gebhart/patrepeval huggingface dataset:
Leishmania major interferes with antigen presentation by infected macrophages (1993)

Impairment of the Ag-presenting capacity of macrophages harboring intracellular Leishmania might represent one of the several mechanisms by which these parasites can evade host-protective T cell responses. Thus, the present study was designed to investigate the ability of macrophages, parasitized with Leishmania major, to present Ag to relevant T cell hybridomas. Results show that bone marrow-derived macrophages from BALB/c mice, after infection with L. major, have a greatly reduced capacity to present OVA, beta-galactosidase, and L. major-derived Ag to specific T cell hybrids derived from mice immunized with those Ag. In contrast, after pulsing with relevant peptide, macrophages containing L. major have a normal Ag-presenting capacity. The inhibition of presentation of native Ag did not appear to result from decreased endocytosis or catabolism. Inasmuch as the inhibition of presentation could not be attributed to an impaired processing of the Ag or an unavailability of MHC class II molecules on the surface of infected cells, these results could indicate that the presence of L. major interferes with the intracellular loading of MHC class II molecules with antigenic peptides.
Cell-Free 59 kDa Immunoreactive Integrin-Linked Kinase (2004)

These data suggest that irILK is an ovarian tumor-associated antigen and implicates its potential not only as a biomarker for early-stage screening but also as a marker for monitoring the clinical condition of patients after treatment.
SEMANTIC SEGMENTATION OF AERIAL IMAGES WITH AN ENSEMBLE OF CNNS (2016)

Abstract. This paper describes a deep learning approach to semantic segmentation of very high resolution (aerial) images. Deep neural architectures hold the promise of end-to-end learning from raw images, making heuristic feature design obsolete. Over the last decade this idea has seen a revival, and in recent years deep convolutional neural networks (CNNs) have emerged as the method of choice for a range of image interpretation tasks like visual recognition and object detection. Still, standard CNNs do not lend themselves to per-pixel semantic segmentation, mainly because one of their fundamental principles is to gradually aggregate information over larger and larger image regions, making it hard to disentangle contributions from different pixels. Very recently two extensions of the CNN framework have made it possible to trace the semantic information back to a precise pixel position: deconvolutional network layers undo the spatial downsampling, and Fully Convolution Networks (FCNs) modify the fully connected classification layers of the network in such a way that the location of individual activations remains explicit. We design a FCN which takes as input intensity and range data and, with the help of aggressive deconvolution and recycling of early network layers, converts them into a pixelwise classification at full resolution. We discuss design choices and intricacies of such a network, and demonstrate that an ensemble of several networks achieves excellent results on challenging data such as the ISPRS semantic labeling benchmark, using only the raw data as input.
MUM1/IRF4 (2010)

MUM1/IRF4 protein is a member of the interferon regulatory factor (IRF) family of transcriptional factors initially described as downstream regulators of interferon signaling. The quantity of this factor varies within the hematopoietic system in a lineage and stage-specific way. It is considered to be a key regulator of several steps in lymphoid, myeloid, and dendritic cell differentiation and maturation. MUM1/IRF4 expression is observed in many lymphoid and myeloid malignancies, and may be a promising target for the treatment of some of these neoplasms. We reviewed the literature on MUM1/IRF4, with emphasis on the pathologic aspects of this marker in reactive and malignant hematologic and nonhematologic conditions.
Judicial independence in the age of democracy: critical perspectives from around the world (2001)

This collection of essays by leading scholars of constitutional law looks at a critical component of constitutional democracy - judicial independence - from an international comparative perspective. Peter H. Russell's introduction outlines a general theory of judicial independence, while the contributors analyze a variety of regimes from the United States and Latin America to Russia and Eastern Europe, Western Europe and the United Kingdom, Australia, Israel, Japan, and South Africa. Russell's conclusion compares these various regimes in light of his own analytical framework.
In vivo adenovirus-mediated p53 tumor suppressor gene therapy for colorectal cancer. (1997)

This form of therapy may provide a novel approach to colorectal cancer.
In Vitro Antibody Evolution Targeting Germline Hot Spots to Increase Activity of an Anti-CD22 Immunotoxin (2004)

