Miracle-dz/UniFAR-FTUs huggingface dataset:
Protocol for the Examination of Specimens from Patients with Melanoma of the Skin

Authors David P. Frishberg, MD, FCAP* Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California Charles Balch, MD Departments of Surgery, Oncology, and Dermatology, Johns Hopkins University, Baltimore, Maryland Bonnie L. Balzer, MD, PhD, FCAP Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California A. Neil Crowson, MD, FCAP Regional Medical Laboratory, Departments of Dermatology, Pathology and Surgery, University of Oklahoma, Tulsa, Oklahoma Mikund Didolkar, MD, FACS Division of Surgical Oncology, Sinai Hospital of Baltimore, Department of Surgery, Johns Hopkins University, Baltimore, Maryland Jennifer M. McNiff, MD, FASCP Departments of Dermatology and Pathology, Yale University School of Medicine Roger R Perry, MD, FACS Department of Surgery, Eastern Virginia Medical School, Norfolk, Virginia Victor G. Prieto, MD, PhD, FCAP Departments of Pathology and Dermatology MD Anderson Cancer Center, University of Texas, Houston, Texas Priya Rao, MD, FCAP Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California M. Timothy Smith, MD Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina Bruce Robert Smoller, MD, FCAP Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, Arkansas Mark R. Wick, MD, FCAP Department of Pathology, University of Virginia Health System, Charlottesville, Virginia For the Members of the Cancer Committee, College of American Pathologists
Protocol for the examination of specimens from patients with primary carcinoma of the colon and rectum.

The College of American Pathologists offers these protocols to assist pathologists in providing clinically useful and relevant information when reporting results of surgical specimen examinations. The College regards the reporting elements in the “Surgical Pathology Cancer Case Summary (Checklist)” portion of the protocols as essential elements of the pathology report. However, the manner in which these elements are reported is at the discretion of each specific pathologist, taking into account clinician preferences, institutional policies, and individual practice. The College developed these protocols as an educational tool to assist pathologists in the useful reporting of relevant information. It did not issue the protocols for use in litigation, reimbursement, or other contexts. Nevertheless, the College recognizes that the protocols might be used by hospitals, attorneys, payers, and others. Indeed, effective January 1, 2004, the Commission on Cancer of the American College of Surgeons mandated the use of the checklist elements of the protocols as part of its Cancer Program Standards for Approved Cancer Programs. Therefore, it becomes even more important for pathologists to familiarize themselves with these documents. At the same time, the College cautions that use of the protocols other than for their intended educational purpose may involve additional considerations that are beyond the scope of this document.
Control of wave climate and meander dynamics on spit breaching and inlet migration

ABSTRACT Chaumillon E. , Ozenne F. , Bertin X. , Long N. , Ganthy F. , 2014. Wave climateand inlet channel meander bend control spit breaching and migration of a new inlet: La Coubre Sandspit, France. In: Green, A.N. and Cooper, J.A. G. (eds.), Proceedings 13th International Coastal Symposium (Durban, South Africa), Journal of Coastal Research, Special Issue No. 70, pp. 109–114, ISSN 0749-0208. This study focuses on the mid-term (infra annual and pluri annual; over the period 1999–2013) morphological evolutions of a sandspit (La Coubre Sandspit, West coast of France), with a particular emphasis on spit breaching, new inlet opening and migration. Morphological evolutions are observed from a large number of aerial photographs and satellite images and are compared with wave parameters and extreme events (periods where significant wave height exceeds the 1% largest waves with water level exceeding the 90% highest water level) obtained from a high resolution hindcast wave modelling. It appears that extreme events are likely to be responsible for spit breaching and new inlet opening. Once opened, the new inlet migrates downdrift, but its migration rate is not correlated with the wave climate variations. Detailed geomorphological observations suggest that the main control on downdrift inlet migration is related to orientation of the meander bend of the tidal inlet main channel. When the meander bend is convex in an updrift direction, it counteracts the littoral drift and slows the inlet migration. Oppositely, when the meander bend is convex in a downdrift direction, the meander-induced transport is in the same direction as wave-induced longshore transport, which allows the inlet to migrate much faster.
Design of Wideband Two-Sided Bandpass Frequency Selective Surface for X, Ka, and Ku Band Application

