gebhart/patrepeval huggingface dataset:
Fuel Pelletization with a Binder: Part I — Identification of a Suitable Binder for Spent Mushroom Compost−Coal Tailing Pellets (2009)

Spent mushroom compost and coal tailings are wastes that could be used as energy sources, through combustion in a fluidized-bed. Our previous pelletization studies produced a denser, yet friable fuel, which produced dust on transport, handling, and feeding. Thus, a suitable binder for these materials was required to enhance pellet properties. Inorganic (caustic soda) and organic (starch) binders were selected for a range of tests. Pelletization at elevated temperatures was also assessed to evaluate the softening of any lignin present in the straw component of the mushroom compost. Small amounts (up to 1 wt %) of both binders increased pellet tensile strength, where starch had more pronounced impacts, doubling the tensile strength to 411 kPa. Pelletization at elevated temperatures (45−75 °C), however, improved overall pellet quality more significantly, increasing the tensile strength to over 600 kPa, although additional temperature increases (up to 125 °C) did not result in further improvements. Whether a binder or elevated temperature is used at the pelletization stage is strongly dependent on the comparative costs of these options, relative to improvements in product quality. The effect of these binders on combustion will also be a crucial factor to consider, which is assessed in the second part of this paper.
Formation of mixed disulfide adducts at cysteine-281 of the lactose repressor protein affects operator and inducer binding parameters (1986)

The lactose repressor protein has been modified with three sulfhydryl-specific reagents which form mixed disulfide adducts. Methyl methanethiosulfonate (MMTS) and 5,5'-dithiobis(2-nitrobenzoic acid) (DTNB) completely reacted with all three cysteine residues, whereas only partial reaction was observed with didansylcystine. Cysteines-107 and -140 reacted stoichiometrically with MMTS and DTNB, while Cys-281 was modified only at higher molar ratios. Didansylcystine reacted primarily with cysteines-107 and -140. Affinity of MMTS-modified repressor for 40 base pair operator DNA was decreased 30-fold compared to unmodified repressor, and this decrease correlated with modification of cysteine-281. DTNB-modified repressor bound operator DNA with a 50-fold weaker affinity than unmodified repressor. Modification of the lac repressor with didanylcystine decreased operator binding only 4-fold, and nonspecific DNA binding increased 3-fold compared to unmodified repressor. No change in the inducer equilibrium binding constant was observed following modification with any of these reagents. In contrast, inducer association and dissociation rate constants were decreased approximately 50-fold for repressor completely modified with MMTS or DTNB, while didansylcystine had minimal effect on inducer binding kinetics. Correlation between modification of Cys-281 and the observed decrease in rate constants indicates that this region of the protein regulates the accessibility of the sugar binding site. The parallel between the increase in the Kd for repressor binding to operator, the altered rate constant for inducer binding, and modification of cysteine-281 suggests that this region of the protein is crucially involved in the function of the repressor protein.
Evaluation of 2‘-modified oligonucleotides containing 2‘-deoxy gaps as antisense inhibitors of gene expression (1993)

We have used a previously described 17-mer phosphorothioate (Monia, B.P., Johnston, J.F., Ecker, D. J., Zounes, M.A., Lima, W.F., and Freier, S.M. (1992) J. Biol. Chem. 267, 19954-19962) for structure-function analysis of 2'-sugar modifications including 2'-O-methyl, 2'-O-propyl, 2'-O-pentyl, and 2'-fluoro. These modifications were analyzed for hybridization affinity to complementary RNA and for antisense activity against the Ha-ras oncogene in cells using a highly sensitive transactivation reporter gene system. Hybridization analysis demonstrated that all of the 2'-modified oligonucleotides hybridized with greater affinity to RNA than an unmodified 2'-deoxy oligonucleotide with the rank order of affinity being 2'-fluoro > 2'-O-methyl > 2'-O-propyl > 2'-O-pentyl > 2'-deoxy. Evaluation of antisense activities of uniformly 2'-modified oligonucleotides revealed that these compounds were completely ineffective in inhibiting Ha-ras gene expression. Activity was restored if the compound contained a stretch of at least five 2'-deoxy residues. This minimum deoxy length correlated perfectly with the minimum length required for efficient RNase H activation in vitro using partially purified mammalian RNase H enzyme. These chimeric 2'-modified/deoxy phosphorothioates displayed greater antisense potencies in inhibiting Ha-ras gene expression, compared with the unmodified uniform deoxy phosphorothioate. Furthermore, antisense potency correlated directly with affinity of a given 2' modification for it's complementary RNA. These results demonstrate the importance of target affinity in the action of antisense oligonucleotides and of RNase H as a mechanism by which these compounds exert their effects.
Thermodynamic performance analysis of a R245fa organic Rankine cycle (ORC) with different kinds of heat sources at evaporator (2018)