Recombinant immunotoxin BL22, containing the Fv portion of an anti-CD22 antibody, produced complete remissions in most patients with drug-resistant hairy cell leukemia but had less activity in leukemias with low CD22 expression. Complementarity-determining region (CDR) mutagenesis is used to increase antibody affinity but can be difficult to perform successfully. We previously showed that antibodies with increased affinity and immunotoxins with increased activity could be obtained by directing mutations at specific DNA residues called hot spots. Because hot spots can arise either by somatic mutation or be present in the germline, we examined which type of hot spot is preferred for increasing antibody affinity. Initially, a second generation antibody phage-display library targeting a germline hot spot (Ser(30)-Asn(31)) within CDR1 of the antibody light chain was mutated. Substitution of serine 30 or asparagine 31 with arginine produced mutant immunotoxins with an affinity (0.8 nM) increased 7-fold over BL22 (5.8 nM) and 3-fold over the first generation mutant HA22 (2.3 nM). More importantly, a 10-fold increase in activity over BL22 and a 2-3-fold increase over HA22 were observed in various B lymphoma cell lines including WSU-CLL that contains only 5500 CD22 sites per cell. For comparison, two phage-display libraries targeting non-germline hot spots in heavy chain CDR1 and CDR3 were generated but did not produce Fv with increased affinity. Our results demonstrate that germline hot spots but not non-germline hot spots are effective for in vitro antibody affinity maturation.
Uncovering myths and transforming realities among low-SES African-American men: implications for reducing prostate cancer disparities. (2004)

These findings suggest factors that may explain the reluctance and limited participation in prostate health and prostate cancer services among medically underserved, socioeconomically disadvantaged, African-American men. Lack of knowledge, which affects all barriers to care, is amenable to change. Therefore, improvements in prostate cancer outcomes are achievable through culturally and linguistically appropriate health education tailored to their specific needs.
Regulators of Sperm function (1996)

The 'major maturation-associated' sperm membrane antigen is the most prominent glycopeptide which appears on the surface of rat spermatozoa during post-testicular sperm maturation. The name describes the fact that its occurrence coincides with the spermatozoa acquiring their major physiological properties of maturation in the distal epididymis. It is shown in this study that this phenomenon is not restricted to the rat. Rather, by immunohistochemical staining, in-situ transcript hybridization and molecular analyses of genomic DNA fragments it is evident that homologous counterparts exist in other mammalian species, including the human. The human homologue is an abundant epididymal gene product that has previously been identified as lymphocyte surface antigen CD52. Thus, following the human standard nomenclature, it seems more appropriate to refer to these molecules as CD52 homologues. Localization of the mRNA for these glycosylphosphatidyl inositol (GPI)-anchored glycopeptides within the epididymal epithelium, and not within the testis, suggests that they may be transferred from epididymal to sperm cell with their GPI-anchor intact.
Discovery of Novel Allosteric Effectors Based on the Predicted Allosteric Sites for Escherichia coli D-3-Phosphoglycerate Dehydrogenase (2014)

D-3-phosphoglycerate dehydrogenase (PGDH) from Escherichia coli catalyzes the first critical step in serine biosynthesis, and can be allosterically inhibited by serine. In a previous study, we developed a computational method for allosteric site prediction using a coarse-grained two-state Gō Model and perturbation. Two potential allosteric sites were predicted for E. coli PGDH, one close to the active site and the nucleotide binding site (Site I) and the other near the regulatory domain (Site II). In the present study, we discovered allosteric inhibitors and activators based on site I, using a high-throughput virtual screen, and followed by using surface plasmon resonance (SPR) to eliminate false positives. Compounds 1 and 2 demonstrated a low-concentration activation and high-concentration inhibition phenomenon, with IC50 values of 34.8 and 58.0 µM in enzymatic bioassays, respectively, comparable to that of the endogenous allosteric effector, L-serine. For its activation activity, compound 2 exhibited an AC50 value of 34.7 nM. The novel allosteric site discovered in PGDH was L-serine- and substrate-independent. Enzyme kinetics studies showed that these compounds influenced Km, kcat, and kcat/Km. We have also performed structure-activity relationship studies to discover high potency allosteric effectors. Compound 2-2, an analog of compound 2, showed the best in vitro activity with an IC50 of 22.3 µM. Compounds targeting this site can be used as new chemical probes to study metabolic regulation in E. coli. Our study not only identified a novel allosteric site and effectors for PGDH, but also provided a general strategy for designing new regulators for metabolic enzymes.
Synthesis of the Formal Diels-Alder Adducts of N-substituted Dehydromaleimides and Anthracene (2000)

