gebhart/patrepeval huggingface dataset:
Multiple suppressive effects of transforming growth factor β1 on the immune response in chickens (1990)

The immunosuppressive effect of human recombinant TGF-beta 1 on chicken immune responses in vitro was evaluated. TGF-beta 1 at 1-10 ng/ml reduced T cell proliferation in response to concanavalin A by 50-80% and B cell proliferation in response to LPS by greater than 90%. In contrast, when added to immune spleen cells, it reduced the secondary PFC response to sheep erythrocytes by less than 50%, particularly when added at the same time as antigen on Day 2 of incubation. When TGF-beta 1 was added during a 2-day incubation to nylon wool-nonadherent immune or normal spleen cells, it caused the maintenance and/or appearance of suppressor cells. These suppressor cells, in coculture with immune spleen cells, inhibited the secondary PFC response in vitro without any further exposure to TGF-beta 1. The phenotype of the cells giving rise to suppressor cells under the influence of TGF-beta 1 was CT8+, TCR2+(alpha,beta), CT4-, TCR1-(gamma,delta) cells. The results suggest that, in addition to direct suppressive effects on the proliferation of B cells and of some T cells, TGF-beta 1 may suppress immune responses by maintaining or by promoting the development of suppressor T cells.
Statistical modeling of the arterial vascular tree (2011)

Automatic examination of medical images becomes increasingly important due to the rising amount of data. Therefore automated methods are required which combine anatomical knowledge and robust segmentation to examine the structure of interest. We propose a statistical model of the vascular tree based on vascular landmarks and unbranched vessel sections. An undirected graph provides anatomical topology, semantics, existing landmarks and attached vessel sections. The atlas was built using semi-automatically generated geometric models of various body regions ranging from carotid arteries to the lower legs. Geometric models contain vessel centerlines as well as orthogonal cross-sections in equidistant intervals with the vessel contour having the form of a polygon path. The geometric vascular model is supplemented by anatomical landmarks which are not necessarily related to the vascular system. These anatomical landmarks define point correspondences which are used for registration with a Thin-Plate-Spline interpolation. After the registration process, the models were merged to form the statistical model which can be mapped to unseen images based on a subset of anatomical landmarks. This approach provides probability distributions for the location of landmarks, vessel-specific geometric properties including shape, expected radii and branching points and vascular topology. The applications of this statistical model include model-based extraction of the vascular tree which greatly benefits from vessel-specific geometry description and variation ranges. Furthermore, the statistical model can be applied as a basis for computer aided diagnosis systems as indicator for pathologically deformed vessels and the interaction with the geometric model is significantly more user friendly for physicians through anatomical names.
Efficient Edge Detection Using Simplified Gabor Wavelets (2009)

Gabor wavelets (GWs) have been commonly used for extracting local features for various applications, such as recognition, tracking, and edge detection. However, extracting the Gabor features is computationally intensive, so the features may be impractical for real-time applications. In this paper, we propose a set of simplified version of GWs (SGWs) and an efficient algorithm for extracting the features for edge detection. Experimental results show that our SGW-based edge-detection algorithm can achieve a similar performance level to that using GWs, while the runtime required for feature extraction using SGWs is faster than that with GWs with the use of the fast Fourier transform. When compared to the Canny and other conventional edge-detection methods, our proposed method can achieve a better performance in the terms of detection accuracy and computational complexity.
Evidence of capsaicin synthase activity of the Pun1-encoded protein and its role as a determinant of capsaicinoid accumulation in pepper (2015)

Using a newly developed protoplast-based assay for de novo capsaicin synthesis and the anti-Pun1 antibodies, we successfully demonstrated that the Pun1 gene and its gene product are involved in capsaicin synthesis. The analysis of the vanillylamine accumulation relative to that of capsaicin indicated that Pun1 was the primary determinant of their accumulation levels.
Human monoclonal antibody directed against gag gene products of the human immunodeficiency virus. (1988)

