gebhart/patrepeval huggingface dataset:
Association of a DNA damage response deficiency (DDRD) assay and prognosis in early-stage esophageal adenocarcinoma. (2014)

4015 Background: The incidence of esophageal adenocarcinoma (EAC) has increased 6-fold in the last 30 years and in early stage EAC 5-year survival remains poor at 25-35%. Neoadjuvant therapy confers a significant improvement in outcomes but the optimal approach for individual patients remains unclear. We assessed a 44 gene DNA Damage Response Deficient (DDRD) assay, previously developed to detect loss of the Fanconi Anaemia (FA)/BRCA pathway in breast cancer, as a predictor of prognosis following DNA damaging chemotherapy in EAC. Methods: This study was conducted using 63 formalin fixed paraffin embedded (FFPE) pre-treatment endoscopic biopsy specimens from early stage EAC patients treated with cisplatin-based neoadjuvant chemotherapy followed by surgical resection between 2004 and 2010 at the NI Cancer Centre. EAC biopsies were profiled using the Xcel array, a cDNA microarray-based technology optimized for archival FFPE tissue (Almac/Affymetrix), and scored for the DDRD assay. The association between the DDRD score and prognosis was assessed by Kaplan-Meier analysis and Cox Proportional Hazards regression. Results: Sufficient quality RNA for analysis was obtained for 62 out of 63 samples (98.4%). A total of 13 samples (21%) were characterised as DDRD positive with the remaining 49 samples (79%) DDRD negative. With a median follow up of 65 months, DDRD assay positivity demonstrated a statistically significant association with disease-free (HR 0.33; 95% CI 0.13-0.87; p=0.024) and overall survival (HR 0.32; 95% CI 0.12-0.82; p=0.017; median DDRD+ve 94.3 months vs DDRD-ve 32.2 months). The assay was not predictive of survival in patients who did not receive chemotherapy. Conclusions: The DDRD assay is the first array-based biomarker using pre-treatment FFPE biopsies to be validated as predictive of prognosis following DNA damaging chemotherapy in early stage EAC. Multivariable analysis of disease-free survival. Hazard ratio Lower 95% CI Upper 95% CI p value DDRD-positive 0.310 0.110 0.877 0.027 Surgical T stage 2 vs 0 & 1 0.343 0.078 1.519 0.159 Surgical T stage 3+ vs 0 & 1 0.470 0.126 1.751 0.261 N stage 1 vs 0 4.793 1.590 14.447 0.005 N stage 2 & 3 vs 0 7.822 2.777 22.034 <0.001
Compressive Sensing Fundamentals (2014)

This chapter discusses sparse models, compressive measurement protocols, and the recovery of sparse signals from compressive measurements. Sparsity is manifestation of the fact that many high-dimensional signals actually have a small number of degrees of freedom. The choice of whether a signal is better described using a synthesis sparsity model or an analysis sparsity model can depend on the context. Synthesis sparsity can be preferable in cases where one views the dictionary elements as ingredients that actually comprise the signal; analysis sparsity can be preferable in cases where the dictionary is merely a set of vectors used for looking at the signal. Greedy algorithms for compressive sensing (CS) reconstruction are an alternative to optimization-based recovery methods. Algorithms can be adopted to exploit the structure of exclusions reduced union of subspaces, and when these algorithms are successfully employed, the CS reconstruction problem can be solved using fewer measurements than would be required using a conventional algorithm suitable for unstructured sparsity models.
Table S1 from Metabolic Reprogramming by MYCN Confers Dependence on the Serine-Glycine-One-Carbon Biosynthetic Pathway (2023)

&lt;p&gt;List of genes regulated by the PHGDH inhibitor NCT-503&lt;/p&gt;
THz Channel Sounding: Design and Validation of a High Performance\n Channel Sounder at 300 GHz (2020)

In this paper, a novel instrument-based time-domain THz channel sounder for\nthe 300 GHz band is introduced. The performance is characterized by conducted\nmeasurements and verified by over-the-air measurements, which confirm the\nsensitivity and highlight the temporal resolution of the setup. Dynamic range,\nmaximum measurable path loss and phase stability are evaluated. The results\nshow that the performance in terms of dynamic range and maximum measurable path\nloss is, to the best knowledge of the authors, unprecedented in this frequency\nrange.\n
Efficient Capacity Provisioning for Firms with Multiple Locations: The Case of the Public Cloud (2022)

