gebhart/patrepeval huggingface dataset:
Comparison of Deconvolution Filters for Photoacoustic Tomography (2016)

In this work, we compare the merits of three temporal data deconvolution methods for use in the filtered backprojection algorithm for photoacoustic tomography (PAT). We evaluate the standard Fourier division technique, the Wiener deconvolution filter, and a Tikhonov L-2 norm regularized matrix inversion method. Our experiments were carried out on subjects of various appearances, namely a pencil lead, two man-made phantoms, an in vivo subcutaneous mouse tumor model, and a perfused and excised mouse brain. All subjects were scanned using an imaging system with a rotatable hemispherical bowl, into which 128 ultrasound transducer elements were embedded in a spiral pattern. We characterized the frequency response of each deconvolution method, compared the final image quality achieved by each deconvolution technique, and evaluated each method's robustness to noise. The frequency response was quantified by measuring the accuracy with which each filter recovered the ideal flat frequency spectrum of an experimentally measured impulse response. Image quality under the various scenarios was quantified by computing noise versus resolution curves for a point source phantom, as well as the full width at half maximum (FWHM) and contrast-to-noise ratio (CNR) of selected image features such as dots and linear structures in additional imaging subjects. It was found that the Tikhonov filter yielded the most accurate balance of lower and higher frequency content (as measured by comparing the spectra of deconvolved impulse response signals to the ideal flat frequency spectrum), achieved a competitive image resolution and contrast-to-noise ratio, and yielded the greatest robustness to noise. While the Wiener filter achieved a similar image resolution, it tended to underrepresent the lower frequency content of the deconvolved signals, and hence of the reconstructed images after backprojection. In addition, its robustness to noise was poorer than that of the Tikhonov filter. The performance of the Fourier filter was found to be the poorest of all three methods, based on the reconstructed images' lowest resolution (blurriest appearance), generally lowest contrast-to-noise ratio, and lowest robustness to noise. Overall, the Tikhonov filter was deemed to produce the most desirable image reconstructions.
Abstract 4450: Silencing NKD2 by promoter region hypermethylation promotes esophageal cancer progression by activating Wnt signaling (2016)

Abstract Background: Despite the use of surgery or chemoradiotherapy to treat, esophageal cancer, its prognosis still remains poor, with a 5-year survival below 15%. Recent insights into the epigenetic mechanisms associated with multi-step carcinogenesis provide new opportunities to develop novel effective targeted therapies for esophageal squamous cell carcinoma. Naked cuticle homolog 2 (NKD2) was found frequently methylated in human breast cancer. The epigenetic changes and mechanisms of NKD2 in human esophageal cancer remain unclear. Methods: Nine esophageal cancer cell lines and 154 cases of primary esophageal cancer samples were analyzed using methylation specific PCR, immunohistochemistry, western blot, flow cytometry techniques and a xenograft mouse model. Results: Loss of NKD2 expression and complete methylation were found in KYSE150 and TE1 cells. Reduced expression and partial methylation were observed in KYSE30, KYSE70, KYSE410, KYSE140 and COLO680 cells. High level expression and unmethylation were detected in KYSE450 and TE8 cells. Re-expression of NKD2 was induced by 5-aza-2’-deoxycytidine in NKD2 unexpressed or reduced cells. NKD2 was methylated in 53.2% (82/154) of human primary esophageal cancer samples, and promoter region hypermethylation was associated with reduced expression of NKD2 significantly (p&amp;lt;0.01). NKD2 methylation was associated with TNM stage and lymph node metastasis (p&amp;lt;0.01). The results suggest that NKD2 is regulated by promoter region methylation and methylation of NKD2 may serve as a prognostic marker in esophageal cancer. Our further studies demonstrate that NKD2 suppresses cell proliferation, colony formation, cell invasion and migration, as well as induces G1/S check point arrest in esophageal cancer cells. NKD2 suppressed xenograft tumor growth and inhibited Wnt signaling in human esophageal cancer cells. Conclusions: NKD2 is frequently methylated in human esophageal cancer, and the expression of NKD2 is regulated by promoter region methylation. NKD2 suppresses esophageal cancer progression by inhibiting Wnt signaling both in vitro and in vivo. Citation Format: Mingzhou Guo, Baoping Cao, Weili Yang, Yongshuai Jin, Meiying Zhang, Tao He, Qimin Zhan, James G. Herman, Guanglin Zhong. Silencing NKD2 by promoter region hypermethylation promotes esophageal cancer progression by activating Wnt signaling. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4450.
Pd/ZnO catalysts for direct CO2 hydrogenation to methanol (2016)

