gebhart/patrepeval huggingface dataset:
Local sensing of absolute refractive index during protein-binding using microlasers with spectral encoding (2022)

Multiplexed, specific and sensitive detection of antigens is critical for the rapid and accurate diagnosis of disease and the informed development of personalized treatment plans. Here, we show that polymer microsphere lasers can be used as photonic sensors to monitor and quantify direct surface binding of biomolecules via changes in the refractive index. The unique spectral signature of each individual laser can be used to find their size and effective refractive index which adds a new encoding dimension when compared to conventional fluorescent beads. We utilize antibody-functionalized microlasers to selectively detect protein binding. Different stages of the multilayer surface modification can be resolved, and protein binding is demonstrated for two different proteins, IgG and CRP. Moreover, by continuously monitoring single lasers, we demonstrate the possibility of real-time monitoring of binding dynamics between antigens in solution phase and the immobilized antibodies. For multiplexed detection, the microlasers are employed in a flow cytometer configuration, with fast spectral detection and identification of microlasers with and without antigen binding. We envision that by combining microlasers with well-established surface modification chemistries and flow geometries, the multiplexing ability of microbead immunoassays can be strongly increased while also opening avenues for single cell profiling within heterogenous cell populations.
The Cacna1h mutation in the GAERS model of absence epilepsy enhances T-type Ca2+ currents by altering calnexin-dependent trafficking of Cav3.2 channels (2017)

Low-voltage-activated T-type calcium channels are essential contributors to the functioning of thalamocortical neurons by supporting burst-firing mode of action potentials. Enhanced T-type calcium conductance has been reported in the Genetic Absence Epilepsy Rat from Strasbourg (GAERS) and proposed to be causally related to the overall development of absence seizure activity. Here, we show that calnexin, an endoplasmic reticulum integral membrane protein, interacts with the III-IV linker region of the Ca<sub>v</sub>3.2 channel to modulate the sorting of the channel to the cell surface. We demonstrate that the GAERS missense mutation located in the Ca<sub>v</sub>3.2 III-IV linker alters the Ca<sub>v</sub>3.2/calnexin interaction, resulting in an increased surface expression of the channel and a concomitant elevation in calcium influx. Our study reveals a novel mechanism that controls the expression of T-type channels, and provides a molecular explanation for the enhancement of T-type calcium conductance in GAERS.
(−)−Epigallocatechin Gallate Overcomes Resistance to Etoposide-Induced Cell Death by Targeting the Molecular Chaperone Glucose-Regulated Protein 78 (2006)

Many beneficial properties have been attributed to (-)-epigallocatechin gallate (EGCG), including chemopreventive, anticarcinogenic, and antioxidant actions. In this study, we investigated the effects of EGCG on the function of glucose-regulated protein 78 (GRP78), which is associated with the multidrug resistance phenotype of many types of cancer cells. Our investigation was directed at elucidating the mechanism of the EGCG and GRP78 interaction and providing evidence about whether EGCG modulates the activity of anticancer drugs through the inhibition of GRP78 function. We found that EGCG directly interacted with GRP78 at the ATP-binding site of protein and regulated its function by competing with ATP binding, resulting in the inhibition of ATPase activity. EGCG binding caused the conversion of GRP78 from its active monomer to the inactive dimer and oligomer forms. Further, we showed that EGCG interfered with the formation of the antiapoptotic GRP78-caspase-7 complex, which resulted in an increased etoposide-induced apoptosis in cancer cells. We also showed that EGCG significantly suppressed the transformed phenotype of breast cancer cells treated with etoposide. Overall, these results strongly suggested that EGCG could prevent the antiapoptotic effect of GRP78, which usually suppresses the caspase-mediated cell death pathways in drug-treated cancer cells, contributing to the development of drug resistance.
Three investigations of piRNA: Making sense of a new class of molecules (2013)

