gebhart/patrepeval huggingface dataset:
Abstract LB-100: Systematic target prioritization and validation from genome-scale loss-of-function screens in large panels of human cancer cell lines (2020)

Abstract Despite its increasing success and revolutionary impact on clinical oncology, Precision Cancer Medicine still has major roadblocks before it becomes applicable to a large proportion of patients. One such roadblock is the limited number of therapeutic targets available. Indeed, for the vast majority of cancer patients, we either do not know what their specific vulnerabilities are or do not have strategies to precisely target their vulnerabilities. In the Cancer Dependency Map Project (DepMap) at the Broad Institute, we aim to overcome these limitations through the use of genome-scale loss-of-function screens in a large panel of cancer cell lines combined with systematic molecular characterization of these cell lines. To date, we have conducted viability screens with genome-wide RNAi and CRISPR/Cas9 libraries on &amp;gt; 800 cell lines, all of which have also been comprehensively profiled with various omics approaches. In order to systematically identify and prioritize potential therapeutic targets, we created an analytical framework that uses a multifaceted approach to score gene dependencies based on the information extracted from screening outcomes, predictive models of sensitivity from all the genetic and molecular information, and the use of priors. To reproducibly validate the nominated targets, we also developed a toolbox of standardized assays that include confirmation of cell viability effects with orthogonal reagents/read-outs and efficient testing for in vivo efficacy across multiple cancer models. Using this approach, we have identified and validated several promising targets, including the WRN DNA helicase that is selectively essential in cancers with microsatellite instability (MSI). The data, framework, and toolbox developed here can inform the nomination and advancement of promising targets for drug development for Precision Cancer Medicine. Citation Format: Tsukasa Shibue, John M. Krill-Burger, Brenton R. Paolella, Benjamin Gaeta, Adhana Asfaw, Joshua M. Dempster, James M. McFarland, David E. Root, Jesse S. Boehm, Aviad Tsherniak, William C. Hahn, Francisca Vazquez. Systematic target prioritization and validation from genome-scale loss-of-function screens in large panels of human cancer cell lines [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr LB-100.
Lifetime identification of single molecules in aqueous solution (1997)

Photon bursts of single rhodamine 6G and rhodamine B molecules in aqueous solution were studied by excitation with a frequency-doubled titanium: sapphire laser. Multichannel scalar traces, fluorescence correlation functions and fluorescence decays determined by time- correlated single-photon counting have been measured simultaneously. The time-resolved fluorescence signals were analyzed with a maximum likelihood estimator. With the setup described it is possible to distinguish single dye molecules of different kind via their characteristic fluorescence lifetimes of 1.79 +/- 0.33 ns for rhodamine B-zwitterion and 3.79 +/- 0.38 ns for rhodamine 6G. ©2005 Copyright SPIE - The International Society for Optical Engineering.
Quantification of RPE Changes in Choroideremia Using a Photoshop-Based Method (2020)

An accurate quantification method for longitudinal RPE change in CHM patients is an important tool for the evaluation of efficacy in any therapeutic trials.
Solid-phase reaction monitoring—Chemical derivatization and off-bead analysis (2000)

The aim of this review is to give a compendium of colorimetric assays and spectrophotometric-based quantification methods applicable to solid-phase organic chemistry. Comprehensive experimental details for commonly employed color tests performed on solid support will be documented.
High-Speed Large-Alphabet Quantum Key Distribution Using Photonic Integrated Circuits (2014)

Abstract : This program theoretically and experimentally investigated the private information capacity of optical channels under experimental constraints. Theoretical work established upper and lower bounds on the Holevo secrecy capacity for optical channels, including channels in turbulent atmosphere, and developed the coding and modulation techniques to approach the maximum key distribution rate over optical channels, in the regime of simultaneously high photon and bandwidth efficiencies. The program also developed two quantum key distribution (QKD) protocols that achieve an information capacity of multiple secure bits per photon pair, providing the first security proofs for experimentally realizable high-dimensional QKD schemes against collective attacks. These protocols represent quantum secure versions of pulse-position- modulation schemes that are commonly employed in energy-constrained electromagnetic channels. Novel adaptive pulseposition modulation and layered coding schemes provide efficient error correction. The experimental effort developed QKD hardware in silicon photonic integrated circuits (PIC), including waveguide-integrated superconducting nanowire single photon detectors. Ultra-bright waveguide-based entangled pair generation was demonstrated with record high entanglement purity measured using dispersion-compensated Franson interferometry. QKD systems were demonstrated with secure key generation in excess of 6 Mbit/second and a photon efficiency in excess of 3 secure bits per detected photon.
Relationship between Amount and Type of Dietary Fat, Postprandial Glycemia, and Insulin Requirements in Type 1 Diabetes (2018)

