gebhart/patrepeval huggingface dataset:
Abstract 4821: Somatic variation scoring and validation for large-scale cancer genome sequencing (2011)

Abstract Complete Genomics has sequenced the genomes of over 100 tumor-normal sample pairs from a variety of cancers (e.g. Lee, et al., Nature 465: 473-477, 2010) using a unique high throughput sequencing platform (Drmanac, et al., Science 327:78-81, 2010). We have assembled a tool set to investigate somatic mutations in these samples, including small variations (SNVs, deletions, insertions and substitutions), as well as larger structural variations, copy number variations and regions of LOH (Loss of Heterozygosity). Included in this sample set are 12 cancer cell lines and matched normal cell lines obtained from the American Type Tissue Culture collection (ATCC), comprising 10 breast cancers and 2 lung cancers. We have developed and characterized somatic variation scoring methods for each variant class that can be tuned for particular applications and sample types. Comparative analyses with previously published data show high specificity and sensitivity of somatic variation detection. We will discuss the application of these methods for somatic variation analysis in larger cancer genome studies. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4821. doi:10.1158/1538-7445.AM2011-4821
Formation of CuIn<sub>1-x</sub>Al<sub>x</sub>Se<sub>2</sub> Thin Films by Selenization of Metallic Precursors in Se Vapor (2007)

CuIn1-xAxlSe2(CIAS) films were obtained by selenization process of metallic precursors. The metallic precursors were deposited sequentially by using sputtering system. As the ratio of Al/(Al+In) in the precursors increased, the chalcopyrite (112) peak shifted to high value and the band-gap of CIAS layer increased to 1.38 eV. However, the bi-layer morphology with well crystallized large grain on the surface and small grain thin bottom layer was observed. Although the sequences of precursors were changed in order to get uniform layer, no distinguishable difference was not observed.
Evolution of methicillin-resistant Staphylococcus aureus towards increasing resistance (2013)

We propose a model for the evolution of S. aureus CC8, involving a split into at least nine phylogenetic lineages and a subsequent series of acquisitions and losses of mobile genetic elements that carry diverse virulence and antimicrobial resistance traits. The evolution of MRSA USA300 towards resistance to additional antibiotic classes is of major concern.
Join optimization of detectors’ fleet settings to maximize global detection power (2018)

In many applications, detection methods are implemented to monitor systems. Detector may be built upon analytical model of the system behaviors, or based on recorded data. Lately lots of efforts have been put in developing methods that enable to transfer a detector from an assessed system to a new one when the 2 systems are similar. These so-called transfer learning approaches have shown efficiency when dealing with a fleet of systems composed of different similar systems. For the detector of each model of system a tradeoff between false alarm and non-detection must be chosen. One question that has not retained much attention up to now is the tuning of these detection systems. The common practice is to tune the detection system associated with each model individually. In this communication we tackle the problem of the global efficiency of this practice. How can we tune all those detection systems together so that the group of detectors satisfies some performance constraint? The formalization of the problem is introduced, discussed and commented based on detector ROC curves. Three toy examples are used to show the gain one could expect from join optimization of detectors and to illustrate optimization issues. Example results show that non detection probability can easily be reduced by up to 50%. In conclusion several extensions of this work are discussed.
Full color generation with Fano-type resonant HfO2 nanopillars designed by a deep-learning approach (2019)

In contrast to lossy plasmonic metasurfaces (MSs), wideband dielectric MSs comprising subwavelength nanostructures supporting Mie resonances are of great interest in the visible wavelength range. Here, for the first time to our knowledge, we experimentally demonstrate a reflective MS consisting of a square-lattice array of hafnia (HfO<sub>2</sub>) nanopillars to generate a wide color gamut. To design and optimize these MSs, we use a deep-learning algorithm based on a dimensionality reduction technique. Good agreement is observed between simulation and experimental results in yielding vivid and high-quality colors. We envision that these structures not only empower the high-resolution digital displays and sensitive colorimetric biosensors but also can be applied to on-demand applications of beaming in a wide wavelength range down to deep ultraviolet.
Heat reject recovery in solar air conditioning (2011)

