bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rodent
Authors: Pérard-Gayot Arsène , Membarth Richard , Leißa Roland , Hack Sebastian , Slusallek Philipp 
Published: July 2019

Monte-Carlo Renderers must generate many color samples to produce a noise-free image, and for each of those, they must evaluate complex mathematical models representing the appearance of the objects in the scene. These models are usually in the form of shaders: Small programs that are executed during rendering in order to compute a value for the current sample.
Renderers often compile and optimize shaders just before rendering, taking advantage of the knowledge of the scene. In principle, the entire renderer could benefit from a-priori code generation. For instance, scheduling can take advantage of the knowledge of the scene in order to maximize hardware usage. However, writing such a configurable renderer eventually means writing a compiler that translates a scene description into machine code.

In this paper, we present a framework that allows generating entire renderers for CPUs and GPUs without having to write a dedicated compiler: First, we provide a rendering library in a functional/imperative language that elegantly abstracts the individual rendering concepts using higher-order functions. Second, we use
partial evaluation
to combine and specialize the individual components of a renderer according to a particular scene.

Our results show that the renderers we generate outperform equivalent high-performance implementations written with state-of-the-art ray tracing libraries on the CPU and GPU.
A learned shape-adaptive subsurface scattering model
Authors: Vicini Delio , Koltun Vladlen , Jakob Wenzel 
Published: July 2019

Subsurface scattering, in which light refracts into a translucent material to interact with its interior, is the dominant mode of light transport in many types of organic materials. Accounting for this phenomenon is thus crucial for visual realism, but explicit simulation of the complex internal scattering process is often too costly. BSSRDF models based on analytic transport solutions are significantly more efficient but impose severe assumptions that are almost always violated, e.g. planar geometry, isotropy, low absorption, and spatio-directional separability. The resulting discrepancies between model and usage lead to objectionable errors in renderings, particularly near geometric features that violate planarity.
This article introduces a new shape-adaptive BSSRDF model that retains the efficiency of prior analytic methods while greatly improving overall accuracy. Our approach is based on a conditional variational autoencoder, which learns to sample from a reference distribution produced by a brute-force volumetric path tracer. In contrast to the path tracer, our autoencoder directly samples outgoing locations on the object surface, bypassing a potentially lengthy internal scattering process.
The distribution is conditional on both material properties and a set of features characterizing geometric variation in a neighborhood of the incident location. We use a low-order polynomial to model the local geometry as an implicitly defined surface, capturing curvature, thickness, corners, as well as cylindrical and toroidal regions. We present several examples of objects with challenging medium parameters and complex geometry and compare to ground truth simulations and prior work.
Procedural phasor noise
Authors: Tricard Thibault , Efremov Semyon , Zanni Cédric , Neyret Fabrice , Martínez Jonàs , Lefebvre Sylvain 
Published: July 2019

Procedural pattern synthesis is a fundamental tool of Computer Graphics, ubiquitous in games and special effects. By calling a single procedure in every pixel - or voxel - large quantities of details are generated at low cost, enhancing textures, producing complex structures within and along surfaces. Such procedures are typically implemented as pixel shaders.
We propose a novel procedural pattern synthesis technique that exhibits desirable properties for modeling highly contrasted patterns, that are especially well suited to produce surface and microstructure details. In particular, our synthesizer affords for a precise control over the profile, orientation and distribution of the produced stochastic patterns, while allowing to grade all these parameters spatially.

Our technique defines a stochastic smooth phase field -
a phasor noise
- that is then fed into a periodic function (e.g. a sine wave), producing an oscillating field with prescribed main frequencies and preserved contrast oscillations. In addition, the profile of each oscillation is directly controllable (e.g. sine wave, sawtooth, rectangular or any 1D profile). Our technique builds upon a reformulation of Gabor noise in terms of a
phasor field
that affords for a clear separation between local intensity and phase.

