gebhart/patrepeval huggingface dataset:
Chromosomal instability determines taxane response (2009)

Microtubule-stabilizing (MTS) agents, such as taxanes, are important chemotherapeutics with a poorly understood mechanism of action. We identified a set of genes repressed in multiple cell lines in response to MTS agents and observed that these genes are overexpressed in tumors exhibiting chromosomal instability (CIN). Silencing 22/50 of these genes, many of which are involved in DNA repair, caused cancer cell death, suggesting that these genes are involved in the survival of aneuploid cells. Overexpression of these "CIN-survival" genes is associated with poor outcome in estrogen receptor-positive breast cancer and occurs frequently in basal-like and Her2-positive cases. In diploid cells, but not in chromosomally unstable cells, paclitaxel causes repression of CIN-survival genes, followed by cell death. In the OV01 ovarian cancer clinical trial, a high level of CIN was associated with taxane resistance but carboplatin sensitivity, indicating that CIN may determine MTS response in vivo. Thus, pretherapeutic assessment of CIN may optimize treatment stratification and clinical trial design using these agents.
ddradseqtools: a software package for in silico simulation and testing of double‐digest RADseq experiments (2016)

Double-digested RADseq (ddRADseq) is a NGS methodology that generates reads from thousands of loci targeted by restriction enzyme cut sites, across multiple individuals. To be statistically sound and economically optimal, a ddRADseq experiment has a preliminary design stage that needs to consider issues related to the selection of enzymes, particular features of the genome of the focal species, possible modifications to the library construction protocol, coverage needed to minimize missing data, and the potential sources of error that may impact upon the coverage. We present ddradseqtools, a software package to help ddRADseq experimental design by (i) the generation of in silico double-digested fragments; (ii) the construction of modified ddRADseq libraries using adapters with either one or two indexes and degenerate base regions (DBRs) to quantify PCR duplicates; and (iii) the initial steps of the bioinformatics preprocessing of reads. ddradseqtools generates single-end (SE) or paired-end (PE) reads that may bear SNPs and/or indels. The effect of allele dropout and PCR duplicates on coverage is also simulated. The resulting output files can be submitted to pipelines of alignment and variant calling, to allow the fine-tuning of parameters. The software was validated with specific tests for the correct operability of the program. The correspondence between in silico settings and parameters from ddRADseq in vitro experiments was assessed to provide guidelines for the reliable performance of the software. ddradseqtools is cost-efficient in terms of execution time, and can be run on computers with standard CPU and RAM configuration.
A New Methodology for Engine Diagnostics and Control Utilizing “Synthetic” Engine Variables: Theoretical and Experimental Results (1998)

Abstract This paper describes new engine diagnostic methodologies and algorithms that simplify and improve combustion quality monitoring and closed loop engine control in order to meet stringent emission standards. The “synthetic” variables these algorithms produce can be used to indicate the work produced by each cylinder combustion event at all engine speeds, and can be effectively used for on-board combustion quality measurements, engine diagnostics, and closed-loop control. The algorithms are very simple in form, and these methodologies can be applied to compression ignition or spark ignition, 2-stroke or 4-stroke engines. Both simulation and experimental results will be given for a two-stroke, two cylinder in-line engine. The rotational dynamics and firing sequence of this configuration of engine is very similar to a four-stroke, four cylinder in-line engine, and nearly identical results will be seen with these two designs. Even more dramatic improvements can be seen with engines of fewer cylinders because of greater variations in their inertial forces. The algorithms can be successfully applied to many other engine configurations as well. Therefore, benefits can be derived from the application of these algorithms and their “synthetic” variables to control strategies for almost all modern small and medium size automotive and marine engines, as well as utility engines used for lawn care, snow removal, and other similar applications.
Compressing Deep Convolutional Networks using Vector Quantization (2014)

Deep convolutional neural networks (CNN) has become the most promising method for object recognition, repeatedly demonstrating record breaking results for image classification and object detection in recent years. However, a very deep CNN generally involves many layers with millions of parameters, making the storage of the network model to be extremely large. This prohibits the usage of deep CNNs on resource limited hardware, especially cell phones or other embedded devices. In this paper, we tackle this model storage issue by investigating information theoretical vector quantization methods for compressing the parameters of CNNs. In particular, we have found in terms of compressing the most storage demanding dense connected layers, vector quantization methods have a clear gain over existing matrix factorization methods. Simply applying k-means clustering to the weights or conducting product quantization can lead to a very good balance between model size and recognition accuracy. For the 1000-category classification task in the ImageNet challenge, we are able to achieve 16-24 times compression of the network with only 1% loss of classification accuracy using the state-of-the-art CNN.
Clinicopathologic Factors and Their Association with Outcomes of Salivary Duct Carcinoma: A Multicenter Experience (2023)