A new class of roof-shaped dibenzobarrelenemaleimide derivatives was prepared by the condensation of a bridged maleic anhydride with amines. A para-substituted bifunctional derivative was proven to be a 1:2 complex with acetone by an X-ray crystallographic study.
Predominant pathogenic role of tumor necrosis factor in experimental colitis in mice (1997)

Antibodies to tumor necrosis factor (TNF)-alpha have been recently proposed as effective treatment for patients with Crohn's disease. Here, we analyze the functional role of TNF-alpha in a mouse model of chronic intestinal inflammation induced by the hapten reagent 2,4,6,-trinitrobenzene sulfonic acid (TNBS) that mimics some characteristics of Crohn's disease in humans. Macrophage-enriched lamina propria (LP) mononuclear cells from mice with TNBS-induced colitis produced 10-30-fold higher levels of TNF-alpha mRNA and protein than cells from control mice. When mice with chronic colitis were treated by intraperitoneal injection of antibodies to TNF-alpha, an improvement of both the clinical and histopathologic signs of disease was found. Isolated macrophage-enriched LP cells from anti-TNF-alpha-treated mice produced strikingly less pro-inflammatory cytokines such as interleukin (IL)-1 and IL-6 in cell culture. The predominant role of TNF-alpha in the mouse TNBS-induced colitis model was further underlined by the finding that striking colonic inflammation and lethal pancolitis was induced in TNF-alpha-transgenic mice upon TNBS treatment. Conversely, no significant TNBS-induced colitis could be induced in mice in which the TNF-alpha gene had been inactivated by homologous recombination. Complementation of TNF-alpha function in TNF-/- mice by the expression of a mouse TNF-alpha transgene was sufficient to reverse this effect. Taken together, the data provide direct evidence for a predominant role of TNF-alpha in a mouse model of chronic intestinal inflammation and encourage further clinical trials with antibodies to TNF-alpha for the treatment of patients with Crohn's disease.
Constancy of pressure-rate product in pacing-induced angina pectoris. (1976)

The pressure-rate product during anginal pain produced by right atrial pacing was studied in 12 patients before, during, and after an angiotensin infusion sufficient to produce a significant rise in blood pressure. During the infusion the pain occurred at a significantly lower heart rate (P less than 0.001). However, the pressure-rate product was similar during anginal pain before and during the angiotensin-induced hypertension and after it wore off. Our studies support the concept that in each individual there is a constant level of myocardial oxygen consumption, as expressed by the pressure-rate product, at which anginal pain occurs.
The effect of dehydration history on associating hydrogels for nucleus pulposus replacement (2003)

A replacement of the nucleus pulposus with a biocompatible, hydrogel blend of polyvinyl alcohol (PVA) and polyvinyl pyrrolidone (PVP) has been proposed. These gels are stable in physiological fluid due to physical crosslinks consisting of intramolecular hydrogen bonds within PVA crystallites and intermolecular hydrogen bonds between PVA and PVP. It has been suggested that the swelling properties of these polymer blends might allow a nucleus replacement surgery to be performed -arthroscopically through a small posteriorly placed cannula. The dehydration of an implant would allow for insertion of the nucleus substitute. Subsequent rehydration once the substitute is positioned within the disc would follow. Here we examine the effects of the extent of dehydration on the properties of the rehydrated hydrogel. It is concluded that the properties of PVA/PVP hydrogel blends are strongly dependent on the material's dehydration history. Partial dehydration/rehydration is a viable process for allowing nucleus pulposus replacement surgery to be performed arthroscopically.
Studies on the Compounds Related to Colistin. V. : Synthesis and Pharmacological Activity of Colistin Analogues (Biological) (1972)