Applications range from texturing to modeling surface displacements, as well as multi-material microstructures in the context of additive manufacturing.
Physically-based statistical simulation of rain sound
Authors: Liu Shiguang , Cheng Haonan , Tong Yiying 
Published: July 2019

A typical rainfall scenario contains tens of thousands of dynamic sound sources. A characteristic of the large-scale scene is the strong randomness in raindrop distribution, which makes it notoriously expensive to synthesize such sounds with purely physical methods. Moreover, the raindrops hitting different surfaces (liquid or various solids) can emit distinct sounds, for which prior methods with unified impact sound models are ill-suited.
In this paper, we present a physically-based statistical simulation method to synthesize realistic rain sound, which respects surface materials. We first model the raindrop sound with two mechanisms, namely the initial impact and the subsequent pulsation of entrained bubbles. Then we generate material sound textures (MSTs) based on a specially designed signal decomposition and reconstruction model. This allows us to distinguish liquid surface with bubble sound and different solid surfaces with MSTs. Furthermore, we build a basic rain sound (BR-sound) bank with the proposed raindrop sound clustering method based on a statistical model, and design a sound source activator for simulating spatial propagation in an efficient manner. This novel method drastically decreases the computational cost while producing convincing sound results. Various experiments demonstrate the effectiveness of our sound simulation model.
DNA methylation reprograms cardiac metabolic gene expression in end-stage human heart failure
Authors: Pepin Mark E. , Drakos Stavros , Ha Chae-Myeong , Tristani-Firouzi Martin , Selzman Craig H. , Fang James C. , Wende Adam R. , Wever-Pinzon Omar 
Published: July 2019

Heart failure (HF) is a leading cause of morbidity and mortality in the United States and worldwide. As a multifactorial syndrome with unpredictable clinical outcomes, identifying the common molecular underpinnings that drive HF pathogenesis remains a major focus of investigation. Disruption of cardiac gene expression has been shown to mediate a common final cascade of pathological hallmarks wherein the heart reactivates numerous developmental pathways. Although the central regulatory mechanisms that drive this cardiac transcriptional reprogramming remain unknown, epigenetic contributions are likely. In the current study, we examined whether the epigenome, specifically DNA methylation, is reprogrammed in HF to potentiate a pathological shift in cardiac gene expression. To accomplish this, we used paired-end whole genome bisulfite sequencing and next-generation RNA sequencing of left ventricle tissue obtained from seven patients with end-stage HF and three nonfailing donor hearts. We found that differential methylation was localized to promoter-associated cytosine-phosphate-guanine islands, which are established regulatory regions of downstream genes. Hypermethylated promoters were associated with genes involved in oxidative metabolism, whereas promoter hypomethylation enriched glycolytic pathways. Overexpression of plasmid-derived DNA methyltransferase 3A in vitro was sufficient to lower the expression of numerous oxidative metabolic genes in H9c2 rat cardiomyoblasts, further supporting the importance of epigenetic factors in the regulation of cardiac metabolism. Last, we identified binding-site competition via hypermethylation of the nuclear respiratory factor 1 (NRF1) motif, an established upstream regulator of mitochondrial biogenesis. These preliminary observations are the first to uncover an etiology-independent shift in cardiac DNA methylation that corresponds with altered metabolic gene expression in HF. NEW & NOTEWORTHY The failing heart undergoes profound metabolic changes because of alterations in cardiac gene expression, reactivating glycolytic genes and suppressing oxidative metabolic genes. In the current study, we discover that alterations to cardiac DNA methylation encode this fetal-like metabolic gene reprogramming. We also identify novel epigenetic interference of nuclear respiratory factor 1 via hypermethylation of its downstream promoter targets, further supporting a novel contribution of DNA methylation in the metabolic remodeling of heart failure.
DNA Methylation Markers for Breast Cancer Detection in the Developing World
Authors: Downs Bradley M. , Mercado-Rodriguez Claudia , Cimino-Mathews Ashley , Chen Chuang , Yuan Jing-Ping , Van Den Berg Eunice , Cope Leslie M. , Schmitt Fernando , Tse Gary M. , Ali Syed Z. , Meir-Levi Danielle , Sood Rupali , Li Juanjuan , Richardson Andrea L. , Mosunjac Marina B. , Rizzo Monica , Tulac Suzana , Kocmond Kriszten J. , de Guzman Timothy , Lai Edwin W. , Rhees Brian , Bates Michael , Wolff Antonio C. , Gabrielson Edward , Harvey Susan C. , Umbricht Christopher B. , Visvanathan Kala , Fackler Mary Jo , Sukumar Saraswati 
Published: July 2019

