gebhart/patrepeval huggingface dataset:
Arrestin domain-containing 3 (Arrdc3) modulates insulin action and glucose metabolism in liver (2020)

Insulin action in the liver is critical for glucose homeostasis through regulation of glycogen synthesis and glucose output. Arrestin domain-containing 3 (<i>Arrdc3</i>) is a member of the α-arrestin family previously linked to human obesity. Here, we show that <i>Arrdc3</i> is differentially regulated by insulin in vivo in mice undergoing euglycemic-hyperinsulinemic clamps, being highly up-regulated in liver and down-regulated in muscle and fat. Mice with liver-specific knockout (KO) of the insulin receptor (IR) have a 50% reduction in <i>Arrdc3</i> messenger RNA, while, conversely, mice with liver-specific KO of <i>Arrdc3</i> (L-<i>Arrdc3</i> KO) have increased IR protein in plasma membrane. This leads to increased hepatic insulin sensitivity with increased phosphorylation of FOXO1, reduced expression of PEPCK, and increased glucokinase expression resulting in reduced hepatic glucose production and increased hepatic glycogen accumulation. These effects are due to interaction of ARRDC3 with IR resulting in phosphorylation of ARRDC3 on a conserved tyrosine (Y382) in the carboxyl-terminal domain. Thus, <i>Arrdc3</i> is an insulin target gene, and ARRDC3 protein directly interacts with IR to serve as a feedback regulator of insulin action in control of liver metabolism.
A role for a lithium-inhibited Golgi nucleotidase in skeletal development and sulfation (2008)

Sulfation is an important biological process that modulates the function of numerous molecules. It is directly mediated by cytosolic and Golgi sulfotransferases, which use 3'-phosphoadenosine 5'-phosphosulfate to produce sulfated acceptors and 3'-phosphoadenosine 5'-phosphate (PAP). Here, we identify a Golgi-resident PAP 3'-phosphatase (gPAPP) and demonstrate that its activity is potently inhibited by lithium in vitro. The inactivation of gPAPP in mice led to neonatal lethality, lung abnormalities resembling atelectasis, and dwarfism characterized by aberrant cartilage morphology. The phenotypic similarities of gPAPP mutant mice to chondrodysplastic models harboring mutations within components of the sulfation pathway lead to the discovery of undersulfated chondroitin in the absence of functional enzyme. Additionally, we observed loss of gPAPP leads to perturbations in the levels of heparan sulfate species in lung tissue and whole embryos. Our data are consistent with a model that clearance of the nucleotide product of sulfotransferases within the Golgi plays an important role in glycosaminoglycan sulfation, provide a unique genetic basis for chondrodysplasia, and define a function for gPAPP in the formation of skeletal elements derived through endochondral ossification.
Model-Based Machine Learning for Communications (2021)

We present an introduction to model-based machine learning for communication systems. We begin by reviewing existing strategies for combining model-based algorithms and machine learning from a high level perspective, and compare them to the conventional deep learning approach which utilizes established deep neural network (DNN) architectures trained in an end-to-end manner. Then, we focus on symbol detection, which is one of the fundamental tasks of communication receivers. We show how the different strategies of conventional deep architectures, deep unfolding, and DNN-aided hybrid algorithms, can be applied to this problem. The last two approaches constitute a middle ground between purely model-based and solely DNN-based receivers. By focusing on this specific task, we highlight the advantages and drawbacks of each strategy, and present guidelines to facilitate the design of future model-based deep learning systems for communications.
Advances in Quantum-Dot-Based Displays (2020)

