gebhart/patrepeval huggingface dataset:
Equity and the JAMA Network (2021)

The key objective of JAMA is "To promote the science and art of medicine and the betterment of the public health"; similar objectives and mission statements are supported by all 12 JAMA Network Journals.Together this family of journals is committed to publishing the best research, reviews, and opinion articles to advance medical science, promote public health, and improve patient care.The ultimate goal is to promulgate truth in science and medicine.On February 23, 2021, a podcast titled "Structural Racism for Doctors-What Is It?" was posted by the JAMA Network and on the following day, a tweet was posted to promote the podcast.Assertions in both that disavowed the presence of structural racism in medicine and among physicians were wrong, misguided, and uninformed.An extensive evidence base strongly supports the presence of structural racism in medicine and its adverse influence on health. 1 The process for reviewing and publishing the podcast and tweet was also flawed.On March 4, 2021, Howard Bauchner, MD, editor in chief of JAMA and the 12 JAMA Network Journals, took responsibility and issued an apology for the podcast and tweet.This editorial team also expresses a profound apology for the misinformation in the podcast and tweet and recognizes the hurt, anger, and outrage that resulted.These events and developments make it clear that JAMA and the JAMA Network Journals can and must do better and advance toward inclusion and antiracism in all journalrelated activities.Even though these journals have made progress, additional commitment and work are needed to build on and intensify these efforts to achieve meaningful, sustainable change.For instance, previous efforts include the more than 650 research, review, and opinion articles on race, racism, and racial and ethnic disparities and inequities that have been published in JAMA and the JAMA Network Journals since 2015, 1 including editorials in JAMA on topics such as race and medical research, 2 race and poverty and medicine, 3 enhancing diversity in medical schools, 4 and equity related to COVID-19 vaccines. 5n addition, within the past year, JAMA Network Open and JAMA Health Forum issued calls for manuscripts on prevention and effects of systemic racism in health 6,7 ; JAMA Psychiatry initiated an editorial fellowship prioritized to earlycareer academic psychiatrists from underrepresented backgrounds; and JAMA Surgery issued a "Call to Action" to all surgery journal editors for diversity in the editorial and peer review process.
151 Using genomics to search for new viral causes and treatments for human cancer (2014)

Although animal polyomaviruses, such as SV40, have been critical models in cancer research for over one-half century, polyomaviruses have not—until recently—been linked to human cancer. Using digital transcriptome subtraction, Merkel cell polyomavirus (MCV) was discovered in 2008 to infect most Merkel cell carcinomas, the most severe form of skin cancer. Normally, MCV is an common and asymptomatic infection of the human skin. In Merkel cell tumors, however, the virus integrates and undergoes mutations that eliminate viral replication but allow continued expression of viral oncogenes. MCV and MCC reveal a new model for carcinogenesis in which a rare combination of xenomutations to healthy skin flora initiate a deadly cancer. Using new sequencing technologies, the causes previously-unsuspected viral cancers can be uncovered and clues for new rational drug therapies can be designed.
Fine-Grained API Evolution for Method Deprecation and Anti-Deprecation (2006)

API evolution is the process of migrating an inter-library interface from one version to another. Such a migration requires checking that all libraries which interact through the interface be updated. Libraries can be updated one by one if there is a transition period during which both updated and non-updated libraries can communicate through some transitional version of the interface. Static type checking can verify that all libraries have been updated, and thus that a transition period may end and the interface be moved forward safely. A fine-grained checker can do so for individual changes to an interface, thus allowing interface changes to be interleaved. Anti-deprecation is a novel type-checking feature that allows static checking for more interface evolutions periods than deprecation alone. Anti-deprecation, along with the more familiar deprecation, is formally studied as an extension to Featherweight Java. This study finds weaknesses in current popular deprecation checkers.
RobFR: Benchmarking Adversarial Robustness on Face Recognition (2020)