This masters thesis is about Piwi-interacting RNA (piRNA) and its object is threefold. We will investigate i) how well a Support Vector Machine (SVM)-based method compares to the currently used software for piRNA cluster detection, namely proTRAC, ii) whether piRNA uses a seed-sequence to connect to protein-coding genes and iii) if piRNA regulates any specific types of protein-coding genes. The results were, respectively i) poorly, as the SVM method was not able to achieve a high level of specificity and sensitivity at the same time. As for ii) by investigating whether potential piRNA seed sequences hit genomic locations depleted for single-nucleotide polymorphisms (SNPs), we found no region of piRNA that seemed more important for binding. Lastly, for iii) by searching the genes hit most often by piRNA for category enrichment, we found no types of protein-coding genes to be preferentially controlled by piRNA. Result i) might be important as far as it shows that a mature machine learning method, the SVM, using a feature vector of attributes known to characterize piRNA, does not measure up to the currently used method for finding piRNA clusters. This indicates that refining proTRAC or similar methods might be a more fruitful avenue for improving piRNA cluster detection. Result ii) is important as the functioning of the still mysterious piRNA is better understood; by knowing how it might bind (using the whole sequence), the functions and regulatory targets of piRNA may become easier to find. The last result iii) likely tells little beyond that our method of finding classes of piRNA-regulated genes was lacking; one reason might be that different clusters of piRNA regulate different genes.
A Convenient and Efficient Synthesis of the First (Nitroimidazolyl)succinic Esters and Their Diacids. (2007)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Correction: Respiratory syncytial virus‐induced exaggeration of allergic airway disease is dependent upon CCR1‐associated immune responses, Vol 35 (1) 2005, DOI 10.1002/eji.200425439 (2005)

Unfortunately, in this article, the RSV strain used was printed incorrectly as A2 in the section entitled ‘RSV-infection and CRA-sensitization protocols’ in the Material and methods. The correct information is as follows below: RSV-infection and CRA-sensitization protocols At 6–8 weeks of age, mice were infected with 1 × 105 pfu human RSV A wild-type strain grown from an original University of Michigan hospital isolate.
Toward a Structural View of hERG Activation by the Small-Molecule Activator ICA-105574 (2019)

Outward current conducted by human <i>ether</i>-<i>à</i>-<i>go</i>-<i>go</i>-related gene type 1 (hERG1) K<sup>+</sup> channels is important for action potential repolarization in the human ventricle. Rapid, voltage-dependent inactivation greatly reduces outward currents conducted by hERG1 channels and involves conformational changes in the ion selectivity filter (SF). Recently, compounds have been found that activate hERG1 channel function by modulating gating mechanisms such as reducing inactivation. Such activating compounds could represent a novel approach to prevent arrhythmias associated with prolonged ventricular repolarization associated with inherited or acquired long QT syndrome. ICA-105574 (ICA), a 3-nitro-<i>n</i>-(4-phenoxyphenyl) benzamide derivative activates hERG1 by strongly attenuating pore-type inactivation. We previously mapped the putative binding site for ICA to a hydrophobic pocket located between two adjacent subunits. Here, we used the recently reported cryoelectron microscopy structures of hERG1 to elucidate the structural mechanisms by which ICA influences the stability of the SF. By combining molecular dynamics simulations, voltage-clamp electrophysiology, and the synthesis of novel ICA derivatives, we provide atomistic insights into SF dynamics and propose a structural link between the SF and S6 segments. Further, our study highlights the importance of the nitro moiety, at the meta position of the benzamide ring, for the activity of ICA and reveals that the (bio)isosteric substitution of this side chain can switch the activity to weak inhibitors. Our findings indicate that ICA increases the stability of the SF to attenuate channel inactivation, and this action requires a fine-tuned compound geometry.
Guidelines for Acquiring and Reporting Clinical Neurospectroscopy (2013)

Since the advent of CPT 76390 in 1998, magnetic resonance spectroscopy (MRS) of the brain, or neurospectroscopy, has moved from the realm of academic research into that of the clinical world. All major MR manufacturers have aided in the endeavor by automating neurospectroscopy so that it no longer requires an MR physicist and is a push-button technique that can be run by technologists just as a typical MR sequence. Thousands of studies have demonstrated the clinical efficacy of neurospectroscopy, and there are many medical reviews of how this technique can be applied across a wide range of neurologic disorders. However, few studies address the practical issue of acquiring and reporting neurospectroscopy in a clinical practice. Based on clinical experience at three different sites across the country and nearly two decades of applications training for technologists and radiologists at international clinical neurospectroscopy courses, the guidelines described in this article demonstrate proven protocols for clinical diagnosis and outline the strategies involved in acquiring, interpreting, and reporting clinical neurospectroscopy successfully. A standard operating procedure used across the three sites is described and high reproducibility across different platforms is shown.
HIF-2α/ITPR1 axis: A new saboteur of NK-mediated lysis (2015)

