gebhart/patrepeval huggingface dataset:
A Noise-level-aware Framework for PET Image Denoising (2022)

In PET, the amount of relative (signal-dependent) noise present in different body regions can be significantly different and is inherently related to the number of counts present in that region. The number of counts in a region depends, in principle and among other factors, on the total administered activity, scanner sensitivity, image acquisition duration, radiopharmaceutical tracer uptake in the region, and patient local body morphometry surrounding the region. In theory, less amount of denoising operations is needed to denoise a high-count (low relative noise) image than images a low-count (high relative noise) image, and vice versa. The current deep-learning-based methods for PET image denoising are predominantly trained on image appearance only and have no special treatment for images of different noise levels. Our hypothesis is that by explicitly providing the local relative noise level of the input image to a deep convolutional neural network (DCNN), the DCNN can outperform itself trained on image appearance only. To this end, we propose a noise-level-aware framework denoising framework that allows embedding of local noise level into a DCNN. The proposed is trained and tested on 30 and 15 patient PET images acquired on a GE Discovery MI PET/CT system. Our experiments showed that the increases in both PSNR and SSIM from our backbone network with relative noise level embedding (NLE) versus the same network without NLE were statistically significant with p&lt;0.001, and the proposed method significantly outperformed a strong baseline method by a large margin.
Endoluminal gastroplication in children with significant gastro-oesophageal reflux disease (2004)

Endoluminal gastroplication is an effective and safe procedure in children/adolescents with significant GORD refractory to, or dependent on, medical anti-GORD therapy.
Photoinduced surface patterning of azobenzene-containing supramolecular dendrons, dendrimers and dendronized polymers (2013)

International audience
Techno-economic analysis of decentralized biomass processing depots (2015)

Decentralized biomass processing facilities, known as biomass depots, may be necessary to achieve feedstock cost, quantity, and quality required to grow the future U.S. bioeconomy. In this paper, we assess three distinct depot configurations for technical difference and economic performance. The depot designs were chosen to compare and contrast a suite of capabilities that a depot could perform ranging from conventional pelleting to sophisticated pretreatment technologies. Our economic analyses indicate that depot processing costs are likely to range from ∼US$30 to US$63 per dry metric tonne (Mg), depending upon the specific technology implemented and the energy consumption for processing equipment such as grinders and dryers. We conclude that the benefits of integrating depots into the overall biomass feedstock supply chain will outweigh depot processing costs and that incorporation of this technology should be aggressively pursued.
IC‐03‐01: IMAGING OF TAU PATHOLOGY IN PATIENTS WITH NON‐ALZHEIMER'S DISEASE TAUOPATHIES BY [11C]PBB3‐PET (2014)

[11 C]PBB3 has been recently developed as a tau imaging PET ligand.The preclinical studies showed high affinity and selectivity of this ligand for tau deposits. Our initial PET study with [11 C]PBB3 demonstrated high [11 C]PBB3 binding in the cerebral cortex including medial temporal lobes in patients with Alzheimer's disease (AD) compared with age-matched controls. The aim of this study is to test the hypothesis that [11 C]PBB3 PET is a sensitive in vivo imaging method for detecting tau lesions in non-AD tauopathies such as progressive supranuclar palsy (PSP) and corticobasal degeneration (CBD). Ten patients with PSP, five patients with corticobasal syndrome (CBS), and 18 age-matched healthy controls (HCs) participated in this study. Sequential PET scans were performed for 70 min following intravenous injection of [11 C]PBB3. PET images were anatomically normalized to the Montreal Neurological Institute space using T1 weighted MRI, and standardized uptake value ratio (SUVR) was calculated using the cerebellar cortex as reference region. One-way ANOVA test was performed among PSP, CBS patients, and HCs using statistical parametric mapping software (SPM 8). Statistical threshold was set to 0.01 with extent threshold of 50 voxels without correction for multiple comparisons. Cerebral beta-amyloid depositions were also estimated using SUVR images at 50-70 min after [11 C]Pittsburgh compound B injection in all patients and HCs. All patients and HCs were PIB-negative except one PIB-positive patient with CBS and one HC. SPM analysis showed high [11 C]PBB3 binding in globus pallidus, putamen, thalamus, subthalamus, midbrain, pons, and peri-rolandic areas in PSP patients compared with HCs. PIB-negative CBS patients (n=4) showed high [11 C]PBB3 binding in peri-rolandic areas, supplementary motor area, subthalamus, and midbrain compared with HCs. SUVR images of one PIB-positive patient with CBS showed high [11 C]PBB3 binding in the whole cerebral cortex including limbic cortex like advanced AD patients. The distribution of [11 C]PBB3 binding in the patients was in accord with the known distribution of tau pathology in PSP and CBD. The present study supports the utility of [11 C]PBB3-PET for detecting tau deposition in non-AD tauopathies including PSP and CBD.
Beyond the Model (2009)

