Miracle-dz/UniFAR-FTUs huggingface dataset:
Proceedings of the 2015 National Toxicology Program Satellite Symposium

The 2015 Annual National Toxicology Program Satellite Symposium, entitled “Pathology Potpourri” was held in Minneapolis, Minnesota, at the American College of Veterinary Pathologists/American Society for Veterinary Clinical Pathology/Society of Toxicologic Pathology combined meeting. The goal of this symposium is to present and discuss diagnostic pathology challenges or nomenclature issues. Because of the combined meeting, both laboratory and domestic animal cases were presented. This article presents summaries of the speakers’ talks, including challenging diagnostic cases or nomenclature issues that were presented, along with select images that were used for audience voting and discussion. Some lesions and topics covered during the symposium included hepatocellular lesions, a proposed harmonized diagnostic approach to rat cardiomyopathy, crop milk in a bird, avian feeding accoutrement, heat exchanger in a tuna, metastasis of a tobacco carcinogen–induced pulmonary carcinoma, neurocytoma in a rat, pituicytoma in a rat, rodent mammary gland whole mounts, dog and rat alveolar macrophage ultrastructure, dog and rat pulmonary phospholipidosis, alveolar macrophage aggregation in a dog, degenerating yeast in a cat liver aspirate, myeloid leukemia in lymph node aspirates from a dog, Trypanosoma cruzi in a dog, solanum toxicity in a cow, bovine astrovirus, malignant microglial tumor, and nomenclature challenges from the Special Senses International Harmonization of Nomenclature and Diagnostic Criteria Organ Working Group.
Adaptive Set-Granular Cooperative Caching

Current Chip Multiprocessors (CMPs) consist of several cores, cache memories and interconnection networks in the same chip. Private last level cache (LLC) configurations assign a static portion of the LLC to each core. This provides lower latency and isolation, at the cost of depriving the system of the possibility of reassigning underutilized resources. A way of taking advantage of underutilized resources in other private LLCs in the same chip is to use the coherence mechanism to determine the state of those caches and spill lines to them. Also, it is well known that memory references are not uniformly distributed across the sets of a set-associative cache. Therefore, applying a uniform spilling policy to all the sets in a cache may not be the best option. This paper proposes Adaptive Set-Granular Cooperative Caching (ASCC), which measures the degree of stress of each set and performs spills between spiller and potential receiver sets, while it tackles capacity problems. Also, it adds a neutral state to prevent sets from being either spillers or receivers when it could be harmful. Furthermore, we propose Adaptive Variable-Granularity Cooperative Caching (AVGCC), which dynamically adjusts the granularity for applying these policies. Both techniques have a negligible storage overhead and can adapt to many core environments using scalable structures. AVGCC improved average performance by 7.8% and reduced average memory latency by 27% related to a traditional private LLC configuration in a 4-core CMP. Finally, we propose an extension of AVGCC to provide Quality of Service that increases the average performance gain to 8.1%.
High Performance and Low Power Architectures: GPU vs. FPGA for Fast Factorized Backprojection

The question if new embedded low power Graphic Processing Units (GPUs) can compete with Field Programmable Gate Arrays (FPGAs) in terms of performance and efficiency is addressed. A Virtex 6 and a Virtex Ultrascale+ FPGA are compared to a Jetson TX2 GPU. Instead of basing the comparison on manufacturer reference numbers, hand optimized high performance implementations of the Fast Factorized Backprojection (FFBP) algorithm for Synthetic Aperture Radar (SAR) image generation have been investigated. Performance is measured in image lines per second and efficiency in performance per power. The Virtex Ultrascale+ provides a runtime speed-up of about 6.5x and an efficiency improvement of about 4.3x compared to the Jetson TX2 GPU.
Primary Human mDC1, mDC2, and pDC Dendritic Cells Are Differentially Infected and Activated by Respiratory Syncytial Virus