This study demonstrates the possibility of using an absorption chiller to produce chilled water for air conditioning, and at the same time recover the rejected heat producing domestic hot water. The absorption chiller considered for this application has been sized to suit a standard household and uses a solution of ammonia and water running on hot water at a temperature ranging from 80 - 120°C produced by thermal solar panels. The system consists of five main components: generator, rectifier, condenser, evaporator and absorber, and is divided in two sections at two different pressures. The section at higher pressure includes the generator, rectifier and condenser whereas the section at lower pressure includes the evaporator and the absorber. Heat in this type of system is usually rejected to the environment from the condenser, rectifier and absorber through a cooling tower or air cooler exchanger. In this paper we describe how to recover this heat to create domestic hot water by providing a quantitative evaluation of the amount of energy recovered by the proposed system, if used in the Australian region.
IDENTIFICATION OF ACOUSTIC MOVING SOURCES USING A TIME-DOMAIN METHOD (2018)

International audience
Association of deoxyribonuclease-sensitive material with adenovirus penton aggregates after treatment of infected cell cultures with sodium deoxycholate (1971)

Sodium deoxycholate treatment of adenovirus-infected cell cultures was found to release rapidly sedimenting penton components with a buoyant density in CsCl of about 1.34 g/ml. The high-density penton material derived from human and simian adenovirus-infected cells occurred in monomeric form, while that derived from canine adenovirus-infected cells was in the form of non-symmetrical groupings of pentons aggregated at the vertex capsomere. Deoxyribonuclease treatment and 3 H-thymidine-DNA labeling experiments revealed that the high-density of the pentons so obtained was due to a small associated segment of nuclease-sensitive material. A possible explanation of the nature of the nuclease-sensitive material is given.
Animal Models of Cognitive Impairment (2006)

The costs associated with a drug's clinical trials are so significant that it has become necessary to validate both its safety and efficacy in animal models prior to the continued study of the drug in humans. Featuring contributions from distinguished researchers in the field of cognitive therapy research, Animal Models of Cognitive Impairmen
Sistema actuador de mandos para una estación remota autochequeada de teleoperaciones (1979)

Referencia OEPM: P0477724.-- Fecha de solicitud: 15/02/1979.-- Titular: Consejo Superior de Investigaciones Cientificas (CSIC).-- Transferida a la empresa Enclavamientos y Senales, S.A. (Barcelona).
Differentiating the Frontal Presentation of Alzheimer's Disease with FDG-PET (2015)

Medial and orbital frontal hypometabolism is greater in AD patients presenting with more frontal/behavioral features, likely reflecting a greater pathological load in these brain regions in FvAD patients. These frontal regions may be more linked to behavioral features than other frontal brain regions.
Tri-tert-butylphosphine (2007)

[12716-12-6] C12H27P (MW 202.32) InChI = 1S/C12H27P/c1-10(2,3)13(11(4,5)6)12(7,8)9/h1-9H3 InChIKey = BWHDROKFUHTORW-UHFFFAOYSA-N (supporting ligand for palladium-1 and rhodium-catalyzed2 cross-coupling reactions) Physical Data: mp 30 °C; bp 102–103 °C/13 Torr; d 0.812 g cm−3. Solubility: sol in most organic solvents; insol in H2O. Form Supplied: colorless liquid or low-melting solid; approx. 10%(w/w) solution in hexane; or as HBF4 salt as a white solid; widely available in all forms. Purification: by vacuum distillation (102–103 °C, 13 Torr). Handling, Storage, and Precautions: the pure material is pyrophoric and must be handled under an oxygen-free atmosphere to avoid spontaneous combustion. In the absence of oxygen, it is indefinitely stable. Solutions (ca. 10%) of tri-tert-butylphosphine are not pyrophoric, but should be handled under an inert atmosphere in order to avoid oxidation to the phosphine oxide. The HBF4 salt is air-stable. Tri-tert-butylphosphine is corrosive and causes burns on contact with skin. It is incompatible with oxidizing agents.
Segmentation of gated Tl-SPECT images for automatic computation of myocardial volume and ejection fraction (2002)