Tonsillar B lymphocytes from an asymptomatic individual infected with HIV were transformed with EBV. A cloned lymphoblastoid cell line was obtained that secreted human mAb (IgG4 subtype) against the known gag gene products of 55,000 and 25,000 Da and a protein of 40,000 Da. The latter p40 protein appears to be a HIV gag-related gene product that is also recognized immunologically by individuals infected by HIV. Although the mAb detects infection of cells by different HIV isolates, it does not neutralize HIV or show activity in an antibody-dependent cytotoxicity assay.
Chain Elongation with Reactor Microbiomes: Open-Culture Biotechnology To Produce Biochemicals (2016)

Chain elongation into medium-chain carboxylates, such as n-caproate and n-caprylate, with ethanol as an electron donor and with open cultures of microbial consortia (i.e., reactor microbiomes) under anaerobic conditions is being developed as a biotechnological production platform. The goal is to use the high thermodynamic efficiency of anaerobic fermentation to convert organic biomass or organic wastes into valuable biochemicals that can be extracted. Several liter-scale studies have been completed and a first pilot-plant study is underway. However, the underlying microbial pathways are not always well understood. In addition, an interdisciplinary approach with knowledge from fields ranging from microbiology and chemical separations to biochemistry and environmental engineering is required. To bring together research from different fields, we reviewed the literature starting with the microbiology and ending with the bioprocess engineering studies that already have been performed. Because understanding the microbial pathways is so important to predict and steer performance, we delved into a stoichiometric and thermodynamic model that sheds light on the effect of substrate ratios and environmental conditions on product formation. Finally, we ended with an outlook.
Abstract 4274: Prolidase directly binds and activates epidermal growth factor receptor and stimulates downstream signaling. (2013)

Abstract Prolidase, also known as Xaa-Pro dipeptidase or peptidase D (PEPD), is a ubiquitously expressed enzyme that hydrolyzes dipeptides with proline or hydroxyproline at the carboxy terminus. Unexpectedly, we have found that recombinant human PEPD directly binds and activates epidermal growth factor receptor (EGFR), and that EGFR activation by PEPD in turn leads to activation of multiple signaling molecules downstream of EGFR, including but may not be limited to AKT, ERK and STAT3. EGFR is a cell surface receptor that plays a major role in a variety of cellular responses, and EGFR activation is known to result in increase in DNA synthesis, cell growth, cell proliferation and cell migration, which perhaps are most clearly demonstrated in cancer cells. The ability of PEPD to activate EGFR signaling is neither cell-specific nor dependent on its enzymatic activity; in the latter case, an enzymatically inactive PEPD mutant was similarly effective in activating EGFR, AKT, ERK and STAT3. PEPD is also a novel inducer of cyclooxygenase-2 (Cox-2), known to play an important role in cancer, inflammation and other diseases, but Cox-2 induction by PEPD also depends on EGFR activation. In line with the pro-survival and pro-proliferation activities of EGFR and Cox-2, PEPD stimulates cell proliferation and DNA synthesis in cultured cells. However, PEPD could activate EGFR only when it was present in the extracellular space, as forced expression of human PEPD via transient gene transfection failed to activate EGFR and the downstream signaling proteins. This result is nonetheless consistent with EGFR being a cell surface receptor. Although PEPD is normally a cytosolic protein, it is apparently released from injured cells and tissues in vivo, and such release appears to result in EGFR activation and activation of its downstream signals. PEPD differs from all known EGFR ligands in that it does not possess an epidermal growth factor (EGF) motif and is not synthesized as a transmembrane precursor. Indeed, there are several notable differences between PEPD and EGF with regard to binding and activation of EGFR and activation of downstream signaling molecules. In conclusion, PEPD is a new ligand of EGFR and presents a novel mechanism of EGFR activation. Citation Format: Lu Yang. Prolidase directly binds and activates epidermal growth factor receptor and stimulates downstream signaling. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4274. doi:10.1158/1538-7445.AM2013-4274
A GPU-based fiber tracking framework using geometry shaders (2009)