A novel wideband bandpass frequency-selective surface functioning at X, Ku, and Ka bands is proposed in this article. The designed FSS has a metallic square loop and a circular ring, and they are printed on both sides of the FR4 substrate. The proposed design FR4-based single-layer FSS is operating from 11.075 GHz to 22.075 GHz with a fractional bandwidth of 66.36%. The parameters of the square loop and circular ring regulate the characteristics of the passband. The optimum dimension of these parameters is obtained with parametric analysis. The proposed structure is measured and fabricated. However, the measured results strongly agree with the simulated results, which authenticate the proposed design performance.
Cross-validation of the ego dissolution scale: implications for studying psychedelics

Introduction Ego dissolution, variously called Ego-Loss, self-loss, and ego disintegration, is a hallmark of psychedelic drug use. We cross-validated the 10-item Ego Dissolution Scale, which we developed to assess ego dissolution in everyday life, and we included comparator variables that expanded our original assessment of construct validity. Methods Undergraduate college student volunteers (N = 527) completed the measures online. Results We replicated the original two factor structure (i.e., subfactors: Ego-Loss and Unity/connectedness with others, the world, universe), and we determined that the total score (Cronbach’s α = 0.79) and subfactors (Ego-Loss = 78; Unity = 0.83) possessed adequate-to-good reliability and strong convergent validity (e.g., mindfulness, hallucination-predisposition, sleep variables, personality variables, positive/negative affect transliminality, dissociation/depersonalization), while neuroticism, social desirability did not correlate highly with ego dissolution. We identified distinct patterns of relations of measures associated with the Ego-Loss vs. Unity subfactors. Discussion We discuss the implications of the use of the EDS for studying everyday aspects of ego dissolution, the long-term effects of psychedelic use, and the value of using the scale in conjunction with measures of the acute effects of psychedelics.
Edge and Texture Analysis for Face Spoofing Detection

With the increasing use of biometric technology in various applications of daily life, face spoofing detection technology plays a crucial role in securing them against fraudulent access. In this paper, a new face anti-spoofing method is proposed that involves a two-stage feature extraction from the YCbCr and HSV face images. The first stage extracts the Binarised Statistical Image Features (BSIF) from the Canny edge face images, while the second stage extracts the Local Binary Patterns (LBP) features from the input face images. The resulting feature vectors from both stages are concatenated to match their identification before being fed into a Support Vector Machine (SVM) classifier. Experiments on the publicly available MSU Mobile Face Spoof Database (MSU-MFSD) confirm that the proposed method achieves promising results compared to state-of-the-art face anti-spoofing techniques.
Vorticity Structures in the Tropical Pacific from a Numerical Simulation

AbstractThe small-scale variability of the tropical Pacific is studied with the simulations from a numerical model in terms of vorticity structures. A Lagrangian method based on the Okubo–Weiss parameter is used to identify the structures and track their main characteristics. Between 8°S and 8°N, the structure characteristics are spatially inhomogeneous compared to higher latitudes. They can be grouped into three categories: anticyclonic and cyclonic structures off the equator and the equatorial structures between 2°S and 2°N. They all have a strong annual cycle with maximum presence from September to March, except during strong El Nino years, when the number of structures becomes very low. Off the equator from 2° to 8°, the anticyclonic structures dominate, but with drastically different characteristics north and south of the equator. In the north, large nonlinear vortices develop (known as the tropical instability vortices) in phase with the 30–35-day oscillation related to an unstable first-meridional-.
Motion Planning Method for Car-Like Autonomous Mobile Robots in Dynamic Obstacle Environments