The first and the second law analyses of a 20 kWeR245fa organic Rankine cycle (ORC) with low grade temperature heat sources were numerically studied. There were three different heat sources such as hot water, saturated steam, and combined hot water/saturated steam used to supply heat at the ORC evaporator. The heat source temperature was varied in a range of 80–110 °C and the pinch temperature difference between the heat source temperature and the evaporating temperature was in a range of 1–10 °C. The ORC condensing temperature was kept constant at 40 °C. The results revealed that the combined hot water/saturated steam heat source provided a highest second law or exergy efficiency due to less irreversibility generated at the evaporator followed by the saturated steam and the hot water heat sources, respectively. The increase of heat source temperature at a specific pinch could increase the second law efficiency of the cycle. However, the increase of pinch value resulted in lower second law efficiency. In addition, for the below pinch zone, with the hot water/saturated steam heat source, the reduction of the hot water flow rate slightly enhanced the ORC second law efficiency as the exergy destruction below pinch was reduced. However, there was a limit that the flow rate should not be reduced below a specific value otherwise a very high heat exchanger area was needed. Keywords: Organic Rankine cycle, Thermodynamic analyses, Thermal performance, Hot water/saturated steam heat source
A protocol for supporting the ABT/DT capability (2002)

With the ATM block transfer with a delayed transmission (ABT/DT) capability, the amount of bandwidth allocated to the different cell flows of a connection (namely the CLP=0+1 and possibly the OAM cell flows) is constant over an ATM block and is referred to as the block cell rate (BCR). Successive BCR values are dynamically negotiated between the user and the network via the exchange of resource management cells. The BCR negotiation for a given ATM block may be initiated either by the source or the destination. As a basic principle, before transmitting an ATM block the source should receive an explicit authorization from the network. This paper gives the existence proof of a protocol for supporting the ABT/DT capability as specified in the May 1996 version of lTU-T Recommendation I.371.
Chemical Compounds Effective Against the Citrus Huanglongbing Bacterium ‘Candidatus Liberibacter asiaticus’ In Planta (2011)

Citrus Huanglongbing (HLB) is one of the most destructive diseases of citrus worldwide and is threatening the survival of the Floridian citrus industry. Currently, there is no established cure for this century-old and emerging disease. As a possible control strategy for citrus HLB, therapeutic compounds were screened using a propagation test system with 'Candidatus Liberibacter asiaticus'-infected periwinkle and citrus plants. The results demonstrated that the combination of penicillin and streptomycin (PS) was effective in eliminating or suppressing the 'Ca. L. asiaticus' bacterium and provided a therapeutically effective level of control for a much longer period of time than when administering either antibiotic separately. When treated with the PS, 'Ca. L. asiaticus'-infected periwinkle cuttings achieved 70% of regeneration rates versus <50% by other treatments. The 'Ca. L. asiaticus' bacterial titers in the infected periwinkle plants, as measured by quantitative real-time polymerase chain reaction, decreased significantly following root soaking or foliar spraying with PS. Application of the PS via trunk injection or root soaking also eliminated or suppressed the 'Ca. L. asiaticus' bacterium in the HLB-affected citrus plants. This may provide a useful tool for the management of citrus HLB and other Liberibacter-associated diseases.
Yersiniabactin Production Requires the Thioesterase Domain of HMWP2 and YbtD, a Putative Phosphopantetheinylate Transferase (2002)

