gebhart/patrepeval huggingface dataset:
Red Blood Cell Stimulation of Platelet Nitric Oxide Production Indicated by Quantitative Monitoring of the Communication between Cells in the Bloodstream (2007)

ATP is a recognized stimulus of nitric oxide synthase and is released from red blood cells (RBCs) upon deformation. The objective of this work is to demonstrate that RBCs stimulate nitric oxide production in platelets by employing a continuous flow analysis system in which the stream contains both RBCs and platelets. Here, two drugs known to improve blood flow in vivo (pentoxyfilline and iloprost) are shown to increase both the release of RBC-derived ATP and the production of platelet-derived NO. A flow-based chemiluminescence assay (in vitro) was employed to quantitatively determine the amount of ATP released from erythrocytes subjected to flow-induced deformation. Prior to being subjected to flow, erythrocytes were incubated in the absence or presence of 4.8 microM pentoxyfilline or 80 nM iloprost. Erythrocytes obtained from rabbits (n=22) that were subjected to flow released 239 +/- 29 nM ATP. When treated with pentoxyfilline, the ATP released from the flowing RBCs increased to 450 +/- 94 nM ATP. An increase in RBC-derived ATP was also measured for iloprost-incubated RBCs in flow (362 +/- 45 nM ATP). Importantly, platelets that were loaded with diaminofluorofluorescein diacetate, an intracellular fluorescence probe for NO, exhibited increases in fluorescence intensity by 16% in the presence of RBCs treated with pentoxyfilline and a 10% increase when treated with iloprost. When the ATP release from the RBCs was inhibited with glybenclamide, the platelet fluorescence intensity decreased by 25 and 51% for RBCs incubated with pentoxyfilline and iloprost, respectively. In an experiment not involving the RBC, inhibition of the P2x receptor on the platelets (an ATP receptor) resulted in no increase in platelet NO production, suggesting that the NO production in the activated platelet is due to ATP.
Gain of 3q and deletion of 11q22 are frequent aberrations in mantle cell lymphoma (1998)

We used comparative genomic hybridization (CGH) to screen for DNA copy number changes in 34 specimens from 27 cases of mantle cell lymphoma (MCL). The most common gains were detected at 3q (52%), 8q (30%), and 15q (26%), whereas the most frequent losses involved 13q (41%), 1p (33%), 6q (30%), 9p (30%), and 11q (30%). The gain of 3q, with a minimal common region at 3q26.1-27, appeared in more than half of the lymphomas, suggesting the location of an important oncogene here. A common deleted region at 11q22 was found in one-third of the patients, which suggests that this region may harbor a tumor suppressor gene important in the tumorigenesis of MCL. The mean number of changes was higher in more aggressive blastoid variants of MCL than in lymphomas with typical morphology. Our results show that the chromosomal regions affected in MCL are highly consistent and are different from those seen in other types of non-Hodgkin's lymphoma.
Mutational analysis of the sequence encoding ICP0 from herpes simplex virus type 1 (1991)

In-frame codon insertion and deletion mutants were constructed in a plasmid containing the sequence that encodes ICP0, a transcriptional activator of herpes simplex virus type 1 (HSV-1). The effect of these mutations was analyzed in a transient expression assay using the promoters for, the IE-0 gene (an immediate early (alpha) gene), the thymidine kinase gene (an early (beta) gene), and the glycoprotein C gene (a late (gamma) gene) fused to reporter cassettes that encoded either beta-galactosidase or chloramphenicol acetyl transferase. Assays were performed in the presence or absence of a plasmid encoding ICP4, the major regulatory protein of HSV-1. Our results demonstrate that ICP0-mediated transactivation varied depending on the position of the insertion in the gene. One region of this protein was consistently shown to be required for full activation of each promoter examined either in the presence or in the absence of ICP4. This region overlaps with a cysteine-rich region and coincides with a transactivator domain identified in another extensive mutational analysis of this sequence. Analysis of the deletion mutants generated in this study demonstrated that the carboxy-terminal regions were required for activation in certain circumstances and that this varied depending on the promoter being assayed and the cell type in which the analysis was performed.
Comparative Risk Analysis of Dioxins in Fish and Fine Particles from Heavy‐Duty Vehicles (2008)