Motion planning between dynamic obstacles is an essential capability to achieve real-world navigation. In this study, we investigated the problem of avoiding dynamic obstacles in complex environments for a car-like mobile robot with an incompletely constrained Ackerman front wheel steering. To address the problems of weak dynamic obstacle avoidance and poor path smoothing in motion planning with the traditional Timed Elastic Band (TEB) algorithm, We proposed a hybrid motion planning algorithm (TEB-CA,Timed Elastic Band-Collision Avoidance) that combines an improved traditional TEB algorithm and Optimal Reciprocal Collision Avoidance (ORCA) model to improve the ability of the robot to predict dynamic obstacles in advance and avoid collisions safely. Moreover, We also add new constraints to the traditional TEB algorithm, including: jerk constraints, smoothness constraints, and curvature constraints. The algorithm is implemented in $C++$ and evaluated experimentally in the Gazebo and Rviz simulation environments of the Robot Operating System (ROS), as well as in actual experimental tests on our car-like autonomous mobile robot “Little Ant” which proves the effectiveness of the method, and that the motion planning scheme is more effective in avoiding dynamic obstacles than the traditional TEB and DWA algorithms.
Applications of Multi-Cycle Earthquake Simulations to Earthquake Hazard

This dissertation seeks to contribute to earthquake hazard analyses and forecasting by conducting a detailed study of the processes controlling the occurrence, and particularly the clustering, of large earthquakes, the probabilities of these large events, and the dynamics of their ruptures. We use the multi-cycle earthquake simulator RSQSim to investigate several fundamental aspects of earthquake occurrence in order to improve the understanding of earthquake hazard. RSQSim, a 3D, boundary element code that incorporates rate- and state-friction to simulate earthquakes in fully interacting, complex fault systems has been successful at modeling several aspects of fault slip and earthquake occurrence. Multi-event earthquake models with time-dependent nucleation based on rate- and state-dependent friction, such as RSQSim, provide a viable physics-based method for modeling earthquake processes. These models can provide a better understanding of earthquake hazard by improving our knowledge of earthquake processes and probabilities. RSQSim is fast and efficient, and therefore is able to simulate very long sequences of earthquakes (from hundreds of thousands to millions of events). This makes RSQSim an ideal instrument for filling in the current gaps in earthquake data, from short and incomplete earthquake catalogs to unrealistic initial conditions used for dynamic rupture models. RSQSim catalogs include foreshocks, aftershocks, and occasional clusters of large earthquakes, the statistics of which are important for the estimation of earthquake probabilities. Additionally, RSQSim finds a near optimal nucleation location that enables ruptures to propagate at minimal stress conditions and thus can provide suites of heterogeneous initial conditions for dynamic rupture models that produce reduced ground motions compared to models with homogeneous initial stresses and arbitrary forced nucleation locations.
The Eeective Energy Transformation Scheme as a Special Continuation Approach to Global Optimization with Application to Molecular Conformation

This paper discusses a generalization of the function transformation scheme for global energy minimization applied to the molecular conformation problem. A mathematical theory for the method as a special continuation approach to global optimization is established. We show that the method can transform a nonlinear objective function into a class of gradually deformed, but \smoother" or \easier" functions. An optimization procedure can then be applied to the new functions successively, to trace their solutions back to the original function. Two types of transformation are deened: isotropic and anisotropic. We show that both transformations can be applied to a large class of nonlinear partially separable functions including energy functions for molecular conformation. Methods to compute the transformation for these functions are given.
Towards Robust Visual Inertial Odometry in Feature Sparse Structured Environments

In conventional Visual Odometry (VO), featureless scenarios, such as facing uniformly textured walls often lead to failure or reliance on fused inertial tracking. Depending on sensor quality, calibration and initialization, this can cause severe drift of the positioning solution, limiting the use of visual methods for practical applications such as first-responder missions in infrastructure-free indoor areas.To overcome this limitation, we present a novel RGB-D Inertial Odometry pipeline that fuses low-cost RGB-D camera and inertial sensor to estimate low-drift trajectories in structured environments. Our method is practical, waiving the need for extensive Inertial Measurement Unit (IMU) calibration and bias initialization while accommodating affordable sensors. We leverage the Manhattan World assumption, which posits that major man-made structures conform to three major orthogonal directions. Utilizing this assumption, we develop a dynamic Manhattan Decision Module that robustly computes absolute orientation in challenging indoor pedestrian tracking scenarios. Moreover, we propose a novel algorithm that partially recovers translational movement using depth sensor information when no visible features are present.Our experiments with commodity sensors demonstrate the superior performance and robustness of our method in estimating low-drift trajectories in challenging environments without dedicated IMU initialization movement or IMU noise parameter estimation.
Physiological and transcriptomic analyses of response of walnuts (Juglans regia) to Pantoea agglomerans infection

