gebhart/patrepeval huggingface dataset:
Compact implementation of dynamic receive apodization in ultrasound scanners (2004)

The image quality in medical ultrasound scanners is determined by several factors, one of which is the ability of the receive beamformer to change the aperture weighting function with depth and beam angle. In digital beamformers, precise dynamic apodization can be achieved by representing that function by numeric sequences. For a 15 cm scan depth and 100 lines per image, a 64-channel, 40 MHz ultrasound beamformer may need almost 50 million coefficients. A more coarse representation of the aperture relieves the memory requirements but does not enable compact and precise beamforming. Previously, the authors have developed a compact beamformer architecture which utilizes sigma-delta A/D conversion, recursive delay generation and sparse sample reconstruction using FIR filters. The channel weights were here fixed. In this paper, a compact implementation of dynamic receive apodization is presented. It allows precise weighting coefficient generation and utilizes a recursive algorithm which shares its starting parameters with the recursive delay generation logic. Thus, only a separate calculation block, consisting of 5 adders and 5 registers, is necessary. A VHDL implementation in a Xilinx XCV2000E-7 FPGA has been made for the whole receive beamformer for assessing the necessary hardware resources and the achievable performance for that platform. The code implements dynamic apodization with an expanding aperture for either linear or phased array imaging. A complete 32-channel beamformer can operate at 129.82 MHz and occupies 1.28 million gates. Simulated in Matlab, a 64-channel beamformer provides gray scale image with around 55 dB dynamic range. The beamformed data can also be used for flow estimation.
Postnatal development of photoreceptor-specific proteins in mice with hereditary retinal degeneration. An immunocytochemical study. (1990)

The postnatal development of immunoreactivity for photoreceptor-specific markers was studied in mice carrying the genes rd (retinal degeneration) and rds (retinal degeneration slow) in different combinations. Antibodies raised against three specific photoreceptor proteins (opsin, alpha-transducin and S-antigen) were applied on retinae from mice with the following allelic combinations at the rd and rds loci: +/+, +/+ (control); rd/rd, +/+; rds/rds, +/+; rds/+, +/+; and rd/rd, rds/rds. Immunoreactivity for each antibody appeared simultaneously in normal and mutants. Thereafter, the immunoreactivity patterns in the mutants diverged from the normal phenotype. Except for a dramatic loss of photoreceptor cells in the mutants, the main divergence from the normal development consisted of a progressive loss of the intracellular immunoreactivity compartmentalization for each protein. As degeneration progressed, the remaining photoreceptors became homogeneously labelled; one this labelling pattern was acquired, it was maintained during subsequent stages of development. It is proposed that this pattern, common for all phenotypes studied, may be due to the loss of structural and biochemical polarity of the photoreceptor cells undergoing degeneration, and that this may be an important primary or secondary aspect of the disease process.
Recognition ofE. coli tryptophan synthase by single-chain Fv fragments: comparison of PCR-cloning variants with the parental antibodies (1997)

The use of a recombinant antibody fragment instead of a complete antibody, as a conformational probe for protein structure and folding studies, can be technically advantageous provided that the recombinant fragment and its parental antibody recognize the antigen through the same mechanism. Monoclonal antibodies mAb19 and mAb93 are directed against the TrpB2 subunit of Escherichia coli tryptophan synthase and they have been extensively used as conformational probes of this protein. DNA sequences coding for single-chain variable fragments (scFv) of mAb19 and mAb93 were cloned and assembled by reverse transcription of the mRNAs from hybridomas and PCR amplification. A specialized plasmid vector, pFBX, was constructed; it enabled to express the scFvs as hybrids with the maltose-binding protein (MalE) in E. coli, and to purify them by affinity chromatography on cross-linked amylose. Six independent clones were sequenced for each hybridoma. All of them had differences in their nucleotide and amino acid sequences. A competition ELISA and the BIAcore biosensor apparatus were used to compare the energetics and kinetics with which the parental antibodies and the hybrids bound TrpB2. The antigen binding properties of the hybrids were close to those of the parental antibodies and they were only weakly affected by the differences of sequence between the clones, with one exception. The stability of one of the hybrids and its antigen binding properties were strongly modified by a change of Gln6 into Glu, introduced into its VH domain by the PCR primers. Simple models of bimolecular interaction did not fully account for the kinetic profiles obtained with the parental antibodies and the hybrids, and this complexity suggested the existence of a conformational heterogeneity in these molecules.
MultiK: an automated tool to determine optimal cluster numbers in single-cell RNA sequencing data (2021)

