gebhart/patrepeval huggingface dataset:
Peroxisome Proliferator-Activated Receptor γ Is Required for Regulatory CD4+ T Cell-Mediated Protection against Colitis (2007)

Peroxisome proliferator-activated receptor (PPAR) gamma activation has been implicated in the prevention of immunoinflammatory disorders; however, the mechanisms of regulation of effector and regulatory CD4+ T cell functions by endogenously activated PPAR-gamma remain unclear. We have used PPAR-gamma-deficient CD4+ T cells obtained from tissue-specific PPAR-gamma null mice (i.e., PPAR-gamma fl/fl; MMTV-Cre+) to investigate the role of endogenous PPAR-gamma on regulatory T cell (Treg) and effector CD4+ T cell function. Overall, we show that the loss of PPAR-gamma results in enhanced Ag-specific proliferation and overproduction of IFN-gamma in response to IL-12. These findings correlate in vivo with enhanced susceptibility of tissue-specific PPAR-gamma null mice to trinitrobenzene sulfonic acid-induced colitis. Furthermore, the transfer of purified PPAR-gamma null CD4+ T cells into SCID recipients results in enteric disease. To test the assertion that the deficiency of PPAR-gamma in Treg impairs their ability to prevent effector T cell-induced colitis, we performed cotransfer studies. These studies demonstrate that PPAR-gamma-expressing, but not PPAR-gamma null Treg, prevent colitis induced by transfer of naive CD4+ T cells into SCID recipients. In line with these findings, the production of IFN-gamma by spleen and mesenteric lymph node-derived CD4+ T cells was down-regulated following transfer of PPAR-gamma-expressing, but not PPAR-gamma null, Treg. In conclusion, our data suggest that endogenous PPAR-gamma activation represents a Treg intrinsic mechanism of down-regulation of effector CD4+ T cell function and prevention of colitis.
Investigating a New Method-Based Internal Joint Operation Law for Optimizing the Performance of a Turbocharger Compressor (2023)

A well-matched relationship between the compressor and turbine plays an important role in improving turbocharger and engine performance. However, in the matching of turbocharger and engine, the internal operation relationship between compressor and turbine is not considered comprehensively. In order to fill this gap, this paper proposed the internal joint operation law (IJOL) method based on the internal operating characteristics of the compressor and turbine using a combination of experimental and simulation methods. On this basis, the optimization method of the compressor was proposed. Firstly, according to the basic conditions of turbocharger, the compressor power consumption and the turbine effective power at a fixed speed were solved. Secondly, the power consumption curve of the compressor and the effective power curve of the turbine were coupled to obtain the power balance point of the turbocharger. Then, the internal joint operating point was solved and coupled to obtain the IJOL method. Finally, the IJOL method was used to optimize the blade number and the blade tip profile of the compressor. The simulation results showed that for the blade number, the 8-blade compressor had the best overall performance. For the blade tip profile, compared with the original compressor, the surge performance of the impeller inlet diameter reduced by 3.12% was better than that of the original compressor. In addition, in order to compare this to engine performance with different compressor structures, a 1D engine model was constructed using GT-Power. The simulation results showed that the maximum torque of the engine corresponding to the impeller designed by the IJOL method was 4.2% higher than that of the original engine, and the minimum brake specific fuel consumption was 3.1% lower. Therefore, compared with the traditional method, the IJOL method was reasonable and practical.
A Comparison of Enzyme-Linked Immunosorbent Assay versus Multiplex Methodology Using an &lt;i&gt;in Vitro&lt;/i&gt; Model of Pulmonary Hypertension and Inflammation (2014)