We analyze a model in which a firm with multiple locations chooses capacity and prices to maximize efficiency. We find that the firm provisions capacity in such a way that the expected fraction of demand that will be unfilled is lower in locations with greater expected demand. The firm also sets lower prices in larger locations. Finally, if a customer is indifferent between multiple locations, then it is more efficient to place this customer in a location with greater expected demand. These theoretical results are consistent with empirical evidence that we present from a major public cloud provider.
Laparoscopic Transdiaphragmatic Access to the Apex of the Left Ventricle of the Heart (2009)

: Laparoscopic transdiaphragmatic approach to the LVOT is a possible route for minimally invasive beating heart aortic valve implantation. This strategy permits a straight transapical line of access to the aortic valve; avoiding the potential for cardiac torsion via a thoracotomy.
Directing Cinematographic Drones (2018)

Quadrotor drones equipped with high-quality cameras have rapidly raised as novel, cheap, and stable devices for filmmakers. While professional drone pilots can create aesthetically pleasing videos in short time, the smooth—and cinematographic—control of a camera drone remains challenging for most users, despite recent tools that either automate part of the process or enable the manual design of waypoints to create drone trajectories. This article moves a step further by offering high-level control of cinematographic drones for the specific task of framing dynamic targets. We propose techniques to automatically and interactively plan quadrotor drone motions in dynamic three-dimensional (3D) environments while satisfying both cinematographic and physical quadrotor constraints. We first propose the Drone Toric Space , a dedicated camera parameter space with embedded constraints, and derive some intuitive on-screen viewpoint manipulators. Second, we propose a dedicated path planning technique that ensures both that cinematographic properties can be enforced along the path and that the path is physically feasible by a quadrotor drone. At last, we build on the Drone Toric Space and the specific path planning technique to coordinate the motion of multiple drones around dynamic targets. A number of results demonstrate the interactive and automated capacities of our approaches on different use-cases.
Finite Atomized Semilattices (2021)

We show that every finite semilattice can be represented as an atomized semilattice, an algebraic structure with additional elements (atoms) that extend the semilattice's partial order. Each atom maps to one subdirectly irreducible component, and the set of atoms forms a hypergraph that fully defines the semilattice. An atomization always exists and is unique up to "redundant atoms". Atomized semilattices are representations that can be used as computational tools for building semilattice models from sentences, as well as building its subalgebras and products. Atomized semilattices can be applied to machine learning and to the study of semantic embeddings into algebras with idempotent operators.
<i>In Vitro</i>: Cytotoxicity, Apoptosis and Ameliorative Potential of <i>Lawsonia inermis</i> Extract in Human Lung, Colon and Liver Cancer Cell Line (2020)

Cancer has emerged as a major public health issue in developed as well as in developing countries. Plant-derived molecules are widely being used in the treatment of cancer due to their minimum side effects. <i>Lawsonia inermis</i> (Henna) is one of the medicinal plants containing many therapeutic properties. In the present study, bioactive components of <i>L. inermis</i> extract were analyzed by LCMS/MS method and validated. Lawsone (3.5%) is primarily responsible for cytotoxic and anti-cancerous activities. These properties were studied on human lung carcinoma (A549), colorectal cancer (DLD1) and Hepatocellular carcinoma (HepG2) cancer cell lines. The activities were assessed by MTT assay, evaluation of apoptosis by measuring the production of Reactive Oxygen Species (ROS) and mitochondrial membrane potential of the cancer cell lines. Moreover, apoptosis in the respective cancer cell lines was also determined by chromatin condensation and DNA fragmentation using Hoechst 33528 and propidium iodide (PI) staining. The preliminary <i>in vitro</i> result of MTT showed that the henna extract induces cytotoxic properties against A549, DLD1, HepG2 with IC<sub>50</sub>values 490, 480 and 610 μg/ml respectively (more than 40% growth inhibition). In addition, the extract induced a concentration-dependent rise in ROS production which was 84, 102, and 110% in HepG2, DLD1 AND A549 respectively at 300 μg/ml, whereas at 400 μg/ml concentration it was 86, 102, and 106% in respective cell lines while decreasing mitochondrial membrane potential was more than 20% in the investigated cell lines. The extract also provoked changes associated with apoptosis and the data indicate that the ROS production leads to a diminution in mitochondrial membrane potential and this correlated with the extract cytotoxicity.
BlockTrail: A Scalable Multichain Solution for Blockchain-Based Audit Trails (2019)