AbstractPurpose:An unmet need in low-resource countries is an automated breast cancer detection assay to prioritize women who should undergo core breast biopsy and pathologic review. Therefore, we sought to identify and validate a panel of methylated DNA markers to discriminate between cancer and benign breast lesions using cells obtained by fine-needle aspiration (FNA).Experimental Design: Two case–control studies were conducted comparing cancer and benign breast tissue identified from clinical repositories in the United States, China, and South Africa for marker selection/training (N = 226) and testing (N = 246). Twenty-five methylated markers were assayed by Quantitative Multiplex-Methylation-Specific PCR (QM-MSP) to select and test a cancer-specific panel. Next, a pilot study was conducted on archival FNAs (49 benign, 24 invasive) from women with mammographically suspicious lesions using a newly developed, 5-hour, quantitative, automated cartridge system. We calculated sensitivity, specificity, and area under the receiver-operating characteristic curve (AUC) compared with histopathology for the marker panel.Results:In the discovery cohort, 10 of 25 markers were selected that were highly methylated in breast cancer compared with benign tissues by QM-MSP. In the independent test cohort, this panel yielded an AUC of 0.937 (95% CI = 0.900–0.970). In the FNA pilot, we achieved an AUC of 0.960 (95% CI = 0.883–1.0) using the automated cartridge system.Conclusions:We developed and piloted a fast and accurate methylation marker–based automated cartridge system to detect breast cancer in FNA samples. This quick ancillary test has the potential to prioritize cancer over benign tissues for expedited pathologic evaluation in poorly resourced countries.
Analysis of Cell-Free DNA from 32,989 Advanced Cancers Reveals Novel Co-occurring Activating RET Alterations and Oncogenic Signaling Pathway Aberrations
Authors: Rich Thereasa A. , Reckamp Karen L. , Chae Young Kwang , Doebele Robert C. , Iams Wade T. , Oh Michael , Raymond Victoria M. , Lanman Richard B. , Riess Jonathan W. , Stinchcombe Thomas E. , Subbiah Vivek , Trevarthen David R. , Fairclough Stephen , Yen Jennifer , Gautschi Oliver 
Published: July 2019

Abstract

Purpose:
RET is an emerging oncogenic target showing promise in phase I/II clinical trials. An understudied aspect of RET-driven cancers is the extent to which co-occurring genomic alterations exist and how they may impact prognosis or therapeutic response.

Experimental Design:
Somatic activating RET alterations were identified among 32,989 consecutive patients with metastatic solid tumors tested with a clinical cell-free circulating tumor DNA (cfDNA) assay. This comprehensive next-generation sequencing (NGS) assay evaluates single-nucleotide variants, and select indels, fusions, and copy number gains in 68–73 clinically relevant cancer genes.

Results:
A total of 176 somatic activating RET alterations were detected in 170 patients (143 fusions and 33 missense mutations). Patients had non–small cell lung (NSCLC, n = 125), colorectal (n = 15), breast (n = 8), thyroid (n = 8), or other (n = 14) cancers. Alterations in other oncogenic signaling pathway genes were frequently identified in RET-positive samples and varied by specific RET fusion gene partner. RET fusions involving partners other than KIF5B were enriched for alterations in MAPK pathway genes and other bona fide oncogenic drivers of NSCLC, particularly EGFR. Molecular and clinical data revealed that these variants emerged later in the genomic evolution of the tumor as mechanisms of resistance to EGFR tyrosine kinase inhibitors.

Conclusions:
In the largest cancer cohort with somatic activating RET alterations, we describe novel co-occurrences of oncogenic signaling pathway aberrations. We find that KIF5B-RET fusions are highly specific for NSCLC. In our study, only non-KIF5B-RET fusions contributed to anti-EGFR therapy resistance. Knowledge of specific RET fusion gene partner may have clinical significance.
Hemodynamic Effects of Mechanical Circulatory Support Devices in Ventricular Septal Defect
Authors: Pahuja Mohit , Schrage Benedikt , Westermann Dirk , Basir Mir B. , Garan Arthur Reshad , Burkhoff Daniel 
Published: July 2019

Background:
Ventricular septal defect (VSD) is a lethal complication of acute myocardial infarction (AMI) and is often associated with cardiogenic shock. The optimal form of percutaneous mechanical circulatory support (MCS) for AMI-VSD is unknown.