Single-cell RNA sequencing (scRNA-seq) provides new opportunities to characterize cell populations, typically accomplished through some type of clustering analysis. Estimation of the optimal cluster number (K) is a crucial step but often ignored. Our approach improves most current scRNA-seq cluster methods by providing an objective estimation of the number of groups using a multi-resolution perspective. MultiK is a tool for objective selection of insightful Ks and achieves high robustness through a consensus clustering approach. We demonstrate that MultiK identifies reproducible groups in scRNA-seq data, thus providing an objective means to estimating the number of possible groups or cell-type populations present.
On the Accuracy Limit of Time-delay Estimation with a Band-limited Signal (2019)

The derivation of tight estimation lower bounds is a key player to design and assess the performance of new estimators. Considering a generic band-limited signal formulation and constant transmitter to receiver propagation delay, we propose a novel compact closed-form expression of the Cramér-Rao bound for time-delay estimation. This new formulation, especially easy to use, allows to derive the best (lowest) Cramér-Rao bound for a band-limited signal of given length and energy, which provides an estimation performance loss metric. These results are illustrated with two representative band-limited signals.
Establishment of Highly Tumorigenic Human Colorectal Cancer Cell Line (CR4) with Properties of Putative Cancer Stem Cells (2014)

The highly tumorigenic and clonogenic CIC-enriched CR4 cell line may provide an important new tool to support the discovery of novel diagnostic and/or prognostic biomarkers as well as the development of more effective therapeutic strategies.
Structural Exploration of (3<i>S</i>,6<i>S</i>)‐6‐Benzhydryl‐<i>N</i>‐benzyltetrahydro‐2<i>H</i>‐pyran‐3‐amine Analogues: Identification of Potent Triple Monoamine Reuptake Inhibitors as Potential Antidepressants (2012)

To further explore the basic structural motifs (3S,6S)-6-benzhydryl-N-benzyltetrahydro-2H-pyran-3-amine and (2S,4R,5R)-2-benzhydryl-5-(benzylamino)tetrahydro-2H-pyran-4-ol, developed by our research group, for monoamine transport inhibition, we designed and synthesized various structurally altered analogues. The new compounds were tested for their affinities for the dopamine transporter (DAT), the serotonin transporter (SERT), and the norepinephrine transporter (NET) in rat brain by measuring their capacity to inhibit the uptake of [(3)H]DA, [(3)H]5-HT, and [(3)H]NE, respectively. Our results point to novel compounds with a TUI, DNRI, SNRI, or SSRI profile. Among the TUIs, compound 2 g exhibited a balanced potency for all three monoamine transporters (K(i): 60, 79, and 70.3 nM for DAT, SERT, and NET, respectively). In the rat forced swim test, compound 2 g produced a significant decrease in immobility in drug-treated rats relative to vehicle, indicating a potential antidepressant property.
Erratum: Modulation on coherent vortex structures by dispersed solid particles in a three-dimensional mixing layer [Phys. Rev. E<b>68</b>, 036309 (2003)] (2004)

We found a mistake in our paper [Phys. Rev. E 68, 036309 (2003)] after its publication. It is due to the use of other computational cases by mistake to plot five figures (Figs. But it should be pointed out that all of these figures represent the same trends, thus the mistake is not essential and the main conclusions in the manuscript are not affected.
Tumor immunology and cancer immunotherapy: summary of the 2014 SITC primer (2015)