Blockchain-based audit trails provide a consensus-driven and tamper-proof trail of system events that are helpful in creating provenance in enterprise solutions. However, taking into account the transaction bulk generated by these applications and the throughput limitations of existing blockchains, a single ledger for record keeping can be inefficient and costly. To that end, we see an imperative need for a new blockchain design that is capable of addressing current challenges, without compromising security and provenance. Hence, we propose BlockTrail, a scalable and efficient blockchain solution for auditing applications. BlockTrail fragments the legacy blockchain systems into layers of co-dependent hierarchies, thereby reducing the time and space complexity, and increasing the throughput. BlockTrail is prototyped on "Practical Byzantine Fault Tolerance" (PBFT) protocol with a custom-built blockchain. Experiments with BlockTrail show that compared to the conventional schemes, BlockTrail is more efficient, and has less storage footprint.
Pathways to defense metabolites and evading fruit bitterness in genus Solanum evolved through 2-oxoglutarate-dependent dioxygenases (2019)

The genus Solanum comprises three food crops (potato, tomato, and eggplant), which are consumed on daily basis worldwide and also producers of notorious anti-nutritional steroidal glycoalkaloids (SGAs). Hydroxylated SGAs (i.e. leptinines) serve as precursors for leptines that act as defenses against Colorado Potato Beetle (Leptinotarsa decemlineata Say), an important pest of potato worldwide. However, SGA hydroxylating enzymes remain unknown. Here, we discover that 2-OXOGLUTARATE-DEPENDENT-DIOXYGENASE (2-ODD) enzymes catalyze SGA-hydroxylation across various Solanum species. In contrast to cultivated potato, Solanum chacoense, a widespread wild potato species, has evolved a 2-ODD enzyme leading to the formation of leptinines. Furthermore, we find a related 2-ODD in tomato that catalyzes the hydroxylation of the bitter α-tomatine to hydroxytomatine, the first committed step in the chemical shift towards downstream ripening-associated non-bitter SGAs (e.g. esculeoside A). This 2-ODD enzyme prevents bitterness in ripe tomato fruit consumed today which otherwise would remain unpleasant in taste and more toxic.
Hand/Arm Forces with Pneumatic Nail Gun Actuation Systems (2014)

A biomechanical model is presented to estimate cumulative user hand/arm force associated with two pneumatic nail gun trigger systems. The contact actuation trigger (CAT) can fire a nail when the user holds the trigger depressed first and then “bumps” the nail gun safety tip against the workpiece. With a full sequential actuation trigger (SAT) the user must press the tip against the workpiece prior to activating the trigger. The SAT is demonstrably safer in reducing traumatic injury risk, but increases the duration (and magnitude) of tip force exertion. Time integrated hand force was calculated for a single user from measurements of the tip contact force with the workpiece and transfer time between nails as inputs to a quasi-dynamic model of nailing in two task orientations. Application of the model shows the hand/arm force dependence upon the orientation of the workpiece in addition to the trigger system. Based on standard time allowances from work measurement systems (i.e. MTM - 1) the model results suggest that efficient application of tip contact force with the SAT would reduce total hand/arm force exertion attributable to this trigger system for this user. The present model is useful for considering differences in cumulative hand/arm force exposure between the SAT and CAT systems and the user perceptions and practices that result from these differences.
A Polymeric Molecular “Handle” for Multiple AFM‐Based Single‐Molecule Force Measurements (2008)

Bindungsstärken per Handgriff: Die mechanische Einzelmolekülentfaltung modularer Proteine kann zur Untersuchung beliebiger Bindungen genutzt werden, indem man ein maßgeschneidertes Kammpolymer einsetzt, das entlang seiner Hauptkette die betreffenden Wechselwirkungen oder Bindungen eingehen kann. Der Ansatz wird zur Untersuchung des Ni-(His)n-NTA-Komplexes verwendet (siehe Bild: rot Ni-NTA, grün His-Markierung; His=Histidin, NTA=Nitrilotriacetat). Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2001/2008/z704526_s.pdf or from the author. 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.
Laser-Induced Crystalline-Phase Transformation for Hematite Nanorod Photoelectrochemical Cells (2020)