Face recognition (FR) has recently made substantial progress and achieved high accuracy on standard benchmarks. However, it has raised security concerns in enormous FR applications because deep CNNs are unusually vulnerable to adversarial examples, and it is still lack of a comprehensive robustness evaluation before a FR model is deployed in safety-critical scenarios. To facilitate a better understanding of the adversarial vulnerability on FR, we develop an adversarial robustness evaluation library on FR named \textbf{RobFR}, which serves as a reference for evaluating the robustness of downstream tasks. Specifically, RobFR involves 15 popular naturally trained FR models, 9 models with representative defense mechanisms and 2 commercial FR API services, to perform the robustness evaluation by using various adversarial attacks as an important surrogate. The evaluations are conducted under diverse adversarial settings in terms of dodging and impersonation, $\ell_2$ and $\ell_\infty$, as well as white-box and black-box attacks. We further propose a landmark-guided cutout (LGC) attack method to improve the transferability of adversarial examples for black-box attacks by considering the special characteristics of FR. Based on large-scale evaluations, the commercial FR API services fail to exhibit acceptable performance on robustness evaluation, and we also draw several important conclusions for understanding the adversarial robustness of FR models and providing insights for the design of robust FR models. RobFR is open-source and maintains all extendable modules, i.e., \emph{Datasets}, \emph{FR Models}, \emph{Attacks\&amp;Defenses}, and \emph{Evaluations} at \url{https://github.com/ShawnXYang/Face-Robustness-Benchmark}, which will be continuously updated to promote future research on robust FR.
Venous Thrombosis as a form of presentation in Inflammatory Bowel Disease - Case report (2023)

Inflammatory bowel disease (IBD) is a chronic disorder of the gastrointestinal tract, with a rising incidence worldwide. It is often associated with numerous extraintestinal manifestations, such as erythema nodosum (EN) and venous thromboembolism (VTE). We report a case of a 17-year-old male seen in a Pediatric consultation due to pain at the inner aspect of the lower left limb associated with bilateral lower limb cutaneous lesions for about a year. A left leg ultrasound revealed signs of phlebitis and the doppler ultrasonography revealed signs of an old occlusive VTE at the level of the great left saphenous vein. Fecal calprotectin was significantly elevated (775 ug/g). Abdominal ultrasound and entero-MRI showed increased thickness of the terminal ileum. Colonoscopy confirmed the diagnosis of Crohn's disease. He began induction treatment with systemic corticosteroids for eight weeks and maintenance treatment with azathioprine. Three months later he was asymptomatic with complete resolution of the erythema nodosum lesions. Extraintestinal manifestations can precede or be concomitant with the diagnosis of IBD and can have a significant impact on the quality of life of these patients. EN is the most common skin manifestation of IBD, with a well-established relationship between these two diseases. Many other extraintestinal manifestations are described, occurring less frequently. The authors aim to bring awareness to the risk of VTE as a rare but non-negligible comorbidity of IBD. This was an uncommon initial presentation of Crohn’s Disease since the patient had never reported any gastrointestinal symptoms. It is important to improve the knowledge of pediatricians about all kinds of extraintestinal manifestations of IBD since they may guide toward the correct diagnosis and allow the prompt initiation of treatment.
In vitro effect of cinnamic aldehyde, a main component of Cinnamomi Cortex, on human platelet aggregation and arachidonic acid metabolism. (1987)

The in vitro effect of cinnamic aldehyde, a main component of Cinnamomi Cortex, on platelet aggregation and arachidonic acid (AA) metabolism in human platelets was studied. Cinnamic aldehyde reduced platelet aggregation of both platelet rich plasma and washed platelets, dose-dependently. This compound also decreased the formation of the metabolites of AA such as thromboxane B2 (TXB2), 12-hydroxy heptadecatrienoic acid and 12-hydroxyeicosatetraenoic acid in collagen-stimulated washed platelets. The conversion of exogenous [14C]AA to cyclooxygenase metabolites or 12-lipoxygenase metabolite was not altered significantly by the addition of cinnamic aldehyde. On the other hand, collagen-induced release of [14C]AA and its metabolites from washed platelets prelabeled with [14C]AA was markedly reduced by the addition of cinnamic aldehyde. These results suggested that cinnamic aldehyde suppressed the release of AA from platelet membrane phospholipids and then reduced the formation of thromboxane A2. This inhibitory effect of cinnamic aldehyde on AA release and TXB2 formation may contribute to reduced platelet aggregation.
Molecular Weight Dependence of Polymersome Membrane Structure, Elasticity, and Stability (2002)

