gebhart/patrepeval huggingface dataset:
A Genomic-Profile Derived Summary Measure of Chromosomal Breakpoints Predicts Response to Treatment with the DNA-Damaging Agent Cisplatin. (2009)

Abstract Cisplatin-based chemotherapy promotes DNA inter- and intra-strand cross-links and is effective treatment in multiple cancer types, yet it is rarely used for first-line therapy of breast cancer. Cisplatin is an effective cytotoxic in BRCA1 mutant cancer cell lines and in breast and ovarian cancers with BRCA1 mutations, prompting speculation that defective DNA double-strand break repair is associated with cisplatin sensitivity. Furthermore, tumors with BRCA1 mutation are presumed to be defective in various aspects of DNA repair and also display increased levels of chromosomal instability. Thus, we hypothesized that the total number of chromosomal breakpoints in a specific tumor may reflect defective DNA repair and/or chromosomal instability, and may therefore be used as a predictor of cisplatin sensitivity. Supporting this relationship, we identified a correlation (r = 0.8, P = 0.08) between the total number of chromosomal breakpoints, estimated by the number of genomic regions showing allelic imbalance, and cisplatin sensitivity in five triple negative breast cancer cell lines. To validate this relationship in a clinical setting we compared the total number of chromosomal breakpoints to therapy response in a cisplatin treated breast cancer cohort. A total of 28 women with stage II or III ER-/PR-/HER2- breast cancer were treated with cisplatin in the neo-adjuvant setting followed by surgery and standard adjuvant chemotherapy. A core biopsy was obtained before treatment commenced, tumor cells were enriched by needle microdissection, and DNA was extracted for genotyping. As only limited amounts of DNA were available, we used a Molecular Inversion Probe assay (in collaboration with Affymetrix), which allowed us to genotype 42,000 SNPs with only 40 ng of starting DNA. We then estimated the total number of putative genomic breakpoints in 21 samples containing at least 75% tumor cells. We compared this summary genomic measure to the response rate as quantitated by the Miller-Payne score determined on the pathological specimen obtained at surgery. This genomic measure showed a remarkably accurate separation of patients by degree of response, correctly classifying 20 out of 21 patients (P &amp;lt; 0.001).These results suggest that the total number of DNA breakpoints may be an accurate biomarker of breast cancers which may be sensitive to cisplatin treatment. The molecular explanations for these findings await further work. Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 111.
Prepolarized magnetic resonance imaging around metal orthopedic implants (2006)

A prepolarized MRI (PMRI) scanner was used to image near metal implants in agar gel phantoms and in in vivo human wrists. Comparison images were made on 1.5- and 0.5-T conventional whole-body systems. The PMRI experiments were performed in a smaller bore system tailored to extremity imaging with a prepolarization magnetic field of 0.4 T and a readout magnetic field of 27-54 mT (1.1-2.2 MHz). Scan parameters were chosen with equal readout gradient strength over a given field of view and matrix size to allow unbiased evaluation of the benefits of lower readout frequency. Results exhibit substantial reduction in metal susceptibility artifacts under PMRI versus conventional scanners. A new artifact quantification technique is also presented, and phantom results confirm that susceptibility artifacts improve as expected with decreasing readout magnetic field using PMRI. This proof-of-concept study demonstrates that prepolarized techniques have the potential to provide diagnostic cross-sectional images for postoperative evaluation of patients with metal implants.
Contribution of Domain Interface Residues to the Stability of Antibody C<sub>H</sub>3 Domain Homodimers (1998)

Dimers of CH3 domains from human IgG1 were used to study the effect of mutations constructed at a domain-domain interface upon domain dissociation and unfolding, "complex stability". Alanine replacement mutants were constructed on one side of the interface for each of the sixteen interdomain contact residues by using a single-chain CH3 dimer in which the carboxyl terminus of one domain was joined to the amino terminus of the second domain via a (G4S)4 linker. Single-chain variants were expressed in Escherichia coli grown in a fermentor and recovered in yields of 6-90 mg L-1 by immobilized metal affinity chromatography. Guanidine hydrochloride-induced denaturation was used to follow domain dissociation and unfolding. Surprisingly, the linker did not perturb the complex stability for either the wild type or two destabilizing mutants. The CH3 domain dissociation and unfolding energetics are dominated by six contact residues where corresponding alanine mutations each destabilize the complex by >2.0 kcal mol-1. Five of these residues (T366, L368, F405, Y407, and K409) form a patch at the center of the interface and are located on the two internal antiparallel beta-strands. These energetically key residues are surrounded by 10 residues on the two external beta-strands whose contribution to complex stability is small (three have a Delta DeltaG of 1.1-1.3 kcal mol-1) or very small (seven have a Delta DeltaG of </=0.7 kcal mol-1). Thus, at the center of the CH3 structural interface there is a small "functional interface" of residues that make significant contributions to complex stability.
Reversal of resistance to Bacillus thuringiensis in Plutella xylostella. (1994)