Respiratory syncytial virus (RSV) causes recurrent infections throughout life. Vaccine development may depend upon understanding the molecular basis for induction of ineffective immunity. Because dendritic cells (DCs) are critically involved in early responses to infection, their interaction with RSV may determine the immunological outcome of RSV infection. Therefore, we investigated the ability of RSV to infect and activate primary mDCs and pDCs using recombinant RSV expressing green fluorescent protein (GFP). At a multiplicity of infection of 5, initial studies demonstrated ∼6.8% of mDC1 and ∼0.9% pDCs were infected. We extended these studies to include CD1c−CD141+ mDC2, finding mDC2 infected at similar frequencies as mDC1. Both infected and uninfected cells upregulated phenotypic markers of maturation. Divalent cations were required for infection and maturation, but maturation did not require viral replication. There is evidence that attachment and entry/replication processes exert distinct effects on DC activation. Cell-specific patterns of RSV-induced maturation and cytokine production were detected in mDC1, mDC2, and pDC. We also demonstrate for the first time that RSV induces significant TIMP-2 production in all DC subsets. Defining the influence of RSV on the function of selected DC subsets may improve the likelihood of achieving protective vaccine-induced immunity.
Cardiovascular Biomarkers in Preeclampsia at Triage

Introduction: To investigate the ability of cardiovascular plasma biomarkers to identify imminent preeclampsia (PE) among pregnant women at triage. Material and Methods: C-terminal pro-arginine vasopressin (copeptin), C-terminal pro-endothelin-1 (CT-proET-1), mid-regional pro-adrenomedullin (MR-proADM), and mid-regional pro-atrial natriuretic peptide (MR-proANP) were prospectively measured in pregnant women presenting at the obstetrical triage units of the University Hospitals of Basel and Zurich, Switzerland. Logistic regression and receiver operating characteristics (ROC) analysis was used to assess and quantify the predictive ability of cardiovascular biomarkers. Results: Of the 147 included women, 27 (18.4%) were diagnosed at admission with PE. All biomarker levels were significantly higher in participants with PE as compared to controls. However, only MR-proANP, MR-proADM and CT-proET-1 were significant and independent predictors of PE, after taking into account the effect of various clinical confounders. The area under the ROC curve (AUC) was 0.62 (95% confidence interval 0.50-0.73) for copeptin, 0.64 (0.52-0.76) for MR-proADM, 0.71 (0.61-0.82) for CT-proET-1, and 0.83 (0.73-0.92) for MR-proANP. The combination of MR-proANP and MR-proADM resulted in the highest diagnostic performance (AUC 0.88; 0.79-0.96). Discussion: Assessment of the cardiovascular plasma biomarkers MR-proANP and MR-proADM holds promise to support diagnosis of PE at triage.
E‐NTPDase1/CD39 modulates renin release from heart mast cells during ischemia/reperfusion: a novel cardioprotective role

Ischemia/reperfusion (I/R) elicits renin release from cardiac mast cells (MC), thus activating a local renin‐angiotensin system (RAS), culminating in ventricular fibrillation. We hypothesized that in I/R, neurogenic ATP could degranulate juxtaposed MC and that ecto‐nucleoside triphosphate diphosphohydrolase 1/CD39 (CD39) on MC membrane could modulate ATP‐induced renin release. We report that pharmacological inhibition of CD39 in a cultured human mastocytoma cell line (HMC‐1) and murine bone marrow‐derived MC with ARL67156 (100 mM) increased ATP‐induced renin release (≥2‐fold), whereas purinergic P2X7 receptors (P2X7R) blockade with A740003 (3 mM) prevented it. Likewise, CD39 RNA silencing in HMC‐1 increased ATP‐induced renin release (≥2‐fold), whereas CD39 overexpression prevented it. Acetaldehyde, an I/R product (300 μM), elicited an 80% increase in ATP release from HMC‐1, in turn, causing an autocrine 20% increase in renin release. This effect was inhibited or potentiated when CD39 was overexpressed or silenced, respectively. Moreover, P2X7R silencing prevented ATP‐ and acetaldehyde‐induced renin release. I/R‐induced RAS activation in ex vivo murine hearts, characterized by renin and norepinephrine overflow and ventricular fibrillation, was potentiated (~2‐fold) by CD39 inhibition, an effect prevented by P2X7R blockade. Our data indicate that by regulating ATP availability at the MC surface, CD39 modulates local renin release and thus, RAS activation, ultimately exerting a cardioprotective effect. —Aldi, S. , Marino, A. , Tomita, K. , Corti, F. , Anand, R. , Olson, K. E. , Marcus, A. J., Levi, R. , E‐NTPDase1/ CD39 modulates renin release from heart mast cells during ischemia/reperfusion: a novel cardioprotective role. FASEB J. 29, 61–69 (2015). www.fasebj. org
A mobile sonification system for stroke rehabilitation