One requirement for the pathogenesis of Yersinia pestis, the causative agent of bubonic plague, is the yersiniabactin (Ybt) siderophore-dependent iron transport system that is encoded within a high-pathogenicity island (HPI) within the pgm locus of the Y. pestis chromosome. Nine gene products within the HPI have demonstrated functions in the nonribosomal peptide synthesis (NRPS)/polyketide (PK) synthesis or transport of Ybt. NRPS/PK synthetase or synthase enzymes are generally activated by phosphopantetheinylation. However, no products with similarities to known phosphopantetheinyl (P-pant) transferases were found within the pgm locus. We have identified a gene, ybtD, encoded outside the HPI and pgm locus, that is necessary for function of the Ybt system and has similarities to other P-pant transferases such as EntD of Escherichia coli. A deletion within ybtD yielded a strain (KIM6-2085+) defective in siderophore production. This strain was unable to grow on iron-deficient media at 37 degrees C but could be cross-fed by culture supernatants from Ybt-producing strains of Y. pestis. The promoter region of ybtD was fused to lacZ; beta-galactosidase expression from this reporter was not regulated by the iron status of the bacterial cells or by YbtA, a positive regulator of other genes of the ybt system. The ybtD mutant failed to express indicator Ybt proteins (high-molecular-weight protein 1 [HMWP1], HMWP2, and Psn), a pattern similar to those seen with several other ybt biosynthetic mutants. In contrast, cells containing a single amino acid substitution (S2908A) in the terminal thioesterase domain of HMWP2 failed to exhibit any ybt regulatory defects but did not elaborate extracellular Ybt under iron-deficient conditions.
Vaginal colonization of pig-tailed macaques by Gardnerella vaginalis. (1984)

Ten pig-tailed macaques inoculated intravaginally with Gardnerella vaginalis organisms were colonized for 11-39 days. In contrast, 4 tamarins and 3 chimpanzees inoculated similarly failed to become colonized. Examination of Gram-stained vaginal smears obtained from infected pig-tailed macaques failed to demonstrate clue cells, a feature which is pathognomonic of non-specific vaginitis in humans. Additionally, the pH value, the levels of non-volatile fatty acids and the anaerobic flora of the macaque vagina differed from these aspects of the human vagina. While these differences indicate that gardnerella-infected macaques are unsuitable as a model of gardnerella-associated vaginitis in humans, such animals may prove useful for studying selected aspects of the biology of G. vaginalis such as the adhesion and interaction of the bacteria with the vaginal mucosa.
Molecular Cloning and Expression of Human and Rat Tumor Necrosis Factor Receptor Chain (p60) and Its Soluble Derivative, Tumor Necrosis Factor-Binding Protein (1990)

Tumor necrosis factor-alpha (TNF-alpha), a protein released by activated macrophages, is involved in a wide variety of human diseases including septic shock, cachexia, and chronic inflammation. TNF binding protein (TNF-BP), a glycoprotein with high affinity to TNF-alpha isolated from urine, acts as an inhibitor of TNF-alpha by competing with the cell-surface TNF receptor. We report here the partial amino acid sequencing of human TNF-BP as well as the isolation, sequence, and expression of cDNA clones encoding a human and rat TNF receptor. The calculated Mr of the mature human and rat TNF receptor chains is 47,526 and 48,072, respectively. The extracellular ligand binding domain represents the soluble TNF-BP which is released by proteolytic cleavage. TNF-BP contains 24 cysteine residues and three potential N-glycosylation sites and shows sequence homology to the extracellular portions of TNF-R p80 chain and nerve growth factor receptor. Transfection of the human TNF receptor cDNA into mammalian cells resulted in increased binding capacity for TNF-alpha and increased reactivity with a monoclonal antibody directed against the human TNF receptor chain p60. When a stop codon was introduced into the cDNA at the site corresponding to the carboxyl terminus of TNF-BP, transfected cells secreted a protein that reacted with antibodies raised against natural TNF-BP.
On the Consistency of Feature Selection using Greedy Least Squares Regression (2009)

This paper studies the feature selection problem using a greedy least squares regression algorithm. We show that under a certain irrepresentable condition on the design matrix (but independent of the sparse target), the greedy algorithm can select features consistently when the sample size approaches infinity. The condition is identical to a corresponding condition for Lasso. Moreover, under a sparse eigenvalue condition, the greedy algorithm can reliably identify features as long as each nonzero coefficient is larger than a constant times the noise level. In comparison, Lasso may require the coefficients to be larger than 0(√s) times the noise level in the worst case, where s is the number of nonzero coefficients.
Simultaneous flow cytometric analysis of two cell surface markers, telomere length, and DNA content (2002)