Enzyme-linked immunosorbent assay (ELISA) is the most widely used method for measuring a single cytokine. Recent developments in cytokine quantification such as multiple arrays measure multiple cytokines simultaneously. Although good correlations between ELISA and multiplex methods have been observed, side by side comparisons are limited. In the present study we hypothesized that ELISA and Luminex techniques are comparable in detecting cytokines in culture medium when pulmonary artery smooth muscle cells (PASMC) are exposed to stress. Primary human PASMC were cultured in modular chambers and exposed to 21% FiO2 and peak inspiratory and positive end expiratory pressure of 24 and 8 cmH2O respectively, and 95% FiO2. At 24 hours, culture medium was collected and assayed for interleukin-6 (IL-6) and IL-8 by quantitative ELISA and by Human Cytokine 25-Plex Panel using a Luminex 200 analyzer. A comparative analysis of agreement between our ELISA and Luminex data was detailed for control and stress conditions using the Bland-Altman plot analysis. Each assay resulted in comparable increased (p < 0.001) levels of IL-6 and IL-8 as compared to control in response to oxidative and biophysical stress. The Bland-Altman analysis demonstrated that 95% of the differences between ELISA and Luminex values were within ±1.96 SD from the mean difference indicated by the 95% limits of agreement for the measurements of IL-6 and IL-8. There was no systematic bias as a function of inflammation level. We conclude that in this cell culture model, ELISA and Luminex are comparable in detecting the levels of IL-6 and IL-8 in the culture medium. If measurements of multiple cytokines are demanded and the amount of sample is limited, Luminex multi-analyte profiling technology is accurate and sensitive.
Functional reconstitution of the MERS CoV receptor binding motif (2022)

In the early 1960's the first human coronaviruses (designated 229E and OC43) were identified as etiologic agents of the common cold, to be followed by the subsequent isolation of three more human coronaviruses similarly associated with cold-like diseases. In contrast to these "mild" coronaviruses, over the last 20 years there have been three independent events of emergence of pandemic severe and acute life-threatening respiratory diseases caused by three novel beta-coronaviruses, SARS CoV, MERS CoV and most recently SARS CoV2. Whereas the first SARS CoV appeared in November 2002 and spontaneously disappeared by the summer of 2003, MERS CoV has continued persistently to spill over to humans via an intermediary camel vector, causing tens of cases annually. Although human-to-human transmission is rare, the fatality rate of MERS CoV disease is remarkably higher than 30%. COVID-19 however, is fortunately much less fatal, despite that its etiologic agent, SARS CoV2, is tremendously infectious, particularly with the recent evolution of the Omicron variants of concern (BA.1 and BA.2). Of note, MERS CoV prevalence in camel populations in Africa and the Middle East is extremely high. Moreover, MERS CoV and SARS CoV2 co-exist in the Middle East and especially in Saudi Arabia and the UAE, where sporadic incidences of co-infection have already been reported. Co-infection, either due to reverse spill-over of SARS CoV2 to camels or in double infected humans could lead to recombination between the two viruses, rendering either SARS CoV2 more lethal or MERS CoV more transmittable. In an attempt to prepare for what could develop into a catastrophic event, we have focused on developing a novel epitope-based immunogen for MERS CoV. Implementing combinatorial phage-display conformer libraries, the Receptor Binding Motif (RBM) of the MERS CoV Spike protein has been successfully reconstituted and shown to be recognized by a panel of seven neutralizing monoclonal antibodies.
Differential spontaneous folding of mycolic acids from Mycobacterium tuberculosis (2013)

Mycolic acids are structural components of the mycobacterial cell wall that have been implicated in the pathogenicity and drug resistance of certain mycobacterial species. They also offer potential in areas such as rapid serodiagnosis of human and animal tuberculosis. It is increasingly recognized that conformational behavior of mycolic acids is very important in understanding all aspects of their function. Atomistic molecular dynamics simulations, in vacuo, of stereochemically defined Mycobacterium tuberculosis mycolic acids show that they fold spontaneously into reproducible conformational groupings. One of the three characteristic mycolate types, the keto-mycolic acids, behaves very differently from either α-mycolic acids or methoxy-mycolic acids, suggesting a distinct biological role. However, subtle conformational behavioral differences between all the three mycolic acid types indicate that cooperative interplay of individual mycolic acids may be important in the biophysical properties of the mycobacterial cell envelope and therefore in pathogenicity.
Endourethral Prostheses for Urethral Stricture (2008)