In terms of their use in displays, quantum dots (QDs) exhibit several advantages, including high illumination efficiency and color rendering, low-cost, and capacity for mass production. Furthermore, they are environmentally friendly. Excellent luminescence and charge transport properties of QDs led to their application in QD-based light-emitting diodes (LEDs), which have attracted considerable attention in display and solid-state lighting applications. In this review, we discuss the applications of QDs which are used on color conversion filter that exhibit high efficiency in white LEDs, full-color micro-LED devices, and liquid-type structure devices, among others. Furthermore, we discuss different QD printing processes and coating methods to achieve the full-color micro-LED. With the rise in popularity of wearable and see-through red, green, and blue (RGB) full-color displays, the flexible substrate is considered as a good potential candidate. The anisotropic conductive film method provides a small controllable linewidth of electrically conductive particles. Finally, we discuss the advanced application for flexible full-color and highly efficient QD micro-LEDs. The general conclusion of this study also involves the demand for a more straightforward QD deposition technique, whose breakthrough is expected.
Benchmark dose analyses of multiple genetic toxicity endpoints permit robust, cross-tissue comparisons of MutaMouse responses to orally delivered benzo[a]pyrene (2017)

Genetic damage is a key event in tumorigenesis, and chemically induced genotoxic effects are a human health concern. Although genetic toxicity data have historically been interpreted using a qualitative screen-and-bin approach, there is increasing interest in quantitative analysis of genetic toxicity dose-response data. We demonstrate an emerging use of the benchmark dose (BMD)-approach for empirically ranking cross-tissue sensitivity. Using a model environmental carcinogen, we quantitatively examined responses for four genetic damage endpoints over an extended dose range, and conducted cross-tissue sensitivity rankings using BMD<sub>100</sub> values and their 90% confidence intervals (CIs). MutaMouse specimens were orally exposed to 11 doses of benzo[a]pyrene. DNA adduct frequency and lacZ mutant frequency (MF) were measured in up to 8 tissues, and Pig-a MF and micronuclei (MN) were assessed in immature (RETs) and mature red blood cells (RBCs). The cross-tissue BMD pattern for lacZ MF is similar to that observed for DNA adducts, and is consistent with an oral route-of-exposure and differences in tissue-specific metabolism and proliferation. The lacZ MF BMDs were significantly correlated with the tissue-matched adduct BMDs, demonstrating a consistent adduct conversion rate across tissues. The BMD CIs, for both the Pig-a and the MN endpoints, overlapped for RETs and RBCs, suggesting comparable utility of both cell populations for protracted exposures. Examination of endpoint-specific response maxima illustrates the difficulty of comparing BMD values for a fixed benchmark response across endpoints. Overall, the BMD-approach permitted robust comparisons of responses across tissues/endpoints, which is valuable to our mechanistic understanding of how benzo[a]pyrene induces genetic damage.
Coexpression of Interleukin-12 Chains by a Self-Splicing Vector Increases the Protective Cellular Immune Response of DNA andMycobacterium bovisBCG Vaccines againstMycobacterium tuberculosis (2002)

More effective vaccines against Mycobacterium tuberculosis may contribute to the control of this major human pathogen. DNA vaccines encoding single mycobacterial proteins stimulate antimycobacterial T-cell responses and induce partial protection against M. tuberculosis in animal models. The protective efficacy of these vaccines encoding a single antigen, however, has been less than that afforded by the current vaccine, Mycobacterium bovis bacillus Calmette-Guérin (BCG). The heterodimeric cytokine interleukin-12 (IL-12) potentiates the induction and maintenance of the type 1 helper T-cell response. We have developed a novel self-splicing vector based on the 2A protein of foot-and-mouth disease virus that permits the coordinate expression of both chains of IL-12 (p2AIL12). Coimmunization with this vector and DNA expressing M. tuberculosis antigen 85B or MPT64 enhanced the specific lymphocyte proliferative response and increased the frequency of specific gamma interferon-secreting T cells against the whole protein and a defined CD8(+) T-cell epitope on MPT64. Further, coimmunizing with p2AIL12 significantly increased the protective efficacy of DNA-85 in the lung against an aerosol challenge with M. tuberculosis to the level achieved with BCG. Therefore, codelivery of an IL-12-secreting plasmid may be a potent strategy for enhancing the protective efficacy of vaccines against M. tuberculosis.
Time Resolved Bit Error Rate Analysis of a Fast Switching Tunable Laser for Use in Optically Switched Networks (2012)