Growing evidence suggests that sonification supports movement perception as well as motor functions. It is hypothesized that real-time sonification supports movement control in patients with sensorimotor dysfunctions efficiently by intermodal substitution of sensory loss. The present article describes a sonification system for the upper extremities that might be used in neuromotor rehabilitation after stroke. A keyfeature of the system is mobility: Arm movements are captured by intertial sensors that transmit their data wirelessly to a portable computer. Hand position is computed in an egocentric reference frame and mapped onto four acoustic parameters. A pilot feasibility study with acute stroke patients resulted in significant effects and is encouraging with respect to ambulatory use.
Glycemia (hemoglobin A1c) and incident venous thromboembolism in the Atherosclerosis Risk in Communities cohort study

Diabetes has been inconsistently associated with increased risk of venous thromboembolism (VTE) and there is little direct evidence on the associations of glycemia levels with VTE. We used data from the Atherosclerosis Risk in Communities study to test the hypothesis that glycemia, as measured by hemoglobin A1c (A1c), is positively associated with VTE. Participants aged 45–64 years (n = 12,298) had A1c measured in 1990 and were followed for incident VTE (n = 345) through 2005. Because A1c is affected by diabetes treatment, analyses were stratified by history of diagnosed diabetes. Owing to evidence of non-linearity, we categorized A1c according to clinical cut-points: <5.7, 5.7–6.4, and ≥6.5% in those with no diagnosed diabetes; <7.0 and ≥7.0% in those with diagnosed diabetes. After adjustment for potential confounders, the hazard ratios (95% CIs) for VTE across increasing A1c categories were 1 (referent), 1.02 (0.77, 1.35) and 0.72 (0.41, 1.29) for those without diagnosed diabetes, and 1.30 (0.77, 2.17) and 1.41 (0.95, 2.09) for those with diagnosed diabetes. To explore the relation, we employed various models to adjust for potential confounding variables and modeled A1c as tertiles. We consistently found elevated hazard ratios in those with diagnosed diabetes, though the association was not statistically significant in every model. Hazard ratios in those without diagnosed diabetes were close to 1. In conclusion, our results are mildly suggestive that diagnosed diabetes and high levels of glucose, per se, may increase the risk of VTE. Elevated glucose was not related to VTE in those without diagnosed diabetes.
The chromatic equivalence class of graph ‾{Bn-6, 12}

By h(G, x) and P (G, λ) we denote the adjoint polynomial and the chromatic polynomial of graph G, respectively. A new invariant of graph G, which is the fourth character R4(G), is given in this paper. Using the properties of the adjoint polynomials, the adjoint equivalence class of graph Bn−6,1,2 is determined, which can be regarded as the continuance of the paper written by Wang et al. [J. Wang, R. Liu, C. Ye and Q. Huang, A complete solution to the chromatic equivalence class of graph Bn−7,1,3, Discrete Math. (2007), doi: 10.1016/j.disc. 2007.07. 030]. According to the relations between h(G, x) and P (G, λ), we also simultaneously determine the chromatic equivalence class of Bn−6,1,2 that is the complement of Bn−6,1,2.
Neurotrophic Factors and Neural Prostheses: Potential Clinical Applications Based Upon Findings in the Auditory System

Spiral ganglion neurons (SGNs) are the target cells of the cochlear implant, a neural prosthesis designed to provide important auditory cues to severely or profoundly deaf patients. The ongoing degeneration of SGNs that occurs following a sensorineural hearing loss is, therefore, considered a limiting factor in cochlear implant efficacy. We review neurobiological techniques aimed at preventing SGN degeneration using exogenous delivery of neurotrophic factors. Application of these proteins prevents SGN degeneration and can enhance neurite outgrowth. Furthermore, chronic electrical stimulation of SGNs increases neurotrophic factor-induced survival and is correlated with functional benefits. The application of neurotrophic factors has the potential to enhance the benefits that patients can derive from cochlear implants; moreover, these techniques may be relevant for use with neural prostheses in other neurological conditions
Bias-Compensated Informed Sound Source Localization Using Relative Transfer Functions

