gebhart/patrepeval huggingface dataset:
Semantic Reconstruction-Based Nuclear Cataract Grading from Slit-Lamp Lens Images (2016)

Cataracts are the leading cause of visual impairment and blindness worldwide. Cataract grading, i.e. assessing the presence and severity of cataracts, is essential for diagnosis and progression monitoring. We present in this work an automatic method for predicting cataract grades from slit-lamp lens images. Different from existing techniques which normally formulate cataract grading as a regression problem, we solve it through reconstruction-based classification, which has been shown to yield higher performance when the available training data is densely distributed within the feature space. To heighten the effectiveness of this reconstruction-based approach, we introduce a new semantic feature representation that facilitates alignment of test and reference images, and include locality constraints on the linear reconstruction to reduce the influence of less relevant reference samples. In experiments on the large ACHIKO-NC database comprised of 5378 images, our system outperforms the state-of-the-art regression methods over a range of evaluation metrics.
Lightweight Establishment of Secure Session (LESS) on CoAP (2018)

Secure yet lightweight protocol for communication over the Internet
for constrained node networks (CNN) is a pertinent problem.
Constrained Application Layer Protocol (CoAP) mandates the use of
Datagram Transport Layer Security (DTLS) for a secure transaction over
CoAP. But DTLS is not a candidate technology for CNNs by design. The
DTLS handshake overhead to establish the credentials for a session
between two end-points in a CNN may not be resource efficient. There
are ongoing efforts to secure one-time exchanges by ensuring object
security at the application layer. But a composite standardized
mechanism for resource-efficient end-to-end security credential
establishment is much needed to cater both one-time exchanges as well
as exchanges over a session. DTLS is essentially a combination of two
operations: (1) the session protocol to establish the credentials (and
this is the resource heavy part), (2) the record protocol to protect
the information (this is the cryptographic part). This draft proposes
to distribute the security responsibilities such that the session
establishment happens in the application layer, leveraging the
lightweight semantics of CoAP, and the record layer encryption happens
by reusing the existing DTLS record-layer protocol. This way the
proposed mechanism enables a resource-efficient session establishment
mechanism besides reusing the existing DTLS encryption. Assuming a
Pre-Shared Key (PSK) environment, this draft proposes an embedding of
handshake for resource efficient end-to-end session establishment into
CoAP. The session establishment procedure produces the necessary and
sufficient inputs for seamless operation of the DTLS record-layer to
secure the channel. Also, this mechanism ensures a direct security
association between the end-applications for systems using middleboxes
like proxies and/or gateways which may not be always trusted. The
proposed approach provides a mechanism to securely traverse through
such middleboxes through an end-to-end trusted channel.
Verification column (2017)

The growing popularity of verification competitions such as VerifyThis Verification Competition and the Competition on Software Verification (SV-COMP), both, incentivize as well as reward tool developers. VerifyThis 2016 was held in Eindhoven colocated with the European Joint Conferences on Theory and Practice of Software (ETAPS) 2016. The competition presents challenges to evaluate a broad range of tools such as Danfy, KeY, VeriFast, CIVL, among others. The first article in the newsletter "CIVL Solutions to VerifyThis 2016 Challenges" by Stephen F. Siegel at University of Delaware presents the solutions to the challenges using The Concurrency Intermediate Verification Language (CIVL) verifier. CIVL supports of a variety of techniques based on symbolic execution and model checking to verify sequential and concurrent programs. The article presents an overview of the framework, a description of the challenges, and how CIVL performs on the benchmarks. The second article "Security by Compilation: An Automated Approach to Comprehensive Side-channel resistance" by Chao Wang from University of Southern California and Patrick Schaumont from Virginia Tech leverage formal verification and program synthesis to detect side challenge attacks on mobile devices. The approach is evaluated on implementations of MAC-Keccak, AES and other cryptographic algorithms. This article bridges the security and verification forums of the newsletter.
Proteomic Studies of Nitrated Alpha-Synuclein Microglia Regulation by CD4+CD25+ T Cells (2009)