Dioxins and airborne fine particles are both environmental health problems that have been the subject of active public debate. Knowledge on fine particles has increased substantially during the last 10 years, and even the current, lowered levels in the Europe and in the United States appear to be a major public health problem. On the other hand, dioxins are ubiquitous persistent contaminants, some being carcinogens at high doses, and therefore of great concern. Our aim was to (a) quantitatively analyze the two pollutant health risks and (b) study the changes in risk in view of the current and forthcoming EU legislations on pollutants. We performed a comparative risk assessment for both pollutants in the Helsinki metropolitan area (Finland) and estimated the health effects with several scenarios. For primary fine particles: a comparison between the present emission situation for heavy-duty vehicles and the new fine particle emission standards set by the EU. For dioxins: an EU directive that regulates commercial fishing of Baltic salmon and herring that exceed the dioxin concentration limit set for fish meat, and a derogation (= exemption) from the directive for these two species. Both of these two decisions are very topical issues and this study estimates the expected changes in health effects due to these regulations. It was found that the estimated fine particle risk clearly outweighed the estimated dioxin risk. A substantial improvement to public health could be achieved by initiating reductions in emission standards; about 30 avoided premature deaths annually in the study area. In addition, the benefits of fish consumption due to omega-3 exposure were notably higher than the potential dioxin cancer risk. Both regulations were instigated as ways of promoting public health.
High-resolution EELS investigation of the electronic structure of ilmenites (2006)

The electronic structure of a series of compounds belonging to the ilmenite family is investigated using high resolution electron energy loss spectroscopy (EELS). The energy loss near edge structure (ELNES) of the O-K, $\mathrm{Ti}\text{\ensuremath{-}}{\mathrm{L}}_{23}$ and transition metal ${\mathrm{L}}_{23}$ edges have been recorded in $\mathrm{Mn}\mathrm{Ti}{\mathrm{O}}_{3}$, $\mathrm{Fe}\mathrm{Ti}{\mathrm{O}}_{3}$, $\mathrm{Co}\mathrm{Ti}{\mathrm{O}}_{3}$, and $\mathrm{Ni}\mathrm{Ti}{\mathrm{O}}_{3}$ with an energy resolution of $0.20--0.25\phantom{\rule{0.3em}{0ex}}\mathrm{eV}$. The formal valency and spin-state of the transition metal are determined unambiguously from the analysis of the ${\mathrm{L}}_{23}$ edges with theoretical ligand field multiplet calculations. The results confirm the evolution of the interatomic distances observed along this series. The O-K edge is analyzed by comparison to the experimental signatures observed in the structurally related ${\mathrm{Ti}}_{2}{\mathrm{O}}_{3}$ compound and using theoretical molecular orbital results.
Influence of infection on exacerbations of multiple sclerosis (1994)

Exacerbations of multiple sclerosis (MS) are triggered by exogenous events, the best documented being viral upper respiratory infections (URIs), which can stimulate secretion of cytokines such as interferon-gamma (IFN-gamma) by immune cells. In conjunction with a recent clinical trial of systemic interferon-beta (IFN-beta) in relapsing-remitting MS, we studied the occurrence of viral infections and their correlation with MS attacks. Thirty patients kept daily logs, noting URI symptoms in themselves, family members, and co-workers. Patients were examined every 3 months, or whenever an attack of MS occurred, and were tested for antibodies to common upper respiratory pathogens. A strong correlation was found between MS attacks and URIs. There were 168 URIs in 2,792 patient-weeks, including 996 weeks at risk (the interval beginning 1 week before and ending 5 weeks after onset of URI symptoms) and 1,796 weeks not at risk. Nearly two-thirds of attacks occurred in periods at risk. Attack rates were 2.92 per year in weeks at risk compared to 1.16 per year in weeks not at risk, a significant difference (p < 0.001). High-dose interferon reduced the frequency of MS attacks, but had no effect on the number of URIs. Although a specific virus could not be incriminated, we concluded that URIs of presumed viral origin are an important trigger of MS attacks, and that treatment with IFN-beta reduces the attack rate, but not by preventing URIs. Rather, it may modulate responses to viral infection that would otherwise lead to immune activation and clinical symptoms.
Toll-Like Receptor Engagement Enhances the Immunosuppressive Properties of Human Bone Marrow-Derived Mesenchymal Stem Cells by Inducing Indoleamine-2,3-dioxygenase-1 via Interferon-β and Protein Kinase R (2009)

