gebhart/patrepeval huggingface dataset:
Trafficking and localization studies of recombinant alpha1, 3- fucosyltransferase VI stably expressed in CHO cells (1998)

Peripheral alpha1,3-fucosylation of glycans occurs by the action of either one of five different alpha1,3-fucosyltransferases (Fuc-Ts) cloned to date. Fuc-TVI is one of the alpha1,3-fucosyltransferases which is capable to synthesize selectin ligands. The major alpha1, 3-fucosyltransferase activity in human plasma is encoded by the gene for fucosyltransferase VI, which presumably originates from liver cells. While the sequence, chromosomal localization, and kinetic properties of Fuc-TVI are known, immunocytochemical localization and trafficking studies have been impossible because of the lack of specific antibodies. Here we report on the development and characterization of a peptide-specific polyclonal antiserum monospecific to Fuc-TVI and an antiserum to purified soluble recombinant Fuc-TVI crossreactive with Fuc-TIII and Fuc-TV. Both antisera were applied for immunodetection in stably transfected CHO cells expressing the full-length form of this enzyme (CHO clone 61/11). Fuc-TVI was found to be a resident protein of the Golgi apparatus. In addition, more than 30% of cell-associated and released enzyme activity was found in the medium. Maturation and release of Fuc-TVI was analyzed in metabolically labeled CHO 61/11 cells followed by immunoprecipitation. Fuc-TVI occurred in two forms of 47 kDa and 43 kDa bands, while the secreted form was detected as a 43 kDa. These two different intracellular forms arose by posttranslational modification, as shown by pulse-chase experiments. Fuc-TVI was released to the supernatant by proteolytic cleavage as a partially endo-H resistant glycoform.
Decoding inflammation, its causes, genomic responses, and emerging countermeasures (2019)

Inflammation is the mechanism of diseases caused by microbial, autoimmune, allergic, metabolic and physical insults that produce distinct types of inflammatory responses. This aetiologic view of inflammation informs its classification based on a cause-dependent mechanism as well as a cause-directed therapy and prevention. The genomic era ushered in a new understanding of inflammation by highlighting the cell's nucleus as the centre of the inflammatory response. Exogenous or endogenous inflammatory insults evoke genomic responses in immune and non-immune cells. These genomic responses depend on transcription factors, which switch on and off a myriad of inflammatory genes through their regulatory networks. We discuss the transcriptional paradigm of inflammation based on denying transcription factors' access to the nucleus. We present two approaches that control proinflammatory signalling to the nucleus. The first approach constitutes a novel intracellular protein therapy with bioengineered physiologic suppressors of cytokine signalling. The second approach entails control of proinflammatory transcriptional cascades by targeting nuclear transport with a cell-penetrating peptide that inhibits the expression of 23 out of the 26 mediators of inflammation along with the nine genes required for metabolic responses. We compare these emerging anti-inflammatory countermeasures to current therapies. The transcriptional paradigm of inflammation offers nucleocentric strategies for microbial, autoimmune, metabolic, physical and other types of inflammation afflicting millions of people worldwide.
Convolutional Architecture Exploration for Action Recognition and Image Classification (2015)

Convolutional Architecture for Fast Feature Encoding (CAFFE) [11] is a software package for the training, classifying, and feature extraction of images. The UCF Sports Action dataset is a widely used machine learning dataset that has 200 videos taken in 720x480 resolution of 9 different sporting activities: diving, golf, swinging, kicking, lifting, horseback riding, running, skateboarding, swinging (various gymnastics), and walking. In this report we report on a caffe feature extraction pipeline of images taken from the videos of the UCF Sports Action dataset. A similar test was performed on overfeat, and results were inferior to caffe. This study is intended to explore the architecture and hyper parameters needed for effective static analysis of action in videos and classification over a variety of image datasets.
An IEEE 802.11ax Interference-Aware MAC Queue (2020)