We recently investigated the role of von Hippel-Lindau (<i>VHL)</i> mutation and the subsequent induction of hypoxia-inducible factor 2α (HIF-2α) in the regulation of renal cell carcinoma (RCC) susceptibility to natural killer (NK) cell-mediated killing. We demonstrated that the resistance of <i>VHL</i>-mutated RCC cell line 786-0 to NK-mediated lysis requires HIF-2α and ITPR1, a direct novel target of HIF-2α, through the activation of autophagy in target cells by NK-derived signals.
Circular Dual Mode Horn Antenna(CDMHA) with Modified Aperture to Improve E/H-Plane Radiation Pattern Symmetry (2013)

본 논문에서는 개구면이 큰 기존 원형 이중 모드 혼의 E/H 평면 방사 패턴 대칭성 향상을 위한 변형된 개구면을 갖는 원형 이중 모드 혼을 제안한다. 제안된 안테나는 급전부, 모드 발생부, 위상정합부로 구성되며, 이 중 위상정합부의 원형 개구면은 E/H 평면의 방사 패턴 대칭성 향상을 위해 타원형 혹은 직사각형으로 변이된 형상을 갖는다. 제안된 안테나와 기존 원형 이중 모드 혼의 성능 비교를 위해 15 GHz에서 동작하는 기존 원형 이중모드 혼과 직사각형 개구면을 갖는 원형 이중 모드 혼을 제작하고 분석하였다. 측정 결과, f/d 비가 1인 반사판 안테나의 최대 개구 효율을 위한 급전 혼의 빔 폭인 -11 dB 빔 폭(<TEX>$53^{\circ}$</TEX>) 내에서 기존 원형 이중 모드 혼의 경우 3.394 dB의 E/H 평면 방사 패턴 차이를 갖는 반면, 제안된 안테나는 오직 0.539 dB 차이를 가진다. In this paper, a circular dual mode horn with modified aperture is proposed to improve a E/H-plane radiation pattern symmetry of a conventional oversized circular dual mode horn. The proposed antenna consists of a feeding section, a mode generation section and a phase matching section which has aperture shape transition from circle to ellipse or rectangle to improve a E/H-plane radiation pattern symmetry. To compare the performances between the proposed antenna and the convenional circular dual mode horn, the conventional circular dual mode horn and the proposed circular dual mode horn with rectangular aperture are fabricated and researched at 15 GHz. The measured results show that the conventional circular dual mode horn has 3.394 dB difference while the proposed antenna has only 0.539 dB difference between E and H-plane radiation patterns within the -11 dB beamwidth(<TEX>$53^{\circ}$</TEX>) which is required beamwidth of the feed horn for the maximum aperture efficiency where f/d ratio of reflector antenna is 1.
The Two Formyl Peptide Receptors Differently Regulate GPR84-Mediated Neutrophil NADPH Oxidase Activity (2021)

Neutrophils express the two formyl peptide receptors (FPR1 and FPR2) and the medium-chain fatty acid receptor GPR84. The FPRs are known to define a hierarchy among neutrophil G protein-coupled receptors (GPCRs), that is, the activated FPRs can either suppress or amplify GPCR responses. In this study, we investigated the position of GPR84 in the FPR-defined hierarchy regarding the activation of neutrophil nicotine adenine dinucleotide phosphate (NADPH) oxidase, an enzyme system designed to generate reactive oxygen species (ROS), which are important regulators in cell signaling and immune regulation. When resting neutrophils were activated by GPR84 agonists, a modest ROS release was induced. However, vast amounts of ROS were induced by these GPR84 agonists in FPR2-desensitized neutrophils, and the response was inhibited not only by a GPR84-specific antagonist but also by an FPR2-specific antagonist. This suggests that the amplified GPR84 agonist response is achieved through a reactivation of desensitized FPR2s. In addition, the GPR84-mediated FPR2 reactivation was independent of β-arrestin recruitment and sensitive to a protein phosphatase inhibitor. In contrast to FPR2-desensitized cells, FPR1 desensitization primarily resulted in a suppressed GPR84 agonist-induced ROS response, indicating a receptor hierarchical desensitization of GPR84 by FPR1-generated signals. In summary, our data show that the two FPRs in human neutrophils control the NADPH oxidase activity with concomitant ROS production by communicating with GPR84 through different mechanisms. While FPR1 desensitizes GPR84 and by that suppresses the release of ROS induced by GPR84 agonists, amplified ROS release is achieved by GPR84 agonists through reactivation of the desensitized FPR2.
<title>Whole-field laser vibrometer for buried land mine detection</title> (2002)