Mesenchymal stem cells (MSC) display unique suppressive properties on T-cell immunity, thus representing an attractive vehicle for the treatment of conditions associated with harmful T-cell responses such as organ-specific autoimmunity and graft-versus-host disease. Toll-like receptors (TLR) are primarily expressed on antigen-presenting cells and recognize conserved pathogen-derived components. Ligation of TLR activates multiple innate and adaptive immune response pathways to eliminate and protect against invading pathogens. In this work, we show that TLR expressed on human bone marrow-derived MSC enhanced the immunosuppressive phenotype of MSC. Immunosuppression mediated by TLR was dependent on the production of immunosuppressive kynurenines by the tryptophan-degrading enzyme indoleamine-2,3-dioxygenase-1 (IDO1). Induction of IDO1 by TLR involved an autocrine interferon (IFN)-beta signaling loop, which was dependent on protein kinase R (PKR), but independent of IFN-gamma. These data define a new role for TLR in MSC immunobiology, which is to augment the immunosuppressive properties of MSC in the absence of IFN-gamma rather than inducing proinflammatory immune response pathways. PKR and IFN-beta play a central, previously unidentified role in orchestrating the production of immunosuppressive kynurenines by MSC.
On some Latin morphological (ir)regularities (2012)

Two Latin irregular case-endings are well-attested in epigraphic sources: the 2nd-declension nominative&#13;\nplural in -eis and the 3rd-declension genitive singular in -us. Although inconsistent with Latin&#13;\nproductive inflectional patterns, these two forms can nevertheless be regarded as prototypicallystructured&#13;\nmorphological classes that are defined by ‘schemas’. Both the synchronic structure and the&#13;\ndiachronic development of these classes provide evidence for the existence of an organized storage&#13;\nthat is midway between rote-learning and rule processing, thus supporting a scalar view of morphological&#13;\n(ir)regularity.
Leakage in data mining (2011)

Deemed "one of the top ten data mining mistakes", leakage is essentially the introduction of information about the data mining target, which should not be legitimately available to mine from. In addition to our own industry experience with real-life projects, controversies around several major public data mining competitions held recently such as the INFORMS 2010 Data Mining Challenge and the IJCNN 2011 Social Network Challenge are evidence that this issue is as relevant today as it has ever been. While acknowledging the importance and prevalence of leakage in both synthetic competitions and real-life data mining projects, existing literature has largely left this idea unexplored. What little has been said turns out not to be broad enough to cover more complex cases of leakage, such as those where the classical i.i.d. assumption is violated, that have been recently documented. In our new approach, these cases and others are explained by explicitly defining modeling goals and analyzing the broader framework of the data mining problem. The resulting definition enables us to derive general methodology for dealing with the issue. We show that it is possible to avoid leakage with a simple specific approach to data management followed by what we call a learn-predict separation, and present several ways of detecting leakage when the modeler has no control over how the data have been collected.
A novel system for continuous protein refolding and on‐line capture by expanded bed adsorption (2005)

A novel two-step protein refolding strategy has been developed, where continuous renaturation-bydilution is followed by direct capture on an expanded bed adsorption (EBA) column. The performance of the overall process was tested on a N-terminally tagged version of human beta2-microglobulin (HAT-hbeta2m) both at analytical, small, and preparative scale. In a single scalable operation, extracted and denatured inclusion body proteins from Escherichia coli were continuously diluted into refolding buffer, using a short pipe reactor, allowing for a defined retention and refolding time, and then fed directly to an EBA column, where the protein was captured, washed, and finally eluted as soluble folded protein. Not only was the eluted protein in a correctly folded state, the purity of the HAThbeta2m was increased from 34% to 94%, and the product was concentrated sevenfold. The yield of the overall process was 45%, and the product loss was primarily a consequence of the refolding reaction rather than the EBA step. Full biological activity of HAT-hbeta2m was demonstrated after removal of the HAT-tag. In contrast to batch refolding, a continuous refolding strategy allows the conditions to be controlled and maintained throughout the process, irrespective of the batch size; i.e., it is readily scalable. Furthermore, the procedure is fast and tolerant toward aggregate formation, a common complication of in vitro protein refolding. In conclusion, this system represents a novel approach to small and preparative scale protein refolding, which should be applicable to many other proteins.
CXCR4 Regulates Migration and Development of Human Acute Myelogenous Leukemia Stem Cells in Transplanted NOD/SCID Mice (2004)

