gebhart/patrepeval huggingface dataset:
Artificial Intelligence-Assisted Serial Analysis of Clinical Cancer Genomics Data Identifies Changing Treatment Recommendations and Therapeutic Targets (2022)

Abstract Purpose: Given the pace of predictive biomarker and targeted therapy development, it is unknown whether repeat annotation of the same next-generation sequencing data can identify additional clinically actionable targets that could be therapeutically leveraged. In this study, we sought to determine the predictive yield of serial reanalysis of clinical tumor sequencing data. Experimental Design: Using artificial intelligence (AI)-assisted variant annotation, we retrospectively reanalyzed sequencing data from 2,219 patients with cancer from a single academic medical center at 3-month intervals totaling 9 months in 2020. The yield of serial reanalysis was assessed by the proportion of patients with improved strength of therapeutic recommendations. Results: A total of 1,775 patients (80%) had ≥1 potentially clinically actionable mutation at baseline, including 243 (11%) patients who had an alteration targeted by an FDA-approved drug for their cancer type. By month 9, the latter increased to 458 (21%) patients mainly due to a single pan-cancer agent directed against tumors with high tumor mutation burden. Within this timeframe, 67 new therapies became available and 45 were no longer available. Variant pathogenicity classifications also changed leading to changes in treatment recommendations for 124 patients (6%). Conclusions: Serial reannotation of tumor sequencing data improved the strength of treatment recommendations (based on level of evidence) in a mixed cancer cohort and showed substantial changes in available therapies and variant classifications. These results suggest a role for repeat analysis of tumor sequencing data in clinical practice, which can be streamlined with AI support.
A negative-index metamaterial design based on metal-core dielectric shell resonators. (2016)

Abstract not provided.
Short Note on Our Research in Cancer: Cell and DNA Damage from the Point of View of a Medical Physicist (2013)

Currently, there are approximately 80 million CT examinations [1] performed in the United States annually. This means that each patient is exposed to about 1013 photons/cm2 during the CT scan and most photon and their secondary electrons have a kinetic energy, which is higher than the ionization potential of patients DNA in cells. To date, due to the increasing number of CT examinations worldwide, the risk of getting cancer has been further increased. According to the literature, direct action of ionizing radiation (e.g. direct cell hits) is seen as less important, because about 2/3 of DNA damage is originated by indirect action of ionizing radiation (e.g. hydroxyl radicals). However, the damage to human DNA by X-ray imaging is a stochastic and also a quantum mechanical process.Therefore, more theoretical and medical physicists should investigate this topic.
Sir Robert Stawell Ball and methodologies of modern screw theory (2002)

The theory of screws was largely developed by Sir Robert Stawell Ball over 100 years ago to investigate general problems in rigid body mechanics. Nowadays, screw theory is applied in many different but related forms including dual numbers, Plilcker coordinates and Lie algebra. An overview of these methodologies is presented along with a perspective on Ball. Screw theory has re-emerged after a hiatus to become an important tool in robot mechanics, mechanical design, computational geometry and multi-body dynamics.
Characterization of GaN-Based Schottky Barrier Ultraviolet (UV) Detectors in the UV and Vacuum Ultraviolet (VUV) Region Using Synchrotron Radiation (2001)

Characterization of GaN-based Schottky barrier ultraviolet (UV) detectors with a comb-shaped electrode using synchrotron radiation ( h ν=2.2–30 eV, λ=41–563 nm) is described. Below h ν=8.0 eV (λ&gt;155 nm), the detectors are available without any photoemission of GaN and Au electrode. Under application of reverse bias, the responsivity is increased to 0.05 A/W at -0.4 V. The photocurrent is controlled by reverse bias. On the other hand, above h ν=8.0 eV (λ&lt;155 nm), the responsivity spectra are dominated by photoemissions of Au and GaN. These results show that these Schottky type detectors with mesa structures are effective to detect vacuum ultraviolet (VUV)-UV light (155&lt;λ&lt;360 nm).
Nitric Oxide in Asthma: Pathogenic, Therapeutic, or Diagnostic? (1999)