This paper discusses the development and performance of a multi-beam laser Doppler vibrometer specifically designed to locate buried landmines with a laser-acoustic technique. The device aims at increasing the speed of landmine detection with this technique by at least one order of magnitude. The present system is capable of simultaneously probing sixteen positions on the ground over a span of one meter, and of measuring the ground velocity at each of these positions with a velocity resolution of about 1 micrometers /s. This architecture could also be scaled to a larger number of beams or into two dimensions. The present system uses a low (100 kHz) carrier frequency, which enables digital signal processing in a simple architecture. This paper also discusses a numerical model to simulate and predict the performance of the multi-beam vibrometer. In particular, the model attempts to address issues associated with speckle dropout, signal/noise, and maximum scanning velocity.
CO<sub>2</sub> Emissions Reduction through a New Multi-Functional Fluid for Simultaneous NOx and Particles Abatement (2020)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;Since the Euro VI/6 regulation came into force in 2013/2014, most of the Diesel applications are equipped with both selective catalytic reduction (SCR) systems and Diesel particulate filters (DPF). On the one hand, SCR requires ammonia for the reduction of nitrogen oxides (NOx) created during the combustion process. An aqueous urea solution (AUS) containing 32.5% wt. urea, such as AdBlue® is injected into the hot exhaust gas upstream of the SCR catalyst to produce ammonia for NOx reduction. On the other hand, DPF demonstrates very high particle filtration efficiency, but requires to be periodically regenerated at high temperature to burn off accumulated soot. The regeneration temperature and duration can be significantly lowered by using fuel additives (fuel-borne catalyst or FBC) or by washcoating a catalyst into the DPF (catalyzed DPF or cDPF). However, this second technique is no longer applicable when SCR catalyst is implemented on filters); continuous combustion of soot is consequently lessened.&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;This paper proposes to use Multi-Functional Fluids (MFFs) with regeneration additives incorporated in the AUS. This approach allows suppressing the fuel additive hardware system used in the case of FBC, and also makes possible an optimal use of the SCR catalyst on filter technology.&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;Physically and chemically stable formulations of efficient MFFs were developed and evaluated on engine test bench. Their efficiency to catalytically promote soot oxidation was demonstrated, during both active regeneration and loading phases (continuous regeneration). These tests also demonstrated that the MFFs keep the NOx reduction reaction at the same efficiency than with non additivated AUS.&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;A simulation phase showed that CO&lt;sub&gt;2&lt;/sub&gt; reductions ranging from 0.5% to 2.9% could be achieved using MFFs. CO&lt;sub&gt;2&lt;/sub&gt; savings vary depending on the application (passenger cars, light-duty or heavy duty vehicles, buses …), the trip characteristics and the regeneration strategies.&lt;/div&gt;&lt;/div&gt;
Combined modality induction therapy without maintenance chemotherapy for small cell carcinoma of the lung. (1984)

One hundred fifty-three patients with limited and 167 with extensive small cell carcinoma of the lung (SCCL) were evaluable for response to treatment with six courses of chemotherapy (cyclophosphamide, doxorubicin, and vincristine), irradiation to intrathoracic disease, and prophylactic cranial irradiation (PCI). No maintenance chemotherapy was given. Fifty-two percent of patients with limited disease (LD) and 10% of extensive disease patients (ED) achieved a complete response. The median survival times for LD and ED patients were 49 and 34 weeks, respectively. These results were compared to a previous experience with 147 patients who were treated with three courses of similar induction chemotherapy and thoracic irradiation, as well as one year of maintenance chemotherapy (CCNU, procarbazine, and methotrexate) but without PCI. Although the use of PCI was found to reduce the frequency of brain metastases as the site of first relapse, detailed comparisons of response rates and survival showed no significant differences between the two study populations. Prolonged maintenance chemotherapy of the type used in the first study does not favorably influence outcome after intensive induction therapy for SCCL.
Unsupervised Fast Visual Localization and Mapping with Slow Features (2021)

