gebhart/patrepeval huggingface dataset:
Analysis of a model for the treatment of wastewater by the activated sludge process (2006)

We investigate a model for the treatment of wastewater in the activated sludge process. This process is based on the aeration of waste water with flocculating biological growth, followed by the separation of treated waste water from biological growth. Part of this growth is then wasted, and the remainder is returned to the system. The wastewater reactor is assumed to be well mixed, so the mathematical formulation for this process can be represented by a continuously stirred tank reactor with recycle. This system is analysed by combining steady-state analysis with path-following techniques. In practice, wastewater is treated by a sequence of tanks arranged in series. By considering the performance of one tank, our work here provides a benchmark for comparing the performances of multiple tanks.
Cytokines and the Pathophysiology of Bone Erosions in Rheumatoid Arthritis (1997)

Rheumatoid arthritis is an inflammatory joint disease in which the chronic synovitis leads to bone and cartilage degradation. Proinflammatory cytokines such as interleukin-1 (IL-1) and tumor necrosis factor alpha are key factors in this process. The specific control of the action of these cytokines can be obtained with blocking antibodies, soluble receptors and receptor antagonists. Many of these products are now in clinical investigation. Some of the anti-inflammatory cytokines such as IL-4, IL-13 and IL-10 appear to affect more directly the consequences of inflammation, reducing destruction and inducing repair. Modulation of cytokine production by the rheumatoid synovitis appears to represent a potential way to control local bone degradation.
Structure−Function Analysis of a Series of Novel GIP Analogues Containing Different Helical Length Linkers (2003)

Glucose-dependent insulinotropic polypeptide (GIP1-42) is a potent glucose-lowering intestinal peptide hormone. The equipotent GIP1-30NH2 was structurally modified by linking N- and C-terminal fragments with several different linkers. Substitution of the middle region of GIP by a flexible aminohexanoic linker resulted in greatly reduced binding affinity and reduction or complete loss of bioactivity. Connection of the bioactive domains GIP1-14 and GIP19-30NH2 by EKEK or AAAA linkers resulted in peptide agonists with approximately 3-4-fold increased bioactivity as compared to GIP1-30NH2. Conformational analysis by CD spectroscopy of GIP fragments and analogues suggests a helical region in the C-terminal (19-30) portion of GIP. It was demonstrated that stabilization of this C-terminal helical region by the introduction of helical linkers favored binding and activation of the GIP receptor. Our results suggest an important contribution of a direct interaction of the first 14 amino acids with the GIP receptor, an appropriate relative orientation of N- and C-terminal parts of GIP, and the presence of helical linkers to be essential for bioactivity.
[Safety of breast-conserving treatment for triple-negative breast cancer]. (2015)

Breast-conserving treatment for TNBC is not associated with increased IBTR compared with non-TNBC subtype. Use of CT information in boost field planning can reduce the risk of ipsilateral breast tumor recurrence for patients undergoing BCT.
Non-negative low rank and sparse graph for semi-supervised learning (2012)

Constructing a good graph to represent data structures is critical for many important machine learning tasks such as clustering and classification. This paper proposes a novel non-negative low-rank and sparse (NNLRS) graph for semi-supervised learning. The weights of edges in the graph are obtained by seeking a nonnegative low-rank and sparse matrix that represents each data sample as a linear combination of others. The so-obtained NNLRS-graph can capture both the global mixture of subspaces structure (by the low rankness) and the locally linear structure (by the sparseness) of the data, hence is both generative and discriminative. We demonstrate the effectiveness of NNLRS-graph in semi-supervised classification and discriminative analysis. Extensive experiments testify to the significant advantages of NNLRS-graph over graphs obtained through conventional means.
Screening of HLA-A24-restricted epitope peptides from prostate-specific membrane antigen that induce specific antitumor cytotoxic T lymphocytes. (2002)

Two novel HLA-A24-restricted PSMA-derived epitopes were identified in this study. These epitopes can be used to further evaluate the clinical utility of DC-based immunotherapeutic strategies for treatment of hormone-refractory prostate cancers.
Antenna shape synthesis using characteristic modes (1982)

An initial effort is described to develop an antenna synthesis procedure by which the shape of a surface of rotation and its current density are deduced from a given far-field radiation pattern which satisfies the conditions of a characteristic mode. Typical results obtained to date are presented to substantiate the method and to illustrate some antenna shapes. A variety of research topics suggested by present efforts are discussed and suggested for future investigation.
Lateral ion implant straggle and mask proximity effect (2003)

