gebhart/patrepeval huggingface dataset:
TUNNELING PHASE LOGIC CELLULAR NONLINEAR NETWORKS (2001)

Based on a simple circuit model of a tunneling phase logic (TPL) element that is driven by a sinusoidal voltage source and biased by a DC voltage source, we present simulations of operations in cellular nonlinear networks (CNN) that could potentially be used to perform general computations in 2D arrays of simple, locally connected nanoscale devices. Some examples are presented to demonstrate the image computation capability of TPL–CNN. In particular, we use a simple 2D TPL–CNN structure to perform edge detection, image enhancement and image segmentation. Some cellular automata (CA)-like behaviors of our 2D TPL-CNN are also presented.
Hypermethylated 14-3-3-σ and ESR1 gene promoters in serum as candidate biomarkers for the diagnosis and treatment efficacy of breast cancer metastasis (2010)

The relationship of 14-3-3-sigma with breast cancer metastasis and progression found in this study suggests a possible application of 14-3-3-sigma as a biomarker to screen for metastasis and to follow up patients treated for metastatic breast cancer, monitoring their disease status and treatment response.
A new approach for the identification and cloning of genes: the pBACwich system using Cre/lox site-specific recombination (2000)

With current plant transformation methods ( Agrobacterium, biolistics and protoplast fusion), insertion of DNA into the genome occurs randomly and in many instances at multiple sites. Associated position effects, copy number differences and multigene interactions can make gene expression experiments difficult to interpret and plant phenotypes less predictable. An alternative approach to random integration of large DNA fragments into plants is to utilize one of several site-specific recombination (SSR) systems, such as Cre/ lox. Cre has been shown in numerous instances to mediate lox site-specific recombination in animal and plant cells. By incorporating the Cre/ lox SSR system into a bacterial artificial chromosome (BAC) vector, a more precise evaluation of large DNA inserts for genetic complementation should be possible. Site-specific insertion of DNA into predefined sites in the genome may eliminate unwanted 'position effects' caused by the random integration of exogenously introduced DNA. In an effort to make the Cre/ lox system an effective tool for site-directed integration of large DNAs, we constructed and tested a new vector potentially capable of integrating large DNA inserts into plant and fungal genomes. In this study, we present the construction of a new BAC vector, pBACwich, for the system and the use of this vector to demonstrate SSR of large DNA inserts (up to 230 kb) into plant and fungal genomes.
Transvenous permanent pacemaker implantation in dextrocardia: technique, challenges, outcome, and a brief review of literature (2014)

Permanent pacemaker implantation in dextrocardia can be challenging because of the distorted anatomy. Use of a technique employing angiography to delineate chamber anatomy and relationship can assist the operator during such difficult PPIs. The medium- and long-term survival after a successful pacemaker implantation in dextrocardia is favourable.
Outcome of Lumbar Epidural Steroid Injection Is Predicted by Assay of a Complex of Fibronectin and Aggrecan From Epidural Lavage (2011)

A molecular complex of fibronectin and aggrecan predicts response to lumbar ESI for radiculopathy with HNP. The biomarker is accurate, objective, and not affected by demographic or psychosocial variables in this series.
Multiscale pore‐network representation of heterogeneous carbonate rocks (2016)

Abstract A multiscale network integration approach introduced by Jiang et al . (2013) is used to generate a representative pore‐network for a carbonate rock with a pore size distribution across several orders of magnitude. We predict the macroscopic flow parameters of the rock utilising (i) 3‐D images captured by X‐ray computed microtomography and (ii) pore‐network flow simulations. To capture the multiscale pore size distribution of the rock, we imaged four different rock samples at different resolutions and integrated the data to produce a pore‐network model that combines information at several length‐scales that cannot be recovered from a single tomographic image. A workflow for selection of the number and length‐scale of the required input networks for the network integration process, as well as fine tuning the model parameters is presented. Mercury injection capillary‐pressure data were used to evaluate independently the multiscale networks. We explore single‐scale, two‐scale, and three‐scale network models and discuss their representativeness by comparing simulated capillary‐pressure versus saturation curves with laboratory measurements. We demonstrate that for carbonate rocks with wide pore size distributions, it may be required to integrate networks extracted from two or three discrete tomographic data sets in order to simulate macroscopic flow parameters.
Dipeptidyl peptidase III: a multifaceted oligopeptide N‐end cutter (2011)

Dipeptidyl peptidase III (DPP III), the sole member and representative of the M49 family of metallopeptidases, is a zinc-dependent aminopeptidase. It sequentially hydrolyses dipeptides from the N-terminal of oligopeptides ranging from three to 10 amino acid residues. Although implicated in an array of pathophysiological phenomena, the precise function of this peptidase is still unclear. However, a number of studies advocate its contribution in terminal stages of protein turnover. Altered expression of DPP III which suggests its involvement in primary ovarian carcinoma, oxidative stress (Nrf2 nuclear localization), pain, inflammation and cataractogenesis has recently led to resurgence of interest in delineating the role of the peptidase in these pathophysiological processes. This review article intends to bring forth the latest updates in this arena which may serve as a base for future studies on the peptidase.
A Transport Metabolon (2001)