The multiparameter Flow-FISH protocol permitted rapid determination of differences in telomere length in subpopulations characterized by two surface markers without prior cell separation.
Construction and Isolation of Recombinant MVA (2004)

Modified vaccinia virus Ankara (MVA) is a valuable tool for the expression of recombinant genes used for such purposes as the study of protein functions or characterization of cellular and humoral immune responses. A major advantage of MVA is its clear safety record, and it can be handled under biosafety level 1 conditions. Despite its replication deficiency in human and most mammalian cells, MVA provides high-level gene expression and has proven to be immunogenic when delivering heterologous antigens in animals and humans. This chapter provides state-of-the-art protocols for generation, plaque isolation, molecular characterization, as well as amplification and purification of MVA vector viruses to obtain recombinant viruses for further evaluation.
Pharmacologic Inhibition of the TGF-β Type I Receptor Kinase Has Anabolic and Anti-Catabolic Effects on Bone (2009)

During development, growth factors and hormones cooperate to establish the unique sizes, shapes and material properties of individual bones. Among these, TGF-beta has been shown to developmentally regulate bone mass and bone matrix properties. However, the mechanisms that control postnatal skeletal integrity in a dynamic biological and mechanical environment are distinct from those that regulate bone development. In addition, despite advances in understanding the roles of TGF-beta signaling in osteoblasts and osteoclasts, the net effects of altered postnatal TGF-beta signaling on bone remain unclear. To examine the role of TGF-beta in the maintenance of the postnatal skeleton, we evaluated the effects of pharmacological inhibition of the TGF-beta type I receptor (TbetaRI) kinase on bone mass, architecture and material properties. Inhibition of TbetaRI function increased bone mass and multiple aspects of bone quality, including trabecular bone architecture and macro-mechanical behavior of vertebral bone. TbetaRI inhibitors achieved these effects by increasing osteoblast differentiation and bone formation, while reducing osteoclast differentiation and bone resorption. Furthermore, they induced the expression of Runx2 and EphB4, which promote osteoblast differentiation, and ephrinB2, which antagonizes osteoclast differentiation. Through these anabolic and anti-catabolic effects, TbetaRI inhibitors coordinate changes in multiple bone parameters, including bone mass, architecture, matrix mineral concentration and material properties, that collectively increase bone fracture resistance. Therefore, TbetaRI inhibitors may be effective in treating conditions of skeletal fragility.
Understanding the Warburg Effect: The Metabolic Requirements of Cell Proliferation (2009)

In contrast to normal differentiated cells, which rely primarily on mitochondrial oxidative phosphorylation to generate the energy needed for cellular processes, most cancer cells instead rely on aerobic glycolysis, a phenomenon termed "the Warburg effect." Aerobic glycolysis is an inefficient way to generate adenosine 5'-triphosphate (ATP), however, and the advantage it confers to cancer cells has been unclear. Here we propose that the metabolism of cancer cells, and indeed all proliferating cells, is adapted to facilitate the uptake and incorporation of nutrients into the biomass (e.g., nucleotides, amino acids, and lipids) needed to produce a new cell. Supporting this idea are recent studies showing that (i) several signaling pathways implicated in cell proliferation also regulate metabolic pathways that incorporate nutrients into biomass; and that (ii) certain cancer-associated mutations enable cancer cells to acquire and metabolize nutrients in a manner conducive to proliferation rather than efficient ATP production. A better understanding of the mechanistic links between cellular metabolism and growth control may ultimately lead to better treatments for human cancer.
The Macrophage Origin of the HIV-Expressing Multinucleated Giant Cells in Hyperplastic Tonsils and Adenoids (1999)