It is not unusual for models developed to predict Absorption, Distribution, Metabolism, Elimination, and Toxicity (ADMET) as well as other endpoints to be nothing more than a black box, supplying only a numerical or categorical value by which users are expected to assess the goodness of a query compound. This type of result is, however, of little use in the overarching goal of developing better and safer drug compounds, that is, providing guidance toward improving the characteristics of the query or formulating chemical hypotheses that can be evaluated through synthetic efforts. As a result, the level of acceptance of predictions by users outside the computational chemistry and molecular modeling groups tends to be very low. In this review, I address three primary domains in which model presentation can be improved, specifically, establishing confidence in the prediction, data interrogation, and model interpretability. It has been my experience that even small efforts in these areas result in a much greater return with respect to acceptance, good faith, and usage from users regardless of the users role within the drug discovery process.
Solution volume studies of a deep cavity inclusion complex of C60: [p-benzylcalix[5]arene ⊂ C60] (1997)

Molecular complexation of C60 with p-benzylcalix[5]arene in toluene is associated with a partial molar volume change of +195 cm3 mol–1 which is consistent with the displacement of two toluene molecules from the cavity of the calixarene.
Parallel Bounded Property Checking with SymC (2005)

Abstract. Today, verification of industrial size designs like multi-million gate ASICs (Application Specific Integrated Circuit) and SoC (System-on-a-Chip) processors consumes up to 75 % of the design effort. The trend to augment functional verification with formal verification tries to alleviate this problem. Efficient property checking algorithms based on binary decision diagrams (BDDs) and satisfiability (SAT) solvers allow automatic verification of medium-sized designs. However, the steadily increasing design sizes still leave verification the major bottleneck, because formal methodologies do not yet scale to very large designs. To address these problems, we developed the bounded property checking tool SymC. SymC takes properties and a system description as inputs and translates them into a symbolically simulatable representation. SymC performs forward state space traversal for verifying the properties. However, for larger designs SymC cannot complete the traversal due to the state space explosion problem. Therefore, we propose a parallel version of SymC. The main idea of our approach is to split the state set into partitions and delegate traversal of these subsets to nodes on a cluster computer. Depending on the property and the quantification operator, detecting an accepting or rejecting state on one node can immediately abort computation on all other nodes and a witness/counterexample is produced. Otherwise, only the current search path is terminated and the remaining paths are traversed further. Parallel computation shows approximately linear speedups in execution time, enables faster verification of properties and we are able to handle larger designs. 1
Dyes and Pigments (2014)

In this article, we report the facile synthesis of metal-free dyes 6 and 7, their solution-based optical and redox properties and their use as sensitizers in dye-sensitized solar cells (DSSCs). Our studies indicate that the addition of the second thiophene unit in dye 7, decreases the oxidation and reduction potential and consequently the band gap of the molecule compared to 6. Furthermore, increasing the length of the conjugated spacer also affects on the properties of the DSSCs, with dye 7 providing a higher power conversion efficiency compared to 6 (h 1⁄4 4.49 versus 3.23%). 2014 The Authors. Published by Elsevier Ltd. All rights reserved.
Titration of recombinant woodchuck hepatitis virus DNA in adult woodchucks (1998)