The chemokine stromal cell-derived factor-1 (SDF-1) and its receptor CXCR4 participate in the retention of normal hematopoietic stem cells within the bone marrow (BM) and their release into the circulation. Homing and engraftment of human stem cells in immunodeficient mice are dependent on cell surface CXCR4 expression and the production of BM SDF-1, which acts also as a survival factor for both human and murine stem cells. However, the role of SDF-1/CXCR4 interactions in the control of human acute myelogenous leukemia (AML) cell trafficking and disease progression is poorly understood. In this study, we report that although some AML cells do not express surface CXCR4, all AML cells tested express internal CXCR4 and SDF-1. Culture of AML cells with SDF-1 promoted their survival, whereas addition of neutralizing CXCR4 antibodies, SDF-1 antibodies, or AMD3100 significantly decreased it. Pretreatment of primary human AML cells with neutralizing CXCR4 antibodies blocked their homing into the BM and spleen of transplanted NOD/SCID/B2m(null) mice. Furthermore, weekly administrations of antihuman CXCR4 to mice previously engrafted with primary AML cells led to a dramatic decrease in the levels of human AML cells in the BM, blood, and spleen in a dose- and time-dependent manner. Interestingly, the same treatment did not affect significantly the levels of normal human progenitors engrafted into NOD/SCID mice. Taken together, our findings demonstrated the importance of the SDF-1/CXCR4 axis in the regulation of in vivo motility and development of human AML stem cells and identified CXCR4 neutralization as a potential treatment for AML.
Synthesis of biologically active cyclic peptides (1981)

Abstract 1. The extent of racemization and the coupling yield in peptide synthesis were studied under high dilution conditions. The azide method yielded the best results. 2. Five linear penta‐peptide precursors related to gramicidin S were subjected to cyclization in order to study how the difference in the sequence influences the yield and the ratio of cyclic dimer to monomer. The azide with the sequence of ‐ L ‐Pro‐ L ‐Val‐ L ‐Orn(Z)‐ L ‐Leu‐ D ‐Phe‐ afforded diZ‐gramicidin S in a high yield of 63%. 3. Alternaria mali toxin III, a cyclotetradepsipeptide phytotoxin, was synthesized. The activated linear tetradepsipeptide containing a D ‐Dap(Z) ( N 3 ‐Z‐ D ‐2,3‐diaminopropionic acid) residue at the N‐terminus afforded the cyclic precursor (53%). The Dap residue in the precursor was converted into a ΔAla residue by Hofmann degradation to give the desired product.
Transition metal atoms on different alumina phases: The role of subsurface sites on catalytic activity (2003)

Transition metals (Pt, Pd, Rh, Cr, etc.) are widely used as catalysts on \ensuremath{\gamma}- and \ensuremath{\eta}-alumina, two phases of ${\mathrm{Al}}_{2}{\mathrm{O}}_{3},$ but the catalytic activity of Cr on \ensuremath{\gamma}-alumina degrades rapidly. We report density-functional calculations that trace the origin of the effect to differences in surface reconstruction caused by different distributions of bulk cation vacancies. On \ensuremath{\eta}-alumina, Cr atoms remain on the surface, threefold-coordinated and reactive; on \ensuremath{\gamma}-alumina, they get trapped in subsurface octahedral sites and become inactive. Some metal atoms (e.g., Mn) also get trapped, but the other catalytic elements (Pt, Pd, Rh) do not. Steric constraints, size effects, or other qualitative considerations are not adequate to account for the results.
Instructable Intelligent Personal Agent (2016)