The pioneers of tumor immunology and cancer immunotherapy, including the late William B. Coley and Lloyd J. Old, have championed the potential for immunotherapy for over a century. Finally, advances in our understanding of the fundamentals of tumor immunology are translating into clinical success, with recent US Food and Drug Administration approval of several immunotherapies that improve clinical outcomes across prostate cancer, metastatic melanoma, non-small cell lung cancer and lymphocytic leukemia. In tandem with these clinical successes, new technologies such as high-throughput DNA/RNA sequencing, genetic engineering, and streamlined ex vivo cell culturing have paved the way for the next generation of immunotherapies and provided new tools for investigating potential biomarkers of response to existing therapies. During the November 2014 Annual Meeting of the Society of the Immunotherapy of Cancer, leaders in tumor immunology and cancer immunotherapy convened at the second annual SITC Primer to review both current knowledge and future directions in the field. Here, we will review the key discussions across a variety of topics, including innate immunity, adaptive immunity, dendritic cells, adoptive T cell therapy, anti-tumor antibodies, cancer vaccines, immune checkpoint blockade, challenges to immunotherapy, monitoring immune responses, and immunotherapy clinical trial design.
Linking clinical phenotypes of chronic lung allograft dysfunction to changes in lung structure (2015)

Chronic lung allograft dysfunction (CLAD) remains the major barrier to long-term success after lung transplantation. This report compares gross and microscopic features of lungs removed from patients receiving a redo-transplant as treatment for CLAD. Lungs donated by patients with either the bronchiolitis obliterans syndrome (BOS) or restrictive allograft syndrome (RAS) phenotype of CLAD and appropriate control lungs (eight per group) were air-inflated, frozen solid and kept frozen while a multi-detector computed tomography (MDCT) was obtained. The lung was then cut into 2-cm thick transverse slices and sampled for micro-CT and histopathology. The MDCT showed reduced lung volume with increased lung weight and density in RAS versus BOS and control (p<0.05). Although pre-terminal bronchioles were obstructed in both phenotypes, RAS lungs showed a reduction of pre-terminal bronchioles (p<0.01). Micro-CT and matched histopathology showed that RAS was associated with reduced numbers of terminal bronchioles/lung compared to BOS and controls (p<0.01), with expansion of the interstitial compartment and obliteration of the alveolar airspaces by fibrous connective tissue. RAS is associated with greater destruction of both pre-terminal and terminal bronchioles. Additionally, the interstitial compartments are expanded and alveolar airspaces are obliterated by accumulation of fibrous connective tissue.
Bilateral exudative retinal detachments as the presenting features of idiopathic orbital inflammation (2005)

Idiopathic orbital inflammation, also known as orbital pseudotumour, is a term describing a spectrum of idiopathic, non-neoplastic, non-infectious, space-occupying orbital lesion without identifiable local or systemic cause. This disease occurs mainly in young adults and typically presents with acute proptosis, chemosis and limited extraocular movement. Herein an unusual case of idiopathic orbital inflammation presenting with bilateral exudative retinal detachment in a 9-year-old girl is described. It demonstrates that prompt diagnosis and corticosteroid treatment can yield good clinical response and significant visual recovery.
Une juriste engagée dans les nanotechnologies (2008)

Séminaire de recherche
An Expeditious Synthesis of 6‐Aminophenanthridines. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Designing Peptide Bunches on Nanocage for Bispecific or Superaffinity Targeting (2016)

Ferritin cage nanoparticles are promising platforms for targeted delivery of imaging and therapeutic agents because their cage structure can accommodate small molecules and their surfaces can be decorated with multiple functionalities. However, selective targeting is still a challenge for translating ferritin-based nanomedicines into the clinic, especially for heterogeneous diseases such as cancer. Targeting peptides can be genetically fused onto the surface of a ferritin cage, forming peptide bunches on nanocages (PBNCs) that offer synergistic increases in binding avidity. Here, we utilized two sites of the ferritin monomer, the N-terminus and the loop between the fourth and fifth helices, which are exposed on the surface of the assembled 24-subunit ferritin cage, to ligate one or two types of peptides to achieve "super affinity" and bispecificity, respectively. PBNCs formed by ligation of the IL-4 receptor-targeting peptide, AP1, to both sites (48AP1-PBNCs) tethered IL-4R, expressing tumor cells with greater affinity than did PBNCs with AP1 ligated to a single site (24AP1-PBNCs). Moreover, bispecific PBNCs containing 24 RGD peptides and 24 AP1 peptides (24RGD/24AP1-PBNCs) were capable of independently targeting cells expressing the corresponding receptors. Bispecific and superaffinity PBNCs could be useful for efficient targeting of ferritin-based therapeutic/diagnostic agents in a clinical setting.
Erweiterung der Modellvorstellung der Zentrifugalentfeuchtung – Berücksichtigung der mechanisch‐thermischen Entfeuchtung (2003)