The authors present an algorithm for automatic assessment of left ventricular ejection fraction (EF) and absolute volume from gated Thallium-SPECT myocardial perfusion images. The system consists of two independent blocs for segmentation and computation of function. The authors introduce a novel formulation for computation of EF based on the epi-cardial contour. The algorithm was validated against manual border tracing from two physicians on different modalities, and gave consistent linear agreement. PET manual vs. Automatic-avg. r=0.91, Tl-SPECT manual vs. auto-r=0.79. The new epicardial method was compared to performance at. High noise. Finally, preliminary comparison were made of EFs computed for PET, /sup 99m/Tc-SPECT and /sup 201/Tl-SPECT to those obtained from planar gated blood pool imaging (GBP) yielding good results. The proposed scheme is specifically designed for /sup 201/Tl-SPECT, but may be used on other image modalities as well. It permits EF computation on relatively noisy images without the need for additional image acquisitions.
Rainbows in the grass II Arbitrary diagonal incidence (2008)

We consider external reflection rainbow caustics due to the reflection of light from a pendant droplet where the light rays are at an arbitrary angle with respect to the horizontal. We compare this theory to observation of glare spots from pendant drops on grass; we also consider the potential application of this theory to the determination of liquid surface tension.
Evolving evidence in the treatment of primary and recurrent posterior cruciate ligament injuries, part 2: surgical techniques, outcomes and rehabilitation (2020)

Abstract Isolated and combined posterior cruciate ligament (PCL) injuries are associated with severe limitations in daily, professional, and sports activities as well as with devastating long‐term effects for the knee joint. As the number of primary and recurrent PCL injuries increases, so does the body of literature, with high‐quality evidence evolving in recent years. However, the debate about the ideal treatment approach such as; operative vs. non‐operative; single‐bundle vs. double‐bundle reconstruction; transtibial vs. tibial inlay technique, continues. Ultimately, the goal in the treatment of PCL injuries is restoring native knee kinematics and preventing residual posterior and combined rotatory knee laxity through an individualized approach. Certain demographic, anatomical, and surgical risk factors for failures in operative treatment have been identified. Failures after PCL reconstruction are increasing, confronting the treating surgeon with challenges including the need for revision PCL reconstruction. Part 2 of the evidence‐based update on the management of primary and recurrent PCL injuries will summarize the outcomes of operative and non‐operative treatment including indications, surgical techniques, complications, and risk factors for recurrent PCL deficiency. This paper aims to support surgeons in decision‐making for the treatment of PCL injuries by systematically evaluating underlying risk factors, thus preventing postoperative complications and recurrent knee laxity. Level of evidence V.
Photomask registration and overlay metrology by means of 193 nm optics (2008)

This paper reports on the current status of PROVE<sup>TM</sup> - a new photomask registration and overlay metrology system currently under development at Carl Zeiss. The scope of the project is to design and build a photomask pattern placement metrology tool which is serving the 32 nm node. Performance specifications of the tool are actually driven by double exposure/ double patterning approaches which will help to extend the 193 nm lithography platforms, while keeping the semiconductor industry conform to ITRS roadmap requirements. A secondary requirement of pattern placement metrology tools is the CD measurement option for design features of interest. Combining both registration and CD measurement reduces the number of process operations a photomask has to encounter during manufacture. Optical design considerations are discussed, which led to the tool being designed for 193 nm illumination corresponding to at-wavelength metrology for most current and future photomask applications. The concept enables registration and CD metrology by transmitted or reflected light. The short wavelength together with a NA of 0.6 also provides sufficient resolution even at working distances compatible with the use of pellicles, hence enabling the tool for qualification of final, production ready masks. Imaging simulations with a rigorous Maxwell solver prove our chosen optical concept to be adequate for the various mask types (e.g. COG, MoSi, EUV) commonly used today and presumably in the future. The open concept does enable a higher NA for future, pellicle free applications.
Quantifying subclinical and longitudinal microvascular changes following episcleral plaque brachytherapy (EPB) using spectral-domain OCT angiography (2019)