Continued success of the most widely used biopesticide, Bacillus thuringiensis, is threatened by development of resistance in pests. Experiments with Plutella xylostella (diamondback moth), the first insect with field populations resistant to B. thuringiensis, revealed factors that promote reversal of resistance. In strains of P. xylostella with 25- to 2800-fold resistance to B. thuringiensis compared with unselected strains, reversal of resistance occurred when exposure to B. thuringiensis was stopped for many generations. Reversal of resistance was associated with restoration of binding of B. thuringiensis toxin CryIA(c) to brush-border membrane vesicles and with increased biotic fitness. Compared with susceptible colonies, revertant colonies had a higher proportion of extremely resistant individuals. Revertant colonies responded rapidly to reselection for resistance. Understanding reversal of resistance will help to design strategies for extending the usefulness of this environmentally benign insecticide.
Identification of a continuous and cross-reacting epitope for Plasmodium falciparum transmission-blocking immunity. (1991)

Identification of continuous epitopes in the target antigens of Plasmodium falciparum transmission-blocking antibodies is likely to facilitate the production of a subunit peptide vaccine. Two such epitopes shared among several sexual-stage antigens were identified with murine monoclonal antibodies. An epitope recognized by four monoclonal antibodies capable of blocking infectivity of gametocytes in the mosquitoes is shared among three antigens (230, 48/45 doublet, and 27 kDa). These antigens are synthesized at different times during the development and maturation of gametocytes, and the blocking epitope appears conserved among parasites from diverse geographical locations. Immune response against such a unique epitope (continuous, cross-reacting, and conserved) is likely to be boosted by natural infection. The 27-kDa protein is reported here as a target of malaria transmission-blocking monoclonal antibodies, and the cross-reacting epitope represents an attractive candidate for a transmission-blocking vaccine.
Bottom-Gate Gallium Indium Zinc Oxide Thin-Film Transistor Array for High-Resolution AMOLED Display (2008)

The fabrication process and the characteristics of bottom-gate Ga <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> -In <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> -ZnO (GIZO) thin-film transistors (TFTs) are reported in detail. Experimental results show that oxygen supply during the deposition of GIZO active layer and silicon oxide passivation layer controls the threshold voltage of the TFT. The field-effect mobility and the threshold voltage of the GIZO TFT fabricated under the optimum process conditions are 2.6 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> /V ldr s and 3.8 V, respectively. A 4-in QVGA active-matrix organic light-emitting diode display driven by the GIZO TFTs without any compensation circuit in the pixel is successfully demonstrated.
Meta-Analysis and Dose-Response Metaregression: Circulating Insulin-Like Growth Factor I (IGF-I) and Mortality (2011)

Both low and high IGF-I concentrations are associated with increased mortality in the general population.
Toward haptic/aural touchscreen display of graphical mathematics for the education of blind students (2011)

We propose the use of a haptic touchscreen to convey graphical and mathematical concepts through aural and/or vibratory tactile feedback. We hypothesize that an important application of such a display will be in teaching visually impaired students concepts that are traditionally learned almost entirely visually. This paper describes initial feasibility studies using a commercially available haptic touchscreen to display grids, points, lines, and shapes - some of the first visual graphical entities students encounter in K-12 mathematics education, and from which more complex lessons can be constructed. We conducted user studies designed to evaluate perception of these objects through haptic feedback alone, auditory feedback alone, and combinations of the two. Our results indicate that both sensory channels can be valuable in user perception.
Conservation of the Notch signalling pathway in mammalian neurogenesis (1997)

The Notch pathway functions in multiple cell fate determination processes in invertebrate embryos, including the decision between the neuroblast and epidermoblast lineages in Drosophila. In the mouse, targeted mutation of the Notch pathway genes Notch1 and RBP-Jk has demonstrated a role for these genes in somite segmentation, but a function in neurogenesis and in cell fate decisions has not been shown. Here we show that these mutations lead to altered expression of the Notch signalling pathway homologues Hes-5, Mash-1 and Dll1, resulting in enhanced neurogenesis. Precocious neuronal differentiation is indicated by the expanded expression domains of Math4A, neuroD and NSCL-1. The RBP-Jk mutation has stronger effects on expression of these genes than does the Notch1 mutation, consistent with functional redundancy of Notch genes in neurogenesis. Our results demonstrate conservation of the Notch pathway and its regulatory mechanisms from fly to mouse, and support a role for the murine Notch signalling pathway in the regulation of neural stem cell differentiation.
Guest editorial - 50th anniversary of CLOS networks (2003)