In vivo transfection of Eastern woodchucks (Marmota monax) with recombinant woodchuck hepatitis virus (WHV) DNA is effective in inducing virus infection for the study of replication, pathogenicity, and oncogenicity of wild-type and mutated WHV. The one drawback to this procedure is the need for preparation of large amounts of WHV DNA. Reduction of the amount of WHV DNA in the transfection protocol necessary to induce infection would save considerable time and resources. Therefore, we conducted a titration of WHV DNA, ranging from 50 micrograms to 50 pg of DNA, in adult woodchucks to determine the minimum infectious dose of recombinant WHV DNA. As little as 50 ng of transfected WHV DNA induced productive infection in adult woodchucks. Thus, transfection with large amounts of recombinant WHV DNA appears to be unnecessary.
Conditional techniques for stream processing kernels (2004)

The stream programming model casts applications as a set of sequential data streams that are operated on by data-parallel computation kernels. Previous work has shown that this model is a powerful representation for media processing applications, such as image- and signal-processing, because it captures the locality and concurrency inherent to an application. This careful handling of important application properties results in kernels that are compute-intensive—i.e., kernels that perform a large number of arithmetic operations per unit of inter-kernel communication bandwidth. Furthermore, the stream model can be implemented with efficient VLSI designs, such as the Imagine Programmable Stream Processor. The Imagine chip supports 48 ALUs on a single die, operating at over 200MHz. This large number of ALUs provides a high peak performance, but makes efficiently executing kernels with conditional code a challenge. 
We will introduce two techniques for efficiently supporting kernel conditionals, such as if-statements, case-statements, and while-loops: conditional routing and conditional streams. Conditional routing is a code transformation that exploits the trade-off of increasing inter-kernel communication in order to increase the performance of kernel inner-loops containing conditional code. The second technique we will discuss is the use of a conditional stream, which is a mechanism to reduce the amount of load-imbalance that arises between parallel processing clusters on a single stream processor chip. Load-imbalance results when different conditional paths are taken on different processing clusters, and causes one or more of the clusters to wait idle for the others to complete a kernel. We will also present a case study of the impact of these techniques on a programmable polygon rendering pipeline that contains many unpredictable conditionals. We show that our techniques improve the performance of this application by 1.9×.
Local Delivery of the K Ca 3.1 Blocker, TRAM-34, Prevents Acute Angioplasty-Induced Coronary Smooth Muscle Phenotypic Modulation and Limits Stenosis (2008)

Blockade of K(Ca)3.1 by delivery of TRAM-34 via balloon catheter prevented smooth muscle phenotypic modulation and limited subsequent restenosis.
Dual Suppression of the Cyclin-Dependent Kinase Inhibitors CDKN2C and CDKN1A in Human Melanoma (2012)

Resistance to BRAF(V600E) inhibitors is associated with reactivation of mitogen-activated protein kinase (MAPK) signaling at different levels in melanoma. To identify downstream effectors of MAPK signaling that could be used as potential additional therapeutic targets for BRAF(V600E) inhibitors, we used hTERT/CDK4R24C/p53DD-immortalized primary human melanocytes genetically modified to ectopically express BRAF ( V600E ) or NRAS ( G12D ) and observed induction of the AP-1 transcription factor family member c-Jun. Using a dominant negative approach, in vitro cell proliferation assays, western blots, and flow cytometry showed that MAPK signaling via BRAF(V600E) promotes melanoma cell proliferation at G1 through AP-1-mediated negative regulation of the INK4 family member, cyclin-dependent kinase inhibitor 2C (CDKN2C), and the CIP/KIP family member, cyclin-dependent kinase inhibitor 1A (CDKN1A). These effects were antagonized by pharmacological inhibition of CDKN2C and CDKN1A targets CDK2 and CDK4 in vitro. In contrast to BRAF ( V600E ) or NRAS ( G12D )-expressing melanocytes, melanoma cells have an inherent resistance to suppression of AP-1 activity by BRAF(V600E)- or MEK-inhibitors. Here, CDK2/4 inhibition statistically significantly augmented the effects of BRAF(V600E)- or MEK-inhibitors on melanoma cell viability in vitro and growth in athymic nude Foxn1 ( nu ) mice (P = .03 when mean tumor volume at day 13 was compared for BRAF(V600E) inhibitor vs BRAF(V600E) inhibitor plus CDK2/4 inhibition; P = .02 when mean tumor volume was compared for MEK inhibitor vs MEK inhibitor plus CDK2/4 inhibition; P values were calculated by a two-sided Welch t test; n = 4-8 mice per group).
3-D Optical Memories For High Performance Computing. (1990)