The gold standard for treating a recurrent urethral stricture in a definitive way remains an open surgical urethroplasty. However, most urologists continue to manage their stricture patients with repeated dilation or urethrotomy, which are typically not curative methods. Since the introduction of urethral stents in the 1980s for the treatment of urethral strictures, two different methods to prevent scarring contraction have been introduced, namely permanent stents versus temporary stents that undergo a staged removal. Examples of permanent urethral stents are the UroLume Wallstent and Memotherm, while that of temporary stents are the UroCoil, Memokath, and Allium. Indications for stent placement are limited and typically for recurrent bulbar urethral strictures. Despite initial enthusiasm, with time, the results obtained with permanent urethral stents have been disappointing. Results with the newer temporary stents are encouraging.
Detector response modeling with asymmetric 2D Gaussian functions for GPU-based image reconstruction of the whole-body dual-ring OpenPET (2014)

We are developing the OpenPET which can provide an open space to make the patient observable and accessible during PET measurements. One of the key technologies for realizing the OpenPET geometry is the depth of interaction (DOI) detectors because the geometry has many oblique lines of response (LORs). Even if the DOI detectors reduce the blurring effect of the thick crystals, it is important to model the detector response function (DRF) in the reconstruction algorithm to achieve high spatial resolution images. In this study, therefore, we developed a new DRF model based on asymmetric 2D Gaussian functions perpendicular to the LOR for on-the-fly DRF calculation by GPUs during image reconstruction. In the proposed model, we virtually separated the detector crystal into two parts: head and tail. The head part has the shape of a cube. We set the center position of the asymmetric 2D Gaussian function at the center of the head part. The parameters of the asymmetric 2D Gaussian functions were calculated according to the size of the head part and tail part components perpendicular to the LOR. The proposed model was implemented on GPUs using the CUDA framework. We compared the proposed model with a simple Gaussian model and a crystal subsampling model which is an analytical model. We found DRFs in the proposed method provided a similar shape to that in the analytical model. In addition, the proposed model could include the blurring effect. The analytical model could represent only the effect of crystal shape, while the simple Gaussian model could represent only the blurring effect. Finally, the proposed method was applied for a prototype whole-body dual-ring OpenPET. As a result, the proposed method could improve the spatial resolution especially in the gap region of the OpenPET.
New Approach to the Practical Synthesis of Tri‐ or Tetrasubstituted Pyrimidine Derivatives: A Four‐Component Coupling Reaction from a Functionalized Silane, Two Types of Aromatic Nitriles, and Acetals. (2006)

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.
Correspondenceless Structure from Motion (2007)

We present a novel approach for the estimation of 3D-motion directly from two images using the Radon transform. The feasibility of any camera motion is computed by integrating over all feature pairs that satisfy the epipolar constraint. This integration is equivalent to taking the inner product of a similarity function on feature pairs with a Dirac function embedding the epipolar constraint. The maxima in this five dimensional motion space will correspond to compatible rigid motions. The main novelty is in the realization that the Radon transform is a filtering operator: If we assume that the similarity and Dirac functions are defined on spheres and the epipolar constraint is a group action of rotations on spheres, then the Radon transform is a correlation integral. We propose a new algorithm to compute this integral from the spherical harmonics of the similarity and Dirac functions. Generating the similarity function now becomes a preprocessing step which reduces the complexity of the Radon computation by a factor equal to the number of feature pairs processed. The strength of the algorithm is in avoiding a commitment to correspondences, thus being robust to erroneous feature detection, outliers, and multiple motions.
Po‐Thur Eve General‐24: Non‐Invasive Imaging Phenotypes of Carotid Atherosclerosis in Subjects: MRI, B‐mode and 3D Ultrasound Measurements (2006)