Introduction Walnut blight is a serious bacterial disease that affects the yield and quality of walnuts. Pantoea agglomerans is one of the main causative agents of walnut blight. However, there have been few studies on the response of walnuts to P. agglomerans infection. Methods In this study, the soluble sugar, photosynthesis, antioxidant enzyme activities, and secondary metabolites were measured, and the transcriptomic analysis was performed to determine the response of walnut tissue cultures to P. agglomerans infection. Results After pathogen inoculation, the soluble sugar content decreased, and photosynthesis was inhibited. Antioxidant enzyme (superoxide dismutase and peroxidase) activities and secondary metabolites (phenol and flavonoid) contents increased, especially in the early stages of inoculation. Transcriptomic analysis revealed that the phenylpropanoid biosynthesis pathway is induced after infection, and pathogen infection promotes ABA and ethylene signal transduction and inhibits auxin signaling. In addition, SA and JA-related gene expression was altered after inoculation with P. agglomerans, and the FLS- and calcium-mediated disease resistance signaling pathways were activated. Furthermore, our results suggested an involvement of the R-protein RPM-mediated disease resistance pathway in the response of walnuts to bacterial infections. Discussion Our findings indicated that phenylpropanoid biosynthesis, hormone signal transduction, and plant-pathogen interaction have key roles in pathogenic inoculation, which provide insights into the molecular mechanisms in the response of walnuts to P. agglomerans infection.
MANTLE CELL LYMPHOMA: AN IMMUNOMORPHOLOGIC STUDY WITH DETECTION OF TRANSLOCATION (11;14)(q 13;q32) BY FLUORESCENT IN SITU HYBRIDIZATION FROM A TERTIARY CANCER CARE CENTER

Background: Mantle cell lymphoma is a rare neoplasm of mature B cells forming 5-7% of non-Hodgkin lymphoma. This observational study evaluates the immunomorphologic features of mantle cell lymphoma with detection of translocation (11;14)(q13;q32) by dual fusion interphase Fluorescent in situ hybridization(FISH) at a tertiary cancer center. Materials and Methods: Interphase FISH for t(11;14) with dual fusion probes was carried out on 69 cases of de novo mantle cell lymphoma over period of 5 years with adequate representative tissue in paraffin blocks. Immunomorphologic and FISH findings were correlated with clinical data. Results: Mantle cell lymphoma formed 5.8% of NHL with male predominance and most presenting with advanced disease. Mean age at presentation was 58 years and affected females at slightly younger age. Cervical lymphadenopathy was the commonest presenting feature, followed by involvement of the gastrointestinal tract. There were 56(81.2%) cases with classic and 13(18.8%) cases with blastoid/pleomorphic morphology.Ki67 proliferation of more than 30% was seen in 53(76.8%) cases and was 30% or less in 16(23.2%) cases. Dual fusion signals on FISH identified t(11;14) in 69 cases and atypical patterns with extra CCND1 copies and more than two fusions were seen in 18 cases, most often in blastoid/pleomorphic variants. Conclusion: This study highlights the distinctive clinical, immunomorphologic and genetic findings in mantle cell lymphoma. Interphase FISH on formalin fixed paraffin sections is a useful technique for identification of t(11;14) . Atypical FISH patterns are more often seen in aggressive variants like blastoid and pleomorphic mantle cell lymphoma.
Association of long-term aspirin use with kidney disease progression