In this single-institution, multicenter retrospective study, the 5-year survival was 42% in patients with SDC. Lymphovascular space invasion, lymph node involvement, and higher staging at diagnosis were associated with lower DMFS and OS.
Adhesion reduction after knee surgery in a rabbit model by Hyaloglide®, a hyaluronan derivative gel (2005)

A randomized controlled experimental trial was performed in a rabbit model of surgical adhesions to investigate the anti-adhesive effects of Hyaloglide, a highly viscous hyaluronan derivative absorbable gel after knee surgery. Twenty New Zealand white rabbits were prepared and randomly divided into two groups of 10 animals each. An intra-articular fibro-adhesive scar was created in the right knee joint of the hind paw of each rabbit using a standardized surgical procedure, and Hyaloglide was administered into the joint cavity of the knee at the end of intervention in the animals belonging to the treatment group. No anti-adhesive treatment was applied in the control group. Additionally, immobilization using a Kirschner wire was applied in order to increase the risk of adhesions. Six weeks after surgery the animals were euthanized and after removal of the immobilization system, adhesions were evaluated both macroscopically and histologically. Results of gross observations using a specific adhesion scoring system showed a significant reduction (p<0.01) of both incidence and severity of adhesions in the hyaluronan-treated group compared to the control group. Histologically, adhesions in the treated group were thinner with less collagenic fibers. In conclusion, Hyaloglide may be considered as a promising absorbable barrier for prevention of post-operative fibrotic adhesions after knee surgery.
TRUE: Re-evaluating Factual Consistency Evaluation (2022)

Or Honovich, Roee Aharoni, Jonathan Herzig, Hagai Taitelbaum, Doron Kukliansy, Vered Cohen, Thomas Scialom, Idan Szpektor, Avinatan Hassidim, Yossi Matias. Proceedings of the 2022 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies. 2022.
A Superior Method for Reducing Phenol Ethers to Dihydro Derivatives and Unsaturated Ketones (1953)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA Superior Method for Reducing Phenol Ethers to Dihydro Derivatives and Unsaturated KetonesA. L. Wilds and Norman A. NelsonCite this: J. Am. Chem. Soc. 1953, 75, 21, 5360–5365Publication Date (Print):November 1, 1953Publication History Published online1 May 2002Published inissue 1 November 1953https://pubs.acs.org/doi/10.1021/ja01117a064https://doi.org/10.1021/ja01117a064research-articleACS PublicationsRequest reuse permissionsArticle Views990Altmetric-Citations108LEARN 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-Alertsclose Get e-Alerts
Trans-Synaptic Stimulation of Cortical Acetylcholine Release after Partial 192 IgG-Saporin-Induced Loss of Cortical Cholinergic Afferents (1996)

Environmental and pharmacological stimulation of cortical acetylcholine (ACh) efflux was determined in rats sustaining partial deafferentation of cortical cholinergic inputs. Rats were bilaterally infused with the selective cholinotoxin 192 IgG-saporin (0.005 microgram/0.5 microliter/site) into the frontoparietal cortex. In the first experiment, animals were pretrained to associate the onset of darkness with presentation of a palatable fruit cereal reward. The ability of this stimulus to enhance frontoparietal ACh efflux alone, and with the benzodiazepine receptor (BZR) weak inverse agonist ZK 93,426 (1.0 or 5.0 mg/kg, i.p.), was determined in lesioned and sham-lesioned rats. Intracortical infusions of 192 IgG-saporin reduced basal cortical ACh efflux by 47% of sham-lesioned values, consistent with reductions in the density of AChE-positive fibers. In spite of this deafferentation, ZK 93,426 produced a transient potentiation of the cortical ACh efflux induced by the darkness/cereal stimulus similar to that observed in control animals. In the second experiment, the ability of the more efficacious BZR partial inverse agonist FG 7142 (8.0 mg/kg, i.p.) to enhance basal cortical ACh efflux was compared in lesioned and sham-lesioned rats. Again, lesioned rats exhibited an increase comparable to control animals after FG 7142. This drug-induced stimulation of cortical ACh efflux was comparably and completely blocked in both groups by co-perfusion with tetrodotoxin (1.0 microM). These results suggest similarities in the modulation of cortical ACh efflux in intact and partially deafferented rats and indicate the potential of BZR inverse agonists for restoring transmission in animals with partial loss of cortical cholinergic inputs.
Mechanistic Studies of Pd(II)−α-Diimine-Catalyzed Olefin Polymerizations1 (2000)

