gebhart/patrepeval huggingface dataset:
How Different DNA-Binding Proteins Affect Long-Range Oxidative Damage to DNA (2001)

Here the effect on DNA-mediated charge transport of binding by a variety of proteins is examined. DNA assemblies were constructed that contain a tethered rhodium intercalator, as photooxidant, as well as two 5'-GG-3' sites flanking the DNA-binding site for the different proteins. By monitoring the ratio of oxidative damage promoted at the guanine doublet situated distal to the protein-binding site versus that at the proximal site as a function of protein binding, the effects of binding the proteins on DNA-mediated charge transport were determined. Proteins examined included both the wild-type and mutant methyltransferase, M.HhaI, which are base-flipping enzymes, the restriction endonuclease R.PvuII, a TATA-binding protein, which kinks the DNA, and the transcription factor Antennapedia homeodomain protein, which binds DNA through a helix-turn-helix motif. In general, it was observed that yields of long-range oxidative damage correlate with protein-dependent alterations in DNA base stacking. Interactions that disturb the DNA pi-stack inhibit DNA charge transport. Alternatively, interactions that promote no helix distortion but, as a result of tight packing, may rigidify the pi-stack, serve instead to enhance the ability of the DNA base pairs to serve as a conduit for charge transport. Thus, protein binding to DNA modulates long-range charge transport both negatively and positively, depending upon the specific protein/DNA interactions in play. Long-range DNA charge transport and this modulation by protein binding may be important to consider physiologically.
Workflow data patterns (2004)

Workflow systems seek to provide an implementation vehicle for complex, recurring business processes. Notwithstanding this common objective, there are a variety of distinct features offered by commercial workflow management systems. These differences result in significant variations in the ability of distinct tools to represent and implement the plethora of requirements that may arise in contemporary business processes. Many of these requirements recur quite frequently during the requirements analysis activity for workflow systems and abstractions of these requirements serve as a useful means of identifying the key components of workflow languages. Previous work has identified a number of workflow control patterns which characterise the range of control flow constructs that might be encountered when modelling and analysing workflow. In this paper, we describe a series of workflow data patterns that aim to capture the various ways in which data is represented and utilised in workflows. By delineating these patterns in a form that is independent of specific workflow technologies and modelling languages, we are able to provide a comprehensive treatment of the workflow data perspective and we subsequently use these patterns as the basis for a detailed comparison of a number of commercially available workflow management systems and business process modelling languages.
Glial cells metabolically cooperate: a potential requirement for gene replacement therapy. (1985)

Immunofluorescently labeled glial cells are shown by radioautography to metabolically cooperate with hypoxanthine phosphoribosyltransferase-deficient fibroblasts. The observations of cooperation without cell contact and of incorporation gradients around the glial cells suggest that cooperation occurs through extracellular transport of radiolabeled purine compounds. The transfer of radiolabeled adenine, adenosine, or methylthioadeninosine is supported by the quantitative loss of cooperation when the recipient cell is also deficient in enzymes required for adenine or adenosine salvage. The demonstration of glial cell cooperation provides impetus for current research toward gene replacement therapy for the neurologic symptoms of the Lesch-Nyhan syndrome.
Concurrent activation of a novel putative transforming gene, myeov, and cyclin D1 in a subset of multiple myeloma cell lines with t(11;14)(q13;q32). (2000)