Generally, a high-temperature postannealing process is required to enhance the photoelectrochemical (PEC) performance of hematite nanorod (NR) photoanodes. However, the thermal annealing time is limited to a short duration as thermal annealing at high temperatures can result in some critical problems, such as conductivity degradation of the fluorine-doped tin oxide film and deformation of the glass substrate. In this study, selective laser processing is introduced for hematite-based PEC cells as an alternative annealing process. The developed laser-induced phase transformation (LIPT) process yields hematite NRs with enhanced optical, chemical, and electrical properties for application in hematite NR-based PEC cells. Owing to its improved properties, the LIPT-processed hematite NR PEC cell exhibits an enhanced water oxidation performance compared to that processed by the conventional annealing process. As the LIPT process is conducted under ambient conditions, it would be an excellent alternative annealing technique for heat-sensitive flexible substrates in the future.
The Critical Response to William Styron (1995)

Series Foreword by Cameron Northouse William Styron's Published Writings: Checklist Introduction Lie Down in Darkness Domestic Tragedy in Virginia by Maxwell Geisman (1951) Memorable First Novel Demolishes Family by Lee Grove (1951) What to Do About Chaos by Louis D. Rubin (1951) Discarded Watermelon Rinds: The Rainbow Aesthetic of Styron's Lie Down in Darkness by William J. Scheick (1978) In Quest of Redemption: The Religious Background of Peyton's Monologue in Lie Down in Darkness by John Lang (1983) a new father, new home: Styron, Faulkner, and Southern Revisionism by Christopher Metress (1990) Darkness Visible and Invisible: The Landscape of Depression in Lie Down in Darkness by Jeffrey Berman (1994) The Long March William Styron by Richard Pearce (1971) Styron's Farewell to Arms: Writings on the Military by Judith Ruderman (1987) Set This House on Fire Review, Thomas F. Curley (1960) Review, Charles Monaghan (1960) The Absurd Hero in American Fiction: Updike, Styron, Bellow, Salinger by David D. Galloway (1970) Styron's Disguises: Provisional Rebel in Christian Masquerade by Samuel Coale (1985) The Confessions of Nat Turner The Fire Last Time by George Steiner (1967) Through the Midst of Jerusalem by Philip Rahv (1967) You've Taken My Nat and Gone by Vincent Harding (1968) The Confessions of Nat Turner: History and Imagination by Floyd C. Watkins (1977) This Unquiet Dust: The Problem of History in Styron's The Confessions of Nat Turner by James M. Mellard (1983) Sophie's Choice Novel of Evil by John Gardner (1979) Evil and William Styron by Pearl K. Bell (1979) Speaking and Unspeakable in Styron's Sophie's Choice by Michael Kreyling (1984) The Thematic Unity of Sophie's Choice by John Kenny Crane (1985) William Styron's Sophie's Choice: The Structure of Oppression by Carolyn A. Durham (1984) The Reach of Fiction: Narrative Technique in Styron's Sophie's Choice by Richard G. Law (1991) Darkness Visible Surmounting the Intolerable: Reconstructing Loss in Sophie's Choice, A Tidewater Morning, and Darkness Visible by Thornton F. Jordan (1994) Bibliography of Criticism Index
Asymmetric Synthesis of Stellettamides A and C (2008)

The first synthesis of the marine indolizidine alkaloids, (+)-stellettamide A and (-)-stellettamide C, has been achieved through a coupling reaction with the aminomethylindolizidine fragment and the chiral or achiral trienecarboxylic acid fragment, both of which could be derived from farnesol as a common precursor.Stellettamide A (1) was isolated from the marine sponge genus Stelletta, which was collected near Shikinejima island of Japan in 1990 by Fusetani and coworkers, 1 as the first example of an indolizidine class of marine alkaloids.Stellettamide A exhibits calmodulin inhibitory activity 2 as well as antifungal and cytotoxic activities against tumor cell lines. 1 The absolute stereochemistry of stellettamide A was
Genetic Variation in Oocyte Phenotype Revealed Through Parthenogenesis and Cloning: Correlation with Differences in Pronuclear Epigenetic Modification1 (2004)