Mechanistic studies of olefin polymerizations catalyzed by aryl-substituted α-diimine−Pd(II) complexes are presented. Syntheses of several cationic catalyst precursors, [(N∧N)Pd(CH3)(OEt2)]BAr‘4 (N∧N = aryl-substituted α-diimine, Ar‘ = 3,5-(CF3)2C6H3), are described. X-ray structural analyses of [ArNC(H)C(H)NAr]Pd(CH3)(Cl) and [ArNC(Me)C(Me)NAr]Pd(CH3)2 (Ar = 2,6-(iPr)2C6H3) illustrate that o-aryl substituents crowd axial sites in these square planar complexes. Low-temperature NMR studies show that the alkyl olefin complexes, (N∧N)Pd(R)(olefin)+, are the catalyst resting states and that the barriers to migratory insertions lie in the range 17−19 kcal/mol. Following migratory insertion, the cationic palladium alkyl complexes (N∧N)Pd(alkyl)+ formed are β-agostic species which exhibit facile metal migration along the chain (“chain walking”) via β-hydride elimination/readdition reactions. Model studies using palladium−n-propyl and −isopropyl systems provide mechanistic details of this process, which is responsible for introducing branching in the polyethylenes made by these systems. Decomposition of the cationic methyl complexes (ArN∧NAr)Pd(CH3)(OEt2)+ (Ar = 2,6-(iPr)2C6H3, 2-tBuC6H4) occurs by C−H activation of β-C−H bonds of the ortho isopropyl and tert-butyl substituents and loss of methane. The rate of associative exchange of free ethylene with bound ethylene in (N∧N)Pd(CH3)(C2H4)+ is retarded by bulky substituents. The relationship of these exchange experiments to chain transfer is discussed.
Multi-center harmonization of flow cytometers for multicolor analyses of a large cohort of patients in the context of the European IMI PROJECT "PRECISESADS". (2016)

International audience
Mechanisms of Neuropathic Pain (2005)

Injury to the peripheral nerve can lead to paradoxical changes in functioning such that there is an ongoing dysesthesia and an altered processing such that low threshold stimuli are responded to in humans and animals as if they were painful. What are the mechanisms underlying these anomalous behaviors? The biological changes induced by nerve injury are complex. To attribute functional relevance to the many changes, systematic preclinical work using well-defined behavioral models of nerve injury has been undertaken. Such studies have provided support for the important role in nerve injury-evoked pain behavior for a number of channels and receptors in the injured nerve, the dorsal root ganglion of the injured nerve, and the dorsal horn. These changes and their effect upon behavior are the subject of this review.
Hermite interpolation of rational space curves using real algebraic surfaces (1989)

We present a simple characterization of the lowest degree, implicitly defined, real algebraic surfaces, which smoothly contain any given number of points and algebraic space curves, of arbitrary degree. The characterization is constructive, yielding efficient algorithms for generating families of such algebraic surfaces. Smooth containment of space curves yields C1-continuous surface fitting, and is a generalization of standard Hermite interpolation applied to fitting curves through point data, equating derivatives at those points. We deal with the containment and matching of “normals” (vectors orthogonal to tangents), possibly varying along the entire span of the space curves. Such Hermite interpolated surfaces prove useful as “blending” or “joining” surfaces for solid models as well as “fleshing” surfaces for curved wireframe models.
Capital Asset Investment: Strategy, Tactics and Tools (2002)

Providing a balanced and practical approach to capital management and budgeting, this book covers the full spectrum of capital investments, from the basics through the latest innovations. It is aimed at managers who are involved in capital investment decisions: setting company capital investment policy; performing project analyses; and drafting recommendations. Those in top management will benefit from discussions of strong and weak points of various methods and concepts.
Included in the arsenal of capital investment tools in this book are concepts of proven usefulness, such as the MAPI method, no longer available in other works on the topic of capital budgeting, and other topics not covered elsewhere, such as abandonment analysis.
Polyphenols: A concise overview on the chemistry, occurrence, and human health (2019)

This review gives an updated picture of each class of phenolic compounds and their properties. The most common classification implies the subdivision of phenolics in two main groups: flavonoids (e.g., anthocyanins, flavanols, flavanones, flavonols, flavonones, and isoflavones) and non-flavonoids (e.g., phenolic acids, xanthones, stilbens, lignans, and tannins) polyphenols. The great interest in polyphenols is associated with their high potential application for food preservation and for therapeutic beneficial use. The relationship between polyphenol intake and human health has been exploited with special reference to cardiovascular diseases, hypertension, diabetes, metabolic syndrome, obesity, and cancer. The use of current existing databases of bioactive compounds including polyphenols is described as key tools for human health research.
Inactivation of human and simian rotaviruses by chlorine dioxide (1990)