Through the application of the NIH/3T3 tumorigenicity assay to DNA from a gastric carcinoma, we have identified a novel transforming gene, designated myeov (myeloma overexpressed gene in a subset of t[11;14]-positive multiple myelomas). Sequence analyses did not reveal any homology with sequences present in the GenBank, except the deduced protein structure predicts a transmembrane localization. Myeov was mapped to chromosome 11q13 and localized by DNA fiber fluorescence in situ hybridization (FISH) 360-kilobase (kb) centromeric of cyclin D1. In 3 of 7 multiple myeloma (MM) cell lines with a t(11;14)(q13;q32) and cyclin-D1 overexpression, Northern blot analysis revealed overexpression of myeov as well. In all 7 cell lines, the translocation breakpoint was mapped within the 360-kb region between myeov and cyclin D1. DNA fiber FISH with a contig of probes covering the constant region of the immunoglobulin heavy chain (IgH) revealed that exclusively in the 3 myeov-overexpressing cell lines (KMS-12, KMS-21, and XG-5), either the 5' E(mu) enhancer or the most telomeric 3' Ealpha enhancer was juxtaposed to myeov. Although cyclin D1 overexpression represents a characteristic feature of all MM cell lines with t(11;14), our results demonstrate aberrant expression of a second putative oncogene in a subset of these cases, due to juxtaposition to IgH enhancers. The clinical relevance of this dual activation remains to be elucidated. (Blood. 2000;95:2691-2698)
The extracellular matrix can regulate vascular cell migration, proliferation, and survival: relationships to vascular disease (2000)

The extracellular matrix (ECM) of the normal artery wall is a collection of fibrous proteins and associated glycoproteins embedded in a hydrated ground substance of glycosaminoglycans and proteoglycans. These distinct molecules are organized into a highly ordered network that are closely associated with the vascular cells that produce them. In addition to providing the architectural framework for the artery wall that imparts mechanical support and viscoelasticity, the ECM can regulate the behaviour of vascular cells, including their ability to migrate, proliferate and survive injury. The composition of the ECM is different within intimal lesions of atherosclerosis, which are composed of monocytes and lymphocytes from the circulation and smooth muscle cells (SMC) that migrate from the media to the intima (Ross 1993, 1999), and these differences may contribute to the altered phenotype of vascular cells within lesions. This review will briefly outline the ECM changes observed in atherosclerosis and restenosis and the potential relationship of these changes to altered vascular cell functions.
Sjogren's Syndrome: A Clinical and Biochemical Analysis (2009)

Sjogren’s syndrome (SS) is a systemic autoimmune disease that presents to eye care&#13;\npractitioners with the hallmark symptom of “dry eye.” Stratifying dry eye patients as Sjogren’s positive or negative is a critical differential diagnosis, as SS patients have numerous systemic complications and a forty times greater risk of developing lymphoma. As such, management of this relatively common dry eye sub-population requires specialized&#13;\ncare. Since a firm diagnosis requires testing that is both invasive and expensive, patients should be protected from these tests if they are not warranted.&#13;\nIn this thesis, studies were therefore undertaken to determine if SS dry eye could be differentiated from other forms of dry eye using two methods: 1) standard clinical tests used in a multi-disciplinary Sjogren’s syndrome clinic and 2) subsequent biological evaluation of collected tear samples and cells from the ocular surface. The former would allow eye care&#13;\npractitioners to conduct appropriate tests and pose suitable questions to ifferentiate these subgroups, and the latter might serve in the future as a relatively non-invasive quantitative means of differentiating such groups through biomarkers.
Role of oxygen-derived free radicals in free growth retardation induced by ischemia-reperfusion in rats (1997)

We investigated the involvement of oxygen-derived free radicals in the pathogenesis of the intrauterine growth retardation (IUGR) induced in Sprague-Dawley rats by ischemia-reperfusion. On day 17 of gestation, rats received saline, superoxide dismutase (SOD, 50,000 U/kg), catalase (CAT, 50,000 U/kg), or SOD + CAT subcutaneously 1 h before induction of 30 min of ischemia of the right uterine horn. On day 21 the placental level of lipid peroxides was significantly increased (P < 0.001 vs. sham-operated group) and IUGR was induced (P < 0.001 vs. left horn) in the saline-treated group n = 6). Pretreatment with SOD + CAT (n = 6) significantly inhibited the increase in placental lipid peroxides and prevented IUGR. The effect of ischemia-reperfusion on uterine blood flow, with or without pretreatment with radical scavengers, was investigated in separate experiments by laser-Doppler flowmetry. The induction of hypoperfusion 3 h after ischemia (blood flow -40 +/- 5%, n = 6, P < 0.05) was blocked by pretreatment with SOD + CAT (n = 6). Results indicate that oxygen-derived free radicals may be important in the development of postischemic uteroplacental hypoperfusion and of ischemia-reperfusion-induced IUGR in the rat.
Inhibitors of mitogen-activated protein kinases differentially regulate costimulated T cell cytokine production and mouse airway eosinophilia (2005)