In this paper, we consider the problem of estimating the target sound direction of arrival (DoA) for a hearing aid (HA) system, which can connect to a wireless microphone worn by the talker of interest. The wireless microphone “informs” the HA system about the noise-free target speech. To estimate the DoA, we consider a maximum-likelihood approach, and we assume that a database of DoA-dependent relative transfer functions (RTFs) has been measured in advance and is available. The proposed DoA estimator is able to take the available noise-free target speech, ambient noise characteristics, and the shadowing effect of the user's head on the received signals into account, and it supports both monaural and binaural microphone array configurations. Moreover, we analytically analyze the bias in the proposed estimator and introduce a modified estimator, which has been compensated for the bias. We demonstrate that the proposed method has lower computational complexity and better performance than recent RTF-based estimators. Furthermore, to decrease the number of parameters required to be wirelessly exchanged between the HAs in binaural configurations, we propose an information fusion strategy, which avoids transmitting microphone signals between the HAs. An important benefit of the proposed IF strategy is that the number of parameters to be exchanged between the HAs is independent of the number of HA microphones. Finally, we investigate the performance of variants of the proposed estimator extensively in different noisy and reverberant situations.
Truth or Lie: Automatically Fact Checking News

In the actual scenario of ever-growing data consumption speed and quantity, factors like news source decentralization, citizen journalism and democratization of media, make the task of manually checking and correcting disinformation across the internet impractical or infeasible . Here, there is an imperative need for a fast and reliable way to account for the veracity of what is produced and spread as information: Automatic fact-checking. In this work we present the problem of fact-checking in the era of big data and post-truth. Some existing approaches for this task are presented and their main features discussed and compared. Concluding, a new approach inspired on the best components of the existing ones is presented.
Motion Correction of 18F-NaF PET for Imaging Coronary Atherosclerotic Plaques

Ruptured coronary atherosclerotic plaques commonly cause acute myocardial infarction. It has recently been shown that active microcalcification in the coronary arteries, one of the features that characterizes vulnerable plaques at risk of rupture, can be imaged using 18F-NaF PET. We aimed to determine whether a motion correction technique applied to gated 18F-NaF PET images could enhance image quality and improve uptake estimates. Methods: Seventeen patients with myocardial infarction (n = 7) or stable angina (n = 10) underwent 18F-NaF PET and prospective coronary CT angiography. PET data were reconstructed in 4 different ways: the first was 1 gated bin (end-diastolic phase with 25% of the counts), the second was 4 gated bins (consecutive 25% segments), the third was 10 gated bins (consecutive 10% segments), and the fourth was ungated. Subsequently, with data from either 4 or 10 bins, gated PET images were registered using a local, nonlinear motion correction method guided by the extracted coronary arteries from CT angiography. Global noise levels and target-to-background ratios (TBR) defined on manually delineated coronary plaque lesions were compared to assess image quality and uptake estimates. Results: Compared with the reference standard of using only 1 bin of PET data, motion correction using 10 bins of PET data reduced image noise by 46% (P < 0.0001). TBR in positive lesions for 10-bin motion-corrected data was 11% higher than for 1-bin data (1.98 [interquartile range, 1.70–2.37] vs. 1.78 [1.58–2.16], P = 0.0027) and 33% higher than for ungated data (1.98 [1.70–2.37] vs. 1.49 [1.39–1.88], P < 0.0001). Conclusion: Motion correction of gated 18F-NaF PET/coronary CT angiography is feasible, reduces image noise, and increases TBR. This improvement may allow more reliable identification of vulnerable coronary artery plaques using 18F-NaF PET.
The Tempo and Mode of Evolution of Transposable Elements as Revealed by Molecular Phylogenies Reconstructed from Mosquito Genomes

Although many mathematical models exist predicting the dynamics of transposable elements (TEs), there is a lack of available empirical data to validate these models and inherent assumptions. Genomes can provide a snapshot of several TE families in a single organism, and these could have their demographics inferred by coalescent analysis, allowing for the testing of theories on TE amplification dynamics. Using the available genomes of the mosquitoes Aedes aegypti and Anopheles gambiae, we indicate that such an approach is feasible. Our analysis follows four steps: (1) mining the two mosquito genomes currently available in search of TE families; (2) fitting, to selected families found in (1), a phylogeny tree under the general time-reversible (GTR) nucleotide substitution model with an uncorrelated lognormal (UCLN) relaxed clock and a nonparametric demographic model; (3) fitting a nonparametric coalescent model to the tree generated in (2); and (4) fitting parametric models motivated by ecological theories to the curve generated in (3).
Behavioral Counseling to Prevent Skin Cancer: A Systematic Review for the U.S. Preventive Services Task Force