Vesicles prepared in water from a series of diblock copolymers“polymersomes”are physically characterized. With increasing molecular weight M̄n, the hydrophobic core thickness for self-assembled bilayers of poly(ethylene oxide)−polybutadiene increases up to ∼20 nm, which is considerably greater than any previously studied lipid or polymersome system. Micromanipulation of vesicles demonstrates an interface-dominated elasticity that is independent of M̄n. Furthermore, membrane stability as defined by the maximal areal strain increases with M̄n, approaching a universal limit predicted by mean-field ideas and set by the interfacial tension. Nonlinear responses and memory effects also emerge with increasing M̄n, indicating the onset of chain entanglements at higher M̄n. The results highlight the interfacial limits and transitions to bulk responses of self-assemblies.
Common Path Side Viewing Monolithic Ball Lens Probe for Optical Coherence Tomography (2015)

Common path probes are highly desirable for optical coherence tomography as they reduce system complexity and cost by eliminating the need of dispersion compensation and polarization controlling optics. In this work, we demonstrate a monolithic ball lens based, common path, side viewing probe that is suitable for Fourier domain optical coherence tomography. The probe design parameters were simulated in Zemax modeling software and the simulated performance parameters were compared with experimental results. We characterized the performance of the probe by measuring its collection efficiency, resolution, and sensitivity. Our results demonstrated that with a source input power of 25 mW, we could achieve sensitivity of 100.5 dB, which is within 7 dB of the maximum possible sensitivity that could be achieved using a separate reference arm. The axial resolution of the system was found to be 15.6 m in air and the lateral resolution (full width half maximum) was approximately 49 m. The probe optics were assembled in a 1 mm diameter hypotube with a 500 m inner diameter. Images of finger skin acquired using this probe demonstrated clear visualization of the stratum corneum, epidermis, and papillary dermis, along with sweat ducts.
Threshold-Responsive Colorimetric Sensing System for the Continuous Monitoring of Gases (2023)

Colorimetric sensors are widely used because of their inherent advantages including accuracy, rapid response, ease-of-use, and low costs; however, they usually lack reusability, which precludes the continuous use of a single sensor. We have developed a threshold-responsive colorimetric system that enables repeated analyte measurements by a single colorimetric sensor. The threshold responsive algorithm automatically adjusts the sensor exposure time to the analyte and measurement frequency according to the sensor response. The system registers the colorimetric sensor signal change rate, prevents the colorimetric sensor from reaching saturation, and allows the sensor to fully regenerate before the next measurement is started. The system also addresses issues common to colorimetric sensors, including the response time and range of detection. We demonstrate the benefits and feasibility of this novel system, using colorimetric sensors for ammonia and carbon dioxide gases for continuous monitoring of up to (at least) 60 detection cycles without signs of analytical performance degradation of the sensors.
Lateral Augmentation Procedures in Anterior Cruciate Ligament Reconstruction: Anatomic, Biomechanical, Imaging, and Clinical Evidence (2018)

Histologically, the ALL appears to be a distinct structure that can be identified with advanced imaging techniques. Biomechanical evidence suggests that the anterolateral structures of the knee, including the ALL, contribute to minimizing anterolateral rotational instability. Cadaveric studies of combined ACLR-LET procedures demonstrated overconstraint of the knee; however, these findings have yet to be reproduced in the clinical literature. The current indications for LET augmentation in the setting of ACLR and the effect on knee kinematic and joint preservation should be the subject of future research.
Automatic 3D Reconstruction by Deep Learning Neural Networks Using Images Acquired via 4D-STEM Stereo Imaging (2022)