A lysine-colistin, an analog of the natural antibiotic colistin, was synthesized by the cyclization of linear decapeptide obtained from acyl-tetrapeptide, formyl-tetrapeptide, and dipeptide by a stepwise reaction. Lysine-colistin is a new peptide containing six moles of lysine instead of six moles of α, γ-diaminobutyric acid in colistin. Lysine-colistin and linear acyl-decapeptide had the same antibiotic activity as colistin against many gram-negative bacterias.
Evolution of Polaron States into Bipolarons in Polypyrrole (1984)

The kinetics of polaron recombination into bipolarons in polypyrrole has been studied by optical-absorption spectroscopy on films doped in situ in an electrochemical cell. ESR studies confirm that the metastable states possess spin, while the stable states do not. The data reveal a slow evolution, consistent with polaron-diffusion rates limited by the mobility of the accompanying counterion.
Synthesis and Characterization of a New Microporous Material. 1. Structure of Aluminophosphate EMM-3 (2006)

Molecular sieves are extensively used in the chemical and petrochemical industry as catalysts, absorbents, and ion exchangers. New molecular sieve structures have the potential to improve the performance of these materials. We have discovered a new microporous material, EMM-3, prepared in both aluminophosphate and silicoaluminophosphate compositions by use of N,N,N,N‘,N‘,N‘-hexamethyl-1,6-hexanediammonium as a template at 160 °C in 20 h. The structure of EMM-3 has been solved and refined from powder data by use of synchrotron X-ray radiation. The unit cell for the calcined AlPO form of EMM-3 has monoclinic space group symmetry, I2/m11, with cell dimensions a = 10.3132(2), b = 12.6975(3), and c = 21.8660(4) and α = 89.656(1)°. The microporous structure contains 12-ring, sinusoidal, unidimensional channels with pore openings of 6.1 × 6.5 Å. This new framework contains two new building chains, not observed in other known framework structures. The 31P and 27Al NMR spectra of the calcined/dehydrated form are in agreement with a fully connected tetrahedral structure containing five unique phosphorus and five unique aluminum atoms. The material is stable upon calcination and absorbs 9−10 wt % hydrocarbons.
MALE ORIENTATION INHIBITOR OF COTTON BOLLWORM: INHIBITORY EFFECTS OF ALCOHOLS IN WIND‐TUNNEL AND IN THE FIELD* (1997)

Abstract The inhibitory effects of several alcohols identified from male hairpencil of cotton bollworm on conspecific male behavior responses were studied. In the wind tunnel dose tests ranging from 4 × lo p4 to 40 pg , male moths of cotton bollworm produced the highest response to the binary components of 29–16: Ald and Z11 —16: Ald in a ratio of 5 : 95 at the dosage of 0.4 μg. When 211–16:OH was added to 0.4 μg dose of binary blend, 5% of the alcohol completely inhibited male orientation behavior. Further increment of percentage of alcohol in binary blend inhibited not only orientation behavior but also takeoff behavior. Comparisons among 211 —16: OH and other three saturated alcohols, 14 : OH, 16 : OH, and 18 : OH as well as structurally similar compound Z9–16: OH indicated that Z11–16: OH was more effective in inhibiting male orientation behavior than other tested alcohols. Field application of 211–16: OH decreased egg hatch rate from untreated 34% to 17% by spraying or coating the alcohal on plastic tubes.
(R)-2-Phenylpyrrolidine Substituted Imidazopyridazines: A New Class of Potent and Selective Pan-TRK Inhibitors (2015)

Deregulated kinase activities of tropomyosin receptor kinase (TRK) family members have been shown to be associated with tumorigenesis and poor prognosis in a variety of cancer types. In particular, several chromosomal rearrangements involving TRKA have been reported in colorectal, papillary thyroid, glioblastoma, melanoma, and lung tissue that are believed to be the key oncogenic driver in these tumors. By screening the Novartis compound collection, a novel imidazopyridazine TRK inhibitor was identified that served as a launching point for drug optimization. Structure guided drug design led to the identification of (R)-2-phenylpyrrolidine substituted imidazopyridazines as a series of potent, selective, orally bioavailable pan-TRK inhibitors achieving tumor regression in rats bearing KM12 xenografts. From this work the (R)-2-phenylpyrrolidine has emerged as an ideal moiety to incorporate in bicyclic TRK inhibitors by virtue of its shape complementarity to the hydrophobic pocket of TRKs.
Carbonylation of heterocycles by homogeneous catalysts (2007)