Microglial inflammatory responses affect Parkinson's disease (PD) associated nigrostriatal degeneration. This is triggered, in measure, by misfolded, nitrated alpha-synuclein (N-alpha-syn) contained within Lewy bodies that are released from dying or dead dopaminergic neurons into the extravascular space. N-alpha-syn-stimulated microglial immunity is regulated by CD4+ T cell subset. Indeed, CD4+CD25+ regulatory T cells (Treg) induce neuroprotective immune responses. This is seen in rodent models of stroke, amyotrophic lateral sclerosis, human immunodeficiency virus associated neurocognitive disorders, and PD. To elucidate the mechanism for Treg-mediated microglial neuroregulatory responses, we used a proteomic platform integrating difference gel electrophoresis and tandem mass spectrometry peptide sequencing. These tests served to determine consequences of Treg on the N-alpha-syn stimulated microglia. The data demonstrated that Treg substantially alter the microglial proteome in response to N-alpha-syn. This is seen through Treg abilities to suppress microglial proteins linked to cell metabolism, migration, protein transport and degradation, redox biology, cytoskeletal, and bioenergetic activities. We conclude that Treg modulate the N-alpha-syn microglial proteome and, in this way, can slow the tempo and course of PD.
Catalytic Reductions and Tandem Reactions of Nitro Compounds Using in Situ Prepared Nickel Boride Catalyst in Nanocellulose Solution (2017)

A mild and efficient method for the in situ reduction of a wide range of nitroarenes and aliphatic nitrocompounds to amines in excellent yields using nickel chloride/sodium borohydride in a solution of TEMPO-oxidized nanocellulose in water (0.01 wt %) is described. The nanocellulose has a stabilizing effect on the catalyst, which increases the turnover number and enables low loading of nickel catalyst (0.1-0.25 mol % NiCl<sub>2</sub>). In addition, two tandem protocols were developed in which the in situ formed amines were either Boc-protected to carbamates or further reacted with an epoxide to yield β-amino alcohols in excellent yields.
RESOLFT Nanoscopy in Living Cells at High Speed (2013)

Among various superresolution methods, RESOLFT nanoscopy has advantages in compatibility with live cell imaging via utilization of genetically encoded reversely-switchable fluorescent proteins (rsFPs). Recent developments in rsFPs allow nanoscopy in living cells at high speed.
Nanoscale optical biosensors based on localized surface plasmon resonance spectroscopy (2003)

The Ag nanoparticle based localized surface plasmon resonance (LSPR) nanosensor yields ultrasensitive biodetection with extremely simple, small, light, robust, and low-cost instrumentation. Using LSPR spectroscopy, the model system, biotinylated surface-confined Ag nanotriangles, was used to detect less than one picomolar up to micromolar concentrations of streptavidin. Additionally, the monitoring of anti-biotin binding to biotinylated Ag nanotriangles exhibited that the system could be used as a solution immunoassay. The system was rigorously tested for nonspecific binding interactions and was found to display virtually no adverse results. These results represent important new steps in the development of the LSPR nanobiosensor for applications in medical diagnostics, biomedical research, and environmental science.
Abstract 3640: Validation of qBiomarker as an accurate and efficient mutation detection method in a comprehensive analysis of patient-derived tumor xenografts (2016)