The stereo-pair approach for revealing the 3D distribution of dislocation structures from the transmission electron micrographs proved to be an effective alternative approach compared to laborious electron tomography Further improvements occurred in the field of stereo 3D reconstruction with the development of a tilt-less imaging technique where a stereo-pair of images can be acquired in a single sample tilt using a convergent probe in scanning TEM mode (STEM) This technique brings many advantages such as the elimination of sample movement between two images and opens the avenue to dynamic imaging However, existing algorithms for post-processing and following 3D reconstruction were still slow and required human intervention.
ERASER: Practical and Accurate Leakage Suppression for Fault-Tolerant Quantum Computing (2023)

Quantum error correction (QEC) codes enable us to toler-<br> ate hardware errors by encoding fault-tolerant logical qubits<br> using redundant physical qubits and detecting errors using<br> parity checks. Leakage errors occur in quantum systems<br> when a qubit leaves its computational basis and enters higher<br> energy states. These errors severely limit the performance of<br> QEC due to two reasons. First, they lead to erroneous parity<br> checks that obfuscate the accurate detection of errors. Second,<br> the leakage spreads to other qubits and creates a pathway for<br> more errors over time. Prior works tolerate leakage errors<br> by using leakage reduction circuits (LRCs) that modify the<br> parity check circuitry of QEC codes. Unfortunately, naively<br> using LRCs always throughout a program is sub-optimal<br> because LRCs add two-qubit operations that (1) facilitate<br> leakage transport, and (2) serve as new sources of errors.<br> Ideally, LRCs should only be used if leakage occurs, so that<br> errors from both leakage as well as additional LRC operations<br> are simultaneously minimized. However, identifying leakage<br> errors in real-time (within a few nanoseconds) is non-trivial.<br> To enable the robust and efficient usage of LRCs, we propose<br> ERASER that speculates the subset of qubits that may have<br> leaked and only uses LRCs for those qubits. Our studies show<br> that the majority of leakage errors impact the parity checks<br> very frequently. We leverage the insight to speculate leaked<br> qubits by identifying patterns in the failed parity checks. We<br> propose ERASER+M that enhances ERASER by detecting<br> leakage more accurately using qubit measurement protocols<br> that can classify qubits into |0〉 , |1〉 and |L〉 states. ERASER<br> and ERASER+M improve the logical error rate by up to 4.3×<br> and 23× respectively compared to Always-LRCs.
Determination of Soft X-ray Emission Spectroscopy Parameters using Experimental Data for Quantitative Microanalysis (2016)

Journal Article Determination of Soft X-ray Emission Spectroscopy Parameters using Experimental Data for Quantitative Microanalysis Get access Hendrix Demers, Hendrix Demers Department of Mining and Materials Engineering, McGill University, Montreal, Quebec, Canada Search for other works by this author on: Oxford Academic Google Scholar Colin M MacRae, Colin M MacRae CSIRO Mineral Resources, Clayton, VIC, Australia Search for other works by this author on: Oxford Academic Google Scholar Nicholas C Wilson, Nicholas C Wilson CSIRO Mineral Resources, Clayton, VIC, Australia Search for other works by this author on: Oxford Academic Google Scholar Pierre Hovington, Pierre Hovington Hydro-Quebec Research Institute, Varennes, Quebec, Canada Search for other works by this author on: Oxford Academic Google Scholar Vladimir Timoshevskii, Vladimir Timoshevskii Hydro-Quebec Research Institute, Varennes, Quebec, Canada Search for other works by this author on: Oxford Academic Google Scholar Raynald Gauvin, Raynald Gauvin Department of Mining and Materials Engineering, McGill University, Montreal, Quebec, Canada Search for other works by this author on: Oxford Academic Google Scholar Karim Zaghib Karim Zaghib Hydro-Quebec Research Institute, Varennes, Quebec, Canada Search for other works by this author on: Oxford Academic Google Scholar Microscopy and Microanalysis, Volume 22, Issue S3, 1 July 2016, Pages 408–409, https://doi.org/10.1017/S1431927616002890 Published: 25 July 2016
Material grain growth consensus control: A multi-zone heating approach applied on a Monte-Carlo model (2016)