Lateral scattering of retrograde well implants is shown to have an effect on the threshold voltage of nearby devices. The threshold voltage of both NMOSFETs and PMOSFETs increases in magnitude for conventional retrograde wells, but for triple-well isolated NMOSFETs the threshold voltage decreases for narrow devices near the edge of the well. Electrical data, SIMS, and SUPREM4 simulations are shown that elucidate the phenomenon.
Core Protein-Coding Sequence, but Not Core Protein, Modulates the Efficiency of Cap-Independent Translation Directed by the Internal Ribosome Entry Site of Hepatitis C Virus (2000)

Among a myriad of putative functions assigned to the hepatitis C virus (HCV) core protein, several studies suggest that it may modulate internal ribosome entry site (IRES)-mediated initiation of translation. We compared the translational activity of dicistronic reporter transcripts containing the HCV IRES within the intercistronic space fused to downstream sequence encoding either 22 amino acids (aa) or 173 aa of the core protein. The inclusion of the nearly full-length core protein-coding sequence significantly suppressed translation in vitro and in transfected HepG2 cells. However, this suppression was not eliminated by frameshift mutations introduced into the core sequence, suggesting that it occurred at the RNA level and not as a result of core protein expression in cis. Similarly, the expression of core protein (aa 1 to 191) in trans from a recombinant baculovirus did not suppress IRES-directed translation from any of these transcripts in transfected Huh-7 cells. While core protein expression did decrease IRES activity in HepG2 cells (up to 79% suppression), the expression of beta-galactosidase from a control baculovirus also suppressed IRES activity (up to 56%), strongly suggesting that this suppression was nonspecific. Finally, the addition of purified recombinant core protein (aa 1 to 179) to in vitro translation reactions at concentrations up to a 10-fold molar excess over the RNA transcripts resulted in no significant reduction in IRES activity. Consistent with these results, a gel retention assay indicated no difference in the affinities of the recombinant HCV core protein and a recombinant Venezuelan equine encephalitis virus capsid protein for HCV IRES-containing RNA transcripts. We conclude that while the inclusion of core protein-coding sequence downstream of the IRES may reduce the efficiency of cap-independent translation on HCV RNA, the core protein itself has no biologically relevant activity in modulating HCV IRES activity.
Prevention of Rapid Intracellular Degradation of ODC by a Carboxyl-Terminal Truncation (1989)

Ornithine decarboxylase (ODC) was converted from a protein with a short intracellular half-life in mammalian cells to a stable protein by truncating 37 residues at its carboxyl terminus. Cells expressing wild-type protein lost ODC activity with a half-life of approximately 1 hour. Cells expressing the truncated protein, however, retained full activity for at least 4 hours. Pulse-chase experiments in which immunoprecipitation and gel electrophoresis were used confirmed the stabilizing effect of the truncation. Thus, a carboxyl-terminal domain is responsible for the rapid intracellular degradation of murine ODC.
Facilitated search for specific genomic targets by p53 c-terminal basic DNA binding domain (2004)

p53 is a unique DNA binding protein with two distinct DNA binding domains, the central domain for sequence-specific DNA binding and the C-terminal basic DNA binding domain (BD domain) for structure-specific DNA binding. In contrast to the apparent inhibitory effect of the BD domain on p53 binding to sequence-specific DNA in vitro, here we demonstrate that the BD domain enhances p53 binding to the endogenous p21(Waf1) promoter and mediates rapid transactivation of p21.(Waf1) This paradox is resolved by the observation that the BD domain is required for rapid binding to non-sequence-specific genomic DNA (NS-DNA) as evident from global chromatin immunoprecipitation analysis of p53 DNA binding in vivo. This finding provides the first in vivo evidence from a eukaryotic system to support binding to NS-DNA as an intermediate step in searching for specific sites as proposed by von Hippel and Berg. Furthermore, we speculate that binding to structure-specific DNA by the BD domain is a mechanism for p53 rapid binding to genomic DNA from its free state to facilitate the search for its target sites in the genome undergoing genotoxic stress.
Is Virtual Colonoscopy A Cost-Effective Option To Screen for Colorectal Cancer? (1999)

To become cost-effective and be able to compete with colonoscopy in screening for colorectal cancer, CT or MR colonography would need be offered at a very low price or result in compliance rates much better than those associated with colonoscopy.
High‐Yield Fabrication of PLGA Non‐Spherical Microarchitectures by Emulsion‐Solvent Evaporation Method (2010)

Recently, it has been recognized the shape of particles plays an essential role in the design of materials with unique properties. In this study, PLGA non-spherical microarchitectures, rods and fibers, were fabricated successfully in high yield by single emulsion-solvent evaporation method in the presence of sodium tripolyphosphate. The assay of PVA residue was carried out and the hydrogen bonds formation was verified as well. The presented data show that viscosity and coagulation agent have a synergistic effect on forming the rod- and fiber-like microarchitectures in the shear response and the formation mechanisms were proposed accordingly.
Alloreactive cloned T cell lines. VI. Multiple lymphokine activities secreted by helper and cytolytic cloned T lymphocytes. (1982)