Abstract Screening of patients for cancer-driving mutations is now used for cancer prognosis, remission scoring and treatment selection. Although recently emerged targeted Next Generation Sequencing (NGS) - based approaches provide accurate results and offer promising diagnostic capabilities, there are still limitations which impede their adoption for large-scale population-based screening. There is a pressing clinical need for a well-validated, rapid, cost-effective and accurate mutation profiling system with optimal analytical performance in patient specimens. Given their speed, and cost-effectiveness, real-time, quantitative qPCR mutation detection techniques are well suited for the clinical environment. The novel qBiomarker somatic mutation PCR array has high sensitivity and shorter turnaround times compared to other methods. However a direct comparison to existing viable alternatives is required to assess its true potential and limitations. In this study, we extensively evaluated a panel of 117 patient-derived tumor xenografts (PDX) by the qBiomarker array and directly compared its efficacy with that of other routinely used methods for mutation detection, including Ion AmpliSeq sequencing, whole exome sequencing (WES), and ultra-sensitive droplet digital PCR (ddPCR) genotyping. Our comprehensive analysis demonstrates that qBiomarker's performance is on par with that of other routinely used but more complex, labor-intensive and expensive methods of cancer mutation detection, and provides a foundation for advancing the adoption of qBiomarker assay for cancer driving mutation profiling in clinical diagnostics. Furthermore, a large-scale direct comparison of different mutation detection approaches will lead to informed choice of screening methodologies, especially in lower budget conditions or timeframe limitations. Citation Format: Mariana Brait, Evgeny Izumchenko, Luciane Kagohara, Samuel Long, Piotr Wysocki, Brian Faherty, Elana Fertig, Tin Khor, Elizabeth Bruckheimer, Gilson Baia, Daniel Ciznadija, Ido Sloma, Ido Ben-Zvi, Keren Paz, David Sidransky. Validation of qBiomarker as an accurate and efficient mutation detection method in a comprehensive analysis of patient-derived tumor xenografts. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3640.
Circulating cardiovascular biomarkers in recurrent atrial fibrillation: data from the GISSI-Atrial Fibrillation Trial (2010)

circulating markers of cardiomyocyte injury/strain and endothelin are related to recurrence of AF in patients in sinus rhythm with a history of recent AF.
DST: Dynamic Substitute Training for Data-free Black-box Attack (2022)

With the wide applications of deep neural network models in various computer vision tasks, more and more works study the model vulnerability to adversarial examples. For data-free black box attack scenario, existing methods are inspired by the knowledge distillation, and thus usually train a substitute model to learn knowledge from the target model using generated data as input. However, the substitute model always has a static network structure, which limits the attack ability for various target models and tasks. In this paper, we propose a novel dynamic substitute training attack method to encourage substitute model to learn better and faster from the target model. Specifically, a dynamic substitute structure learning strategy is proposed to adaptively generate optimal substitute model structure via a dy-namic gate according to different target models and tasks. Moreover, we introduce a task-driven graph-based structure information learning constrain to improve the quality of generated training data, and facilitate the substitute model learning structural relationships from the target model multiple outputs. Extensive experiments have been conducted to verify the efficacy of the proposed attack method, which can achieve better performance compared with the state-of-the-art competitors on several datasets. Project page: https://wxwangiris.github.io/DST
Remote Sensing and Earth System Dynamics: The Helmholtz Association Alliance (2014)

The main objective of the five year funded German Helmholtz Alliance “Remote Sensing and Earth System Dynamics” is the development and evaluation of novel bio/geo-physical information products derived from data acquired by a new generation of remote sensing satellites; and their integration in Earth system models for improving understanding and modelling the ability of global environmental processes and ecosystem change. The Alliance is organized in 4 research topics, each one dedicated to a specific Earth sphere with a specific scientific goal: • Biosphere: Global forest structure and biomass dynamics are evaluated for forest and biodiversity monitoring and the quantification of the global carbon cycle; • Geosphere: The ability to measure topographic variations with millimetre accuracy is explored for improving the understanding of earthquake and volcano activities; • Hydrosphere: The quantification of soil moisture and its variations at high spatial resolution is assessed with respect to hydrological models and the global water cycle; • Cryosphere: The estimation of melting processes in snow, ice and permafrost regions is addressed in terms of global climate change. The Alliance has been founded in June 2012 and comprises around 120 scientists with a financial support of 50 PhDs and PostDocs having different backgrounds and nationalities. 18 national research centers and university are participating which represents a unique opportunity to exploit and widen the expertise of all participating centres and to maximize their role and contribution in the international environmental change science. In this presentation the objectives of the Alliance and research highlight are presented obtained during the 2.5 years of operation.
Mutations in the principal neutralization determinant of human immunodeficiency virus type 1 affect syncytium formation, virus infectivity, growth kinetics, and neutralization (1992)