The inactivation of single-particle stocks of human (type 2, Wa) and simian (SA-11) rotaviruses by chlorine dioxide was investigated. Experiments were conducted at 4 degrees C in a standard phosphate-carbonate buffer. Both virus types were rapidly inactivated, within 20 s under alkaline conditions, when chlorine dioxide concentrations ranging from 0.05 to 0.2 mg/liter were used. Similar reductions of 10(5)-fold in infectivity required additional exposure time of 120 s at 0.2 mg/liter for Wa and at 0.5 mg/liter for SA-11, respectively, at pH 6.0. The inactivation of both virus types was moderate at neutral pH, and the sensitivities to chlorine dioxide were similar. The observed enhancement of virucidal efficiency with increasing pH was contrary to earlier findings with chlorine- and ozone-treated rotavirus particles, where efficiencies decreased with increasing alkalinity. Comparison of 99.9% virus inactivation times revealed ozone to be the most effective virucidal agent among these three disinfectants.
EFFECT OF EXTERNAL FACTORS ON PHYSICOCHEMICAL TRANSFORMATIONS Photostimulated Currents and Magnetic Spin Effects in Organic p-n Polymeric Heterostructures (2012)

photovoltaic characteristics of cells based on polymeric p–n heterostructures: an increase in short circuit photocurrent (by more than an order of magnitude for a volume interface and by several times for a diffusion interface) was observed, and free running voltage increased (to 1.2–1.4 V). This allows the energy effective� ness of photovoltaic cells to be substantially increased at a moderate increase in temperature (by no more than
Impact of cardiopulmonary comorbidities on pulmonary hemodynamics (2015)

Introduction: Cardiopulmonary comorbidities are known risk factors for pulmonary hypertension (PH) and may contribute to pulmonary arterial pressure (PAP) elevation. However, in clinical practice it is difficult to differentiate whether these conditions should be considered as coexisting comorbidities in the setting of PH or as the underlying cause for PH.
Platelet Nanocrystals Resulting from the Disruption of Waxy Maize Starch Granules by Acid Hydrolysis (2003)

Colloidal aqueous suspensions of starch nanocrystals were prepared by submitting native granules from A-type amylopectin-rich waxy maize to a hydrochloric acid hydrolysis. The insoluble residue contains polydisperse and more or less individualized platelet nanocrystals corresponding to the lamellae formed by the association of amylopectin side branches into parallel arrays of double helices. After 2 weeks of hydrolysis, 5-7 nm thick lamellae still connected by alpha(1-->6) linkages were seen edge-on using transmission electron microscopy. As the hydrolysis progressed up to 6 weeks, more alpha(1-->6) branching points located in the inter-lamellar areas were severed and the platelets were thus observed in planar view. Despite a variety of shapes, characteristic geometrical features of the nanocrystalsa were recognized, such as marked 60-65 degrees acute angles and constituting parallelepipedal blocks with a length of 20-40 nm and a width of 15-30 nm. X-ray and electron diffraction showed that these nanoplatelets retain the crystalline A-type of the parent granules.
New YARN Non-Exclusive Resource Management Scheme through Opportunistic Idle Resource Assignment (2018)

Efficiently managing resources and improving throughput in a large-scale cluster has become a crucial problem with the explosion of data processing applications in recent years. Hadoop YARN and Mesos, as two universal resource management platforms, have been widely adopted in the commodity cluster for co-deploying multiple data processing frameworks, such as Hadoop MapReduce and Apache Spark. However, in the existing resource management, a certain amount of resources are exclusively allocated to a running task and can only be re-assigned after that task is completed. This exclusive mode unfortunately leads to a potential problem that may under-utilize the cluster resources and degrade system performance. To address this issue, we propose a novel opportunistic and efficient resource allocation scheme, named OpERA, which breaks the barriers among the encapsulated resource containers by leveraging the knowledge of actual runtime resource utilizations to re-assign opportunistic available resources to the pending tasks. OpERA avoids incurring severe performance interference to active tasks by further using two approaches to efficiently balances the starvations of reserved tasks and normal queued tasks. We implement and evaluate OpERA in Hadoop YARN v2.5. Our experimental results show that OpERA significantly reduces the average job execution time and increases the resource (CPU and memory) utilizations.
Multithreaded Java program test generation (2002)

We describe ConTest, a tool for detecting synchronization faults in multithreaded Java™ programs. The program under test is seeded with a sleep( ), yield( ), or priority( ) primitive at shared memory accesses and synchronization events. At run time, ConTest makes random or coverage-based decisions as to whether the seeded primitive is to be executed. Thus, the probability of finding concurrent faults is increased. A replay algorithm facilitates debugging by saving the order of shared memory accesses and synchronization events.