Abstract Background I-125 episcleral plaque brachytherapy (EPB) is standard-of-care for globe-conserving treatment of medium-sized choroidal melanomas. Radiation retinopathy is a potential consequence of treatment, characterized by deleterious effects on retinal microvasculature. We investigated the application of Optical Coherence Tomography Angiography (OCTA) for detecting and longitudinally monitoring I-125 episcleral plaque brachytherapy induced radiation retinopathy. Methods High resolution OCTA of the central 3×3mm macula were obtained from I-25 episcleral plaque brachytherapy treated and untreated fellow eyes of 62 patients. Capillary density (vessel skeleton density, VSD) and caliber (vessel diameter index, VDI) were quantified using previously validated semi-automated algorithms. Nonperfusion was also quantified as flow impairment regions (FIR). Exams from treated and fellow eyes obtained pre-treatment and at 6-month, 1-year, and 2-year intervals were compared using generalized estimating equation linear models. Dosimetry maps were used to evaluate spatial correlation between radiation dose and microvascular metrics. Results Mean time from treatment to last follow-up was 10.8 months. Mean±SD and median radiation dose at the fovea were 64.5 ± 76 Gy and 32.0 Gy, respectively. Preoperative logMAR (Snellen) mean visual acuity was 0.26 ± 0.05 (∼20/35) and 0.08 ± 0.02 (∼20/25) in treated and fellow eyes, respectively. At 6 months, treated eyes had significantly lower VSD (0.147 ± 0.003 vs 0.155 ± 0.002; p = 0.023) and higher FIR (1.95 ± 0.176 vs 1.45 ± 0.099; p = 0.018) compared to fellow eyes. There was a significant decrease in VSD and a corresponding increase in FIR even for treated eyes without clinically identifiable retinopathy at 6 months. VDI was significantly higher in treated eyes than in fellow eyes at 2 years (2.93 ± 0.022 vs 2.84 ± 0.016; p = 0.002). Microvascular changes were spatially correlated with a radiation gradient of 85-250 Gy across the fovea. Conclusions OCTA can be used to quantify and monitor EPB induced radiation, and can detect vascular abnormalities even in the absence of clinically observable retinopathy. OCTA may therefore be useful in investigating treatment interventions that aim to delay EPB-induced radiation retinopathy.
Apolar Acetylenic Liquid Crystals (1984)

Abstract A large number of bicyclic†;, apolar, acetylenic mesogens with the C, C-triple bond situated either in the central core unit or in the terminal chains have been synthesized. Where possible, their nematic or smectic thermal stabilities are compared with those of the corresponding dimethylene-bridged analogs.
The anti‐diabetic drug miglitol is protective against anginal ischaemia through a mechanism independent of regional myocardial blood flow in the dog (2005)

1. In the present study, we attempted to clarify whether the antidiabetic drug miglitol, an alpha-glucosidase inhibitor, has a protective effect against anginal ischaemia. We had reported previously that miglitol reduces myocardial infarct size through inhibition of glycogenolysis during ischaemia in rabbits. However, the effect of miglitol on anginal ischaemia remains unknown. 2. In open-chest beagle dogs with a severely stenosed left anterior descending coronary artery, an epicardial electrode was attached to the surface of the risk area of the left ventricle and a microdialysis probe was implanted into the myocardium to measure ST segment changes and interstitial lactate accumulation. The first episode of anginal ischaemia was induced by atrial pacing and phenylephrine infusion (50-100 microg/min) for 10 min. The second episode of anginal ischaemia was induced 210 min after the first episode. Miglitol (10 mg/kg, i.v.) was administered to the miglitol group (n = 10) 30 min before the second episode of anginal ischaemia, whereas saline was administered to the control group (n = 10). Regional myocardial blood flow was measured using coloured microspheres. 3. There was no significant difference in regional myocardial blood flow in the risk and non-risk areas between the first and second episodes of anginal ischaemia and between the miglitol and control groups. During the first and second episodes of anginal ischaemia, the ST segment was decreased to a similar extent in the control group. Although ST segment depression during the first episode of anginal ischaemia was similar in both groups, ST segment depression during the second episode of anginal ischaemia was significantly attenuated in the miglitol-treated group compared with the control group (1.3 +/- 0.4 vs 2.2 +/- 0.4 mV, respectively). Miglitol significantly attenuated myocardial interstitial lactate accumulation in the risk area. 4. In conclusion, in the present study miglitol improved ST segment depression and attenuated the accumulation of myocardial interstitial lactate during anginal ischaemia without altering regional myocardial blood flow. Miglitol has an anti-anginal ischaemia effect via a mechanism that is independent of regional myocardial blood flow.
Cobalt Bromide (2011)