ADA recommends individuals with type 1 diabetes (T1D) are taught to adjust insulin for dietary fat however optimal adjustments are not yet clear. This study aimed to determine 1) the relationship between the ‘amount’ and ‘type’ of dietary fat and glycemia and 2) the optimal insulin adjustments for dietary fat. Six adults with T1D using insulin pump therapy attended the research clinic on 9 to 12 occasions. On the first 6 visits, participants consumed meals containing 45g CHO with either 0g, 20g, 40g, or 60g fat and either saturated (SFA), monounsaturated (MUFA) or polyunsaturated (PUFA) fat. Insulin was dosed using individual insulin: carbohydrate ratio as a dual-wave 50/50% split over 2h. On subsequent visits, participants repeated the 20 to 60g fat meals with the insulin dose estimated using a model predictive bolus, with up to 2 repeats/meal until glycemic control achieved. With the same insulin dose, mean 5h incremental area under the curve (iAUC) was increased by 46%, 23% and 139% for the 3 fat loads relative to the 0g fat meal (0g: 509 ± 153; 20g: 742 ± 742; 40g: 626 ± 74; 60g: 1216 ± 434mmol/L.min; ns). The type of fat made small but non-significant differences to the 5h iAUC. To achieve glycemic control, on average, participants required 20-60% more insulin, delivered as a dual-wave over 1.25-2h. This study provides foundation for mealtime insulin dosing recommendations for dietary fat in T1D. Disclosure K. Bell: Other Relationship; Self; Novo Nordisk Inc.. S. Duke: None. K.M. Alexander: None. M. McGill: Advisory Panel; Self; Abbott. Speaker's Bureau; Self; AstraZeneca. Advisory Panel; Self; Merck Sharp &amp; Dohme Corp.. Speaker's Bureau; Self; Merck Sharp &amp; Dohme Corp. J. Wong: Speaker's Bureau; Self; Novo Nordisk A/S, AstraZeneca, Eli Lilly and Company. G. Fulcher: Other Relationship; Self; Novo Nordisk Inc., Janssen Scientific Affairs, LLC., Boehringer Ingelheim GmbH, Merck Sharp &amp; Dohme Corp. S.M. Twigg: Advisory Panel; Self; Abbott. Consultant; Self; Abbott. Advisory Panel; Self; Novo Nordisk Inc., Sanofi-Aventis, AstraZeneca, Boehringer Ingelheim Pharmaceuticals, Inc., Eli Lilly and Company. Speaker's Bureau; Self; AstraZeneca, Merck Sharp &amp; Dohme Corp.. Other Relationship; Self; Abbott. J. Brand-Miller: Board Member; Self; Glycemic Index Foundation. Other Relationship; Self; Hachette Australia. Stock/Shareholder; Spouse/Partner; Novo Nordisk A/S. Other Relationship; Self; Pam Krauss Books. G.M. Steil: Consultant; Self; Profusa, Eli Lilly and Company.
Molecular cloning and functional characterization of porcine CCL28: Possible involvement in homing of IgA antibody secreting cells into mammary gland (2008)

International audience
Unraveling the Unconventional Order of a High-Mobility Indacenodithiophene–Benzothiadiazole Copolymer (2021)

A new class of donor-acceptor (D-A) copolymers found to produce high charge carrier mobilities competitive with amorphous silicon (>1 cm<sup>2</sup> V<sup>-1</sup> s<sup>-1</sup>) exhibit the puzzling microstructure of substantial local order, however lacking long-range order and crystallinity previously deemed necessary for achieving high mobility. Here, we demonstrate the application of low-dose transmission electron microscopy to image and quantify the nanoscale and mesoscale organization of an archetypal D-A copolymer across areas comparable to electronic devices (≈9 μm<sup>2</sup>). The local structure is spatially resolved by mapping the backbone (001) spacing reflection, revealing nanocrystallites of aligned polymer chains throughout nearly the entire film. Analysis of the nanoscale structure of its ordered domains suggests significant short- and medium-range order and preferential grain boundary orientations. Moreover, we provide insights into the rich, interconnected mesoscale organization of this new family of D-A copolymers by analysis of the local orientational spatial autocorrelations.
Triple Collocation Analysis for Two Error-Correlated Datasets: Application to L-Band Brightness Temperatures over Land (2020)