Culture supernatants generated by alloantigenic or lectin stimulation of a cloned helper T lymphocyte, designated L2, contain interleukin 2 (IL 2), granulocyte/macrophage colony-stimulating factor (CSF), B cell stimulating factor (BCSF), macrophage (Ia+)-recruiting factor (MIRF), (Ia+)-inducing activity, gamma-interferon, Fc receptor-enhancing activity, macrophage migration inhibitory factor (MIF), macrophage activation factor (MAF), interleukin 3 (IL 3), and a factor responsible for prolonging the synthesis and secretion of the fourth and second components of complement by guinea pig peritoneal macrophages. Erythropoietin was not detected. A spontaneously arising variant of L2, designated L2V, produces much lower quantities of macrophage-stimulating activities, IL 2, and interferon. However, when compared to L2, L2V produces much higher levels of BCSF, equivalent amounts of IL 3, and slightly smaller amounts of CSF. Unlike L2V, a cytolytic clone, designated L3, secretes lymphokines that primarily affect macrophage function. The time course of lymphokine production by L2 cells indicates that for the six lymphokine activities studied there are three different times at which maximal or near maximal levels are reached, as follows: 1) IL 2, 12 to 24 hr; 2) IL 3 and CSF, 24 to 48 hr; and 3) (Ia+)-inducing activity, MAF, and interferon, 48 hr or later. Only IL 2 activity disappears during the 8-day culture cycle. The time course data and the differential production of activities by the three types of lymphocyte clones suggest that at least four terminal effector lymphokine molecules account for the ten biologic activities tested.
Microsatellite alterations as clonal markers for the detection of human cancer. (1994)

Microsatellite instability has been reported to be an important feature of tumors from hereditary nonpolyposis colorectal carcinoma (HNPCC) patients. The recent discovery of genetic instability in small cell lung carcinoma, a neoplasm not associated with HNPCC, led us to investigate the possible presence of microsatellite alterations in other tumor types. We examined 52 microsatellite repeat sequences in the DNA of normal and tumor pairs from 100 head and neck, bladder, and lung cancer patients by the polymerase chain reaction. Although alterations were rare in dinucleotide repeats, larger (tri- or tetranucleotide) repeats were found to be more prone to expansion or deletion. We screened 100 tumors with a panel of nine tri- and tetranucleotide repeat markers and identified 26 (26%) that displayed alterations in at least one locus. This observation prompted us to examine the possibility of using microsatellite alterations as markers to detect clonal tumor-derived cell populations in pathologic samples. The identical microsatellite alterations detected in the primary tumors were successfully identified in corresponding urine, sputum, and surgical margins from affected patients. This study demonstrates that appropriately selected microsatellite loci are commonly altered in many cancers and can serve as clonal markers for their detection.
Dengue 1 virus binding to human hepatoma HepG2 and simian Vero cell surfaces differs (1996)

We analysed the binding and infectivity of dengue virus serotype 1 (DEN-1) for the human hepatoma cell line HepG2 in comparison with the simian kidney cell line Vero. The higher susceptibility of Vero cells to DEN-1 correlated with greater binding affinity of DEN-1 to these cells. In contrast, the capacity of virus attachment was higher for HepG2 than for Vero cells. Profiles of DEN-1 binding at different pH were markedly different between the two cell types. A type-specific neutralizing monoclonal antibody reduced initial virus binding to both cell types similarly but complex- and group-specific neutralizing antibodies affected virus adhesion differently. Altogether, these results suggest the involvement of different receptors or receptors presented in a different environment on the cell surface in the two cell lines. The sensitivity to proteolytic enzymes and to ionic detergent of the binding sites on the two cell types was tested and results indicated that they may be multimeric proteins or protein complexes.
The psychophysiology of crying (1994)

Two conflicting views have emerged as to why people cry when they are sad. One suggests that crying serves homeostasis by facilitating recovery; the other suggests that crying produces an aversive high-arousal state that motivates behavior aimed at ending the tears. To test hypotheses drawn from these views, we showed a short film known to elicit sadness to 150 women. During this film, 33 subjects spontaneously cried and 117 did not. Subjects who cried exhibited more expressive behavior and reported feeling more sadness and pain than did subjects who did not cry. Crying also was associated with increases in somatic and autonomic nervous system activity. The increases in autonomic activity could not be accounted for solely by the increases in somatic activity. Crying is thus associated with an aversive state, including negative emotion and a complex mixture of sympathetic, parasympathetic, and somatic activation, and we speculate about the functional implications of these findings.
Sex determination and polyploid gigantism in the dwarf surfclam (Mulinia lateralis Say). (1994)