These results demonstrate that the MAPKs ERK and JNK may be suitable targets for anti-inflammatory therapy of asthma, whereas inhibition of p38 seems to be an unlikely target.
Long-term potentiation of horizontal connections provides a mechanism to reorganize cortical motor maps (1994)

1. Field potential recordings were used in rat motor cortex (MI) slice preparations to investigate the potential for activity-dependent modifications in the effectiveness of synaptic connections formed by layer II/III horizontal projections. 2. Long-term potentiation (LTP) of synaptic efficacy in MI horizontal pathways could be produced at short (0.5 mm) and long (1.0 mm) distances by theta burst stimulation (TBS), but only during local, transient application of the gamma-aminobutyric acid-A (GABAA) receptor antagonist, bicuculline methiodide (bic) immediately before TBS. Mean increase of the field potential amplitude measured 25-35 min after LTP induction ranged between 24 and 34%. Cooperative effects of conjoint TBS of two horizontal pathways on LTP induction were observed. 3. These results demonstrate that persistent changes in the functional interactions of cortical neurons can arise by activity-dependent mechanisms within the local horizontal connections and suggest a likely mechanism to recognize cortical representation patterns.
Dry etching: path to coherent refractive microlens arrays (1993)

Reactive ion etching (RIE) is used to fabricate infrared refractive micro-optics in silicon. Three methods are used: binary optics technology which uses iterative steps of photolithography and RIE to create a multistep approximation to an aspheric profile; direct etching of a preshaped polymer microlens etch mask into the substrate; and analog etching of a lens profile directly into the substrate through a pinhole mask.
Nernst Limit in Dual-Gated Si-Nanowire FET Sensors (2010)

Field effect transistors (FETs) are widely used for the label-free detection of analytes in chemical and biological experiments. Here we demonstrate that the apparent sensitivity of a dual-gated silicon nanowire FET to pH can go beyond the Nernst limit of 60 mV/pH at room temperature. This result can be explained by a simple capacitance model including all gates. The consistent and reproducible results build to a great extent on the hysteresis- and leakage-free operation. The dual-gate approach can be used to enhance small signals that are typical for bio- and chemical sensing at the nanoscale.
Feature selection for DNA methylation based cancer classification (2001)

Molecular portraits, such as mRNA expression or DNA methylation patterns, have been shown to be strongly correlated with phenotypical parameters. These molecular patterns can be revealed routinely on a genomic scale. However, class prediction based on these patterns is an under-determined problem, due to the extreme high dimensionality of the data compared to the usually small number of available samples. This makes a reduction of the data dimensionality necessary. Here we demonstrate how phenotypic classes can be predicted by combining feature selection and discriminant analysis. By comparing several feature selection methods we show that the right dimension reduction strategy is of crucial importance for the classification performance. The techniques are demonstrated by methylation pattern based discrimination between acute lymphoblastic leukemia and acute myeloid leukemia.
Integrated Three-Dimensional Craniofacial Mapping: Background, Principles, andPerspectlves (2001)

This article reviews the origins and history of three-dimensional (3D) measurement in orthodontics. Some principles of integrated 3D craniofacial measurement are discussed and illustrated, Present and future perspectives of 3D measurement in orthodontics are examined through the prism of the author's experience at the Craniofacial Research Instrumentation Laboratory (CRIL) of the University of the Pacific School of Dentistry.(Semin Orthod 2001;7:223-232,) Copyright © 2001 by W.B. Saunders Company
Preparation of Polymer-Coated Functionalized Silver Nanoparticles (1999)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTPreparation of Polymer-Coated Functionalized Silver NanoparticlesLuca Quaroni and George ChumanovView Author Information Department of Chemistry Iowa State University, Ames, Iowa 50011 Cite this: J. Am. Chem. Soc. 1999, 121, 45, 10642–10643Publication Date (Web):October 30, 1999Publication History Received21 June 1999Published online30 October 1999Published inissue 1 November 1999https://pubs.acs.org/doi/10.1021/ja992088qhttps://doi.org/10.1021/ja992088qrapid-communicationACS PublicationsCopyright © 1999 American Chemical SocietyRequest reuse permissionsArticle Views5035Altmetric-Citations230LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Layers,Metal nanoparticles,Nanoparticles,Polymer particles,Silver Get e-Alerts
Administration of herpes simplex-thymidine kinase-expressing donor T cells with a T-cell-depleted allogeneic marrow graft (2001)