Nitrogen monoxide, more commonly called nitric oxide or simply NO, is a fascinating free radical molecule, which participates in a broad range of important physiologic processes, including vasodilation, neurotransmission, and host defense. NO is generated from L -arginine by the enzyme nitric oxide synthase (NOS), of which there are three known isoforms. Types I and III NOS, found predominantly in neurons and endothelium, respectively, are constitutively expressed and are dependent upon calcium for activity. The third isoform, NOS II, can be expressed by a wide range of cells primarily after it has been induced by certain cytokines, microbes, or microbial products (1, 2). All three isoforms are dimeric, with each subunit containing iron protoporpyrin IX, tetrahydrobiopterin, flavin adenine dinucleotide, flavin mononucleotide, and binding sites for
Sieving for shortest vectors in ideal lattices: a practical perspective (2017)

The security of many lattice-based cryptographic schemes relies on the hardness of finding short vectors in integral lattices. We propose a new variant of the parallel Gauss sieve algorithm to compute such short vectors. It combines favourable properties of previous approaches resulting in reduced run time and memory requirement per node. Our publicly available implementation outperforms all previous Gauss sieve approaches for dimensions 80, 88, and 96. When computing short vectors in ideal lattices, we show how to reduce the number of multiplications and comparisons by using a symbolic Fourier transform. We computed a short vector in a negacyclic ideal lattice of dimension 128 in less than nine days on 1,024 cores, more than twice as fast as the recent record computation for the same lattice on the same computer hardware.
ZSM-based Management and Orchestration of 3GPP Network Slicing: An Architectural Framework and Deployment Options (2022)

Driven by closed-loop automation, the Zero-Touch Network and Services Management (ZSM) framework offers invigorating features for the end-to-end management and orchestration of a sliced network. Although ZSM is considered a promising framework by 3GPP, there is a lack of concrete ZSM-based solutions for the 3GPP Network Slicing management. This article presents an architectural framework of a ZSM-based management system for 3GPP Network Slicing. The proposed framework employs recursive ZSM management domains to meet the specific management requirements of the standard 3GPP Network Slicing framework. Two deployment options are considered for the presented framework. The first option features the integration of the standard services of the 3GPP Management System within ZSM. The other one considers ZSM as a complementary system for the standard 3GPP Management System. From these deployment options, some key questions are identified on ZSM's interoperability with the existing 3GPP Network Slicing systems. Finally, for each option, the architectural and operational feasibility of the ZSM interoperation with 3GPP Network Slicing systems is shown through an example use case.
Adjuvanted Recombinant BCG Vaccine increases protection against TB (2012)

Poster - Session 2
Interpreting and predicting tactile signals for the SynTouch BioTac (2021)

In the human hand, high-density contact information provided by afferent neurons is essential for many human grasping and manipulation capabilities. In contrast, robotic tactile sensors, including the state-of-the-art SynTouch BioTac, are typically used to provide low-density contact information, such as contact location, center of pressure, and net force. Although useful, these data do not convey or leverage the rich information content that some tactile sensors naturally measure. This research extends robotic tactile sensing beyond reduced-order models through (1) the automated creation of a precise experimental tactile dataset for the BioTac over a diverse range of physical interactions, (2) a 3D finite-element (FE) model of the BioTac, which complements the experimental dataset with high-density, distributed contact data, (3) neural-network-based mappings from raw BioTac signals to not only low-dimensional experimental data, but also high-density FE deformation fields, and (4) mappings from the FE deformation fields to the raw signals themselves. The high-density data streams can provide a far greater quantity of interpretable information for grasping and manipulation algorithms than previously accessible. Datasets, CAD files for the experimental testbed, FE model files, and videos are available at https://sites.google.com/nvidia.com/tactiledata .
Evaluation of a biomimetic optical-filter based chemical sensor for detection of hazardous chemical vapors in the infrared (2016)

