gebhart/patrepeval huggingface dataset:
Quality control of radiomic features using 3D-printed CT phantoms (2021)

<b>Purpose</b>: The lack of standardization in quantitative radiomic measures of tumors seen on computed tomography (CT) scans is generally recognized as an unresolved issue. To develop reliable clinical applications, radiomics must be robust across different CT scan modes, protocols, software, and systems. We demonstrate how custom-designed phantoms, imprinted with human-derived patterns, can provide a straightforward approach to validating longitudinally stable radiomic signature values in a clinical setting. <b>Approach</b>: Described herein is a prototype process to design an anatomically informed 3D-printed radiomic phantom. We used a multimaterial, ultra-high-resolution 3D printer with voxel printing capabilities. Multiple tissue regions of interest (ROIs), from four pancreas tumors, one lung tumor, and a liver background, were extracted from digital imaging and communication in medicine (DICOM) CT exam files and were merged together to develop a multipurpose, circular radiomic phantom (18 cm diameter and 4 cm width). The phantom was scanned 30 times using standard clinical CT protocols to test repeatability. Features that have been found to be prognostic for various diseases were then investigated for their repeatability and reproducibility across different CT scan modes. <b>Results</b>: The structural similarity index between the segment used from the patients' DICOM image and the phantom CT scan was 0.71. The coefficient variation for all assessed radiomic features was <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mo><</mml:mo> <mml:mn>1.0</mml:mn> <mml:mo>%</mml:mo></mml:mrow> </mml:math> across 30 repeat scans of the phantom. The percent deviation (pDV) from the baseline value, which was the mean feature value determined from repeat scans, increased with the application of the lung convolution kernel, changes to the voxel size, and increases in the image noise. Gray level co-occurrence features, contrast, dissimilarity, and entropy were particularly affected by different scan modes, presenting with <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mi>pDV</mml:mi> <mml:mo>></mml:mo> <mml:mo>±</mml:mo> <mml:mn>15</mml:mn> <mml:mo>%</mml:mo></mml:mrow> </mml:math> . <b>Conclusions</b>: Previously discovered prognostic and popular radiomic features are variable in practice and need to be interpreted with caution or excluded from clinical implementation. Voxel-based 3D printing can reproduce tissue morphology seen on CT exams. We believe that this is a flexible, yet practical, way to design custom phantoms to validate and compare radiomic metrics longitudinally, over time, and across systems.
A Novel Experimental Porcine Model to Assess the Impact of Differential Pulmonary Blood Flow on Primary Graft Dysfunction After Unilateral Lung Transplantation (2020)

Abstract Background Primary graft dysfunction (PGD) remains a major obstacle after lung transplantation. We developed a novel approach to selectively assess reperfusion injury in transplanted lung and investigated the impact of pulmonary flow. Materials Twelve porcine left lung transplants were divided in two groups (n = 6, in low (LF) and high flow (HF) group). Donor lungs were stored for 24 hours on ice, followed by left lung transplantation. Recipient animals were observed for 6h after reperfusion with partially clamping of right PA in HF group. Results Survival at 6 hours was 100% in both groups. P a O 2 /F i O 2 (P/F) ratio of the transplanted lung was lower (229.1 mmHg vs 308.9 mmHg, p=0.01), mPAP was higher (34.62 mmHg vs 29.88 p=0.01) in HF versus LF group. Wet-to-dry (W/D) ratios of right native and left transplanted lung were not different after 6 h of reperfusion. Conclusions Lung transplantation in large animal settings is feasible. P/F ratio in allograft is dependent on PA flow. Our innovative approach to control blood flow to transplanted lung demonstrates that higher flows induce more PGD and allows to further study development and treatment of PGD. Our findings might have an important impact on sequential intra-operative approach during lung transplantation.
Gate-first high-k/metal gate DRAM technology for low power and high performance products (2015)