Visual localization is the task of accurately estimating the camera’s position in a known environment. State-of-the-art methods use the 3D structure of a scene for precise visual localization. However, 3D scene reconstruction is resource-intensive in terms of hardware requirements and computation time, making it infeasible to run on low-cost embedded hardware. Unsupervised spatial representation learning with Slow Feature Analysis (SFA) enables computationally inexpensive localization and mapping. This paper analyzes SFA-based and the well-known structure-based localization, i.e., Active Search, in two distinct settings: short-term temporal and extreme spatial generalization. We present the experimental results from an outdoor environment and compare both methods w.r.t localization accuracy and computation time. Results show that the SFA-based approach is 886x faster in mapping time and 34x faster in localization than Active Search while achieving comparable localization accuracy in our test scenario.
Hydrogen Enrichment Impact on Gas Turbine Combustion Characteristics (2020)

Abstract The current research provides the impact of hydrogen enrichment on gas turbine combustion characteristics. The uniqueness of this study is it isolates the hydrogen effects while minimizing the impact of other parameters that are known to influence combustion characteristics. Experiments are carried out under high operating pressure and a wide range of firing temperatures that extend from the Lean Blow Out (LBO) limit to beyond J class firing temperature. Aerodynamic effects are isolated by using a perforated plate burner to provide a simple flame structure. The study is conducted under perfectly premixed conditions to exclude the mixing effects from the problem under investigation. Air flow, residence time, pressure and temperature are all held constant to enable back to back comparison. Hydrogen enrichment is varied from 0 to 25 percent by volume while holding the combustor exit temperature constant. No cooling air or effusion air is used in the combustion zone to ensure that there is no impact on the problem under investigation and to focus the study on kinetics effects and flame shape variation. NOx, CO emissions, LBO limits as well as flame luminosity are reported. Oxygen and carbon dioxide are measured at the combustor exit and used to ensure test integrity and for confirmation of the exit temperature. A reactor network model is used to mimic the experimental work and study sensitivity. The effective residence time in the model is varied slightly to mimic the slight change observed in flame length with hydrogen addition. This basic research provides a key resolution to the contradictory results that are typically reported in the literature for the impact of hydrogen on NOx emissions.
G protein‐coupled receptors can control the Hippo/YAP pathway through Gq signaling (2021)

The Hippo pathway is an evolutionarily conserved kinase cascade involved in the control of tissue homeostasis, cellular differentiation, proliferation, and organ size, and is regulated by cell-cell contact, apical cell polarity, and mechanical signals. Miss-regulation of this pathway can lead to cancer. The Hippo pathway acts through the inhibition of the transcriptional coactivators YAP and TAZ through phosphorylation. Among the various signaling mechanisms controlling the hippo pathway, activation of G12/13 by G protein-coupled receptors (GPCR) recently emerged. Here we show that a GPCR, the ghrelin receptor, that activates several types of G proteins, including G12/13, Gi/o, and Gq, can activate YAP through Gq/11 exclusively, independently of G12/13. We revealed that a strong basal YAP activation results from the high constitutive activity of this receptor, which can be further increased upon agonist activation. Thus, acting on ghrelin receptor allowed to modulate up-and-down YAP activity, as activating the receptor increased YAP activity and blocking constitutive activity reduced YAP activity. Our results demonstrate that GPCRs can be used as molecular switches to finely up- or down-regulate YAP activity through a pure Gq pathway.
A doctoral thesis proposal: Implementation, Evaluation and Modeling of IP Network Bandwidth Measurement Methods (2006)

A doctoral thesis proposal: Implementation, Evaluation and Modeling of IP Network Bandwidth Measurement Methods
Prediction of delayed graft function after kidney transplantation: comparison between logistic regression and machine learning methods (2015)

The discriminative capacities of LDA, linear SVM, radial SVM and LR are the only ones above 80 %. None of the pairwise AUROC comparisons between these models is statistically significant, except linear SVM outperforming LR. Additionally, the sensitivity of linear SVM to identify recipients with DGF is amongst the three highest of all models. Due to both reasons, the authors believe that linear SVM is most appropriate to predict DGF.