Detection of concealed hazardous materials is a pressing need for the global defense community. To address this need, the development of reliable and readily-deployable sensing devices is a key area of research. A multitude of infrared sensing techniques are being studied which allow for reliable sensing of concealed threats. Continued development in this field is working to increase the selectivity of such infrared sensors, while at the same time reducing their complexity, size and cost. We have recently developed a biomimetic optical filter based approach, based on human color vision, that utilizes multiple, broadband, overlapping infrared (IR) filters to clearly discriminate between hazardous target chemicals and interferents with very similar mid-IR spectral signatures. This technique was extensively studied in order to select filters which provide optimum selectivity for specific chemical sets. Using this knowledge, we designed and assembled a gas-phase sensor which uses three broadband mid-IR filters to detect and discriminate between a target chemical, fuel oil, and various interferents with strongly overlapping IR absorption bands in the carbon – hydrogen stretch region of the IR absorption spectrum 2700 cm<sup>-1</sup> - 3300 cm<sup>-1</sup> (3.0 &mu;m - 3.7 &mu;m). We present an overview of the design and performance of this filter-based system and explore the ability of this system to detect and discriminate between strongly overlapping target and interferent chemicals. The detection results using the filter-based system are compared to numerical methods to demonstrate the operation of this methodology. We present the results of experiments with both target and interferent chemicals present with chemicals both in and out of the detection set, and discuss future field development and application of this approach.
ChemInform Abstract: 2,6‐Diketopiperazines from Amino Acids: From Solution‐Phase to Solid‐Phase Organic Synthesis. (2002)

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.
Towards environmentally friendly, dry deposited, water developable molecular glass photoresists (2007)

Photoresists based on molecular glasses are gaining more and more importance as resist material to replace polymer based photoresist. In addition environmental issues have to be considered in the long-term. Therefore the paper describes novel negative photoresists containing a ternary mixture of a glassy low molecular functional polyphenol where the film preparation is possible by solvent-free physical vapor deposition. After UV light exposure and a thermal annealing process to enable acid catalyzed crosslinking between the molecular glass and the crosslinker, the photoresist was developed using only water to give well-defined patterns. In order to experimentally study efficiently the multiple parameters such as composition, exposure dose, and development times combinatorial PVD techniques were utilized.
Corrigendum: Inducing Social Self‐Sorting in Organic Cages To Tune The Shape of The Internal Cavity (2020)

The authors would like to draw attention to an error in Figure 5 of this Research Article. The top line of Figure 5 does not show the correct cage ([L1+2B1]); rather, [L1+2B1N] has been shown twice. The corrected figure is shown below. This mistake does not affect the scientific conclusions of the paper. Side-, window-, and top-views of the electrostatic potential inside the cavities of the socially sorted [L1+2B1X] cages, mapped onto the 0.0004 a.u. total electron density isosurface calculated at the M06-2X/6-311+G(d,p) level of theory.
Laser-assisted synthesis of gold–graphene oxide nanocomposites: effect of pulse duration (2020)

Laser photoreduction of metal ions onto graphene oxide (GO) is a facile, environmentally friendly method to produce functional metal-GO nanocomposites for a variety of applications. This work compares Au-GO nanocomposites prepared by photoreduction of [AuCl<sub>4</sub>]<sup>-</sup> in aqueous GO solution using laser pulses of nanosecond (ns) and femtosecond (fs) duration. The presence of GO significantly accelerates the [AuCl<sub>4</sub>]<sup>-</sup> photoreduction rate, with a more pronounced effect using ns laser pulses. This difference is rationalized in terms of the stronger interaction of the 532 nm laser wavelength and long pulse duration with the GO. Both the ns and fs lasers produce significant yields of sub-4 nm Au nanoparticles attached to GO, albeit with different size distributions: a broad 5.8 ± 1.9 nm distribution for the ns laser and two distinct distributions of 3.5 ± 0.8 and 10.1 ± 1.4 nm for the fs laser. Despite these differences, both Au-GO nanocomposites had the same high catalytic activity towards p-nitrophenol reduction as compared to unsupported 4-5 nm Au nanoparticles. These results point to the key role of GO photoexcitation in catalyzing metal ion reduction and indicate that both ns and fs lasers are suitable for producing functional metal-GO nanocomposites.
Fast reaction studies of the gycolytic pathway from aldolase to glyceraldehyde-3-phosphate dehydrogenase with physiological concentrations of enzymes: another oxygen-debt mechanism (1987)