This article summarizes the recent developments (particularly the uses of homogeneous organometallic catalysts) in ring-opening carbonylations, ring-opening carbonylative polymerizations and ring-expansion carbonylations of heterocycles such as epoxides, aziridines, lactones and oxazolines.
2‐Aminobenzimidazole Derivatives Strongly Inhibit and Disperse Pseudomonas aeruginosa Biofilms (2012)

Bakterielle Biofilme bergen ernstzunehmende Gesundheitsrisiken. Sie sind mit herkömmlichen Antibiotika nur schwer zu bekämpfen, doch 2-Aminobenzimidazol-Derivate (siehe Schema) hemmen das Wachstum von Pseudomonas-aeruginosa-Biofilmen stark oder lösen diese auf. Die Verbindungen, die das Quorum Sensing in Reporterlinien modulieren, zählen zu den stärksten Hemmstoffen für P.-aeruginosa-Biofilme. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Enzymatic synthesis of duplex circular X174 DNA containing phosphoramidate bonds in the (-) strand. (1976)

Duplex circular phiX174 DNA (RF I) containing some phosphoramidate links in the backbone chain of the (-) strand was synthesized by reaction of 5'-amino-5'-deoxythymidine 5'-triphosphate, dCTP, dGTP, and 3H-dATP with DNA polymerase I and DNA ligase (T4) on a (+) strand phiX174 amber 3 DNA template. The yield of duplex DNA was higher when dTTP was included along with the amino analog in the initial reaction system or was added late in the synthesis. RF I DNA was observed as a rapidly sedimenting species in an alkaline sucrose gradient, and the presence of phosphoramidate linkages was demonstrated by the unusual lability of the duplex DNA in a weakly acidic solution.
geoADDICTION-flexible handling of complex geometries in IC layout tools (2003)

A layout CAD (computer-aided design) system is presented that allows the flexible handling of different geometries to be used for IC design. The proposed parameterizable geometry model allows the user to make only the geometric features available to his CAD tools that are suitable for the current technology, hence providing the maximum efficiency for the tools' operation. Presently the system provides six geometry classes including circles and circle segments. The model has been designed so that it is easily expandable even to arbitrarily shaped geometric structures. The flexible geometry model is incorporated into ADDICTION, the control data management unit of the layout CAD system IMAGE.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Teaching Visual Literacies: The Case of the Great American Dust Bowl. (2019)

Teachers and students require a range of tools to engage with visual texts. Using The Great American Dust Bowlby Don Brown (2013) as an exemplar text, we outline four conceptions of visual literacy: rhetorical, instructional, industrial and visuo-spatial and discuss their use in our literacy education practice. In addition, we provide a brief model of a second text, The Arrival (Tan, 2013) and a list of suggested texts for students at different levels (elementary, middle, and high school). We argue that these tools have the potential to deepen conceptions of visual literacies and empower teachers and students to understand the many ways in which visual texts operate to send message and evoke response and engagement.
Twister ribozymes as highly versatile expression platforms for artificial riboswitches (2016)

The utilization of ribozyme-based synthetic switches in biotechnology has many advantages such as an increased robustness due to in cis regulation, small coding space and a high degree of modularity. The report of small endonucleolytic twister ribozymes provides new opportunities for the development of advanced tools for engineering synthetic genetic switches. Here we show that the twister ribozyme is distinguished as an outstandingly flexible expression platform, which in conjugation with three different aptamer domains, enables the construction of many different one- and two-input regulators of gene expression in both bacteria and yeast. Besides important implications in biotechnology and synthetic biology, the observed versatility in artificial genetic control set-ups hints at possible natural roles of this widespread ribozyme class.