We investigate the use of different direct detection modulation formats in a wavelength switched optical network. We find the minimum time it takes a tunable sampled grating distributed Bragg reflector laser to recover after switching from one wavelength channel to another for different modulation formats. The recovery time is investigated utilizing a field programmable gate array which operates as a time resolved bit error rate detector. The detector offers 93 ps resolution operating at 10.7&#x00A0;Gb/s and allows for all the data received to contribute to the measurement, allowing low bit error rates to be measured at high speed. The recovery times for 10.7&#x00A0;Gb/s non-return-to-zero on&#x2013;off keyed modulation, 10.7&#x00A0;Gb/s differentially phase shift keyed signal and 21.4&#x00A0;Gb/s differentially quadrature phase shift keyed formats can be as low as 4&#x00A0;ns, 7&#x00A0;ns and 40&#x00A0;ns, respectively. The time resolved phase noise associated with laser settling is simultaneously measured for 21.4&#x00A0;Gb/s differentially quadrature phase shift keyed data and it shows that the phase noise coupled with frequency error is the primary limitation on transmitting immediately after a laser switching event.
MiR-200c-3p maintains stemness and proliferative potential in adipose-derived stem cells by counteracting senescence mechanisms (2021)

Adipose-derived mesenchymal stem cells (ASCs) are promising therapeutic tools in regenerative medicine because they possess self-renewal, differentiation and immunomodulatory capacities. After isolation, ASCs are passaged multiple times in vitro passages to obtain a sufficient amount of cells for clinical applications. During this time-consuming procedure, ASCs become senescent and less proliferative, compromising their clinical efficacy. Here, we sought to investigate how in vitro passages impact ASC proliferation/senescence and expression of immune regulatory proteins. MicroRNAs are pivotal regulators of ASC physiology. Particularly, miR-200c is known to maintain pluripotency and targets the immune checkpoint Programmed death-ligand 1 (PD-L1). We therefore investigated its involvement in these critical characteristics of ASCs during in vitro passages. We found that when transiently expressed, miR-200c-3p promotes proliferation, maintains stemness, and contrasts senescence in late passaged ASCs. Additionally, this miRNA modulates PD-L1 and Indoleamine 2,3-Dioxygenase (IDO1) expression, thus most likely interfering with the immunoregulatory capacity of ASCs. Based on our results, we suggest that expression of miR-200c-3p may prime ASC towards a self-renewing phenotype by improving their in vitro expansion. Contrarily, its inhibition is associated with senescence, reduced proliferation and induction of immune regulators. Our data underline the potential use of miR-200c-3p as a switch for ASCs reprogramming and their clinical application.
In vivo whole brain microvascular imaging in mice using transcranial 3D Ultrasound Localization Microscopy (2022)

This study was supported by the European Research Council under the European Union's Seventh Framework Program (FP/2007-2013) / ERC Grant Agreement n° 311025 and by the Fondation Bettencourt-Schueller under the program "Physics for Medicine". We acknowledge the ART (Technological Research Accelerator) biomedical ultrasound program of INSERM.
Advanced MRI of articular cartilage (2011)

Musculoskeletal MRI is advancing rapidly, with innovative technology and significant potential for immediate clinical impact. In particular, cartilage imaging has become a topic of increasing interest as our aging population develops diseases such as osteoarthritis. Advances in MRI hardware and software have led to increased image quality and tissue contrast. Additional developments have allowed the assessment of cartilage macromolecular content, which may be crucial to the early detection of musculoskeletal diseases. This comprehensive article considers current morphological and physiological cartilage imaging techniques, their clinical applications, and their potential to contribute to future improvements in the imaging of cartilage.
A framework for actuator placement in large scale power systems: Minimal strong structural controllability (2013)

This paper addresses the problem of minimal placement of actuators in large-scale linear time invariant (LTI) systems, such as large-scale power systems, for dynamic controller design. A novel sufficient and necessary condition to ensure a strong structurally controllable (SSC) system is proposed. Specifically, the paper addresses the problem of obtaining the minimal number of dedicated inputs, i.e., inputs which actuate only a single state variable, and the respective state variables they should be assigned to, such that the LTI system is SSC. In addition, an efficient and scalable algorithm, with polynomial implementation complexity, to achieve such minimal placement of dedicated inputs is proposed. An illustration of the proposed design methodology is provided on the IEEE 5-bus test system, thereby identifying the minimal number of physical state variables to be actuated for ensuring strong structural controllability.
Phage Display Technology as a Powerful Platform for Antibody Drug Discovery (2021)