The design of high performance computers such as array processors has reached a critical stage. These machines are increasingly using parallel processing methods to achieve higher performance. They require low cost memory systems with much higher capacities and bandwidths than available today while retaining small volume, weight, and power consumption characteristics. Massively interconnected optical computers will require even higher performance memory systems. This paper reviews various 3-D memory concepts that are proposed to meet these demands.
A Split-Phase Interface for Parallel File Systems (1997)

We describe the effects of a new user-level library for the Galley Parallel File System. This library allows some pre-existing sequential programs to make use of the Galley Parallel File System with minimal modification. It permits programs to efficiently use the parallel file system because the user-level library groups accesses together. We examine the performance of our library, and we show how code needs to be modified to use the library. 1 Introduction Many parallel applications are limited by the performance of the I/O system, and the performance of many I/O systems is currently limited by the file system. The Galley Parallel File System [NK97] has demonstrated that it can provide parallel applications with high-throughput access to their data files, if they use new file-system interfaces. Unfortunately, it is sometimes inconvenient for programmers to rewrite their application code to fit the new interface. In this paper, we describe a new user-level library that runs on top of ...
ExoSkin (2016)

There is a long tradition for crafting wearable objects directly on the body, such as garments, casts, and orthotics. However, these high-skill, analog practices have yet to be augmented by digital fabrication techniques. In this paper, we explore the use of hybrid fabrication workflows for on-body printing. We outline design considerations for creating on-body fabrication systems, and identify several human, machine, and material challenges unique to this endeavor. Based on our explorations, we present ExoSkin, a hybrid fabrication system for designing and printing digital artifacts directly on the body. ExoSkin utilizes a custom built fabrication machine designed specifically for on-body printing. We demonstrate the potential of on-body fabrication with a set of sample workflows, and share feedback from initial observation sessions.
Methaemoglobin reduction test: a new, simple, in vitro test for identifying primaquine-sensitivity. (1960)

The 8-aminoquinolines, and many other drugs, cause an acute intravascular haemolysis, known as primaquine-sensitivity, in a certain percentage of persons, particularly the darker-skinned peoples of the world. Massive drug programmes for the eradication of malaria in whole population groups frequently call for the use of primaquine; in addition, the use of other haemolytic or potentially haemolytic drugs in clinical medicine is widespread. Thus it is becoming increasingly important to be able to identify primaquine-sensitive individuals in field and clinical laboratories. Two modifications of a new test for primaquine-sensitivity, the methaemoglobin reduction test, are described in detail in this paper. The more simple modification, the field screening test, is practical for surveying large population groups in the field. The more accurate clinical test is also suitable for field use if a clinical spectrophotometer or photoelectric colorimeter is available.
Catalytic Performance of Rh/CeO2 in the Gasification of Cellulose to Synthesis Gas at Low Temperature (2001)