BACKGROUND More than 2 million cases of skin cancer are diagnosed annually in the United States, and melanoma incidence is increasing. PURPOSE To assist the U.S. Preventive Services Task Force in updating its 2003 recommendation on behavioral counseling to prevent skin cancer. DATA SOURCES Existing systematic reviews, database searches through February 2010, and outside experts. STUDY SELECTION English-language, primary care-relevant counseling trials to promote sun-protective behaviors and studies examining the association between sun-protective behaviors and skin cancer outcomes or potential adverse effects were included. DATA EXTRACTION Each study was appraised by using design-specific quality criteria. Important study details were abstracted into evidence tables. DATA SYNTHESIS 11 fair- or good-quality, randomized, controlled trials examined the counseling interventions' effect on sun-protective behaviors. In young women, appearance-focused behavioral interventions decrease indoor tanning and ultraviolet exposure. In young adolescents, computer support can decrease midday sun exposure and increase sunscreen use. Thirty-five mainly fair-quality observational studies examined the relationship between ultraviolet exposure or sunscreen use and skin cancer. Increasing intermittent sun exposure in childhood is associated with an increased risk for squamous cell carcinoma, basal cell carcinoma, and melanoma. Evidence suggests that regular or early use of indoor tanning may increase melanoma risk. On the basis of 1 fair-quality trial, regular sunscreen use can prevent squamous cell carcinoma, but it is yet unclear if it can prevent basal cell carcinoma or melanoma. LIMITATIONS There are limited rigorous counseling trials. Observational studies are limited by the complexity of measuring ultraviolet exposure and sunscreen use, and inadequate adjustment for important confounders. CONCLUSION Randomized, controlled trials suggest that primary care-relevant counseling can increase sun-protective behaviors and decrease indoor tanning.
Evolution of environment‐dependent galaxy properties in the Sloan Digital Sky Survey

We use photometric redshifts to analyse the effect of local environment on galaxy colours at redshifts z ≤ 0.63 in the Sloan Digital Sky Survey (SDSS) data release 6 (DR6). We construct mock SDSS-DR6 catalogues using semi-analytic galaxies to study possible systematic effects on the characterization of environment and colour statistics due to the uncertainty in the determination of redshifts. We use the projected galaxy density derived from the distance to the nearest neighbours with a suitable radial velocity threshold to take into account the uncertainties in the photometric redshift estimates. Our findings indicate that the use of photometric redshifts greatly improves estimates of projected local galaxy density when galaxy spectra are not available. We find a tight relationship between spectroscopic and photometric derived densities, both in the SDSS-DR6 data (up to z = 0.3) and in mock catalogues (up to z = 0.63). At z = 0, faint galaxies show a clear increase of the red galaxy fraction as the local density increases. Bright galaxies, on the other hand, show a constant red galaxy fraction. We are able to track the evolution of this fraction to z = 0.55 for galaxies brighter than M r = -21.5 and find that the fraction of blue galaxies with respect to the total population progressively becomes higher as the redshift increases, at a rate of 15 per cent/Gyr. Also, at any given redshift, bright galaxies show a larger red population, indicating that the star formation activity shifts towards smaller objects as the redshift decreases.
A newly diagnosed case of polymorphous low-grade neuroepithelial tumor of the young

Polymorphous low-grade neuroepithelial tumor of the young (PLNTY) is a recently described variant of low-grade neuroepithelial tumors that exhibits infiltrative growth, histopathological variability with frequently prominent oligodendroglioma-like components, intense labeling for CD34, absence of 1P/19Q codeletion, a distinct DNA methylation signature and genetic alterations involving MAP kinase pathway constituents of either the B-Raf proto-oncogene BRAF or fibroblast growth factor receptors 2 or 3 (FGFR2 and FGFR3). We here report a newly diagnosed case of PLNTY involving the temporal lobe in a 31-year-old man with chronic focal epilepsy. This tumor had histologic and immunophenotypic features similar to the recently described PLNTY and proved BRAF V600E mutant. Biomolecular profiling is becoming increasingly important in characterizing neuroepithelial tumors. Furthermore, biomolecular features such as CD34 expression and BRAF mutation have been reported to be significantly associated with the clinical behavior of these tumors. Like other low-grade neuroepithelial tumors, PLNTYs appear to be generally indolent with excellent seizure relief after total surgical resection. It is important to recognize cases of PLNTY in order to guide clinical management including the indication for surgery.