The principal neutralization determinant (PND) of human immunodeficiency virus type 1 envelope glycoprotein gp120 contains a conserved GPG sequence. The effects of a 29-amino-acid deletion of most of the PND, a 3-amino-acid deletion in the GPG sequence, and 16 single-amino-acid substitutions in the GPG sequence were determined in a transient expression assay. All mutant envelope glycoproteins were expressed at levels comparable to that of the wild-type envelope, and mutations in the GPG sequence did not affect processing to gp120 or, except for the 29-amino-acid deletion, binding to CD4. Of all of the mutants, only the GHG and GFG mutants induced formation of syncytia similar in size and number to those induced by the wild-type envelope. When the envelope expression level was increased 10-fold or more, several additional mutants (APG, GAG, GSG, GQG, GVG, and GPF) also induced syncytium formation. Transfection with infectious proviral molecular clones containing the GHG, GFG, APG, GAG, GSG, or GPF mutations induced production of viral particles; however, only the GPG, GHG, and GFG viruses produced active infections in CD4-bearing cells. Furthermore, whereas the wild-type virus was efficiently neutralized by PND polyclonal and monoclonal antibodies, the GHG- and GFG-containing viruses were not. These results show that mutations in the GPG sequence found within the PND do not affect envelope expression and do not significantly affect CD4 binding or production of viral particles but that they do affect the ability of the envelope to induce syncytia and those of the viral particles to infect CD4 cells and be neutralized by PND antibodies.
Compensation of Temperature and Concanavalin A Concentratration Effects for Glucose Determination by the Viscometric Affinity Assay (2000)

A viscometer suitable for rapid measurements in small volumes of highly viscous liquids is described. Using this device the viscometric affinity assay for glucose was studied under variable conditions in order to obtain basic information for the design of a viscometric glucose sensor. The viscosity of the dextran/Concanavalin A (ConA) solution is sensitive to glucose in a broad range of the shear stress. However, for measuring the glucose concentration with this sensitive liquid the strong dependence of the absolute viscosity on temperature and ConA concentration has to be taken into account. For the purpose of calibration a parameter more suitable than the absolute viscosity is the relative fluidity (F(r)) that is defined by the actual measured viscosity at a given glucose concentration, the reference viscosity at a standard glucose concentration, and a constant linearization coefficient. F(r) shows a linear dependence on the glucose concentration in the therapeutically interesting range up to 30 mM and is not significantly changed by moderate variations of the ConA concentration or temperature.
Anywhere decoding: Low-overhead basestation cooperation for interference- and fading-limited wireless environments (2015)

In the context of interference channels with multiple transmitters and receivers, we propose a novel decoding scheme called anywhere decoding that does not pre-assign the receiver at which each message should be decoded, but rather requires that each message must be decoded at some receiver. This paper illustrates how system performance can improve if we allow for this flexibility. After developing a system model based upon the classical two-user, discrete-memoryless interference channel, we present two decoding schemes based upon the anywhere decoding concept, each requiring extremely low overhead to enable cooperation among the receivers. Both of these schemes offer the same achievable rate region, for which we outline the proof in the discrete-memoryless case and state the result for the Gaussian case with independent and identically distributed Gaussian inputs. When cast into a cellular setting with two cooperating basestations experiencing path-loss and multipath fading, we assess performance in terms of two system metrics: the common outage probability and the symmetric throughput. Asymptotic analysis of the outage probability of the anywhere decoding schemes demonstrates that they achieve full spatial diversity through multiple decoding opportunities, and they are no more than 1.5 decibels (dB) from full basestation cooperation at high signal-to-noise ratio (SNR).
The Simplicity Project: Managing Complexity in a Diverse ICT World (2004)

As technology develops, people are using an ever broader range of heterogeneous ICT (Information and Communication Technology) devices and network-based services. New areas of research, such as pervasive computing, will further increase the diversity of the devices and services with which users have to deal. The result is an enormous burden of complexity for users, service providers and network operators. This creates obstacles to effective exploitation and acceptance of Beyond 3G systems such as ambient intelligence, context-aware services and novel access technologies. The goal of the Simplicity project is to reduce this complexity by: i) providing automatic customization of user access to services and the network; ii) automatically adapting services to terminal characteristics and user preferences; iii) orchestrating network capabilities.
Role of Nativity in End of Life Care Planning (2021)