Antibody drugs with a high affinity and specificity are effective and safe for intractable diseases, such as cancers and autoimmune diseases. Furthermore, they have played a central role in drug discovery, currently accounting for eight of the top 20 pharmaceutical products worldwide by sales. Forty years ago, clinical trials on antibody drugs that were thought to be a magic bullet failed, partly due to the immunogenicity of monoclonal antibodies produced in mice. The recent breakthrough in antibody drugs is largely because of the contribution of phage display technology. Here, we reviewed the importance of phage display technology as a powerful platform for antibody drug discovery from various perspectives, such as the development of human monoclonal antibodies, affinity enhancement of monoclonal antibodies, and the identification of therapeutic targets for antibody drugs.
New loci for body fat percentage reveal link between adiposity and cardiometabolic disease risk (2020)

To increase our understanding of the genetic basis of adiposity and its links to cardiometabolic disease risk, we conducted a genome-wide association meta-analysis of body fat percentage (BF%) in up to 100,716 individuals. Twelve loci reached genome-wide significance (P<5 × 10−8), of which eight were previously associated with increased overall adiposity (BMI, BF%) and four (in or near COBLL1/GRB14, IGF2BP1, PLA2G6, CRTC1) were novel associations with BF%. Seven loci showed a larger effect on BF% than on BMI, suggestive of a primary association with adiposity, while five loci showed larger effects on BMI than on BF%, suggesting association with both fat and lean mass. In particular, the loci more strongly associated with BF% showed distinct cross-phenotype association signatures with a range of cardiometabolic traits revealing new insights in the link between adiposity and disease risk.
Fiber Bundle Image Relay for Monocentric Lenses (2014)

We characterize the spatially variant transfer function of a fiber coupled monocentric lens imager, and show image processing techniques to reduce defects caused by the fiber bundle, improve image uniformity and increase spatial resolution.
Prevention of experimental allergic encephalomyelitis (EAE) in the SJL/J mouse by whole body ultraviolet irradiation. (1984)

The cellular requirements for the in vivo induction of experimental allergic encephalomyelitis (EAE) were investigated in the SJL/J mouse. Exposure of mice to whole body ultraviolet (UV) irradiation, a treatment that has been shown in other systems to interfere selectively with antigen-presenting cell function, prevented the development of clinical and pathologic signs of acute EAE. Splenic T cells from UV-treated animals did not adoptively transfer resistance to EAE, making it unlikely that UV irradiation resulted in the generation of a specific suppressor cell population responsible for protection from EAE. UV irradiation was effective in preventing EAE when administered before initial immunization; UV irradiation was ineffective in modifying ongoing EAE or in preventing relapses of EAE induced by reimmunization. In additional experiments, adult thymectomized, lethally x-irradiated mice reconstituted with syngeneic marrow cells depleted of mature T lymphocytes were found to be resistant to the induction of EAE. Susceptibility was restored by the addition of splenic T cells, demonstrating that EAE induction is T cell-dependent in the mouse. The prevention of an experimental autoimmune demyelinating disease by whole body UV irradiation suggests that interference with the function of Ia-bearing accessory cells may represent an approach for immunotherapy in autoimmune disorders.
Image Sensing Technology. Control System for Optical Image Stabilization. (2002)

A control system for stabilizing the image in camcorders has been developed. Optimization of the control system through computer simulation maximized the effect of compensating for image fluctuations, resulting in a high image-stabilization rate (-37dB). The results of computer simulation were consistent with those of experiments using trial models, resulting in reduced development time. Establishment of this simulation technology has made it easier to adjust the image-stabilization characteristics. The load placed on the control microprocessor was reduced by reducing the drive frequency of the image-stabilization lens. As a result, camera control and the image-stabilization process are both implemented in a one-chip microprocessor, which prevents enlargement of the control circuit.
Introduction to the Special Issue on Networking and Information Theory (2006)