Atherosclerosis is a chronic inflammatory disease, characterized by the accumulation of lipids and fibrous elements within the inner‐most layer of the artery wall. Vulnerable atherosclerotic plaques may eventually rupture, resulting in emboli that can obstruct blood flow and result in stroke or myocardial infarction. Direct measurements of atherosclerosis include non‐invasive imaging phenotypes such as MRI and 3DUS derived plaque and wall volume measurements and B‐mode US measurements of the intima media thickness (IMT). Here we report the first comparison of IMT with 3D Ultrasound and MRI‐derived atherosclerosis phenotypes measured in five subjects with moderate carotid atherosclerosis . Five research subjects with carotid plaque area ⩾ 0.5 cm 2 were studied and all subjects were undergoing treatment for hyperlipidemia. Mean age was 66 yrs with no significant difference between males and females. Subjects underwent MRI, 3DUS and 2D B‐mode US of the left and right carotid arteries. A single observer carried out 3DUS vessel wall volume measurements (VWV) in 10 subject images at both time points, a second observer measured MRI vessel wall volume; a third observer measured IMT. Both 3DUS VWV and MRI VWV measurements were repeated five times to determine intra‐observer variability and variability between time points. At baseline 3DUS and MRI VWV measurements were not significantly different. No significant differences was observed for mean 3DUS VWV and MRI VWV at test and retest. No significant difference between mean IMT at test and retest was found. IMT measurements had the highest intra‐class correlation coefficients and the lowest coefficient of variation values.
Tetrahedral vs. polyhedral mesh size evaluation on flow velocity and wall shear stress for cerebral hemodynamic simulation (2010)

Haemodynamic factors, in particular wall shear stresses (WSSs) may have significant impact on growth and rupture of cerebral aneurysms. Without a means to measure WSS reliably in vivo, computational fluid dynamic (CFD) simulations are frequently employed to visualise and quantify blood flow from patient-specific computational models. With increasing interest in integrating these CFD simulations into pretreatment planning, a better understanding of the validity of the calculations in respect to computation parameters such as volume element type, mesh size and mesh composition is needed. In this study, CFD results for the two most common aneurysm types (saccular and terminal) are compared for polyhedral- vs. tetrahedral-based meshes and discussed regarding future clinical applications. For this purpose, a set of models were constructed for each aneurysm with spatially varying surface and volume mesh configurations (mesh size range: 5119-258, 481 volume elements). WSS distribution on the model wall and point-based velocity measurements were compared for each configuration model. Our results indicate a benefit of polyhedral meshes in respect to convergence speed and more homogeneous WSS patterns. Computational variations of WSS values and blood velocities are between 0.84 and 6.3% from the most simple mesh (tetrahedral elements only) and the most advanced mesh design investigated (polyhedral mesh with boundary layer).
Abstract B021: Single domain antibodies targeting CTLA-4 demonstrate a critical role for Fc in the antitumor response (2016)

Abstract Monoclonal antibodies targeting CTLA-4 are now a central part of the standard of care for metastatic melanoma, and have shown efficacy against diverse tumor types. However, the extent to which direct blockade of CTLA-4 contributes to the efficacy of these antibodies remains incompletely understood. Mice lacking FcγRIV fail to respond to αCTLA-4 therapy, and maintain robust tumor infiltrating Treg populations. These findings suggest that anti-CTLA-4 antibody therapy enhances antitumor responses through Treg depletion, though a requirement for FcγR in other aspects of the antitumor response has not been excluded, and the importance of CTLA-4 blockade alone has not be directly assessed. We have developed an alpaca-derived single domain antibody (H11) that binds CTLA-4 with high affinity, occluding the B7 binding motif as determined by x-ray crystallography. We are able to use this single domain antibody in 18F immuno-PET to produce a comprehensive image of CTLA-4 expression in a tumor-bearing live mouse, confirming penetration of H11 into the tumor microenvironment. Therapeutically, we find that H11 potently blocks CTLA-4 co-inhibition in vitro, but fails to elicit protective immunity in vivo. Therapeutic activity is restored when H11 is attached to the Fc region of murine IgG2a, but not when half-life alone is increased through H11 dimerization or conjugation to PEG, confirming a central role for Fc-dependent function in αCTLA-4 responses, as well as the minimal efficacy of CTLA-4 blockade alone. We further find that the efficacy of αCTLA-4 therapy can be enhanced through blockade of CD47, consistent with an important role for Treg depletion by myeloid cells in the activity of this therapy. These findings have implications for the development of combinations immune therapies. Citation Format: Michael Dougan, Jessica Ingram, Olga Blomberg, Mohammad Rashidian, Edmund Keliher, Ralph Weissleder, Steven Almo, Hidde Ploegh. Single domain antibodies targeting CTLA-4 demonstrate a critical role for Fc in the antitumor response [abstract]. In: Proceedings of the Second CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; 2016 Sept 25-28; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(11 Suppl):Abstract nr B021.
Lock Mass (2016)