The clinical application of fiber tracking becomes more widespread. Thus it is of high importance to be able to produce high quality results in a very short time. Additionally, research in this field would benefit from fast implementation and evaluation of new algorithms. In this paper we present a GPU-based fiber tracking framework using latest features of commodity graphics hardware such as geometry shaders. The implemented streamline algorithm performs fiber reconstruction of a whole brain using 30,000 seed points in less than 120 ms on a high-end GeForce GTX 280 graphics board. Seed points are sent to the GPU which emits up to a user-defined number of fiber points per seed vertex. These are recorded to a vertex buffer that can be rendered or downloaded to main memory for further processing. If the output limit of the geometry shader is reached before the stopping criteria are fulfilled, the last vertices generated are then used in a subsequent pass where the geometry shader continues the tracking. Since all the data resides on graphics memory the intermediate steps can be visualized in real-time. The fast reconstruction not only allows for an interactive change of tracking parameters but, since the tracking code is implemented using GPU shaders, even for a runtime change of the algorithm. Thus, rapid development and evaluation of different algorithms and parameter sets becomes possible, which is of high value for e.g. research on uncertainty in fiber tracking.
Processing of Tellurite‐Based Glass with Low OH Content (2010)

We report results on the processing and characterization of tellurite‐based glass in the TeO 2 –Bi 2 O 3 –ZnO (TBZ) glass family and efforts to reduce their absorption loss due to residual hydroxyl (OH) content. We show that the introduction of alkaline or alkaline earth in the glass network, drying of the batch with fluorine‐based raw materials before melting, and melting of the glass in O 2 ‐rich atmosphere can lead to a significant reduction in OH content. Employing these steps in TBZ glass processing resulted in a 93% reduction of OH content as compared with a reference composition. The reduction in OH content was verified by a decrease of the absorption band center at 3000 cm −1 as well as a decrease of the free volume in the glass. The addition of F in the glass network was found to reduce the fraction of nonbridging oxygen associated with OH. X‐ray fluorescence spectrometry was used to determine the amount of remaining F.
A wearable UV-LED medical device for automatic disinfection of stethoscope membrane (2014)

Background 

The medical literature has demonstrated the importance of healthcare-associated infections (HAIs) and their negative consequences which are often due to inadequate management of cleaning, disinfection and sterilization. Stethoscope is the most used medical device in the world. The lack of stethoscope hygiene favors the transmission of microorganisms and can be a potential source of HAIs. This study proposes and evaluates an innovative health technology solution for stethoscopes’ disinfection.

Methods 

A prototype of a portable and …
Numerical Simulation of Injection and Mixing on New Power Systems of Liquid-Fueled Pulse Detonation Engines (2010)

Pulse detonation engines (PDE) have received significant attention in recent years due to their potential advantages over conventional propulsion systems, including high thermodynamics cycle efficiency, high thrust/weight and specific impulse. The fuel-air injection and mixing is one of important research issues. To optimize the fuel-air injection and mixing, a three-dimensional computation model of PDE is established. The mixing process for twin-fluid air-assisted atomizers for air supplied with tangential inlet and axial inlet is numerically analyzed by using the software Fluent as platform to solve the three-dimensional Navier-Stokes equations, and the relationship between drop size and air mass and gasoline/air ratio is arrived at. Numeric simulations results of the process with different inlets show that well mixing but bad concentration distribution occurs with tangential inlet especially along the central axis which makes PDE difficult to work in high frequency, while bad mixing but well-proportioned distribution occurs through axial inlet. And with the same gasoline/air ratio initialized, as the air mass increases, the droplet size decreases, and the result is also correct for the case in which the gasoline/air ratio decreases with the same air mass initialized. These results are found to be in good agreement with the limited experimental data that is currently available. The conclusions are available for the design of liquid-fueled PDE.
A low power multi-mode CMOS image sensor with integrated on-chip motion detection (2013)