The direct hydrogenation of CO2 into methanol is crucial for providing a means of CO2 fixation and a way to store cleanly produced hydrogen in a more energy-dense and transportable form. Here we have prepared two series of Pd/ZnO catalysts, both by immobilisation of PVA-protected Pd colloids and by Pd impregnation of PdCl2 to investigate structure activity relationships for direct CO2 hydrogenation. Very different performances were found for the different preparation methods, and the Pd loading and pre-reduction of the catalysts were shown to be important factors for optimising methanol yield. The crucial factor for high methanol yield is the formation of a Pd–Zn alloy, either during the reaction itself, or better by high temperature pre-reduction. The formation of the alloy greatly reduces CO production by the reverse water gas shift reaction. The catalysts prepared by sol-immobilisation were relatively stable to thermal treatment. In contrast, the impregnated catalysts were much less thermally stable, due to the presence of remnant chloride on the surface of the catalyst, which was absent for the case of sol immobilisation preparation. The results illustrate the importance of controlling the PdZn particle size and its surface structure for the catalysts to achieve high methanol selectivity (60%, the rest being CO) and conversion (11%) at 250 °C and 20 bar. Selectivity for sol-immobilised catalysts decreases from 60% at 3 nm average diameter, to 20% at 7 nm.
Computational features of tumor-infiltrating lymphocyte architecture of residual disease after chemotherapy on H&E images as prognostic of overall and disease-free survival for triple-negative breast cancer. (2021)

584 Background: Approximately 30% of all breast cancers are characterized as triple-negative (TNBC). TNBC typically occurs in younger women and is associated with a poorer prognosis relative to other breast cancer subtypes. High levels of tumor-infiltrating lymphocytes (TILs) in residual disease after Neoadjuvant chemotherapy (NACT) have previously been shown to be associated with better prognosis in TNBC. In this work, we sought to evaluate the prognostic value of computationally derived measures of TIL spatial architecture in residual TNBC after NACT. Methods: H&amp;E-stained samples from 92 patients (pts) with TNBC (41 died, 45 had disease recurrence) and residual disease after NACT were retrospectively collected from 2 sites: Instituto Nacional de Enfermedades Neoplásicas (S1) and University Hospitals (S2). 45 pts (16 deaths, 23 recurrences) from S1 formed the training set and 47 pts (25 deaths, 22 recurrences) from S2 formed the independent validation cohort. Samples were digitized at 20x. Computerized algorithms automatically identified 2 types of nuclei (TILs and non-TILs) and built clusters for each nuclei type based on cell proximity. The spatial arrangement of these clusters was then quantified using network graph metrics. The top 5 features, determined by least absolute shrinkage and selection operator, were used to train a Cox regression model that assigned a risk of death and recurrence to each patient on the training set. The percentile 33 risk score was used as a threshold for stratifying pts on the validation set as either low or high risk. For comparison, we also employed a model based on TIL density alone. Survival analysis was used to evaluate the performance of both approaches on disease-free survival (DFS) and overall survival (OS). Results: Pts in S2 (n=47) identified as “high risk” by the model based on spatial architecture of residual TILs had a significantly shorter survival time. The median OS for pts at high risk was 25 months vs. 55 months for low-risk pts. The median DFS for pts at high risk was 32 months vs 51 months for low-risk pts. Univariable analysis showed this model was prognostic for both OS (Hazard Ratio (HR) = 2.57, 95% Confidence Interval (CI): 1.07-6.16, p=0.03) and DFS (HR=2.38, CI: 1.01-5.62, p=0.04). In contrast, the model based on TIL density was not prognostic for OS (HR=1.24, CI: 0.33-4.63, p=0.73) nor DFS (HR=1.19, CI: 0.32-4.34, p=0.78). Conclusions: A computerized image analysis model based on measurements of spatial arrangement of residual TILs and surrounding cells was found to be prognostic in TNBC pts who received NACT. This method appears to be more prognostic than TIL density alone. Additional multisite validation and multivariable analysis is needed to further establish the independent prognostic utility of TIL based image biomarkers in the post-NACT TNBC.
Digital Microfluidics Sample Analyzer (2010)