Unlike traditional machine learning methods, humans often learn from natural language instruction. As users become increasingly accustomed to interacting with mobile devices using speech, their interest in instructing these devices in natural language is likely to grow. We introduce our Learning by Instruction Agent (LIA), an intelligent personal agent that users can teach to perform new action sequences to achieve new commands, using solely natural language interaction. LIA uses a CCG semantic parser to ground the semantics of each command in terms of primitive executable procedures defining sensors and effectors of the agent. Given a natural language command that LIA does not understand, it prompts the user to explain how to achieve the command through a sequence of steps, also specified in natural language. A novel lexicon induction algorithm enables LIA to generalize across taught commands, e.g., having been taught how to "forward an email to Alice," LIA can correctly interpret the command "forward this email to Bob." A user study involving email tasks demonstrates that users voluntarily teach LIA new commands, and that these taught commands significantly reduce task completion time. These results demonstrate the potential of natural language instruction as a significant, under-explored paradigm for machine learning.
Sensing surface shape by touch (2002)

The design and construction of a tactile sensor that has been developed to measure the surface shape of objects held between the fingers of a robot gripper are described. A robotic tactile sensory workcell has been assembled to investigate touch-mediated grasping and object manipulation. This system requires sensors to provide surface profile information for experiments involving object manipulation and shape determination. A piezoresistive tactile sensor originally developed for the workcell proved to be generally unsuitable because its stiff sensing surface gave little surface shape information. A solution was provided by a tactile sensor designed to have a compliant structure.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The AmMYB308 and AmMYB330 Transcription Factors from Antirrhinum Regulate Phenylpropanoid and Lignin Biosynthesis in Transgenic Tobacco (1998)

MYB-related transcription factors are known to regulate different branches of flavonoid metabolism in plants and are believed to play wider roles in the regulation of phenylpropanoid metabolism in general. Here, we demonstrate that overexpression of two MYB genes from Antirrhinum represses phenolic acid metabolism and lignin biosynthesis in transgenic tobacco plants. The inhibition of this branch of phenylpropanoid metabolism appears to be specific to AmMYB308 and AmMYB330, suggesting that they recognize their normal target genes in these transgenic plants. Experiments with yeast indicate that AmMYB308 can act as a very weak transcriptional activator so that overexpression may competitively inhibit the activity of stronger activators recognizing the same target motifs. The effects of the transcription factors on inhibition of phenolic acid metabolism resulted in complex modifications of the growth and development of the transgenic plants. The inhibition of monolignol production resulted in plants with at least 17% less lignin in their vascular tissue. This reduction is of importance when designing strategies for the genetic modification of woody crops.
DNA Variation at therp49Gene Region ofDrosophila simulans: Evolutionary Inferences From an Unusual Haplotype Structure (2001)

An approximately 1.3-kb region including the rp49 gene plus its 5' and 3' flanking regions was sequenced in 24 lines of Drosophila simulans (10 from Spain and 14 from Mozambique). Fifty-four nucleotide and 8 length polymorphisms were detected. All nucleotide polymorphisms were silent: 52 in noncoding regions and 2 at synonymous sites in the coding region. Estimated silent nucleotide diversity was similar in both populations (pi = 0.016, for the total sample). Nucleotide variation revealed an unusual haplotype structure showing a subset of 11 sequences with a single polymorphism. This haplotype was present at intermediate frequencies in both the European and the African samples. The presence of such a major haplotype in a highly recombining region is incompatible with the neutral equilibrium model. This haplotype structure in both a derived and a putatively ancestral population can be most parsimoniously explained by positive selection. As the rate of recombination in the rp49 region is high, the target of selection should be close to or within the region studied.
Differential Expression of Tissue Repair Genes in the Pathogenesis of Chronic Obstructive Pulmonary Disease (2010)

The progression of COPD is associated with the differential expression of a cluster of genes that favor the degradation of the tissue surrounding the small conducting airways.
Computer aids in drug design--highlights. (1997)

An outline of some procedures used for computer aided drug design has been given. The emphasis is on lead generation, both primary and secondary, and on current lead optimization processes which rely on an appreciation of ligand-receptor interactions. The areas covered include techniques for structure based drug design and lead optimization, ligand-receptor interaction studies using molecular surfaces and docking, extraction of pharmacophore pattern to obtain new leads, expert system application etc.