In this paper, we propose a novel low power multimode CMOS smart image sensor node with integrated focal-plane motion detection and video compression. An 80×80 image pixel array is fabricated in 0.5 μm 3M2P standard CMOS technology, occupying 3×3 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> silicon area. The proposed imager enables various operational modes, including 1) event generator mode, 2) motion tracking mode and 3) video output mode in full-resolution or compression by region of interest (ROI). An ultra low power focal-plane motion detection block, consisting of analog memory and dual-threshold comparator, is integrated in the pixel-level circuit for on-chip motion detection. A hardware-friendly motion tracking algorithm is developed that indicates ROIs according to a strategy based on the detection results. A 12-bit on-chip, off-array ADC is employed to convert the captured light intensity into digital readouts. In order to further reduce the power consumption, lower image resolution is used under the first two modes. A trade-off analysis between the image resolution and detection accuracy is proposed in this paper. In simulation, the total power consumption is 10μW at a frame rate of 30fps and a supply voltage of 3.3V in motion tracking mode. A compression ratio of 14% and an average PSNR of 42dB is achieved in compressive video output mode.
Mitophagy Protects the Retina Against Anti-Vascular Endothelial Growth Factor Therapy-Driven Hypoxia via Hypoxia-Inducible Factor-1α Signaling (2021)

Anti-VEGF drugs are first-line treatments for retinal neovascular diseases, but these anti-angiogenic agents may also aggravate retinal damage by inducing hypoxia. Mitophagy can protect against hypoxia by maintaining mitochondrial quality, thereby sustaining metabolic homeostasis and reducing reactive oxygen species (ROS) generation. Here we report that the anti-VEGF agent bevacizumab upregulated the hypoxic cell marker HIF-1α in photoreceptors, Müller cells, and vascular endothelial cells of oxygen-induced retinopathy (OIR) model mice, as well as in hypoxic cultured 661W photoreceptors, MIO-MI Müller cells, and human vascular endothelial cells. Bevacizumab also increased expression of mitophagy-related proteins, and mitophagosome formation both <i>in vivo</i> and <i>in vitro</i>, but did not influence cellular ROS production or apoptosis rate. The HIF-1α inhibitor LW6 blocked mitophagy, augmented ROS production, and triggered apoptosis. Induction of HIF-1α and mitophagy were associated with upregulation of BCL2/adenovirus E1B 19-kDa protein-interacting protein 3 (BNIP3) and FUN14 domain containing 1 (FUNDC1), and overexpression of these proteins in culture reversed the effects of HIF-1α inhibition. These findings suggest that bevacizumab does induce retinal hypoxia, but that concomitant activation of the HIF-1α-BNIP3/FUNDC1 signaling pathway also induces mitophagy, which can mitigate the deleterious effects by reducing oxidative stress secondary. Promoting HIF-1α-BNIP3/FUNDC1-mediated mitophagy may enhance the safety of anti-VEGF therapy for retinal neovascular diseases and indicate new explanation and possible new target of the anti-VEGF therapy with suboptimal effect.
Transient and Average Unsteady Dynamics of Single Polymers in Large-Amplitude Oscillatory Extension (2016)