Administration of donor T cells expressing the herpes simplex-thymidine kinase (HS-tk) with a hematopoietic stem cell (HSC) transplantation could allow, if graft-versus-host disease (GVHD) was to occur, a selective in vivo depletion of these T cells by the use of ganciclovir (GCV). The study evaluates the feasibility of such an approach. Escalating numbers of donor HS-tk-expressing CD3(+) gene-modified cells (GMCs) are infused with a T-cell-depleted bone marrow transplantation (BMT). Twelve patients with hematological malignancies received 2 x 10(5) (n = 5), 6 x 10(5) (n = 5), or 20 x 10(5) (n = 2) donor CD3(+) GMCs/kg with a BMT from a human leukocyte antigen (HLA)-identical sibling. No acute toxicity was associated with GMC administration. An early increase of circulating GMCs followed by a progressive decrease and long-lasting circulation of GMCs was documented. GCV treatment resulted in significant rapid decrease in circulating GMCs. Three patients developed acute GVHD, with a grade of at least II, while one patient developed chronic GVHD. Treatment with GCV alone was associated with a complete remission (CR) in 2 patients with acute GVHD, while the addition of glucocorticoids was necessary to achieve a CR in the last case. Long-lasting CR occurred with GCV treatment in the patient with chronic GVHD. Unfortunately, Epstein-Barr virus-lymphoproliferative disease occurred in 3 patients. Overall, the administration of low numbers of HS-tk-expressing T cells early following an HLA-identical BMT is associated with no acute toxicity, persistent circulation of the GMCs, and GCV-sensitive GVHD. Such findings open the way to the infusion of higher numbers of gene-modified donor T cells to enhance post-BMT immune competence while preserving GCV-sensitive alloreactivity.
Visualizing quaternion rotation (1994)

Quaternions play a vital role in the representation of rotations in computer graphics, primarily for animation and user interfaces. Unfortunately, quaternion rotation is often left as an advanced topic in computer graphics education due to difficulties in portraying the four-dimensional space of the quaternions. One tool for overcoming these obstacles is the quaternion demonstrator, a physical visual aid consisting primarily of a belt. Every quaternion used to specify a rotation can be represented by fixing one end of the belt and rotating the other. Multiplication of quaternions is demonstrated by the composition of rotations, and the resulting twists in the belt depict visually how quaternions interpolate rotation. This article introduces to computer graphics the exponential notation that mathematicians have used to represent unit quaternions. Exponential notation combines the angle and axis of the rotation into concise quaternion expression. This notation allows the article to present more clearly a mechanical quaternion demonstrator consisting of a ribbon and a tag, and develop a computer simulation suitable for interactive educational packages. Local deformations and the belt trick are used to minimize the ribbon's twisting and simulate a natural-appearing interactive quaternion demonstrator.
Quantitative MR microscopy of enzymatically degraded articular cartilage (2000)

Structural changes in bovine patellar articular cartilage, induced by component selective enzymatic treatments, were investigated by measuring tissue T(2) relaxation at 9.4 T. This MRI parameter was compared with Young's modulus, a measure of elastic stiffness and loadbearing ability of cartilage tissue. Collagenase was used to digest the collagen network and chondroitinase ABC to remove proteoglycans. Polarized light microscopy and digital densitometry were used to assess enzyme penetration after 44 hr of enzymatic digestion. T(2) relaxation in superficial cartilage increased significantly only in samples treated with collagenase. A statistically significant decrease in Young's modulus was observed in both enzymatically treated sample groups. These results confirm that T(2) of articular cartilage is sensitive to the integrity of collagen in the extracellular matrix. Nonetheless, it does not appear to be an unambiguous indicator of cartilage stiffness, which is significantly impaired in osteoarthrosis.
Assessment of Accuracy and Analysis Time of a Novel Device to Monitor Sleep and Breathing in the Home (1995)