Abstract No abstracts.
Simple direct block-oriented system identification for hydraulic motion control (2016)

Block-oriented system modelling allows to define physically meaningful connection points between logically separated parts of a system. This work presents a class of systems in block oriented structure, which allow to apply a simple way of databased modelling. The definition of the class via a few key properties is given, as well as a suitable identification approach. Afterwards it is shown, that the very common system of a hydraulic motion control with servo pumps fits into this system class and the presented method is applied and verified in a simulation example.
Symbolic Analysis Of Higher-Order Side Channel Countermeasures (2016)

In this paper, we deal with the problem of efficiently assessing the higher order vulnerability of a hardware cryptographic circuit. Our main concern is to provide methods that allow a circuit designer to detect early in the design cycle if the implementation of a Boolean-additive masking countermeasure does not hold up to the required protection order. To achieve this goal, we promote the search for vulnerabilities from a statistical problem to a purely symbolical one and then provide a method for reasoning about this new symbolical interpretation. Eventually we show, with a synthetic example, how the proposed conceptual tool can be used for exploring the vulnerability space of a cryptographic primitive.
Heterogeneous memory management for 3D-DRAM and external DRAM with QoS (2013)

This paper presents an innovative memory management approach to utilize both 3D-DRAM and external DRAM (ex-DRAM). Our approach dynamically allocates and relocates memory blocks between the 3D-DRAM and the ex-DRAM to exploit the high memory bandwidth and the low memory latency of the 3D-DRAM as well as the high capacity and the low cost of the ex-DRAM. Our simulation shows that in workloads that are not memory intensive, our memory management technique transfers all active memory blocks to the 3D-DRAM which runs faster than the ex-DRAM. In memory intensive workloads, our memory management technique utilizes both the 3D-DRAM and the ex-DRAM to increase the memory bandwidth to alleviate bandwidth congestion. Our approach supports Quality of Service (QoS) for “latency sensitive”, “bandwidth sensitive”, and “insensitive” applications. To improve the performance and satisfy a certain level of QoS, memory blocks of different application types are allocated differently. Compared to the scratchpad memory management mechanism, the average memory access latency of our approach decreases by 19% and 23%, while performance improves by up to 5% and 12% in single threaded benchmarks and multi-threaded benchmarks respectively. Moreover, using our approach, applications do not need to manage memory explicitly like in the scratchpad case. Our memory block relocation comes with negligible performance overhead, particularly for applications which have high spatial memory locality.
Metabolic remodeling of white adipose tissue in obesity (2014)