It is the first time that the high-k/metal gate technology was used at peripheral transistors for fully integrated and functioning DRAM. For cost effective DRAM technology, capping nitride spacer was used on cell bit-line scheme, and single work function metal gate was employed without strain technology. The threshold voltage was controlled by using single TiN metal gate with La2O3 and SiGe/Si epi technology. The optimized DRAM high-k/metal gate peripheral transistors showed current gains of 65%/55% and DIBL improvements of 52%/46% for nMOSFET and pMOSFET, respectively. The results in process yield, performance, and reliability characteristics of the technology on 4Gb DRAM have shown that the gate-first high-k/metal gate DRAM technology can be regarded as one of the major candidates for next-generation low power DRAM products.
Neuronal KGB-1 JNK MAPK signaling regulates the dauer developmental decision in response to environmental stress in C. elegans (2021)

Abstract In response to stressful growth conditions of high population density, food scarcity and elevated temperature, young larvae of nematode Caenorhabditis elegans can enter a developmentally arrested stage called dauer that is characterized by dramatic anatomic and metabolic remodeling. Genetic analysis of dauer formation of C. elegans has served as an experimental paradigm for the identification and characterization of conserved neuroendocrine signaling pathways. Here, we report the identification and characterization of a conserved JNK-like mitogen-activated protein kinase (MAPK) pathway that is required for dauer formation in response to environmental stressors. We observed that loss-of-function mutations in the MLK-1-MEK-1-KGB-1 MAPK pathway suppress dauer entry. Loss-of-function mutation in the VHP-1 MAPK phosphatase, a known negative regulator of KGB-1 signaling, results in constitutive dauer formation which is dependent on the presence of dauer pheromone but independent of diminished food levels or elevated temperatures. Our data suggest that KGB-1 pathway acts in the sensory neurons, in parallel to established insulin and TGF- β signaling pathways, to transduce the dauer-inducing environmental cues of diminished food levels and elevated temperature.
Microsphere Technology and Applications (2013)

Microparticulate carriers can be classified based on its structural architecture and design into microcapsules, microspheres, and microparticles. These micron-sized particles may differ from one another in terms of morphology, matrix vs. shell, and internal structure. This entry discusses applications of microspheres and evaluates their potential advantages in the current field of microsphere research, and highlights the various preparation techniques and emphasizes their advantages and limitations.
A neutralizing anti–G-CSFR antibody blocks G-CSF–induced neutrophilia without inducing neutropenia in nonhuman primates (2017)

Neutrophils are the most abundant WBCs and have an essential role in the clearance of pathogens. Tight regulation of neutrophil numbers and their recruitment to sites of inflammation is critical in maintaining a balanced immune response. In various inflammatory conditions, such as rheumatoid arthritis, vasculitis, cystic fibrosis, and inflammatory bowel disease, increased serum G-CSF correlates with neutrophilia and enhanced neutrophil infiltration into inflamed tissues. We describe a fully human therapeutic anti-G-CSFR antibody (CSL324) that is safe and well tolerated when administered via i.v. infusion to cynomolgus macaques. CSL324 was effective in controlling G-CSF-mediated neutrophilia when administered either before or after G-CSF. A single ascending-dose study showed CSL324 did not alter steady-state neutrophil numbers, even at doses sufficient to completely prevent G-CSF-mediated neutrophilia. Weekly infusions of CSL324 (≤10 mg/kg) for 3 wk completely neutralized G-CSF-mediated pSTAT3 phosphorylation without neutropenia. Moreover, repeat dosing up to 100 mg/kg for 12 wk did not result in neutropenia at any point, including the 12-wk follow-up after the last infusion. In addition, CSL324 had no observable effect on basic neutrophil functions, such as phagocytosis and oxidative burst. These data suggest that targeting G-CSFR may provide a safe and effective means of controlling G-CSF-mediated neutrophilia as observed in various inflammatory diseases.
Supplementary Table S6 from Discovery of Candidate DNA Methylation Cancer Driver Genes (2023)

&lt;p&gt;Description of analyzed TCGA data.&lt;/p&gt;
Supplementary Figure 2 from Mechanistic Contribution of Ubiquitous 15-Lipoxygenase-1 Expression Loss in Cancer Cells to Terminal Cell Differentiation Evasion (2023)

&lt;p&gt;PDF file - 73KB&lt;/p&gt;
A new family of bis-DCM based dopants for red OLEDs (2005)