Obstructive sleep apnea is increasingly recognized as a common and debilitating disorder. As a result, a variety of diagnostic technologies have evolved to potentially decrease cost and improve access and ease of assessment. In this study we compared the Healthdyne NightWatch (NW) System (a home sleep diagnostic methodology) to standard polysomnography (PSG) in two sleep centers. Two separate studies were completed. NW was compared to a simultaneously obtained PSG in 30 patients (IN-LAB study). Seventy additional patients were studied in both the home with NW and in the laboratory with PSG (HOME-LAB study). The NW system records eye movement, leg movement, SaO2, nasal-oral airflow, chest and abdominal wall motion, body position and heart rate on a solid state recorder, which permits sleep staging based on body and eye movement and standard respiratory assessment. For the PSG, standard paper recording techniques were used. The IN-LAB study revealed a correlation between NW and PSG for total sleep time of r = 0.72, with NW tending to score some awake time as nonrapid eye movement sleep. The correlation for apnea-hypopnea index (AHI) was r = 0.94 between systems, with a sensitivity of 100% and specificity of 63.6% at an AHI threshold of 10. The HOME-LAB study demonstrated understandably poor correlations between NW and PSG for most measures of sleep, which is likely a product of night-to-night variability in sleep, home versus laboratory effects and the differences in sleep staging methodology. However, the correlation for AHI was r = 0.92, with a sensitivity of 90.7% and a specificity of 70.4% at an AHI threshold of 10. Using a new methodology to assess agreement between diagnostic systems, we observed 78.6% diagnostic agreement between NW and PSG in the HOME-LAB study, with NW underestimating AHI 4.3% of the time and overestimating it in 17.1% of cases. This may relate to night-to-night variability in AHI or greater NW computer sensitivity to subtle hypopneas. We conclude that NW provides an accurate determination of AHI in both the home and laboratory, using limited instrumentation. The analysis time for NW is also reduced compared to PSG, and patients generally prefer the NW evaluation.
Test circuits for substrate noise evaluation in CMOS digital ICs (2002)

A Transition Controllable Noise Source (TCNS) generates substrate noises with controlled transitions in size, interstage delay, and direction. The noises are measured in a 100 ps 100 /spl mu/V resolution by a linear substrate voltage detector that uses a front-end PMOS source follower probing substrate potential and a back-end latch comparator for sampling/digitizing the source follower output. A 0.4 /spl mu/m CMOS test chip demonstrates the effectiveness of these circuits in performing advanced research on substrate noise.
Construction of a yeast artificial chromosome contig spanning the spinal muscular atrophy disease gene region. (1993)

The childhood spinal muscular atrophies (SMAs) are the most common, serious neuromuscular disorders of childhood second to Duchenne muscular dystrophy. A single locus for these disorders has been mapped by recombination events to a region of 0.7 centimorgan (range, 0.1-2.1 centimorgans) between loci D5S435 and MAP1B on chromosome 5q11.2-13.3. By using PCR amplification to screen yeast artificial chromosome (YAC) DNA pools and the PCR-vectorette method to amplify YAC ends, a YAC contig was constructed across the disease gene region. Nine walk steps identified 32 YACs, including a minimum of seven overlapping YAC clones (average size, 460 kb) that span the SMA region. The contig is characterized by a collection of 30 YAC-end sequence tag sites together with seven genetic markers. The entire YAC contig spans a minimum of 3.2 Mb; the SMA locus is confined to roughly half of this region. Microsatellite markers generated along the YAC contig segregate with the SMA locus in all families where the flanking markers (D5S435 and MAP1B) recombine. Construction of a YAC contig across the disease gene region is an essential step in isolation of the SMA-encoding gene.