NETWORKING and information theory have long promised interesting connections. Yet, for many years the most fruitful exchange between these two fields lay in the
Disparity estimation using a region-dividing technique and energy-based regularization (2004)

A two-stage algorithm is proposed for locating smooth and detailed disparity vector fields in a stereo image pair. The algorithm consists of hierarchical disparity estimation using a region-dividing technique and edge-preserving regularization. The hierarchical region-dividing disparity estimation increases the efficiency and reliability of the estimation process. At the second stage, the vector fields are regularized with an energy model that produces smooth fields while preserving discontinuities resulting from object boundaries. The minimization problem is addressed by solving a corresponding partial differential equation using a finite-difference method. Experiments show that the proposed algorithm provides accurate and spatially correlated disparity vector fields in various types of stereo images, even in the case of images with large displacements.
MHC class II restricted recognition of FMDV peptides by bovine T cells. (1991)

A putative synthetic vaccine for foot-and-mouth disease (FMDV15) has proved less successful in a host species, cattle, than predicted by results in a small-animal model. Possible reasons for this include non-recognition by T cells influenced by major histocompatibility complex (MHC)-linked immune response gene control. It is now possible to type for human leucocyte antigen (HLA) DR-like bovine MHC (BoLA) class II polymorphisms with a one-dimensional isoelectric focusing (IEF) technique. Using this method 14 unrelated cattle were selected with eight different BoLA class II IEF types. After immunization with FMDV15, 13 cattle generated a T-cell response to FMDV15. However, the fine specificity and magnitude of the response was related to BoLA class II type. The non-response by one animal and low response by two other animals were associated with two of the BoLA class II types. Response to the region 149-158 was immunodominant and animals which did not respond to this region had low responses to the whole peptide. Using FMDV-specific T-cell lines five BoLA class II types associated with responder animals were able to present FMDV15 in an MHC class II-restricted fashion, indicating that this peptide is capable of binding to different MHC class II molecules and may account for the broad response observed. The restriction patterns of the lines indicated that the IEF method does not distinguish all functional polymorphisms. At least two of the IEF-defined types could each be split into two distinct specificities and revealed that the three sets of animals with identical IEF types in fact expressed distinct restriction elements.
Macromol. Symp. 281 (2009)

Cover: The “48 th Microsymposium: Polymer Colloids: From Design to Biomedical and Industrial Applications” was held in Prague in July 20–24, 2008. The covers shows the stepwise preparation of structured magnetic latex particles and is from the article by A. Elaissari, p. 14.
PepS: An Innovative Microfluidic Device for Bedside Whole Blood Processing before Plasma Proteomics Analyses (2020)

Immunoassays have been used for decades in clinical laboratories to quantify proteins in serum and plasma samples. However, their limitations make them inappropriate in some cases. Recently, mass spectrometry (MS) based proteomics analysis has emerged as a promising alternative method when seeking to assess panels of protein biomarkers with a view to providing protein profiles to monitor health status. Up to now, however, translation of MS-based proteomics to the clinic has been hampered by its complexity and the substantial time and human resources necessary for sample preparation. Plasma matrix is particularly tricky to process as it contains more than 3000 proteins with concentrations spanning an extreme dynamic range (1010). To address this preanalytical challenge, we designed a microfluidic device (PepS) automating and accelerating blood sample preparation for bottom-up MS-based proteomics analysis. The microfluidic cartridge is operated through a dedicated compact instrument providing fully automated fluid processing and thermal control. In less than 2 h, the PepS device allows bedside plasma separation from whole blood, volume metering, depletion of albumin, protein digestion with trypsin, and stabilization of tryptic peptides on solid-phase extraction sorbent. For this first presentation, the performance of the PepS device was assessed using discovery proteomics and targeted proteomics, detecting a panel of three protein biomarkers routinely assayed in clinical laboratories (alanine aminotransferase 1, C-reactive protein, and myoglobin). This innovative microfluidic device and its associated instrumentation should help to streamline and simplify clinical proteomics studies.