Conference Article| October 01 1987 Fast reaction studies of the gycolytic pathway from aldolase to glyceraldehyde-3-phosphate dehydrogenase with physiological concentrations of enzymes: another oxygen-debt mechanism M. R. HOLLAWAY; M. R. HOLLAWAY 1Department of Biochemistry, University College London, Gower Street, London WC1E 6BT, U.K. Search for other works by this author on: This Site PubMed Google Scholar S. M. DUNN; S. M. DUNN 1Department of Biochemistry, University College London, Gower Street, London WC1E 6BT, U.K. Search for other works by this author on: This Site PubMed Google Scholar P. W. CHAPMAN P. W. CHAPMAN 1Department of Biochemistry, University College London, Gower Street, London WC1E 6BT, U.K. Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (1987) 15 (5): 985–987. https://doi.org/10.1042/bst0150985 Article history Received: April 10 1987 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn MailTo Cite Icon Cite Get Permissions Citation M. R. HOLLAWAY, S. M. DUNN, P. W. CHAPMAN; Fast reaction studies of the gycolytic pathway from aldolase to glyceraldehyde-3-phosphate dehydrogenase with physiological concentrations of enzymes: another oxygen-debt mechanism. Biochem Soc Trans 1 October 1987; 15 (5): 985–987. doi: https://doi.org/10.1042/bst0150985 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Society Transactions Search Advanced Search Keywords: GPD, glyceraldehyde-3-phosphate dehydrogenase, TIM, triose phosphate isomerase, FBP, fructose-1,6-bisphosphate, GOD, glycerol phosphate dehydrogenase, FBP, fructose 1.6-bisphosphate, G3P, glyceraldehyde 3-phosphatc, DHAP, dihydroxyacetone phosphate, DPG, 1.3-diphosphoglycerate, N, NAD+, NH, NADH This content is only available as a PDF. © 1987 Biochemical Society1987 Article PDF first page preview Close Modal You do not currently have access to this content.
Free-space optical communications link at 1550 nm using multiple-quantum-well modulating retroreflectors in a marine environment (2005)

A 1550-nm eye-safe, free-space optical communications link is demonstrated at rates up to 5 Mbits/s over a distance of 2 km in the Chesapeake Bay, using quantum-well-based modulating retroreflectors. Tests are conducted under various atmospheric conditions over a time period of about a year. The experimental and theoretical link budgets are compared and statistical measurements of the effects of scintillation are collected.
An Evaluation of Service Composition Technologies Applied to Network Management (2007)

Service composition is a technique that may help the development of management systems by aggregating smaller services to produce more sophisticated ones. Service composition can be realized by using traditional management technologies, although these technologies have not been conceived taking composition support as one of their main aspects. Current service-oriented architecture (SOA)-related efforts, however, define specific standards for Web services composition, such as the Web services business process execution language (WS-BPEL). Web services for network management have been investigated by the management community at least in the last four years, but up to today no research evaluating Web services composition applied to network management has been carried out. In this paper we present such an evaluation where compositions based on the IETF Script MIB, ad-hoc Java Web services, and WS- BPEL are compared against one another in a managed network where BGP routers are investigated in order to identify route advertisement anomalies.
Genetic variation in the immune system and malaria susceptibility in infants: a nested case–control study in Nanoro, Burkina Faso (2021)

These findings indicate that genetic polymorphisms in genes driving innate immune responses are associated to malaria susceptibility during the first year of life, possibly by modulating production of inflammatory mediators.
Experimental validation of autonomous converter control in a HVDC grid (2014)