Background Chronic microinflammation contributes to the progression of chronic kidney disease (CKD). Aspirin (ASA) has been used to treat inflammation for centuries. The effects of long-term low-dose ASA on CKD progression are unclear. Methods We examined the association of long-term use of newly initiated low-dose ASA (50–200 mg/day) with all-cause mortality using Cox proportional hazard models; with cardiovascular/cerebrovascular (CV) mortality and with end stage kidney disease (ESKD) using Fine and Gray competing risk regression models; with progression of CKD defined as patients’ eGFR slopes steeper than −5 mL/min/1.73m2/year using logistic regression models in a nationwide cohort of US Veterans with incident CKD. Among 831,963 patients, we identified 385,457 who either initiated ASA (N = 21,228) within 1 year of CKD diagnosis or never received ASA (N = 364,229). We used propensity score matching to account for differences in key characteristics, yielding 29,480 patients (14,740 in each group). Results In the matched cohort, over a 4.9-year median follow-up period, 11,846 (40.2%) patients (6,017 vs. 5,829 ASA users vs. non-users) died with 25.8% CV deaths, and 934 (3.2%) patients (476 vs. 458) reached ESKD. ASA users had a higher risk of faster decline of kidney functions, i.e., steeper slopes (OR 1.30 [95%CI: 1.18, 1.44], p < 0.01), but did not have apparent benefits on mortality (HR 0.97 [95%CI: 0.94, 1.01], p = 0.17), CV mortality (Sub-Hazard Ratio [SHR]1.06 [95%CI: 0.99–1.14], p = 0.11), or ESKD (SHR1.00 [95%CI: 0.88, 1.13], p = 0.95). Conclusion Chronic low-dose ASA use was associated with faster kidney function deterioration, and no association was observed with mortality or risk of ESKD.
Deep Reinforcement Learning with Convolutional Networks Applied to Autonomous Navigation of Real Robots Using Virtual Scenario Training

Industrial applications of autonomous mobile robotic systems have demanded the development of autonomous navigation algorithms using artificial intelligence. This paper proposes a method based on deep reinforcement learning algorithm and convolutional network (DQN-CNN: Deep Q-Network with Convolutional Network) to allow autonomous navigation of robots equipped with RGB cameras. The training phase of this algorithm is performed in the Coppelia VREP simulation environment with real practical implementation based on the NVIDIA Jetson Nano development board. The proposed methodology includes training in a simulation environment and integration with a real system. For prototyping, a navigation track is used, where the robot is controlled by a DQN reinforcement learning algorithm. The results confirm the effectiveness of the proposal, as the real robot was able to successfully perform the planned mission. It is expected that this work can contribute to the advancement of mobile robotics and reinforcement learning, as well as provide a useful methodology for researchers and developers working with these technologies. The video of the practical experiment is available at: https://bit.ly/3IK1Rb5.
North‐eastern Laurentide, western Greenland and southern Innuitian ice stream dynamics during the last glacial cycle

Precise relationships between high‐frequency ice sheet dynamics and late Quaternary climate variability are still poorly understood, notably with regard to their relative timing and causal mechanisms. Baffin Bay is of particular interest in this regard due to the influence of ice streaming activities from the north‐eastern Laurentide, southern Innuitian and western Greenland ice margins on its sedimentary regimes during glacial times. Here we document such ice margin dynamics using a sedimentological analysis performed on a piston core from central Baffin Bay and spanning the last 115 ka. Lithofacies analysis and mineralogical assemblages are used to reconstruct sediment sources (using the SedUnMix program) and depositional mechanisms. Coarse detrital carbonate (DC, dolomite‐rich) layers are attributed either to north‐eastern Laurentide and Innuitian ice stream surges or to pervasive ice rafted debris delivery processes at distinct periods. Out‐of‐phase fine‐grained glaciomarine sediments with a mineralogical signature from western Greenland, linked to Uummannaq ice streaming activity, are interbedded with the coarse DC layers. The new results suggest that during the last glacial cycle, the north‐eastern Laurentide and southern Innuitian ice streams were sensitive to high‐frequency climate fluctuations, such as the Dansgaard–Oeschger events, while the western Greenland margins were more sensitive to large‐scale climatic/oceanic reorganizations, such as relative sea‐level changes and/or advection of warmer Atlantic waters into the bay.