The gasification of cellulose has been investigated on Rh catalysts supported on CeO2, ZrO2, Al2O3, TiO2, MgO, and SiO2 at very low temperatures (723−823 K) in a laboratory-scale fluidized-bed reactor using air as a gasifying agent. Of the catalysts, only Rh/CeO2 showed the excellent catalytic performance in the cellulose gasification at above 823 K, resulting in 100% carbon conversion to gas. The details of reaction conditions that affected the performance of the catalyst have been optimized. The best results have been found at above 823 K using the total flow rate of 170 cm3 min-1 of inlet gases. The total carbon conversion was achieved when 50 mg of cellulose was used in a batch. The Rh loading of 1.2 × 10-4 mol (g of catalyst)-1 on CeO2 and W/F of 1.8 gh mol-1 were optima for the total conversion of carbon to gases. Fresh and used catalysts were characterized by a Brunauer−Emmett−Teller (BET) analysis and transmission electron microscopy (TEM). The BET surface area has been decreased from 59 to 24 m2/g during the first batch reaction; however, this value decreased to 21 m2/g during the next 20 batches. No Rh particle was observed in the TEM image of the fresh catalyst; however, in the used catalyst, it was observed, and the particle size was 1.5−2.2 nm on CeO2.
The impact of tumor profiling approaches and genomic data strategies for cancer precision medicine (2016)

Large tumor-only targeted panels are sufficient for most somatic variant identification and mutational load prediction if paired with expanded germline analysis strategies and molecular pathologist review. Paired germline sequencing reduced overall false positive mutation calls and WES provided the most neoantigens. Without patient-matched germline data, large germline databases are needed to minimize false positive mutation calling and mitigate ethnic disparities.
An E3 ubiquitin ligase-independent role of LUBAC (2014)

In this issue of Blood, Dubois et al show a catalytic-independent role of the linear ubiquitin chain assembly complex (LUBAC) in lymphocyte activation and B-cell malignancy.1 These data add a new layer of versatility to the recently established role of LUBAC in nuclear factor-kB (NF-kB) signaling.
Development Status of the WetLab-2 Project: New Tools for On-orbit Real-time Quantitative Gene Expression. (2013)

The primary objective of NASA Ames Research Centers WetLab-2 Project is to place on the ISS a research platform to facilitate gene expression analysis via quantitative real-time PCR (qRT-PCR) of biological specimens grown or cultured on orbit. The WetLab-2 equipment will be capable of processing multiple sample types ranging from microbial cultures to animal tissues dissected on-orbit. In addition to the logistical benefits of in-situ sample processing and analysis, conducting qRT-PCR on-orbit eliminates the confounding effects on gene expression of reentry stresses and shock acting on live cells and organisms. The system can also validate terrestrial analyses of samples returned from ISS by providing quantitative on-orbit gene expression benchmarking prior to sample return. The ability to get on orbit data will provide investigators with the opportunity to adjust experimental parameters for subsequent trials based on the real-time data analysis without need for sample return and re-flight. Finally, WetLab-2 can be used for analysis of air, surface, water, and clinical samples to monitor environmental contaminants and crew health. The verification flight of the instrument is scheduled to launch on SpaceX-5 in Aug. 2014.Progress to date: The WetLab-2 project completed a thorough study of commercially available qRT-PCR systems and performed a downselect based on both scientific and engineering requirements. The selected instrument, the Cepheid SmartCycler, has advantages including modular design (16 independent PCR modules), low power consumption, and rapid ramp times. The SmartCycler has multiplex capabilities, assaying up to four genes of interest in each of the 16 modules. The WetLab-2 team is currently working with Cepheid to modify the unit for housing within an EXPRESS rack locker on the ISS. This will enable the downlink of data to the ground and provide uplink capabilities for programming, commanding, monitoring, and instrument maintenance. The project is currently designing a module that will lyse the cells and extract RNA of sufficient quality for use in qRT-PCR reactions while using a housekeeping gene to normalize RNA concentration and integrity. Current testing focuses on two promising commercial products and chemistries that allow for RNA extraction with minimal complexity and crew time.
Dirac Spectra and Edge States in Honeycomb Plasmonic Lattices (2009)

We study theoretically the dispersion of plasmonic honeycomb lattices and find Dirac spectra for both dipole and quadrupole modes. Zigzag edge states derived from Dirac points are found in ribbons of these honeycomb plasmonic lattices. The zigzag edge states for out-of-plane dipole modes are closely analogous to the electronic ones in graphene nanoribbons. The edge states for in-plane dipole modes and quadrupole modes, however, have rather unique characters due to the vector nature of the plasmonic excitations. The conditions for the existence of plasmonic edge states are derived analytically.