The first wave of IEEE 802.11ax capable devices have already hit the market, aiming at enhancing the Quality of Experience (QoE) for the users in dense deployments, by enabling novel features to improve throughput and spectrum efficiency. One of these features is Spatial Reuse (SR) mechanism, which is introduced for coping with the exposed node problem. Under the SR operation, nodes belonging on different Basic Service Sets (BSSs) are allowed to initiate concurrent transmissions, utilising the spectrum resources and improving throughput. However, the main challenge for this enabling technology is the increased interference level that is introduced by the concurrent transmissions. Even though, there are a few algorithms available in the literature that study this issue for the IEEE 802.11ax, in this article we look into that issue from a different perspective. We propose an Interference-Aware scheduler for the Medium Access Control (MAC) queue based on the interference level observed and other characteristics that can be obtained from the channel and the inter-BSS frames. This paper considers only downlink traffic for the evaluation of the proposed scheme with simulation-based results showing a clear performance improvement of up to 34% against the legacy First-In First-Out (FIFO) MAC queue by introducing new policies and leave room for further exploration and enhancements.
Protein Interacting with C-Kinase 1/Protein Kinase Cα-Mediated Endocytosis Converts Netrin-1-Mediated Repulsion to Attraction (2006)

In vertebrates, the receptor families deleted in colorectal cancer (DCC) and UNC5 mediate responses to the bifunctional guidance cue netrin-1. DCC mediates attraction, whereas a complex of DCC and UNC5 mediates repulsion. Thus, a primary determinant of the responsiveness of an axon to netrin-1 is the presence or absence of UNC5 family members on the cell surface. Currently, little is known about the role of receptor trafficking in regulating neuronal responses to netrin-1. We show that protein interacting with C-kinase 1 (PICK1) recruits activated protein kinase Calpha (PKCalpha) to MycUNC5A at the plasma membrane, stimulating its endocytosis. We identify two PKCalpha phosphorylation sites at serines 408 and 587, as well as dileucine internalization motifs, which are required for this endocytosis. We find that PKCalpha-stimulated internalization of UNC5A alters the functional response of developing hippocampal axons to netrin-1, preventing UNC5A-mediated growth cone collapse and converting netrin-1-stimulated chemorepulsion to attraction. To address whether this conversion in axonal response occurs in neurons expressing endogenous levels of UNC5, we show that mouse cerebellar granule axons exhibit chemorepulsion in a netrin-1 gradient and that this chemorepulsion is converted to chemoattraction after PKCalpha activation. We demonstrate that this repulsion depends on UNC5A because Unc5a-/- axons are not repelled and show this conversion depends on PICK1 because PICK1-/- axons are not converted to chemoattraction after PKCalpha activation. Together, these data provide a potential mechanism to explain how developing neurons alter their responsiveness to netrin-1 at intermediate choice points as they navigate to their targets.
Surface energy modification of a Na-mordenite thin layer treated by an alkaline solution (2015)

International audience
Trusted Computing in Mobile Action (2006)

Due to the convergence of various mobile access technologies like UMTS, WLAN, and WiMax the need for a new supporting infrastructure arises. This infrastructure should be able to support more efficient ways to authenticate users and devices, potentially enabling novel services based on the security provided by the infrastructure. In this paper we exhibit some usage scenarios from the mobile domain integrating trusted computing, which show that trusted computing offers new paradigms for implementing trust and by this enables new technical applications and business scenarios. The scenarios show how the traditional boundaries between technical and authentication domains become permeable while a high security level is maintained.
Supplementary Materials and Methods from ZIC5 Drives Melanoma Aggressiveness by PDGFD-Mediated Activation of FAK and STAT3 (2023)

&lt;p&gt;Supplementary Materials and Methods of plasmids, siRNA, shRNA, transfections, western blot analysis, reagents, luciferase reporter assays, chromatin immunoprecipitation, immunocytochemistry, immunohistochemistry, scratch assays, cell proliferation assays, cell cycle analysis, quantitative real-time PCR, migration and invasion assays, animal experiments, microarray analysis, apoptosis assays, and generation of vemurafenib-resistant cell lines.&lt;/p&gt;
Noninvasive evaluation of renal pH homeostasis after ischemia reperfusion injury by CEST‐MRI (2017)