The error characterization of satellite observations is crucial for blending observations from multiple platforms into a unique dataset and for assimilating them into numerical weather prediction models. In the last years, the triple collocation (TC) technique has been widely used to assess the quality of many geophysical variables acquired with different instruments and at different scales. This paper presents a new formulation of the triple collocation (Correlated Triple Collocation (CTC)) for the case of three datasets that resolve similar spatial scales, with two of them being error-correlated datasets. Besides, the formulation is designed to ensure fast convergence of the error estimators. This approach is of special interest in cases such that finding more than three datasets with uncorrelated errors is not possible and the amount of data is limited. First, a synthetic experiment has been carried out to assess the performance of CTC formulation. As an example of application, the error characterization of three collocated L-band brightness temperature (TB) measurements over land has been performed. Two of the datasets come from ESA (European Space Agency) SMOS (Soil Moisture and Ocean Salinity) mission: one is the reconstructed TB from the operational L1B v620 product, and the other is the reconstructed TB from the operational L1B v620 product resulting from application of an RFI (Radio Frequency Interference) mitigation technique, the nodal sampling (NS). The third is an independent dataset, the TB acquired by a NASA (National Aeronautics and Space Administration) SMAP (Soil Moisture Active Passive) radiometer. Our analysis shows that the application of NS leads to TB error reduction with respect to the current version of SMOS TB in 80% of the points in the global map, with an average reduction of approximately 1 K over RFI-free regions and approximately 1.45 K over strongly RFI-contaminated areas.
What’s the target: understanding two decades of in silico microRNA-target prediction (2019)

An interactive implementation of our recommendations including materials shown in the manuscript is freely available at https://www.ccb.uni-saarland.de/mtguide.
Industrial IoT with Distributed Cloud Experiments using 5G LTE (2019)

With the evolution of 5G it is envisioned that industrial applications with different requirements on latency and availability can be offloaded to a distributed cloud infrastructure. For example, some applications with stringent timing requirements can be hosted at the edge of the mobile network, closer to the control hardware, whereas some applications with relaxed timing requirements can be hosted in a cloud located geographically further away.This paper presents a feasibility study of hosting control applications based on OPC UA communication in a distributed cloud with LTE connectivity to the control hardware. The study includes measurements of communication round-trip time and availability of the network comparing cases where the application is hosted at a local or regional cloud. The results indicate that it is feasible to deploy industrial applications in a distributed cloud with timing requirements in the order of 100ms.
Intermolecular Interactions of Lithocholic Acid Derivatives with Phospholipid as Bilayer Membrane (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTIntermolecular Interactions of Lithocholic Acid Derivatives with Phospholipid as Bilayer MembraneZi-Chen Li, Fu-Mian Li, Shinya Arase, Shinji Takeoka, and Eishun TsuchidaCite this: Langmuir 1995, 11, 8, 3161–3166Publication Date (Print):August 1, 1995Publication History Published online1 May 2002Published inissue 1 August 1995https://pubs.acs.org/doi/10.1021/la00008a048https://doi.org/10.1021/la00008a048research-articleACS PublicationsRequest reuse permissionsArticle Views152Altmetric-Citations1LEARN 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
Determination of sublimation pressures of a fullerene (C60/C70) solid solution (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDetermination of sublimation pressures of a fullerene (C60/C70) solid solutionC. Pan, M. S. Chandrasekharaiah, D. Agan, R. H. Hauge, and J. L. MargraveCite this: J. Phys. Chem. 1992, 96, 16, 6752–6755Publication Date (Print):August 1, 1992Publication History Published online1 May 2002Published inissue 1 August 1992https://doi.org/10.1021/j100195a041RIGHTS & PERMISSIONSArticle Views482Altmetric-Citations24LEARN 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 InReddit PDF (2 MB) Get e-Alerts
The Easter Egg Weevil (Pachyrhynchus) genome reveals syntenic patterns in Coleoptera across 200 million years of evolution (2021)

Patterns of genomic architecture across insects remain largely undocumented or decoupled from a broader phylogenetic context. For instance, it is unknown whether translocation rates differ between insect orders. We address broad scale patterns of genome architecture across Insecta by examining synteny in a phylogenetic framework from open-source insect genomes. To accomplish this, we add a chromosome level genome to a crucial lineage, Coleoptera. Our assembly of the Pachyrhynchus sulphureomaculatus genome is the first chromosome scale genome for the hyperdiverse Phytophaga lineage and currently the largest insect genome assembled to this scale. The genome is significantly larger than those of other weevils, and this increase in size is caused by repetitive elements. Our results also indicate that, among beetles, there are instances of long-lasting (>200 Ma) localization of genes to a particular chromosome with few translocation events. While some chromosomes have a paucity of translocations, intra-chromosomal synteny was almost absent, with gene order thoroughly shuffled along a chromosome. This large amount of reshuffling within chromosomes with few inter-chromosomal events contrasts with patterns seen in mammals in which the chromosomes tend to exchange larger blocks of material more readily. To place our findings in an evolutionary context, we compared syntenic patterns across Insecta in a phylogenetic framework. For the first time, we find that synteny decays at an exponential rate relative to phylogenetic distance. Additionally, there are significant differences in decay rates between insect orders, this pattern was not driven by Lepidoptera alone which has a substantially different rate.
Readout circuitry for continuous high-rate photon detection with arrays of InP Geiger-mode avalanche photodiodes (2012)