Presents the guest editorial for this issue of the publication.
Syntheses of all-(Z)-5,8,11,14,17-Eicosapentaenoic Acid and all-(Z)-4,7,10,13,16,19-Docosahexaenoic Acid from (Z)-1,1,6,6-tetraisopropoxy-3-hexene (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSyntheses of all-(Z)-5,8,11,14,17-Eicosapentaenoic Acid and all-(Z)-4,7,10,13,16,19-Docosahexaenoic Acid from (Z)-1,1,6,6-tetraisopropoxy-3-hexeneJacqueline Sandri and Jacques VialaCite this: J. Org. Chem. 1995, 60, 20, 6627–6630Publication Date (Print):October 1, 1995Publication History Published online1 May 2002Published inissue 1 October 1995https://pubs.acs.org/doi/10.1021/jo00125a065https://doi.org/10.1021/jo00125a065research-articleACS PublicationsRequest reuse permissionsArticle Views950Altmetric-Citations38LEARN 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 (2)»Supporting Information Supporting Information Get e-Alerts
Broad-Band Mirror (1.12–1.62&amp;lt;tex&amp;gt;$mu$&amp;lt;/tex&amp;gt;m) Using a Subwavelength Grating (2004)

We report the first experimental demonstration of a novel single-layer subwavelength grating (SWG) that has >500-nm-wide reflection spectrum from 1.12-1.62 μm and very high reflectivity (>98.5%). This SWG is scalable for different wavelengths by simply changing the grating dimensions, which, thus, facilitates monolithic integration of devices over a wide range of wavelengths.
Cardiac dose evaluation for 3Dimensional conformal partial breast irradiation compared with whole breast irradiation (2009)

To compare the radiation dose to normal cardiac tissue for 3Dimensional (3D) conformal external beam partial breast irradiation (PBI) and standard whole breast irradiation (WBI), and examine the effect of tumor bed location. For 14 patients with left breast tumors randomized on the National Surgical Adjuvant Breast and Bowel Project B-39 protocol, computer-generated radiotherapy treatment plans were devised for WBI and PBI. Tumor bed location was designated according to whether more than 50% of the excision cavity was medial or lateral to the nipple line. The volume of heart receiving doses of 2.5, 5, 10, and 20 Gy was calculated for all PBI and WBI plans. Dose to 5% of the heart volume (D5) and mean heart dose were also calculated. The biologically-equivalent dose (BED) was calculated to account for the different fractionation used in PBI and WBI. Of the 14 patients, 8 had lateral tumor beds, and 6 had medial tumor beds. The volumes of heart receiving 2.5, 5, 10, and 20 Gy were significantly lower for lateral PBI compared with WBI. For medial PBI, significant cardiac sparing was only seen at a dose of 20 Gy. The difference of D5 values was significant for lateral PBI compared with WBI (p=0.008), but not for medial PBI compared with WBI (p=0.84). The mean dose was also significantly lower for lateral PBI compared with WBI (p=0.008), but not for medial PBI (p=0.16). The results from BED calculations did not change this outcome. Both 3D conformal PBI and standard WBI can deliver relatively low doses to the heart. For patients with lateralized tumor beds, PBI offers significant cardiac sparing compared with WBI. Patients with medial lesions have relatively similar heart dosimetry with PBI and WBI. 3D conformal PBI is an emerging treatment modality and continued participation on clinical trials is encouraged. Patients with left-sided lesions and lateralized tumor beds warrant special consideration for PBI, given the significant cardiac dose sparing.
A Chiral and Colorful Redox Switch: Enhanced π Acidity in Action (2010)

Deep blue diving: π Acidities up to a new record of −4.74 eV are made possible with simple sulfur redox chemistry (see scheme). This attractive method is able to generate exceptional electron affinities and anion transport efficiencies for applications in optoelectronic devices, medicinal chemistry, and anion–π catalysis. 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.
Sustained Effectiveness of Converting-Enzyme Inhibition in Patients with Severe Congestive Heart Failure (1980)