We have synthesized a series of novel bis-DCM derivatives as candidate red dopants for use in organic light-emitting devices (OLEDs), by introducing various donor-substituted aryl rings. Compared to DCJTB (621 nm), the novel dopants (637–677 nm) showed more red-shifted emission in 1,2-dichloroethane. Using bis-DCMNEtOBu (7) as a dopant, we fabricated OLEDs with the configuration of ITO/4,4′,4″-tris(3-methylphenylamino)triphenylamine (m-MTDATA) (20 nm)/N,N′-bis(1-naphthyl)-diphenyl-1,1′-biphenyl-4,4′-diamine (NPB) (40 nm)/tris(8-quinolinolato)aluminium (Alq3) : red dopant (35 nm, x wt%)/Alq3 (35 nm) LiF/Al. The device with a doping concentration of 1.25 wt% showed pure red emission at λmax = 654 nm (chromaticity coordinate: x = 0.67, y = 0.33) and a maximum brightness of 2500 cd m−2. The chromaticity coordinates were almost independent of current density. Moreover, highly efficient red emission (x = 0.63, y = 0.36) was obtained in the 0.74 wt% doped device. The maximum external quantum efficiency was 4.46% at 7 V, the current efficiency was 3.43 cd A−1, and the power efficiency was 1.64 lm W−1. The highest brightness of 8300 cd m−2 was obtained at 19.6 V.
Performance evaluation of a prototype Positron Emission Tomography scanner using Digital Photon Counters (DPC) (2012)

We show performance results of a prototype Positron Emission Tomography scanner based on digital SiPMs, or Digital Photon Counters (DPC), developed by the Philips Digital Photon Counting unit. The scalability of the DPC technology is demonstrated by an excellent system coincidence timing resolution of 266 ps FWHM and an energy resolution of 10.7 % FWHM. Even while using 4 mm × 4 mm × 22 mm LYSO crystals, the spatial resolution is close to 2.4 mm. Although not optimized yet, the image homogeneity is 5.8 %. We show that the system performance is maintained even at highest count rates encountered in PET scans.
Hepcidin‐dependent and hepcidin‐independent regulation of erythropoiesis in a mouse model of anemia of chronic inflammation (2014)

Increased hepcidin antimicrobial peptide correlates with hypoferremia and anemia in various disease states, but its requirement for anemia of inflammation has not been adequately demonstrated. Anemia of inflammation is usually described as normocytic and normochromic, while diseases associated with over expression of hepcidin, alone, are often microcytic and hypochromic. These differences in erythrocyte parameters suggest anemia in many inflammatory states may not be fully explained by hepcidin-mediated iron sequestration. We used turpentine-induced sterile abscesses to model chronic inflammation in mice with targeted disruption of Hepcidin 1 [Hepc1 (-/-)] or its positive regulator, Interleukin-6 [IL-6 (-/-)], to determine whether these genes are required for features characteristic of anemia of inflammation. Although hemoglobin levels did not decline in Hepc1 (-/-) mice with sterile abscesses, erythrocyte numbers were significantly reduced compared to untreated Hepc1 (-/-) mice. In contrast, both hemoglobin concentration and erythrocyte number declined significantly in wild type and IL-6 (-/-) mice with sterile abscesses. Both Hepc1 (-/-) and IL-6 (-/-) mice had increased erythrocyte mean cell volume and mean cell hemoglobin following sterile abscesses, while wild types had no change. Thus, IL-6 (-/-) mice with sterile abscesses exhibit an intermediate phenotype between wild type and Hepc1 (-/-). Our results demonstrate the requirement of Hepc1 for the development of anemia in this rodent model. Simultaneously, our results demonstrate hepcidin-independent effects of inflammation on the suppression of erythropoiesis. Our results suggest chronic anemia associated with inflammation may benefit from interventions protecting erythrocyte number in addition to anti-hepcidin interventions aimed at enhancing iron availability.
Increasing cellular capacity using ISM band side-channels (2014)