Abstract Given the rapidly aging population, optimal end-of-life (EOL) consistent with individual wishes is a public health priority. Advanced Care Planning (ACP) involves Advanced Directives (AD) and establishing a Power of Attorney (POA). AD describe EOL Care preferences including options to limit treatment, withhold treatment, provide comfort care, and prolong treatments. Nativity can provide meaningful guidance in decision-making at the end of life. Data from this study came from the Health and Retirement Study, nationally representative longitudinal study of U.S. residents. The sample included 4,015 older adults, 65 and above years of age who died during study follow-up. Nativity was categorized as U.S born and Foreign born. ACP variables included presence of AD and POA, and EOLC preferences included provide comfort care, limit, withhold, or prolong treatment. Covariates included age, gender, race, marital status, education, and subjective health at baseline. Cox Proportional Hazards (Cox PH) and Weibull Models were used to identify associations between nativity and end of life care. Results: Compared to U.S born, Foreign born participants were less likely to have POA (HR: 0.75; 95% CI:0.64-0.89) in Cox PH and POA (HR: 0.63; 95 % CI:0.53-0.75) Weibull models in unadjusted models, limited treatment (HR: 1.58; 95 % CI: 1.2, 2.1), and prolong treatment (HR: 0.23; 95 % CI:0.06-0.99) and Cox PH and (HR: 0.20; 95 % CI: 0.05-0.83) in Weibull modes. Conclusion: There are differences in Advanced Care Planning by nativity. Country of origin should be considered when helping individuals plan for end-of-life care.
Multiscale texture segmentation of dip‐cube slices using wavelet‐domain hidden Markov trees (1999)

PreviousNext No AccessSEG Technical Program Expanded Abstracts 1999Multiscale texture segmentation of dip‐cube slices using wavelet‐domain hidden Markov treesAuthors: Ivan Magrin‐ChagnolleauHyeokho ChoiRutger van SpaendonckPhilippe SteeghsRichard G. BaraniukIvan Magrin‐ChagnolleauRice University, Houston, Texas, Hyeokho ChoiRice University, Houston, Texas, Rutger van SpaendonckRice University, Houston, Texas, Philippe SteeghsRice University, Houston, Texas, and Richard G. BaraniukRice University, Houston, Texashttps://doi.org/10.1190/1.1820808 SectionsAboutPDF/ePub ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InRedditEmail Permalink: https://doi.org/10.1190/1.1820808FiguresReferencesRelatedDetails SEG Technical Program Expanded Abstracts 1999ISSN (print):1052-3812 ISSN (online):1949-4645Copyright: 1999 Pages: 2061 publication data© 1999 Copyright © 1999 Society of Exploration GeophysicistsPublisher:Society of Exploration Geophysicists HistoryPublished: 04 Jan 2005 CITATION INFORMATION Ivan Magrin‐Chagnolleau, Hyeokho Choi, Rutger van Spaendonck, Philippe Steeghs, and Richard G. Baraniuk, (1999), "Multiscale texture segmentation of dip‐cube slices using wavelet‐domain hidden Markov trees," SEG Technical Program Expanded Abstracts : 1512-1515. https://doi.org/10.1190/1.1820808 Plain-Language Summary PDF DownloadLoading ...
Assessment of bio-fuel options for solid oxide fuel cell-based auxiliary power units (2011)

It is now illegal in many states to idle heavy-duty trucks to supply the cabin electrical needs of the driver. An alternative approach is the solid oxide fuel cell-based auxiliary power unit (APU), which can produce electrical power with much higher efficiency and lower greenhouse gas emissions. The “standard” APU system includes a fuel reformer, which converts on-board diesel fuel into a hydrogen-rich effluent that is delivered to the anode side of the fuel cell stack. As renewable bio-fuels begin to realize greater market penetration, there is a need to determine which bio-fuel option provides the optimal pathway to economic value and emissions reduction when converted for use in a fuel cell APU system. The results of this study indicate that biodiesel from waste cooking oil may be the optimal bio-fuel option because of its relatively low energy use and greenhouse gas (GHG) emissions, as well as chemical and physical properties that are similar to those of petroleum-based diesel fuel.