Adipose tissue metabolism is a critical regulator of adiposity and whole body energy expenditure; however, metabolic changes that occur in white adipose tissue (WAT) with obesity remain unclear. The purpose of this study was to understand the metabolic and bioenergetic changes occurring in WAT with obesity. Wild-type (C57BL/6J) mice fed a high-fat diet (HFD) showed significant increases in whole body adiposity, had significantly lower V̇(O₂), V̇(CO₂), and respiratory exchange ratios, and demonstrated worsened glucose and insulin tolerance compared with low-fat-fed mice. Metabolomic analysis of WAT showed marked changes in lipid, amino acid, carbohydrate, nucleotide, and energy metabolism. Tissue levels of succinate and malate were elevated, and metabolites that could enter the Krebs cycle via anaplerosis were mostly diminished in high-fat-fed mice, suggesting altered mitochondrial metabolism. Despite no change in basal oxygen consumption or mitochondrial DNA abundance, citrate synthase activity was decreased by more than 50%, and responses to FCCP were increased in WAT from mice fed a high-fat diet. Moreover, Pgc1a was downregulated and Cox7a1 upregulated after 6 wk of HFD. After 12 wk of high-fat diet, the abundance of several proteins in the mitochondrial respiratory chain or matrix was diminished. These changes were accompanied by increased Parkin and Pink1, decreased p62 and LC3-I, and ultrastructural changes suggestive of autophagy and mitochondrial remodeling. These studies demonstrate coordinated restructuring of metabolism and autophagy that could contribute to the hypertrophy and whitening of adipose tissue in obesity.
Development of Dosimetric Verification System for Patient-Specific Quality Assurance of High-Dose-Rate Brachytherapy (2021)

<b>Purpose:</b> The aim of this study was to develop a dosimetric verification system (DVS) using a solid phantom for patient-specific quality assurance (QA) of high-dose-rate brachytherapy (HDR-BT). <b>Methods:</b> The proposed DVS consists of three parts: dose measurement, dose calculation, and analysis. All the dose measurements were performed using EBT3 film and a solid phantom. The solid phantom made of acrylonitrile butadiene styrene (ABS, density = 1.04 g/cm<sup>3</sup>) was used to measure the dose distribution. To improve the accuracy of dose calculation by using the solid phantom, a conversion factor [CF(r)] according to the radial distance between the water and the solid phantom material was determined by Monte Carlo simulations. In addition, an independent dose calculation program (IDCP) was developed by applying the obtained CF(r). To validate the DVS, dosimetric verification was performed using gamma analysis with 3% dose difference and 3 mm distance-to-agreement criterion for three simulated cases: single dwell position, elliptical dose distribution, and concave elliptical dose distribution. In addition, the possibility of applying the DVS in the high-dose range (up to 15 Gy) was evaluated. <b>Results:</b> The CF(r) between the ABS and water phantom was 0.88 at 0.5 cm. The factor gradually increased with increasing radial distance and converged to 1.08 at 6.0 cm. The point doses 1 cm below the source were 400 cGy in the treatment planning system (TPS), 373.73 cGy in IDCP, and 370.48 cGy in film measurement. The gamma passing rates of dose distributions obtained from TPS and IDCP compared with the dose distribution measured by the film for the simulated cases were 99.41 and 100% for the single dwell position, 96.80 and 100% for the elliptical dose distribution, 88.91 and 99.70% for the concave elliptical dose distribution, respectively. For the high-dose range, the gamma passing rates in the dose distributions between the DVS and measurements were above 98% and higher than those between TPS and measurements. <b>Conclusion:</b> The proposed DVS is applicable for dosimetric verification of HDR-BT, as confirmed through simulated cases for various doses.
Abstract 19676: A Positive Genotype Predicts Clinical Outcomes in a Large Cohort With Dilated Cardiomyopathy (2017)

Introduction: Expansion of genetic testing in Dilated Cardiomyopathy (DCM) has increased mutation detection in patients. Nevertheless, genotype-phenotype correlations are still poorly understood. Hypothesis: To explore the genetic landscape of a large DCM cohort, assessing the effect of carrier status and association between specific genotypes and outcomes. Methods: Four hundred eighty-seven patients with available genetic testing analysis were analyzed and grouped into “gene clusters” with similar functions. Primary prognostic measures included all causes of mortality, heart transplantation or ventricular assist device implantation (D/HTx/VAD). Two secondary end-points were also considered: heart failure (HF)-related death/HTx/VAD (DHF/HTx/VAD) and sudden death (SCD)/major ventricular arrhythmias (MVA). Results: A total of 186 pathogenic/likely pathogenic variants were found in 180 patients (37%). The genetic clusters identified were: 55 (11%) TTNtv; 19 (4%) LMNA; 24 (5%) Structural Cytoskeleton-Z Disk g...