This document contains recommendations for terminology in mass spectrometry. Development of standard terms dates back to 1974 when the IUPAC Commission on Analytical Nomenclature issued recommendations on mass spectrometry terms and definitions. In 1978, the IUPAC Commission on Molecular Structure and Spectroscopy updated and extended the recommendations and made further recommendations regarding symbols, acronyms, and abbreviations. The IUPAC Physical Chemistry Division Commission on Molecular Structure and Spectroscopy’s Subcommittee on Mass Spectroscopy revised the recommended terms in 1991 and appended terms relating to vacuum technology. Some additional terms related to tandem mass spectrometry were added in 1993 and accelerator mass spectrometry in 1994. Owing to the rapid expansion of the field in the intervening years, particularly in mass spectrometry of biomolecules, a further revision of the recommendations has become necessary. This document contains a comprehensive revision of mass spectrometry terminology that represents the current consensus of the mass spectrometry community.
The prognostic significance of postoperative neutrophil-to-lymphocyte ratio after radical prostatectomy for localized prostate cancer (2016)

Our results demonstrate that postoperative neutrophil-to-lymphocyte ratio is an independent factor for biochemical recurrence and overall survival in patients who underwent radical prostatectomy for prostate cancer. These findings suggest that neutrophil-to-lymphocyte ratio can be a potentially valuable tool for stratifying high-risk patients and facilitating choices of postoperative therapy in patients with prostate cancer.
Time-Varying Model Predictive Control for Highly Dynamic Motions of Quadrupedal Robots (2021)

Obtaining highly dynamic motions in robots is a difficult task. In recent years, sophistication in mechanical design, improved algorithms, and high computational power allows new robots to perform natural gaits and dynamic motions such as backflips. Offline optimization is often necessary to obtain good performance in those difficult motions. However, when an athlete does a backflip, he will adapt “online” to any change, and that is shown in the robustness of the movements. One of the biggest challenges in robotics is to perform those movements using online optimization with the dynamics of the robot. Here, we present an approach to deal with complicated tasks using online optimization. We obtain 90° rotational jumps and jumps over sloped terrain in the Mini-Cheetah hardware, and online-optimized backflips, sideflips, and frontflips in a real-time physical simulator with full-body dynamics.
Knock Prediction Using a Simple Model for Ignition Delay (2016)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;An earlier paper has shown the ability to predict the phasing of knock onset in a gasoline PFI engine using a simple ignition delay equation for an appropriate surrogate fuel made up of toluene and PRF (TPRF). The applicability of this approach is confirmed in this paper in a different engine using five different fuels of differing &lt;i&gt;RON&lt;/i&gt;, sensitivity, and composition - including ethanol blends. An Arrhenius type equation with a pressure correction for ignition delay can be found from interpolation of previously published data for any gasoline if its &lt;i&gt;RON&lt;/i&gt; and sensitivity are known. Then, if the pressure and temperature in the unburned gas can be estimated or measured, the Livengood-Wu integral can be estimated as a function of crank angle to predict the occurrence of knock. Experiments in a single cylinder DISI engine over a wide operating range confirm that this simple approach can predict knock very accurately. The data presented should enable engineers to study knock or other auto-ignition phenomena e.g. in premixed compression ignition (PCI) engines without explicit chemical kinetic calculations.&lt;/div&gt;&lt;/div&gt;