Three innovations address the needs of the medical world with regard to microfluidic manipulation and testing of physiological samples in ways that can benefit point-of-care needs for patients such as premature infants, for which drawing of blood for continuous tests can be life-threatening in their own right, and for expedited results. A chip with sample injection elements, reservoirs (and waste), droplet formation structures, fluidic pathways, mixing areas, and optical detection sites, was fabricated to test the various components of the microfluidic platform, both individually and in integrated fashion. The droplet control system permits a user to control droplet microactuator system functions, such as droplet operations and detector operations. Also, the programming system allows a user to develop software routines for controlling droplet microactuator system functions, such as droplet operations and detector operations. A chip is incorporated into the system with a controller, a detector, input and output devices, and software. A novel filler fluid formulation is used for the transport of droplets with high protein concentrations. Novel assemblies for detection of photons from an on-chip droplet are present, as well as novel systems for conducting various assays, such as immunoassays and PCR (polymerase chain reaction). The lab-on-a-chip (a.k.a., lab-on-a-printed-circuit board) processes physiological samples and comprises a system for automated, multi-analyte measurements using sub-microliter samples of human serum. The invention also relates to a diagnostic chip and system including the chip that performs many of the routine operations of a central labbased chemistry analyzer, integrating, for example, colorimetric assays (e.g., for proteins), chemiluminescence/fluorescence assays (e.g., for enzymes, electrolytes, and gases), and/or conductometric assays (e.g., for hematocrit on plasma and whole blood) on a single chip platform.
Sensors and related devices for IoT, medicine and s mart-living (2018)

The evolutions of medicine covering genome to exposome (i.e. all types of environmental exposures) [1] opened new paths of development for electronics including low power sensors. Additionally, the frontiers for new generations of sensors between smart-living, environment and health are fading. In this paper, we will give examples based on our developments in emerging autonomous sensors and medical devices, and show how they can be included in our daily life.
STATISTICAL PROPERTIES OF URBAN WCDMA CHANNEL FOR MOBILE POSITIONING APPLICATIONS (2004)

The goal of this paper is to present the results of a comprehensive statistical analysis of the urban wireless channels, based on WCDMA field-measurements data. The applications of our study are in the area of WCDMA-based mobile phone positioning. The objective here is the analysis of the Line-of-Sight (LOS) and Non Line-of-Sight (NLOS) situations and the statistical distributions of their parameters, such as the delays and amplitudes. The distribution of the first arriving path is tested against several theoretical distributions, such as the Rayleigh, Rician, and Nakagami-m distributions. The estimated delay of the first arriving path is compared to the LOS delay estimated via GPS so as to detect NLOS situations. The estimation of the mobile speed based on field-measurements data is also carried out and compared to the speed estimation based on the GPS link. The measurements were conducted in urban environment, downtown Helsinki.
Innovative Model for the Efficiency Optimization for High-Speed Trains through the Recovery of Braking Energy (2018)

Nowadays, the competitors of railway systems are going through a strong development phase, concerning the energy savings and the emissions in the environment, typically fields where railway vehicles assume a position of advantage. Due to the diffusion of distributed traction in railway vehicles, the recovery of braking energy, through appropriate technical solutions, represents an important purpose of research. In this work, the authors, as partner of the Tesys rail project (an Italian project which involves important academic and industrial partners), have developed an innovative model, which includes a vehicle dynamical model, coupled with an electrical model of the feeding line, using the innovative object oriented Matlab-Simscape language. The line model is made up of the contact line, the electrical substations, and stationary and on-board energy storage devices. The authors have focused their attention on the performances of high-speed trains. In particular, the proposed model has been validated through a set of experimental measurements performed on the Italian high-speed train ETR 1000 within the Firenze-Roma 3 kV direct current line. Once proved the good accuracy of the results, the model permits to perform a feasibility analysis of the energetic perspectives of a high-speed railway system, concerning different operating scenarios and various energy storage systems configurations. Through appropriate driving strategies and energy storage configurations, the results show that it is possible to recover a significant percentage of the braking energy. Finally, the proposed model proved to be characterized by a great computational efficiency: it is possible to simulate the behaviour of the train along a 250 km distance in only 5 seconds of simulation.
Initiation of focal adhesion assembly by talin and kindlin: A dynamic view (2020)