This paper considers the control of the grain growth in a copper thin film using a multi-zone micro heater array. The overall system is a multi-input/multi-output (MIMO) control system: currents of 10 micro heaters as input and local microstructure (mean grain sizes) as output. We develop a biased Monte-Carlo (MC) model to simulate complete microstructure evolution in response to the temperature field controlled by the heater input. An FEM temperature model is approximated by Artificial Neural Network (ANN) and coupled with the MC model to predict grain growth under controlled temperature field. Focusing on the metrics of mean grain size, a multi-region empirical model is generalized for efficient control analysis and tuning. We first apply consensus-based output feedback to track a desired grain size trajectory. Stability is verified by passivity theorem using the loop transformation. As an alternate approach, we have also applied Particle Swarm Optimization (PSO) based Model Predictive Control (MPC) to take constraints and the full state into account. Simulations are conducted on the empirical model for controller tuning. Both methods achieve consensus and follow the reference trajectory well. MPC is able to reach consensus faster, but relies on model accuracy. Consensus-based output feedback may not realize optimal performance, but is more robust with respect to the variability of material properties and experimental parameters. The consensus controller is then applied to the MC model to with desirable performance demonstrated as well.
Nucleophilic substitution at the central allyl carbon atom of a (.pi.-allyl)platinum complex (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNucleophilic substitution at the central allyl carbon atom of a (.pi.-allyl)platinum complexKouichi Ohe, Hideki Matsuda, Tsumoru Morimoto, Sensuke Ogoshi, Naoto Chatani, and Shinji MuraiCite this: J. Am. Chem. Soc. 1994, 116, 9, 4125–4126Publication Date (Print):May 1, 1994Publication History Published online1 May 2002Published inissue 1 May 1994https://pubs.acs.org/doi/10.1021/ja00088a077https://doi.org/10.1021/ja00088a077research-articleACS PublicationsRequest reuse permissionsArticle Views671Altmetric-Citations70LEARN 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-AlertscloseSupporting Info (2)»Supporting Information Supporting Information Get e-Alerts
Regulation of Ca2+/calmodulin kinase II by a small C-terminal domain phosphatase (2008)

We present here the identification and characterization of an SCP3 (small C-terminal domain phosphatase-3) homologue in smooth muscle and show, for the first time, that it dephosphorylates CaMKII [Ca(2+)/CaM (calmodulin)-dependent protein kinase II]. SCP3 is a PP2C (protein phosphatase 2C)-type phosphatase that is primarily expressed in vascular smooth muscle tissues and specifically binds to the association domain of the CaMKIIgamma G-2 variant. The dephosphorylation is site-specific, excluding the Thr(287) associated with Ca(2+)/CaM-independent activation of the kinase. As a result, the autonomous activity of CaMKIIgamma G-2 is not affected by the phosphatase activity of SCP3. SCP3 co-localizes with CaMKIIgamma G-2 on cytoskeletal filaments, but is excluded from the nucleus in differentiated vascular smooth muscle cells. Upon depolarization-induced Ca(2+) influx, CaMKIIgamma G-2 is activated and dissociates from SCP3. Subsequently, CaMKIIgamma G-2 is targeted to cortical adhesion plaques. We show here that SCP3 regulates phosphorylation sites in the catalytic domain, but not those involved in regulation of kinase activation. This selective dephosphorylation by SCP3 creates a constitutively active kinase that can then be differentially regulated by other phosphorylation-dependent regulatory mechanisms.
An End-to-End Segmentation Pipeline for Dixon Adipose and Muscle by Neural Nets (DAMNN) (2023)

An end-to-end pipeline was developed that processes whole-body Dixon MRI data sets from UK Biobank and corrects for overlapping slices, inhomogeneous signal intensities, and fat-water swaps to produce high quality 3D data sets. Segmentation maps for subcutaneous/visceral fat and left/right thigh muscles from these 3D data sets were then produced using neural networks, and muscle and fat volume phenotypes were extracted. The Jaccard index for the validation data sets was 93.3% for the fat segmentation and 96.9% for the muscle segmentation. Excellent correspondence was obtained with the extracted muscle and fat volumes and similar metrics from a commercially available package.