Methods and Results:
We used a previously validated cardiovascular model to simulate AMI-VSD with parameters adjusted to replicate average hemodynamics reported in the literature, including a pulmonary-to-systemic blood flow ratio of 3.0. We then predicted effects of different types of percutaneous MCS (including intra-aortic balloon pumping, Impella, TandemHeart, and extracorporeal membrane oxygenation) on pressures and flows throughout the cardiovascular system. The simulation replicated all major hemodynamic parameters reported in the literature with AMI-VSD. Inotropes and vasopressors worsened left-to-right shunting, whereas vasodilators decreased shunting at the expense of worsening hypotension. All MCS devices increased forward blood flow and arterial pressure but other effects varied among devices. Impella 5.0 provided the greatest degree of pulmonary capillary wedge pressure reductions and decreased left-to-right shunting. Extracorporeal membrane oxygenation worsened pulmonary capillary wedge pressure and shunting, which could be improved by adding Impella or passive left ventricular vent. Pulmonary-to-systemic blood flow ratio could not be reduced below 2.0, and pulmonary flows remained high with all forms of MCS.

Conclusions:
Although no form of percutaneous MCS normalized hemodynamics in AMI-VSD, pulmonary capillary wedge pressure and shunting were worsened by extracorporeal membrane oxygenation and improved by Impella. Accordingly, based on hemodynamics alone, Impella provides the optimal form of support in AMI-VSD. However, other factors, including team experience, device availability, potential for tissue ingestion, and clinical characteristics, need to be considered when choosing a percutaneous MCS device for AMI-VSD.
Cathepsin S Deficiency Mitigated Chronic Stress–Related Neointimal Hyperplasia in Mice
Authors: Wang Hailong , Meng Xiangkun , Piao Limei , Inoue Aiko , Xu Wenhu , Yu Chenglin , Nakamura Kae , Hu Lina , Sasaki Takeshi , Wu Hongxian , Unno Kazumasa , Umegaki Hiroyuki , Murohara Toyoaki , Shi Guo‐Ping , Kuzuya Masafumi , Cheng Xian Wu 
Published: July 2019

Background
Exposure to chronic psychosocial stress is a risk factor for atherosclerosis‐based cardiovascular disease. We previously demonstrated the increased expressions of cathepsin S (CatS) in atherosclerotic lesions. Whether CatS participates directly in stress‐related neointimal hyperplasia has been unknown.

Methods and Results

Male wild‐type and CatS‐deficient mice that underwent carotid ligation injury were subjected to chronic immobilization stress for morphological and biochemical studies at specific times. On day 14 after stress/surgery, stress enhanced the neointima formation. At the early time points, the stressed mice had increased plaque elastin disruption, cell proliferation, macrophage accumulation,
mRNA
and/or protein levels of vascular cell adhesion molecule‐1, angiotensin
II
type 1 receptor, monocyte chemoattractant protein‐1, gp91
phox
, stromal cell–derived factor‐1, C‐X‐C chemokine receptor‐4, toll‐like receptor‐2, toll‐like receptor‐4,
SC
35, galectin‐3, and CatS as well as targeted intracellular proliferating‐related molecules (mammalian target of rapamycin, phosphorylated protein kinase B, and p‐glycogen synthase kinase‐3α/β). Stress also increased the plaque matrix metalloproteinase‐9 and matrix metalloproteinase‐2
mRNA
expressions and activities and aorta‐derived smooth muscle cell migration and proliferation. The genetic or pharmacological inhibition of CatS by its specific inhibitor (Z‐
FL
‐COCHO) ameliorated the stressed arterial targeted molecular and morphological changes and stressed aorta‐derived smooth muscle cell migration. Both the genetic and pharmacological interventions had no effect on increased blood pressure in stressed mice.