Acute kidney injury (AKI) in mice caused by sustained ischemia followed by reperfusion is associated with acute tubular necrosis and renal dysfunctional blood flow. Although the principal role of the kidney is the maintenance of acid-base balance, current imaging approaches are unable to assess this important parameter, and clinical biomarkers are not robust enough in evaluating the severity of kidney damage. Therefore, novel noninvasive imaging approaches are needed to assess the acid-base homeostasis in vivo. This study investigates the usefulness of MRI-chemical exchange saturation transfer (CEST) pH imaging (through iopamidol injection) in characterizing moderate and severe AKI in mice following unilateral ischemia reperfusion injury. Moderate (20 min) and severe (40 min) ischemia were induced in Balb/C mice, which were imaged at several time points thereafter (Days 0, 1, 2, 7). A significant increase of renal pH values was observed as early as one day after the ischemia reperfusion damage for both moderate and severe ischemia. MRI-CEST pH imaging distinguished the evolution of moderate from severe AKI. A recovery of normal renal pH values was observed for moderate AKI, whereas a persisting renal pH increase was observed for severe AKI on Day 7. Renal filtration fraction was significantly lower for clamped kidneys (0.54-0.57) in comparison to contralateral kidneys (0.84-0.86) following impairment of glomerular filtration. The severe AKI group showed a reduced filtration fraction even after 7 days (0.38 for the clamped kidneys). Notably, renal pH values were significantly correlated with the histopathological score. In conclusion, MRI-CEST pH mapping is a valid tool for the noninvasive evaluation of both acid-base balance and renal filtration in patients with ischemia reperfusion injury.
Source Data for "Tuning charge transport dynamics via clustering of doping in organic semiconductor thin films" (2019)

README.txt and source data files included in one .zip file
Nuclear Spin Gyroscope based on the Nitrogen Vacancy Center in Diamond (2020)

A rotation sensor is one of the key elements of inertial navigation systems and compliments most cellphone sensor sets used for various applications. Currently, inexpensive and efficient solutions are mechanoelectronic devices, which nevertheless lack long-term stability. Realization of rotation sensors based on spins of fundamental particles may become a drift-free alternative to such devices. Here, we carry out a proof-of-concept experiment, demonstrating rotation measurements on a rotating setup utilizing nuclear spins of an ensemble of NV centers as a sensing element with no stationary reference. The measurement is verified by a commercially available MEMS gyroscope.
Differential Targeting and Shifts in the Immunodominance of Epstein‐Barr Virus–Specific CD8 and CD4 T Cell Responses during Acute and Persistent Infection (2005)

The evolution of Epstein-Barr virus (EBV)-specific T cell responses that occurs during the acute and persistent stages of infection remains poorly characterized despite its importance for developing immune interventions for EBV-associated disorders. This study assessed T cell responses to 113 EBV-derived epitopes in 40 subjects with acute or persistent EBV infection. Although no significant differences were seen in the breadth of CD8 and CD4 T cell responses, their magnitude differed significantly over time; acutely infected subjects generated especially strong responses to lytic viral antigens. The cross-sectional shift in immunodominance was also confirmed in subjects followed longitudinally from acute to persistent infection. In addition, human leukocyte antigen-matched siblings with discordant histories of symptomatic EBV infection showed no significant differences in their response patterns, suggesting that symptomatic EBV infection does not lead to unique persistent-stage responses. These data provide an assessment of immunodominance patterns and guidance for developing immunotherapeutic interventions for EBV-associated disorders.
Measurement of Vector Magnetic Properties of a Non-oriented Electrical Steel Sheet under Shear Stress (2013)

It is well known that magnetic properties of electrical steel sheets are influenced due to mechanical stress strongly. We have been measured residual stress distribution with a X-ray stress measurement device and clarified not only the tensile and compressive stress but also the shear stress in a rotating machine core. In particular, the influence of the shear stress on the magnetic property has not been reported. We try to develop a new measurement system of vector magnetic property under the shear stress. This paper presents a mechanism to apply the shear stress and the measured vector magnetic property of a non-oriented electrical steel sheet under the shear stress. As these results, the difference of the vector magnetic property of the non-oriented electrical steel sheet was obtained according to the shear stress.
Human Nasal Reflexes (2016)