The rise of ISM band radios, notably for WiFi, with near-default inclusion in smartphones, has been phenomenal. The use of ISM band radios is largely controlled by end-users for data access, either directly connecting to a WiFi access point or wireless tethering. We study an additional use of ISM bands to manage interference in cellular bands, by creating ISM ``side-channels" between mobile clients. Our objective is to increase the network capacity in cellular bands, when there is no opportunity of data offloading to WiFi. We first study the likelihood of finding a WiFi-free environment, specifically on highways, to establish an ISM side-channel between smartphones. The likelihood is found by experimentally studying the range of WiFi links between smartphones with our designed Android applications, combined with rush hour traffic data on highways; the result is that there is high probability of finding at least one smartphone within the ISM band range. Finally, we show that the proposed use of ISM side-channels can significantly reduce interference in a MIMO wireless system and increase the overall cellular network capacity, by flexibly accommodating both multiuser beam-forming and full-duplex operation.
Biomimetic self-assembly of helical electrical circuits using orthogonal capillary interactions (2002)

This letter describes the biomimetic self-assembly of mm-sized polyhedra into helical aggregates. The system used two orthogonal, capillary interactions that acted in parallel. The design of the self-assembly process, and of the resulting structures, was modeled on the formation and structure of tobacco mosaic virus. The self-assembled, helical aggregates carried one, two, or four isolated, electrical circuits.
Optimization of Alkaline Earth Metal Oxide and Hydroxide Catalysts for Base‐Catalyzed Reactions (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Supplementary Figure 1 from Mutated <i>BCR-ABL</i> Generates Immunogenic T-cell Epitopes in CML Patients (2023)

&lt;p&gt;PDF file, 210K, Forty-five distinct peptides were predicted to bind with IC50&lt; 1000 nM, with 60 peptide-allele combinations.&lt;/p&gt;
Development of a Fixed Repertoire of Blood Transcriptome Modules Based on Co-expression Patterns Across Immunological States (2020)

Abstract As the capacity for generating large scale data continues to grow the ability to extract meaningful biological knowledge from it remains a limitation. Here we describe the development of a new fixed repertoire of transcriptional modules. It is meant to serve as a stable reusable framework for the analysis and interpretation of blood transcriptome profiling data. It is supported by customized resources, which include analysis workflows, fingerprint grid plots data visualizations, interactive web applications. These provide access to a vast number of module-specific functional profiling reports, reference transcriptional profiles, and give users the ability to visualize changes in transcript abundance across the modular repertoire at different granularity levels. A use case focusing on a set of six modules comprising interferon-inducible genes is also provided. Taken together, this well-characterized set of modules may be employed for the interpretation and benchmarking of blood transcriptome profiles obtained within and across patient cohorts.
Resonant tunneling of acoustic waves through a double barrier consisting of two phononic crystals (2005)

International audience
Hierarchical Instruction Register Organization (2008)

This paper analyzes a range of architectures for efficient delivery of VLIW instructions for embedded media kernels. The analysis takes an efficient filter cache as a baseline and examines the benefits from 1) removing the tag overhead, 2) distributing the storage, 3) adding indirection, 4) adding efficient NOP generation, and 5) sharing instruction memory. The result is a hierarchical instruction register organization that provides a 56% energy and 40% area savings over an already efficient filter cache.
Formation and X-ray structure of the hostguest adduct [Pd3(dppm)3(CO)(NO3)]+ and the mechanism of its electrochemical reduction (2006)

[Pd 3 (dppm) 3 (CO)] 2+ , [Pd 3 ] 2+ , reacts with NO 3  to form the hostguest adduct [Pd 3 (dppm) 3 (CO)(NO 3 )] + , [Pd 3 (NO 3 )] + . The presence of NO 3  inside the cavity is confirmed by X-ray crystallography. Using a qualitative relationship between λ max (UVvis) and the association constant of various adducts, the relative binding between NO 3  and [Pd 3 ] 2+ is in the same order of magnitude of that between CF 3 CO 2  and [Pd 3 ] 2+ . Based on Pd···O distances, the NO 3  ion is relativity more weakly associated to [Pd 3 ] 2+ in comparison with the known [Pd 3 (CF 3 CO 2 )] + . Using variation of [NO 3  ] in the presence of [Pd 3 ](PF 6 ) 2 and variation of scan rates, the resulting cyclic voltammogramms (CV) were simulated to extract both kinetic and thermodynamic constants associated to a square scheme. Both the anodic and cathodic scans of the title cluster exhibits ECE mechanisms (E = electrochemical process; C = chemical process). For the anodic scan, the EEC event is not ruled out, at least as a minor process.Key words: nitrate, palladium cluster, adduct, electrochemistry, X-ray structure, rate constant, equilibrium constant.
<title>Interactive algorithms for rapid enumeration of hybridization signals in individual whole-cell nuclei inside intact-tissue specimens</title> (1995)