Focal adhesions (FAs) are integrin-containing protein complexes regulated by a network of hundreds of protein-protein interactions. They are formed in a spatiotemporal manner upon the activation of integrin transmembrane receptors, which is crucial to trigger cell adhesion and many other cellular processes including cell migration, spreading and proliferation. Despite decades of studies, a detailed molecular level understanding on how FAs are organized and function is lacking due to their highly complex and dynamic nature. However, advances have been made on studying key integrin activators, talin and kindlin, and their associated proteins, which are major components of nascent FAs critical for initiating the assembly of mature FAs. This review will discuss the structural and functional findings of talin and kindlin and their immediate interaction network, which will shed light upon the architecture of nascent FAs and how they act as seeds for FA assembly to dynamically regulate diverse adhesion-dependent physiological and pathological responses.
Hormonal regulation of apoptosis in early antral follicles: follicle-stimulating hormone as a major survival factor. (1996)

Hormonal regulation of apoptosis has been studied in cultured preovulatory follicles. Because early antral follicles are most vulnerable to undergo atretic degeneration under physiological conditions in vivo, the present studies were designed to investigate the hormonal regulation of apoptosis using in vitro culture of early antral follicles. Rats were implanted with diethylstilbestrol at 24 days of age to stimulate the development of early antral follicles, and ovaries were collected at day 27 of age. Early antral follicles were dissected and cultured (four per vial) for 24 h with or without hormonal treatments. After culture, DNA was extracted from follicles, and the degree of apoptotic DNA fragmentation was determined using 3'-end labeling and gel electrophoresis. In situ analysis of apoptotic DNA fragmentation revealed that granulosa cells in these follicles are the main cell type undergoing apoptosis. Follicles cultured in the absence of hormones showed a 12-fold increase in the level of apoptotic DNA fragmentation which was prevented by treatment with FSH in a dose-dependent manner (60% maximal suppression and apparent ED50 of 30 ng/ml). Similarly, treatment with (Bu)2cAMP also suppressed follicle apoptosis. Treatment with LH or human CG, however, minimally suppressed apoptotic DNA fragmentation (35% maximal suppression). Insulin-like growth factor-I (IGF-I) also suppressed apoptosis by 45%. Moreover, the suppressive effect of FSH on apoptosis was partially reversed by coincubation with IGF-binding protein-3, suggesting a potential mediatory role of endogenous IGF-I. However, recombinant bovine GH had no effect on follicle apoptosis despite its ability to stimulate IGF-I messenger RNA (mRNA) levels. Incubation of follicles with epidermal growth factor (EGF) and basic fibroblast growth factor maximally suppressed follicle apoptosis by only 32% and 42%, respectively. Ligand binding analysis indicated the minimal effectiveness of EGF on apoptosis in early antral follicles, as compared with its potent action in preovulatory follicles reported earlier, may be due to a 3.5 fold increase in EGF receptor concentration in the mature follicles. High doses (150 or 500 ng/ml) of interleukin-1beta also suppressed apoptosis by 48% whereas treatment with an NO generator, sodium nitroprusside, or a cyclic GMP analog suppressed apoptosis as effectively as that of FSH. Furthermore, treatment with activin resulted in a dose-related suppression of follicle apoptosis, reaching a maximal 40% suppression. In contrast, cotreatment of activin with its binding protein, follistatin, abolished this effect. Collectively, these data demonstrated a stage-dependent difference in the hormonal regulation of follicle apoptosis. Although FSH, LH/human CG, GH, IGF-I, EGF, basic fibroblast growth factor, and interleukin-1beta are all effective survival factors for preovulatory follicles, FSH is a major survival factor for early antral follicles, the stage during which a majority of follicle undergo atresia under physiological conditions.
Bronchoscopy is useful for diagnosing smear-negative tuberculosis in HIV-infected patients: Table 1– (2010)

To the Editors:
5-Aminolevulinic acid with ferrous iron improves early renal damage and hepatic steatosis in high fat diet-induced obese mice (2018)