Conclusions
These results demonstrate an essential role of CatS in chronic stress–related neointimal hyperplasia in response to injury, possibly via the reduction of toll‐like receptor‐2/toll‐like receptor‐4–mediated inflammation, immune action, and smooth muscle cell proliferation, suggesting that CatS will be a novel therapeutic target for stress‐related atherosclerosis‐based cardiovascular disease.
Toward Optimization of Rheology in Sea Ice Models through Data Assimilation
Authors: Stroh J. N. , Panteleev Gleb , Yaremchuk Max , Francis Oceana , Allard Richard 
Published: July 2019

AbstractSea ice models that allow for deformation are primarily based on rheological formulations originally developed in the 1970s. In both the original viscoplastic (VP) and elastic-VP schemes, the internal pressure term is modeled as a function of variable sea ice thickness and concentration with spatially and temporally constant empirical parameters for ice strength. This work considers a spatially variable extension of the rheology parameters as well as wind stress in a one-dimensional VP sea ice data assimilation system. In regions of total ice cover, experiments that assimilate synthetic ice-state observations using variable rheological parameters show larger improvements than equivalent experiments using homogeneous parameters. For partially ice-covered regions where internal ice stresses are relatively unimportant, experiments assimilating synthetic sea ice velocity observations demonstrate reasonable reconstruction of spatially variable wind stresses. These results suggest practical benefits for sea ice–state reconstruction and forecasts by using sea ice velocity, thickness, and concentration observations to optimize spatially varying rheological parameters and to improve wind stress forcing.
Characteristics of Typhoon Eyewalls According to World Wide Lightning Location Network Data
Authors: Permyakov Mikhail , Kleshcheva Tatiana , Potalova Ekaterina , Holzworth Robert H. 
Published: July 2019

Abstract
Methods for the estimation of typhoon eyewall characteristics (the center location, the radius and the width, and radii of inner and outer boundaries) based on World Wide Lightning Location Network (WWLLN) data are presented and discussed in this work. The center locations, the eyewall radii, and inner boundary radii estimated from WWLLN data for the typhoons of the northwestern Pacific from 2011 to 2015 were compared with the typhoon centers, radii of maximum winds, and the radii of the eyes obtained from Advanced Scatterometer (ASCAT) wind data, the Japan Meteorological Agency (JMA) archives, and the Joint Typhoon Warning Center (JTWC) archives. It is shown that the eyewall characteristics estimates based on the lightning discharge data are most closely related to characteristics of the ASCAT wind speed fields, and the radii of the eyewalls and their inner boundaries are linearly related to the radii of maximum winds and the radii of the eyes, with correlation coefficients reaching approximately 0.9 and 0.8, respectively. It was shown that the distances between locations of the eyewalls and typhoon centers estimated according to the WWLLN and those of the ASCAT, JMA, and JTWC data on average were 19, 16, and 17 km, respectively. The eyewall widths varied from 15 to 69 km, with an average of ~30 km.
Outcomes of conversion THA after failed porous tantalum implant for osteonecrosis of the femoral head: a comparative matched study
Authors: Ma Jinhui , Wang Bailiang , Yue Debo , Sun Wei , Wang Weiguo , Li Zirong 
Published: July 2019

Background: As a joint-preserving surgery, porous tantalum implantation (PTI) provides an additional treatment option for osteonecrosis of the femoral head (ONFH). However, conversion to a total hip arthroplasty (THA) after failed PTI is considered a challenging procedure. The purpose of this study was to compare the clinical and radiologic outcomes and complications of THA after failed PTI with those of primary THA without any previous surgery for ONFH. Methods: This retrospective study included 32 patients undergoing THA after failed PTI and 25 age, sex, and body mass index matched patients who underwent primary THA without any previous surgery for ONFH between December 2009 and March 2014. All patients were followed for at least 36 months. The postoperative clinical and radiological evaluations were based on Harris Hip Score (HHS) and plain radiographs. The independent sample test and the chi-square test were used for the statistical analysis. Results: The HHS in the PTI group was similar to that in the primary group at the latest follow-up ( p = 0.274), but longer operation time and greater intraoperative blood loss were observed in the PTI group ( p < 0.001, respectively). No significant differences in radiological parameters and postoperative complications were found between the 2 groups ( p > 0.05). Conclusions: THA after PTI showed similar clinical and radiological outcomes to primary THA except for longer operation time and greater intraoperative blood loss.