Oscillatory rheometry has been widely used in bulk rheological measurements of complex fluids such as polymer solutions and melts. Despite recent progress on bulk oscillatory rheology, however, the vast majority of single polymer studies has focused on chain dynamics in simple on/off step strain-rate experiments. In order to fully understand dynamic polymer microstructure and to establish connections with bulk rheology, there is a clear need to study the dynamics of single polymers in more realistic, nonidealized model flows with transient forcing functions. In this work, we study the dynamics of single polymers in large amplitude oscillatory extensional (LAOE) flow using experiments and Brownian dynamics (BD) simulations, and we characterize transient polymer stretch, orientation angle, and average unsteady stretch as functions of the flow strength (Weissenberg number, Wi) and probing frequency (Deborah number, De). Small and large amplitude sinusoidal oscillatory extensional flow are generated in a cross-slot microfluidic geometry, which is facilitated by using an automated flow device called the Stokes trap. This approach allows the conformational dynamics of single DNA molecules to be observed in oscillatory extensional flow for long times. In this way, we observe a characteristic periodic motion of polymers in LAOE including compression, rotation, and stretching between the time-dependent principal axes of extension and compression. Interestingly, distinct polymer conformations are observed in LAOE that appear to be analogous to buckling instabilities for rigid or semiflexible filaments under compression. Average unsteady polymer extension is further characterized for single polymers in oscillatory extension across a wide range of Wi and De. In the limit of low Wi, average polymer stretch is interpreted using analytical results based on a Hookean dumbbell model, which can be used to define a critical Wi at the linear to nonlinear transition in oscillatory extension. These results reveal the existence of a master curve for average polymer stretch when plotted as a function of an effective Weissenberg number Wieff. Experimental results are compared to BD simulations, and we observe good agreement between simulations and experiments for transient and average unsteady dynamics. Finally, average transient dynamics in oscillatory extensional flow are further interpreted in the context of Pipkin space, defined by the two-dimensional space described by Wi and De.
Quinoxaline Studies. XIII. N-(2-Quinoxaloyl)-α-amino Acids<sup>1,2</sup> (1966)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTQuinoxaline Studies. XIII. N-(2-Quinoxaloyl)-α-amino Acids1,2Shlomo Gerchakov, Peter J. Whitman, and Harry P. SchultzCite this: J. Med. Chem. 1966, 9, 2, 266–268Publication Date (Print):March 1, 1966Publication History Published online1 May 2002Published inissue 1 March 1966https://doi.org/10.1021/jm00320a042RIGHTS & PERMISSIONSArticle Views65Altmetric-Citations10LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (364 KB) Get e-Alertsclose Get e-Alerts
Differential expression of crown gall tumor markers in transformants obtained after <i>in vitro Agrobacterium tumefaciens</i> -induced transformation of cell wall regenerating protoplasts derived from <i>Nicotiana tabacum</i> (1981)

To obtain transformation of plant cells, we incubated 3-day-old cell wall-regenerating protoplasts from tobacco with Agrobacterium tumefaciens harboring tumor-inducing plasmids. Putative transformed tobacco cells were selected by phytohormone autotrophic growth and were shown to be transformed by the detection of the tumor cell specific enzymes lysopine dehydrogenase or nopaline dehydrogenase. This was substantiated by the detection, in transformed tumor tissues, of DNA sequences homologous to sequences in the tumor-inducing plasmid. Segregation of tumor markers has been observed among the transformants and it is suggested that this happened during the initiation of the transformation. The stable character of the transformed state was shown by the retention of tumor markers in subcloning of primary transformants under nonselective conditions. Suppression of the neoplastic state of transformants could take place, resulting in the development of transformed shoots. Indications were obtained for the inheritance of tumor markers through meiosis from seedlings obtained from seeds of flowering transformed plants that still expressed nopaline synthesis.
RASID: A robust WLAN device-free passive motion detection system (2012)

WLAN Device-free passive (DfP) indoor localization is an emerging technology enabling the localization of entities that do not carry any devices nor participate actively in the localization process using the already installed wireless infrastructure. This technology is useful for a variety of applications such as intrusion detection, smart homes and border protection. We present the design, implementation and evaluation of RASID, a DfP system for human motion detection. RASID combines different modules for statistical anomaly detection while adapting to changes in the environment to provide accurate, robust, and low-overhead detection of human activities using standard WiFi hardware. Evaluation of the system in two different testbeds shows that it can achieve an accurate detection capability in both environments with an F-measure of at least 0.93. In addition, the high accuracy and low overhead performance are robust to changes in the environment as compared to the current state of the art DfP detection systems.