712–717). These include: the utility of transgenic mouse models to investigate β-adrenergic receptor (β-AR) signaling and pharmacology; the relative sensitivity of biological preparations to