An asynchronous readout integrated circuit (ROIC) has been developed for hybridization to a 32x32 array of single-photon sensitive avalanche photodiodes (APDs). The asynchronous ROIC is capable of simultaneous detection and readout of photon times of arrival, with no array blind time. Each pixel in the array is independently operated by a finite state machine that actively quenches an APD upon a photon detection event, and re-biases the device into Geiger mode after a programmable hold-off time. While an individual APD is in hold-off mode, other elements in the array are biased and available to detect photons. This approach enables high pixel refresh frequency (PRF), making the device suitable for applications including optical communications and frequency-agile ladar. A built-in electronic shutter that de-biases the whole array allows the detector to operate in a gated mode or allows for detection to be temporarily disabled. On-chip data reduction reduces the high bandwidth requirements of simultaneous detection and readout. Additional features include programmable single-pixel disable, region of interest processing, and programmable output data rates. State-based on-chip clock gating reduces overall power draw. ROIC operation has been demonstrated with hybridized InP APDs sensitive to 1.06-&mu;m and 1.55-&mu;m wavelength, and fully packaged focal plane arrays (FPAs) have been assembled and characterized.
Modeling of an Electric Drive for a HEV Supervisory Level Power Flow Control Problem (2005)

In this paper, a supervisory level power flow control model for a parallel hybrid electric vehicle (HEV) is developed. The HEV studied utilizes power flow from an internal combustion engine ICE and from an electric-motor-generator, EM-GEN, (30 kW) and battery pack consisting of thirty 25 Ah 12 V lead acid batteries connected in series. The EM-GEN unit is an induction machine operated under maximum torque/amp control. This paper summarizes the non EM-GEN aspects of the HEV power flow control model developed earlier but focuses primarily on the development of a viable EM-GEN model amenable to a supervisory level power flow control problem.
An expert system for switch operation planning on line dispatching (1994)

Abstract An expert system is presented that produces the operation sequence for disconnecting apparatus from a power system under normal operating conditions. To maintain the reliability of power supply on the network during the operation, the operation sequence must be produced in due consideration of network states, such as load factors and routes of transmission line. Besides, since the network which the system manages includes many high‐voltage consumers, the operation sequence for each consumer should be divided into detailed switch operation sequence. To produce a detailed switching operation sequence simultaneously with macronetwork operation sequence, we introduce the multilayered object‐oriented network model for the knowledge base of this expert system. Each layer of this model represents network configuration in the different degree of detail, and the consistency between states of layers is maintained by an interlayer message‐passing mechanism. On the layer which represents apparatus and their connections in detail, the inference engine can generate the switching operation sequence. On another layer which represents control centers and consumers, the inference engine can search for routes of power supply and can generate the sequence of changing over the network. Therefore, by using each layer properly, the inference engine can produce various kinds of operation sequences. Furthermore the object‐oriented network model facilitates maintenance and extension of the system.
ChemInform Abstract: Biocatalytic Synthesis of Chiral Polyoxygenated Compounds: Modulation of the Selectivity Upon Changes in the Experimental Conditions. (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Predicting changes in blood flow in patient-specific operative plans for treating aortoiliac occlusive disease (2005)

Traditionally, a surgeon will select a procedure for a particular patient on the basis of past experience with patients with a similar state of disease. The experience gained from this patient will be selectively used when treating the next patient with similar symptoms. This article describes a surgical planning system that was developed to enable a vascular surgeon to create and test alternative operative plans prior to surgery for a given patient. One-dimensional and three-dimensional hemodynamic (i.e., blood flow) simulations were performed for rest and exercise for operative plans for two aorto-femoral bypass patients and compared with actual postoperative data. The information obtained from one-dimensional (volume flow distribution and pressure losses) and three-dimensional (flow, pressure, and wall shear stress) hemodynamic simulations may be clinically relevant to vascular surgeons planning interventions.
Flexible Microfluidic Devices With Three-Dimensional Interconnected Microporous Walls (2011)

Microfluidics is emerging as one of the fastest growing fields for chemical and biological applications. The demand has also increased for methods of fabricating low-cost prototype microfluidic devices rapidly with compatible materials and novel functional attributes. One attractive feature that can be incorporated into microfluidic devices is a porous membrane or porous channel wall [1]. Devices with such features can potentially be used for multiphase catalytic reactions in chemical and pharmaceutical applications similar to the gas-liquid-solid hydrogenation reactions reported by Kobayahi et al. [2] or gas-liquid syntheses by Park and Kim [3].