Mulinia lateralis, the dwarf surfclam, is a suitable model for bivalve genetics because it is hardy and has a short generation time. In this study, gynogenetic and triploid M. lateralis were successfully induced. For gynogenesis, eggs were fertilized with sperm irradiated with ultraviolet light and subsequently treated with cytochalasin B to block the release of the second polar body (PB2). Triploidy was induced by blocking PB2 in normally fertilized eggs. The survival of gynogenetic diploids was very low, only 0.7% to 8 days post-fertilization (PF), compared with 15.2% in the triploid groups and 27.5% in the normal diploid control. Larvae in all groups metamorphosed at 8-10 days PF, and there was no significant post-larval mortality. At sexual maturation (2-3 months PF), all gynogenetic diploids were female, and there was no significant difference (P > 0.05) in sex ratio between diploids and triploids. These results suggested that the dwarf surfclam may have an XX-female, XY-male sex determination with Y-domination. Compared with diploids, triploids had a relative fecundity of 59% for females and 80% for males. Eggs produced by triploid females were 53% larger (P < 0.001) in volume than those from diploid females. In both length and weight measurements at three months PF, the gynogenetic diploids were not significantly (P > 0.33) different from normal diploid females, suggesting that inbreeding depression was minimal in meiosis II gynogens. Triploid clams were significantly larger (P < 0.001) than normal diploids. We hypothesize that the increased body-size in triploids was caused by a polyploid gigantism due to the increased cell volume and a lack of cell-number compensation.
Alkoxide-accelerated Smiles rearrangements. Synthesis of N-(2-hydroxyethyl)anilines from N-(2-hydroxyethyl)(aryloxy)acetamides (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAlkoxide-accelerated Smiles rearrangements. Synthesis of N-(2-hydroxyethyl)anilines from N-(2-hydroxyethyl)(aryloxy)acetamidesWilliam R. BakerCite this: J. Org. Chem. 1983, 48, 25, 5140–5143Publication Date (Print):December 1, 1983Publication History Published online1 May 2002Published inissue 1 December 1983https://pubs.acs.org/doi/10.1021/jo00173a076https://doi.org/10.1021/jo00173a076research-articleACS PublicationsRequest reuse permissionsArticle Views312Altmetric-Citations13LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Lipid A and resistance of Salmonella typhimurium to antimicrobial granule proteins of human neutrophil granulocytes (1984)

Granule extracts from human polymorphonuclear leukocytes were prepared and fractionated by chromatography on Sephadex G75-SF. One fraction exhibited potent antimicrobial activity against an Rd1 lipopolysaccharide (LPS) mutant of Salmonella typhimurium. Susceptibility of the mutant to antimicrobial activity appeared to be due to binding of granule proteins to lipid A because isolated native LPS succeeded in blocking the antimicrobial activity of granule extracts whereas base-hydrolyzed LPS failed to do so. Centrifugation of control and base-hydrolyzed LPS-protein mixtures in cesium chloride gradients suggested that only control LPS formed complexes with antimicrobial proteins. Further evidence that bactericidal proteins from polymorphonuclear leukocyte granules interact with lipid A was that sublethal concentrations of polymyxin B (an antibiotic known to bind to lipid A) rendered target bacteria phenotypically resistant to granule proteins. Moreover, a mutant of S. typhimurium which synthesized a lipid A with decreased electronegativity due to increased 4-amino-4-deoxy-L-arabinosylation at the 4'-phosphate exhibited increased resistance to both polymyxin B and granule proteins. These results suggest that polymyxin B and antimicrobial proteins derived from polymorphonuclear leukocyte granules interact with lipid A in an analogous manner.
4-Pentenoic Acid (2002)

[591-80-0] C5H8O2 (MW 100.12) InChI = 1S/C5H8O2/c1-2-3-4-5(6)7/h2H,1,3-4H2,(H,6,7) InChIKey = HVAMZGADVCBITI-UHFFFAOYSA-N (reagent used for protection of amines and activation of certain alcohols1) Physical Data: mp −22.5 °C; bp 83–84 °C/12 mmHg; d 0.981 g cm−3. Solubility: soluble in alcohol, diethyl ether, and most organic solvents. Form Supplied in: colorless liquid; widely available. Purification: fractional distillation using a Vigreux column. Handling, Storage, and Precautions: corrosive organic acid with an acrid odor. Use in a well-ventilated fume hood with gloves, eye protection, and protective clothing to avoid contact. Moderately toxic by ingestion. LD50 (rat, oral): 470 mg/kg.