Previous studies revealed that oocytes of different genetic strains (e.g, C57BL/6 and DBA/2) modify maternal and paternal pronuclei differently, affecting early preimplantation development. To determine whether these strain-dependent effects would also apply to oocyte modifications of somatic cell nuclei introduced during cloning procedures, we compared the efficiency of development of parthenogenetic and cloned embryos made with DBA/2, C57BL/6, and (B6D2)F1 oocytes. Our results reveal significant differences in the ability of oocytes of different genetic backgrounds to support parthenogenetic development in different culture media. Additionally, our results reveal oocyte strain-dependent differences in the ability to support cloned embryo development beyond what can be accounted for on the basis of differences in parthenogenesis. Thus, the previously documented differences in oocyte-directed parental genome modification are accompanied in the same strains by differences in the ability of oocytes to modify somatic cell nuclei and support clonal development, raising the possibility that these oocyte functions may be mediated by related mechanisms. These results provide a genetic basis for further studies seeking to identify specific genes that determine oocyte phenotype, as well as genes that determine the success of nuclear reprogramming and clonal development.
Physical and pH Properties of Gastroesophagopharyngeal Refluxate: A 24-hour Simultaneous Ambulatory Impedance and pH Monitoring Study (2004)

Concurrent impedance and pH recordings detect significantly more events qualifying as reflux in the pharynx than pH recordings alone. A substantial majority of these events are gaseous refluxes both with and without minor pH drops. Gas reflux events with weak acidity appear to be more common among patients with reflux-attributed laryngeal lesions compared to GERD patients and controls.
Evaluation of Biomass-Derived Distillate Fuel as Renewable Heating Oil (2015)

The utilization of advanced biofuels in stationary applications, such as home heating, is considered as an early entry point for biomass-derived fuels into the distillate fuel market sector. Two renewable fuels produced by a biomass fluidized catalytic cracking (BFCC) process, followed by hydroprocessing and fractionation, were tested. The evaluation was performed on a pure (100%) distillate fraction, 50% blend of the distillate fraction with petroleum-based heating oil, and 20% blend of a heavier gas oil fraction. Combustion experiments were carried out in a transparent quartz chamber and a typical oil-fired residential boiler. The flame stability, size, and shape produced by the fuels were examined. The flue gas was analyzed for O2, CO, NOx, and smoke. The elastomer compatibility test was performed with nitrile slabs at 43 °C for 1 month. Fuel stability was examined at 80 °C for 1 week. The results from the combustion studies suggest that the distillate fuel blends could be used as alternative fuels to No. 2 heating oil, even up to 100% without any operational issues. The distillate fuels were found to be stable. and the nitrile slab volume swell (∼10%) suggests that the fuel could be compatible to legacy elastomers.
TraB family proteins are components of ER-mitochondrial contact sites and regulate ER-mitochondrial interactions and mitophagy (2022)

ER-mitochondrial contact sites (EMCSs) are important for mitochondrial function. Here, we have identified a EMCS complex, comprising a family of uncharacterised mitochondrial outer membrane proteins, TRB1, TRB2, and the ER protein, VAP27-1. In Arabidopsis, there are three TraB family isoforms and the trb1/trb2 double mutant exhibits abnormal mitochondrial morphology, strong starch accumulation, and impaired energy metabolism, indicating that these proteins are essential for normal mitochondrial function. Moreover, TRB1 and TRB2 proteins also interact with ATG8 in order to regulate mitochondrial degradation (mitophagy). The turnover of depolarised mitochondria is significantly reduced in both trb1/trb2 and VAP27 mutants (vap27-1,3,4,6) under mitochondrial stress conditions, with an increased population of dysfunctional mitochondria present in the cytoplasm. Consequently, plant recovery after stress is significantly perturbed, suggesting that TRB1-regulated mitophagy and ER-mitochondrial interaction are two closely related processes. Taken together, we ascribe a dual role to TraB family proteins which are component of the EMCS complex in eukaryotes, regulating both interaction of the mitochondria to the ER and mitophagy.
Genotypic resistance profiles of HIV-2-treated patients in West Africa (2014)

We observed adequate drug plasma concentrations and virological suppression in a high proportion of HIV-2-infected patients. However, in cases of virological failure, the limited HIV-2 therapeutic arsenal and cross-resistance dramatically reduced treatment options.
Cancer patients' attitudes towards Chinese medicine: a Hong Kong survey (2009)

Chinese medicine is commonly used among Hong Kong cancer patients. The interviewed cancer patients in Hong Kong considered integrative Chinese and Western medicine is an effective cancer treatment.