Fluorescence in situ hybridization (FISH) is useful for analyzing specific nucleic acid sequences in individual cells. Its application to tissue sections has been limited however because of the difficulties of performing the hybridization and analysis in sections that are thick enough to contain intact nuclei. Recent improvements in FISH permit hybridization with chromosome-specific, centromeric probes throughout 20 micrometers formalin fixed, paraffin- embedded sections, which do contain many intact nuclei. This paper describes software to facilitate analysis of these 3D hybridizations. We have developed two algorithms for analyzing 3D, confocal images of thick sections. One displays 2D, maximum-intensity, projection images through the original 3D image at different angles. When projections are viewed sequentially, the 3D image appears semi-transparent and rotates. The second algorithm allows interactive enumeration of FISH signals. Each signal is marked by the analyst. Then, for each pair of marked signals, a 2D slice image along the line connecting both marked signals and parallel to the z (depth) axis is displayed. From this slice, the analyst decides if the signals are in the same or different nuclei, or if the signals should be rejected because they are in a nucleus truncated by the upper or lower surface of the section. After consideration of all pairs of signals, the algorithm produces a map of the tissue section showing the numbers of signals in each of the intact nucleus. The algorithms enable analysis of small, premalignant and early malignant lesions and infiltrative lesions that cannot be analyzed by other molecular techniques and permit the direct correlation of FISH information with histology/cytology.
Enabling Better Thermal Management of Indoor Spaces through Adaptive Zonal Heat Transfer (2018)

In multi-zone indoor spaces with thermal dependencies between zones and limited heating/cooling sources, choosing optimal zonal thermostat or heat input settings is often not enough to attain desired zonal temperatures. In such scenarios, simple changes that affect the thermal transfer between different zones, or between the individual zones and the ambient - actuated through opening/closing of doors and windows, for example - can significantly improve the the zonal temperatures or reduce energy costs. In this paper, we consider the problem of determining how the thermal flow in-between the different zones of the indoor space, or between the zones and the ambient, should be adapted towards improving the overall thermal environment in the multi-zone space. Despite the complex structure of the problem, we show how such the question of optimal zonal heat transfer adaptation - which involves determining the optimal zonal heat input settings as well - can be formulated and solved efficiently. We also determine conditions under which the problem has a convex structure. Finally, we evaluate the benefits of zonal heat transfer adaptation through simulations on a dynamic thermal model of a 6-zone indoor space. Our results show that zonal heat transfer adaptation can result in significant improvement of zonal temperatures and/or energy costs, particularly when not all zones are equipped with heat sources.
Experiments and Simulations of Time-Dependant Phenomena in a Hydrothermal Oxidation Tubular Reactor (2003)

The scaling up of a hydrothermal oxidation (HTO) facility depends on the development of simulation tools. In this way, a new approach to simulate the reactor thermal behavior during a nonstationary regime such as the start, stop, or emergency stop of the unit is developed. A numerical procedure of nonstationary temperature profile simulation in the reactor is described in order to predict the reactor thermal behavior. This new model is validated from experimental data obtained with a quasi-adiabatic reactor, which allows one to follow the temperature profile evolution along the reactor during the HTO process. Performances of the numerical procedure are tested with the simulation of three kinds of real nonstationary conditions: facility start, pump defect, and waste concentration dilution. The simulation gives the evolution of temperature profiles of a reactive mixture versus time and models the external wall temperature of the reactor tube versus time. These three simulations show that the HTO reactor thermal operation can be considered as stable and sure. Furthermore, they put in a prominent position that the risks of reactor damage are limited.
Retinal Laser Therapy Preserves Photoreceptors in a Rodent Model of MERTK-Related Retinitis Pigmentosa (2019)

Availability of retinal lasers in ophthalmic practice enables rapid translation of our study to clinical testing and may help preserve the sight in patients with photoreceptor degeneration.