Eight patients with severe congestive heart failure refractory to conventional therapy, including vasodilators, were given captopril (seven patients) or teprotide (one patient). All had dyspnea, edema, elevated pulmonary wedge pressure (28.0 +/- 2.6 mm Hg), low cardiac index (1.6 +/- 0.1 liters per minute per square meter), and elevated levels of serum creatinine (2.3 +/- 0.2 mg per deciliter [203.3 +/- 17.7 mumol per liter]), blood urea nitrogen (48 +/- 5 mg per deciliter [17.1 +/- 1.8 mmol of urea per liter]), plasma renin activity (21 +/- 7 ng of angiotensin I per milliliter per hour), plasma angiotensin II (271 +/- 51 pg per milliliter), and plasma aldosterone (65 +/- 14 ng per deciliter). After one week of therapy, all indexes improved. Creatinine and p-aminohippurate clearances were also increased (P less than 0.01). Improvement was sustained (more than six months) and was associated with a statistically significant increase in the cardiac ejection fraction (12 +/- 3 to 26 +/- 7 per cent). With a mean follow-up of seven months, the New York Heart Association Functional Class has been reduced from IV to II, and the number of days of hospitalization to less than 10 per cent of that before captopril therapy. We conclude that captopril reduces afterload in advanced congestive heart failure and induces sustained improvements in clinical status and renal function.
Evaluation of a Decentralized Architecture for Large Scale Collaborative Intrusion Detection (2007)

An important problem in network intrusion detection is how to detect large scale coordinated attacks such as scans, worms and denial-of-service attacks. These coordinated attacks can be difficult to detect at an early stage, since the evidence of the attack may be widely distributed across different subnetworks in the Internet. A critical issue for research is how to detect these large scale attacks by correlating information from multiple intrusion detection systems in an efficient manner. Several collaborative detection systems have been proposed in the literature. However, these proposals have lacked large scale testing in real networks, and the practicalities of how to optimize the trade-off between detection accuracy and reaction time of these systems has not been demonstrated. To address these challenges, we propose LarSID, a scalable decentralized large scale intrusion detection framework. LarSID provides a service for defending against attacks by sharing potential evidence of intrusions between participant intrusion detection systems via a distributed hash table (DHT) architecture. In particular, we investigate how to optimize the trade-off between detection accuracy and reaction time of LarSID based on an analysis of a large, real-world intrusion detection dataset (DShield Dataset), which has been collected from over 1600 firewall administrators across the world. LarSID has been deployed and tested on the PlanetLab testbed, and is built on top of OpenDHT - a public DHT service. Our experimental results show significant reductions in detection latency compared to a centralized detection architecture. Currently, LarSID has been deployed on 128 PlanetLab nodes as a large scale intrusion detection service.
MARCKS Protein Is a Key Molecule Regulating Mucin Secretion by Human Airway Epithelial Cells in Vitro (2001)

Hypersecretion of airway mucin characterizes numerous respiratory diseases. Although diverse pathological stimuli can provoke exocytotic release of mucin from secretory cells of the airway epithelium, mechanisms involved remain obscure. This report describes a new paradigm for the intracellular signaling mechanism regulating airway mucin secretion. Direct evidence is provided that the myristoylated alanine-rich C kinase substrate (MARCKS) is a central regulatory molecule linking secretagogue stimulation at the cell surface to mucin granule release by differentiated normal human bronchial epithelial cells in vitro. Down-regulation of MARCKS expression or disruption of MARCKS function in these cells inhibits the secretory response to subsequent stimulation. The intracellular mechanism controlling this secretory process involves cooperative action of two separate protein kinases, protein kinase C and cGMP-dependent protein kinase. Upon stimulation, activated protein kinase C phosphorylates MARCKS, causing translocation of MARCKS from the plasma membrane to the cytoplasm, where it is then dephosphorylated by a protein phosphatase 2A that is activated by cGMP-dependent protein kinase, and associates with both actin and myosin. Dephosphorylated cytoplasmic MARCKS would also be free to interact with mucin granule membranes and thus could link granules to the contractile cytoskeleton, mediating their movement to the cell periphery and subsequent exocytosis. These findings suggest several novel intracellular targets for pharmacological intervention in disorders involving aberrant secretion of respiratory mucin and may relate to other lesions involving exocytosis of membrane-bound granules in various cells and tissues.
M<sup>2</sup>EC: A multi-tenant resource orchestration in multi-access edge computing systems (2018)

Multi-access Edge Computing (MEC) is envisioned as a key technology in the 5G landscape, able to bring computing capabilities to the edge of the network, closer to the end users. This would help to fulfill the next generation network requirements in terms of low latency and high bandwidth. ETSI has started specifying MEC as an operator-owned system to run third party's applications, which can leverage the benefits inherent to the MEC environment for added value services to the end users. In this paper we explore a novel paradigm for third parties to access the MEC system: renting part of MEC facilities leveraging on the network slicing paradigm to expand the business opportunities for both the system provider and the MEC tenants. We introduce the concept of MEC broker as an entity exposing administration and management capabilities while handling heterogeneous tenant privileges. Our concept is validated by developing an orchestration solution, namely M <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> EC, to optimally allocate requested resources in compliance with the tenants service level agreements.