INTRODUCTION The conditions of inhaled air activate trigeminal type A and C afferent neurons. Distinct subpopulations of afferent neurons are presumed to have unique combinations of afferent sensor proteins, sodium, and other ion channels. These are involved in neural depolarization and the spread of the action potential throughout the extensively branched nasal ramification of nerve endings, and transmission to the dorsal root ganglion cell bodies and central nervous system. Some of the branched neurons release neurotransmitters locally in the nasal mucosa to generate the axon response of “neurogenic inflammation.” The axon response in human nasal mucosa leads to glandular secretion without any change in vascular processes. This activation-exocytosis loop is a very rapid onset nasal defense mechanism. Depolarization of dorsal root ganglion cells may alter the amount and identity of sensor proteins and neurotransmitters and so alter the functions of these neurons (“neural plasticity”).
Regularization design for breast lesion detection in penalized maximum likelihood image reconstruction (2012)

Detecting cancerous lesion is a major clinical application in emission tomography. In a previous work, we have shown that penalized maximum likelihood image reconstruction can improve lesion detection at a fixed location by designing a shift-invariant quadratic penalty function. Here we extend this work to detection of tumors at unknown positions. We present a method to design a shift-variant quadratic penalty function that maximizes the detectability of lesions at all possible locations. We conducted computer-based Monte Carlo simulations to compare the optimized shift-variant penalty with the conventional penalty for detecting a breast lesion. Lesion detectability was assessed by a channelized Hotelling observer and human observer. The results showed a statistically significant improvement in lesion detection by using the optimized shift-variant penalty function compared to using the conventional penalty function.
Fatigue Property of High Strength Steel with Artificial Defects under Cyclic Torsion with a Shear Stress Ratio of 0.1 (2018)

In this paper, torsional fatigue tests of high strength spring steel were conducted for bar-shaped specimens with artificial small defects of various sizes at a stress ratio of R＝0.1. The shear fatigue limit decreased with the increase in defect size. The relationship between fatigue limit and the square root of the projected area of the defect was evaluated. The relationship was defined by El Haddad’s short crack correlation substituting an intrinsic defect size for an intrinsic crack depth. The relationship was characterized by the approximate formulation using the parameter; thus, the fatigue limit with a small defect can be accurately estimated by the parameter.
3D motion flow estimation using local all-pass filters (2016)

Fast and accurate motion estimation is an important tool in biomedical imaging applications such as motion compensation and image registration. In this paper, we present a novel algorithm to estimate motion in volumetric images based on the recently developed Local All-Pass (LAP) optical flow framework. The framework is built upon the idea that any motion can be regarded as a local rigid displacement and is hence equivalent to all-pass filtering. Accordingly, our algorithm aims to relate two images, on a local level, using a 3D all-pass filter and then extract the local motion flow from the filter. As this process is based on filtering, it can be efficiently repeated over the whole image volume allowing fast estimation of a dense 3D motion. We demonstrate the effectiveness of this algorithm on both synthetic motion flows and in-vivo MRI data involving respiratory motion. In particular, the algorithm obtains greater accuracy for significantly reduced computation time when compared to competing approaches.
AntBot is able to go home like desert ants (2019)

Designed to move, sense and behave like desert ants, AntBot is a robot able to navigate autonomously without GPS. Fully 3d-printed, this open-source project aims at providing autonomous vehicles with new robust and accurate navigation systems. - submission by Julien Dupeyroux, Stéphane Viollet, Julien R. Serres
Synthesis of 4,5-Bis- and 4,4′,5,5′-Tetrakis(2-hydroxyethylthio) tetrathiafulvalene: The Assembly of Tris- and Pentakis(tetrathiafulvalene) Macromolecules (1994)

Efficient syntheses are reported of the novel pentakis- and tris(tetrathiafulvalene) derivatives 11 and 12, respectively, by esterification of tetraol and diol derivatives 8 and 10 with TTF-carbonyl chloride.
Silencing of Mcl-1 overcomes resistance of melanoma cells against TRAIL-armed oncolytic adenovirus by enhancement of apoptosis (2021)