Replication and storage of virus are characteristic features of hyperplastic lymphoid tissues in HIV infection. In opportunistic infections, HIV is synthesized by phagocytic mononuclear and Langhans'-type multinucleated macrophages that coexpress the dendritic cell-associated S-100 and p55 antigens. However, similar cells in hyperplastic tonsils and adenoids from HIV+ individuals were alternatively identified as macrophages or, on the basis of the same S-100 and p55 staining, as dendritic cells. To consider establishing the role of these HIV-rich cells in HIV disease, it is important to reconcile this apparent discrepancy in identity. Hyperplastic tonsils and adenoid specimens were analyzed by HIV RNA in situ hybridization (ISH), light and transmission electron microscopy (TEM), and immunohistochemistry (IHC) (HIV Gag p24 protein, S-100, p55, CD68, HAM56, lysozyme, alpha-1-anti-trypsin, and alpha-1-anti-chymotrypsin). In HIV+ pediatric and adult surgical specimens (n = 11), the giant cells and their mononuclear counterpart were positive for both macrophage and p55 and S-100 IHC markers. In addition, TEM, p24 IHC, and ISH showed HIV expression by cells with typical features of macrophages. Furthermore, these cells were not unique to HIV+ specimens, being seen in 20% of hyperplastic T&A surgical specimens (n = 57) lacking HIV as well as in several types of granulomatous processes, such as sarcoidosis. These cells appear to represent an activated phenotype that can develop independent of HIV, but that may represent a viral host in HIV-infected individuals. Thus, the giant and mononuclear cells that produce striking amounts of HIV in tonsils and adenoids are of macrophage origin, yet, as in opportunistic infections, share dendritic cell-associated antigens, reflecting a common CD34+ bone marrow progenitor.
The orphan nuclear receptor DAX1 is up-regulated by the EWS/FLI1 oncoprotein and is highly expressed in Ewing tumors (2005)

The Ewing family of tumors harbors chromosomal translocations that join the N-terminal region of the EWS gene with the C-terminal region of several transcription factors of the ETS family, mainly FLI1, resulting in chimeric transcription factors that play a pivotal role in the pathogenesis of Ewing tumors. To identify downstream targets of the EWS/FLI1 fusion protein, we established 293 cells expressing constitutively either the chimeric EWS/FLI1 or wild type FLI1 proteins and used cDNA arrays to identify genes differentially regulated by EWS/FLI1. DAX1 (NR0B1), an unusual orphan nuclear receptor involved in gonadal development, sex determination and steroidogenesis, showed a consistent up-regulation by EWS/FLI1 oncoprotein, but not by wild type FLI1. Specific induction of DAX1 by EWS/FLI1 was confirmed in two independent cell systems with inducible expression of EWS/FLI1. We also analyzed the expression of DAX1 in Ewing tumors and derived cell lines, as well as in other nonrelated small round cell tumors. DAX1 was expressed in all Ewing tumor specimens analyzed, and in seven out of eight Ewing tumor cell lines, but not in any neuroblastoma or embryonal rhabdomyosarcoma. Furthermore, silencing of EWS/FLI1 by RNA interference in a Ewing tumor cell line markedly reduced the levels of DAX1 mRNA and protein, confirming that DAX1 up-regulation is dependent upon EWS/FLI1 expression. The high levels of DAX1 found in Ewing tumors and its potent transcriptional repressor activity suggest that the oncogenic effect of EWS/FLI1 may be mediated, at least in part, by the up-regulation of DAX1 expression.
Correlation of PD-L1 Surface Expression on Leukemia Cells with the Ratio of PD-L1 mRNA Variants and with Electrophoretic Mobility (2016)

The expression on the surface of tumor cells of ligands for the PD-1 inhibitory receptor prevents the antitumor immune response and is considered to be a negative prognostic factor in a variety of solid tumors as well as in hematologic malignancies. To determine if it were possible to analyze PD-L1 with PCR-based methods, we assessed the expression of PD-L1 in primary samples from patients with acute myeloid leukemia, in healthy donors, and in a panel of cell lines, by means of flow cytometry, RT-PCR, and Western blotting. Although the surface density of the protein was not correlated with the amount of expressed full-length mRNA, we found a statistically significant positive correlation between PD-L1 surface density and the ratio of two transcript variants (variant 1/variant 2). Our PCR-based method allows for retrospective examination of PD-L1 surface expression from frozen cDNA samples, without the need for a reference gene. Our results also suggest that variant 2, which is produced by alternative splicing, negatively regulates PD-L1 protein expression on the cell surface. In addition, PD-L1 exposition on the cell surface is clearly associated with a shift of electrophoretic mobility, observed on Western blots. This finding can explain the relatively large variability in PD-L1 apparent molecular weight reported in the literature and offers an alternate means for the assessment of PD-L1 surface expression. Cancer Immunol Res; 4(10); 815-9. ©2016 AACR.