5-Aminolevulinic acid, a natural amino acid, activates mitochondrial respiration and induces heme oxygenase-1 expression. Obesity and type 2 diabetes mellitus are associated with age-related mitochondrial respiration defect, oxidative stress and inflammation. The aim of this study is to investigate the effects of 5-aminolevulinic acid with sodium ferrous citrate on early renal damage and hepatic steatosis. 7-Month-old C57BL/6 mice were fed with a standard diet or high fat diet for 9 weeks, which were orally administered 300 mg/kg 5-aminolevulinic acid combined with 47 mg/kg sodium ferrous citrate (5-aminolevulinic acid/sodium ferrous citrate) or vehicle for the last 5 weeks. We observed that 5-aminolevulinic acid/sodium ferrous citrate significantly decreased body weight, fat weight, hepatic lipid deposits and improved levels of blood glucose and oral glucose tolerance test. In addition, 5-aminolevulinic acid/sodium ferrous citrate suppressed increased glomerular tuft area in high fat diet-fed mice, which was associated with increased heme oxygenase-1 protein expression. Our findings demonstrate additional evidence that 5-aminolevulinic acid/sodium ferrous citrate could improve glucose and lipid metabolism in diabetic mice. 5-Aminolevulinic acid/sodium ferrous citrate has potential application in obesity or type 2 diabetes mellitus-associated disease such as diabetic nephropathy and nonalcoholic fatty liver disease.
Full Ring Evaluation of X70 Grade UOE Line Pipes for Sour Service (2012)

High-strength large-diameter UOE line pipes over X70 grade are difficult to apply to actual fields, including H2S, because of a deterioration of sour resistance and a lack of past performance. However, API X70 grade large-diameter UOE line pipes for sour service have been manufactured stably by optimizing the continuous casting process, controlling the shape of inclusions and decreasing coarse precipitates. A full-ring test can simulate fairly well the actual applied conditions of line pipes and evaluate hydrogen induced cracking (HIC), sulfide stress cracking (SSC) and stress oriented hydrogen induced cracking (SOHIC) of line pipes for sour service simultaneously. It was confirmed that the X70 grade UOE line pipes have a good sour resistance from standard HIC tests, four-point bent beam SSC tests and the full-ring test including a seam weld under severe sour conditions (NACE solution A with 0.1 MPa H2S). In addition, the SSC resistance of a girth welded portion was also investigated by using simulated HAZ.
Description of depolarization effects in double-quantum solid state nuclear magnetic resonance experiments using multipole-multimode Floquet theory (2006)

Using an analytical model based on multipole-multimode Floquet theory (MMFT), we describe the polarization loss (or depolarization) observed in double-quantum (DQ) dipolar recoupling magic angle spinning (MAS) experiments. Specifically, the factors responsible for depolarization are analyzed in terms of higher order corrections to the spin Hamiltonian in addition to the usual phenomenological decay rate constant. From the MMFT model and the effective Hamiltonians, we elucidate the rationale behind the inclusion of a phenomenological damping term in DQ recoupling experiments. As a test of this theoretical approach, the recoupling efficiency of one class of (13)C-(13)C and (13)C-(15)N resonance width dipolar recoupling experiments are investigated at different magnetic field strengths and compared with the more exact numerical simulations. In contrast to existing analytical treatments, the role of higher order corrections is clearly explained in the context of the MMFT approach leading to a better understanding of the underlying spin physics. Furthermore, the analytical model presented herein provides a general framework for describing coherent and incoherent effects in homonuclear and heteronuclear DQ MAS recoupling experiments.
NOVEL ISOCOUMARIN DERIVATIVES FROM ACHLYS TRIPHYLLA (BERBERIDACEAE) (1990)

Three new phenolic compounds with a novel skeleton were isolated from the underground parts of Achlys triphylla (Berberidaceae). The structures were established by means of spectroscopic methods to be 7-geranyl-6, 8-dihydroxy-3-(4'-hydroxyphenylethyl)isocoumarin (1__∼) for achlisocoumarin I, 7-geranyl-6, 8-dihydroxy-3-(4'-hydroxyphenylethenyl)isocoumarin (2__∼) for achlisocoumarin II, and 6, 8-dihydroxy-3-(3', 4'-dihydroxyphenylethenyl)isocoumarin (3__∼) for achlisocoumarin III, respectively.