Arming of oncolytic viruses with tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) has been shown as a viable approach to increase the antitumor efficacy in melanoma. However, melanoma cells may be partially or completely resistant to TRAIL or develop TRAIL resistance, thus counteracting the antitumor efficiency of TRAIL-armed oncolytic viruses. Recently, we found that TRAIL resistance in melanoma cells can be overcome by inhibition of antiapoptotic Bcl-2 protein myeloid cell leukemia 1 (Mcl-1). Here, we investigated whether the cytotoxicity of AdV-TRAIL, an oncolytic adenovirus, which expresses TRAIL after induction by doxycycline (Dox), can be improved in melanoma cells by silencing of Mcl-1. Two melanoma cell lines, the TRAIL-resistant MeWo and the TRAIL-sensitive Mel-HO were investigated. Treatment of both cell lines with AdV-TRAIL resulted in a decrease of cell viability, which was caused by an increase of apoptosis and necrosis. The proapoptotic effects were dependent on induction of TRAIL by Dox and were more pronounced in Mel-HO than in MeWo cells. SiRNA-mediated silencing of Mcl-1 resulted in a further significant decrease of cell viability and a further increase of apoptosis and necrosis in AdV-TRAIL-infected MeWo and Mel-HO cells. However, while in absolute terms, the effects were more pronounced in Mel-HO cells, in relative terms, they were stronger in MeWo cells. These results show that silencing of Mcl-1 represents a suitable approach to increase the cytotoxicity of a TRAIL-armed oncolytic adenovirus in melanoma cells. KEY MESSAGES: • Cytotoxicity of TRAIL-expressing adenovirus can be enhanced by silencing of Mcl-1. • The effect occurs in TRAIL-sensitive and TRAIL-resistant melanoma cells. • Increase of apoptosis is the main mechanism induced by Mcl-1 silencing.
Data from Circulating Levels of Soluble KIT Serve as a Biomarker for Clinical Outcome in Gastrointestinal Stromal Tumor Patients Receiving Sunitinib following Imatinib Failure (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; To evaluate changes in circulating levels of soluble KIT (sKIT) extracellular domain as a potential biomarker for clinical outcome in gastrointestinal stromal tumor patients treated with the multitargeted tyrosine kinase inhibitor sunitinib following imatinib failure in a previously reported phase III study.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; Patients received sunitinib 50 mg/d (&lt;i&gt;n&lt;/i&gt; = 243) or placebo (&lt;i&gt;n&lt;/i&gt; = 118) daily in 6-week cycles (4 weeks on, 2 weeks off treatment). Plasma sKIT levels were sampled every 2 weeks in cycle 1 and on days 1 and 28 of subsequent cycles; analyzed by ELISA; and evaluated using Prentice criteria, Cox proportional hazards models, and proportion of treatment effect (PTE) analysis.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; From 4 weeks on treatment and onward, significant differences were shown between treatment groups (&lt;i&gt;P&lt;/i&gt; &lt; 0.0001) in sKIT level changes from baseline (median levels decreased with sunitinib and increased with placebo). Decreases in sKIT levels were a significant predictor of longer time to tumor progression (TTP). Patients with reduced levels at the end of cycle 2 had a median TTP of 34.3 weeks versus 16.0 weeks for patients with increased levels [hazard ratio, 0.71; 95% confidence interval (95% CI), 0.61-0.83; &lt;i&gt;P&lt;/i&gt; &lt; 0.0001], and changes in sKIT levels replaced treatment as a stronger predictor of TTP (PTE, 0.80; 95% CI, 0.34-3.70), showing even greater surrogacy on cycle 3 day 1 (PTE, 0.98; 95% CI, 0.39-3.40).&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; The results suggest that circulating plasma sKIT levels seem to function as a surrogate marker for TTP in gastrointestinal stromal tumor patients. Additional studies are warranted to confirm and expand these findings. (Clin Cancer Res 2009;15(18):5869–77)&lt;/p&gt;&lt;/div&gt;
A fast method for the calculation of foil winding losses (2015)

This paper introduces a new two-dimensional (2D) modeling approach for the fast calculation of inductor and transformer foil winding losses. The proposed modeling procedure is derived from the Partial Element Equivalent Circuit (PEEC) method, which is originally a full three-dimensional (3D) electromagnetic solution technique. With the presented modifications, the PEEC method can take into account the influence of an air gap fringing field and core material boundaries as well as skin- and proximity effect. A comparison to 2D Finite Element Method (FEM) simulations shows that the developed PEEC-based approach exhibits similar accuracy but shorter calculation times than the classical FEM modeling techniques typically employed for the calculation of non-uniform current distribution within foil windings. The new modeling approach is experimentally verified by calorimetric loss measurements of a gapped foil winding E-core inductor. Due to the fast calculation speed of the new approach, optimizations of inductive components with foil windings over a wide design space are finally possible.