[7789-43-7] Br2Co (MW 218.74) InChI = 1S/2BrH.Co/h2*1H;/q;;+2/p-2 InChIKey = BZRRQSJJPUGBAA-UHFFFAOYSA-L (catalyst for C-metal,1-7 C-heteroatom8-11 and CC12-27 bond formations, addition to unsaturated bonds,28-37 cyclizations,38-50 functional group transformations,51, 52 polymerization,53, 54 oxidations55-73 and reductions,74-76 carbonylations77-79) Physical Data: mp 678 °C, d 4.909 g cm−3. Solubility: water, methanol, ethanol, acetone, methyl acetate, acetonitrile, and dimethylformamide. Form Supplied in: green powder when anhydrous; widely available. Typical impurities are sodium, nickel, iron, and silicium salts. Analysis of Reagent Purity: silver nitrate titration. Purification: when becoming pink under effect of moisture, it should be heated (at 100–110 °C) until the green color is regenerated. Handling, Storage, and Precautions: hygroscopic, so should be handled under nitrogen atmosphere for strictly anhydrous conditions. Moisture and ammonia sensitive. Handle away from oxidants and alkali metals. This reagent is toxic and an irritant.
Large Strain Deformation of Single-Phase Copper Solid Solutions by Machining (2006)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
Cooperative Jamming for Secure Transmission With Both Active and Passive Eavesdroppers (2020)

Secrecy transmission is investigated for a cooperative jamming scheme, where a multi-antenna jam-mer generates artificial noise (AN) to confuse eavesdroppers. Two kinds of eavesdroppers are considered: passive eavesdroppers who only overhear the legitimate information, and active eavesdroppers who not only overhear the legitimate information but also jam the legitimate signal. Existing works only treat the passive and active eavesdroppers separately. Different from the existing works, we investigate the achievable secrecy rate in presence of both active and passive eavesdroppers. For the considered system model, we assume that the instantaneous channel state information (CSI) of the active eavesdroppers is available at the jammer, while only partial CSI of the passive eavesdroppers is available at the jammer. A new zero-forcing beamforming scheme is proposed in the presence of both active and passive eavesdroppers. For both the perfect and imperfect CSI cases, the total transmission power allocation between the information and AN signals is optimized to maximize the achievable secrecy rate. Numerical results show that imperfect CSI between the jammer and the legitimate receiver will do more harm to the achievable secrecy rate than imperfect CSI between the jammer and the active eavesdropper.
CITED2 Cooperates with ISL1 and Promotes Cardiac Differentiation of Mouse Embryonic Stem Cells (2016)

The transcriptional regulator CITED2 is essential for heart development. Here, we investigated the role of CITED2 in the specification of cardiac cell fate from mouse embryonic stem cells (ESC). The overexpression of CITED2 in undifferentiated ESC was sufficient to promote cardiac cell emergence upon differentiation. Conversely, the depletion of Cited2 at the onset of differentiation resulted in a decline of ESC ability to generate cardiac cells. Moreover, loss of Cited2 expression impairs the expression of early mesoderm markers and cardiogenic transcription factors (Isl1, Gata4, Tbx5). The cardiogenic defects in Cited2-depleted cells were rescued by treatment with recombinant CITED2 protein. We showed that Cited2 expression is enriched in cardiac progenitors either derived from ESC or mouse embryonic hearts. Finally, we demonstrated that CITED2 and ISL1 proteins interact physically and cooperate to promote ESC differentiation toward cardiomyocytes. Collectively, our results show that Cited2 plays a pivotal role in cardiac commitment of ESC.