Much research has been done regarding the control and coordination of VSC converters in a Multiterminal HVDC network or grid. Amongst those, one underlying concept is the most common- the DC voltage droop control.
Degradation of DMSP in Antarctic winter sea ice: Who is responsible? (2015)

Dimethylsulfoniopropionate (DMSP) is frequently found in high concentrations in polar sea ice, especially when the phytoplankton biomass is high. It is synthesized by various types of phytoplankton and serves, for example, as compatible solute and cryoprotectant, an adaptation to the physico-chemical conditions in sea ice.&#13;\nDMSP can be cleaved to the climate cooling gas dimethylsulfide (DMS) by the phytoplankton or by bacteria. The more common pathway, however, is bacterial demethylation, which leads to the formation of 3-mercaptopropionate and subsequently methanethiol. Different groups of Proteobacteria are known to possess genes for DMSP-cleavage or DMSP-demethylation pathways, or both. Proteobacteria of the gamma-, alpha, and beta-subclass, and members of the Bacteroidetes phylum are the dominating bacterial groups in sea ice. However, DMSP degradation pathways were investigated in oceanic bacterial strains and information on the processes in sea ice is scarce. &#13;\nWe performed incubation experiments to investigate DMSP degradation by sea ice bacterial communities during the AWECS (Antarctic Winter Ecosytem Climate Study) cruise on RV Polarstern (ANT29-6) in the Weddell Sea. Sea ice was crushed and submerged in filtered sea water for incubation in gastight 1L glass-bottles at 0°C. The treatments were amended with DMSP and incubated under different light conditions or nutrient additions. During the experiment, DMSP concentrations decreased and DMS concentrations increased. Bacterial growth was higher in the DMSP amended treatments than in control incubations without DMSP addition, and the fraction of gamma-Proteobacteria increased in all treatments. Dominant species were Polaribacter sp. (Flavobacteria), Oleispiera sp. and Colwellia sp. (gamma-Proteobacteria). Model strains of the aforementioned species contain the cleavage pathway gene dddD as well as the demethylation pathway genes in their genome. However, the confirmation of the presence of the DMSP-cleavage and demethylation genes in our incubations is currently still underway.&#13;\n
Post-translational modification and folding of a lasso-type gene-encoded antimicrobial peptide require two enzymes only in Escherichia coli (2007)

International audience
A reference dataset for deformable image registration spatial accuracy evaluation using the COPDgene study archive (2013)

Landmark point-pairs provide a strategy to assess deformable image registration (DIR) accuracy in terms of the spatial registration of the underlying anatomy depicted in medical images. In this study, we propose to augment a publicly available database (www.dir-lab.com) of medical images with large sets of manually identified anatomic feature pairs between breath-hold computed tomography (BH-CT) images for DIR spatial accuracy evaluation. Ten BH-CT image pairs were randomly selected from the COPDgene study cases. Each patient had received CT imaging of the entire thorax in the supine position at one-fourth dose normal expiration and maximum effort full dose inspiration. Using dedicated in-house software, an imaging expert manually identified large sets of anatomic feature pairs between images. Estimates of inter- and intra-observer spatial variation in feature localization were determined by repeat measurements of multiple observers over subsets of randomly selected features. 7298 anatomic landmark features were manually paired between the 10 sets of images. Quantity of feature pairs per case ranged from 447 to 1172. Average 3D Euclidean landmark displacements varied substantially among cases, ranging from 12.29 (SD: 6.39) to 30.90 (SD: 14.05) mm. Repeat registration of uniformly sampled subsets of 150 landmarks for each case yielded estimates of observer localization error, which ranged in average from 0.58 (SD: 0.87) to 1.06 (SD: 2.38) mm for each case. The additions to the online web database (www.dir-lab.com) described in this work will broaden the applicability of the reference data, providing a freely available common dataset for targeted critical evaluation of DIR spatial accuracy performance in multiple clinical settings. Estimates of observer variance in feature localization suggest consistent spatial accuracy for all observers across both four-dimensional CT and COPDgene patient cohorts.