The cytoplasmic carboxyl-terminal domain of AE1, the plasma membrane chloride/bicarbonate exchanger of erythrocytes, contains a binding site for carbonic anhydrase II (CAII). To examine the physiological role of the AE1/CAII interaction, anion exchange activity of transfected HEK293 cells was monitored by following the changes in intracellular pH associated with AE1-mediated bicarbonate transport. AE1-mediated chloride/bicarbonate exchange was reduced 50-60% by inhibition of endogenous carbonic anhydrase with acetazolamide, which indicates that CAII activity is required for full anion transport activity. AE1 mutants, unable to bind CAII, had significantly lower transport activity than wild-type AE1 (10% of wild-type activity), suggesting that a direct interaction was required. To determine the effect of displacement of endogenous wild-type CAII from its binding site on AE1, AE1-transfected HEK293 cells were co-transfected with cDNA for a functionally inactive CAII mutant, V143Y. AE1 activity was maximally inhibited 61 +/- 4% in the presence of V143Y CAII. A similar effect of V143Y CAII was found for AE2 and AE3cardiac anion exchanger isoforms. We conclude that the binding of CAII to the AE1 carboxyl-terminus potentiates anion transport activity and allows for maximal transport. The interaction of CAII with AE1 forms a transport metabolon, a membrane protein complex involved in regulation of bicarbonate metabolism and transport.
Probing RNA recognition by human ADAR2 using a high-throughput mutagenesis method (2016)

Adenosine deamination is one of the most prevalent post-transcriptional modifications in mRNA. In humans, ADAR1 and ADAR2 catalyze this modification and their malfunction correlates with disease. Recently our laboratory reported crystal structures of the human ADAR2 deaminase domain bound to duplex RNA revealing a protein loop that binds the RNA on the 5' side of the modification site. This 5' binding loop appears to be one contributor to substrate specificity differences between ADAR family members. In this study, we endeavored to reveal detailed structure-activity relationships in this loop to advance our understanding of RNA recognition by ADAR2. To achieve this goal, we established a high-throughput mutagenesis approach which allows rapid screening of ADAR variants in single yeast cells and provides quantitative evaluation for enzymatic activity. Using this approach, we determined the importance of specific amino acids at 19 different positions in the ADAR2 5' binding loop and revealed six residues that provide essential structural elements supporting the fold of the loop and key RNA-binding functional groups. This work provided new insight into RNA recognition by ADAR2 and established a new tool for defining structure-function relationships in ADAR reactions.
Macrophages and smooth muscle cells express lipoprotein lipase in human and rabbit atherosclerotic lesions. (1991)

Lipoprotein lipase (LPL; EC 3.1.1.34) may promote atherogenesis by producing remnant lipoproteins on the endothelial surface and by acting on lipoproteins in the artery wall. In vitro, smooth muscle cells and macrophages synthesize LPL, but in human carotid lesions only a few smooth muscle cells were reported to contain LPL protein. Endothelial cells do not synthesize LPL in vitro, but in normal arteries intense immunostaining for LPL is present on the endothelium. We used Northern blot analysis, in situ hybridization, and immunocytochemistry of human and rabbit arteries to determine cellular distribution and the site of the synthesis of LPL in atherosclerotic lesions. Northern blot analysis showed that LPL mRNA was detectable in macrophage-derived foam cells isolated from arterial lesions of "ballooned" cholesterol-fed rabbits. In situ hybridization studies of atherosclerotic lesions with an antisense riboprobe showed a strong hybridization signal for LPL mRNA in some, but not all, lesion macrophages, which were mostly located in the subendothelial and edge areas of the lesions. Also, some smooth muscle cells in lesion areas also expressed LPL mRNA. Immunocytochemistry of frozen sections of rabbit lesions with a monoclonal antibody to human milk LPL showed intense staining for LPL protein in macrophage-rich intimal lesions. The results suggest that lesion macrophages and macrophage-derived foam cells express LPL mRNA and protein. Some smooth muscle cells in the lesion areas also synthesize LPL. These data are consistent with an important role for LPL in atherogenesis.
Phospho‐proteomic immune analysis by flow cytometry: from mechanism to translational medicine at the single‐cell level (2006)

Understanding a molecular basis for cellular function is a common goal of biomedicine. The complex and dynamic cellular processes underlying physiological processes become subtly or grossly perturbed in human disease. A primary objective is to demystify this complexity by creating and establishing relevant model systems to study important aspects of human disease. Although significant technological advancements over the last decade in both genomic and proteomic arenas have enabled progress, accessing the complexity of cellular interactions that occur in vivo has been a difficult arena in which to make progress. Moreover, there are extensive challenges in translating research tools to clinical applications. Flow cytometry, over the course of the last 40 years, has revolutionized the field of immunology, in both the basic science and clinical settings, as well as having been instrumental to new and exciting areas of discovery such as stem cell biology. Multiparameter machinery and systems exist now to access the heterogeneity of cellular subsets and enable phenotypic characterization and functional assays to be performed on material from both animal models and humans. This review focuses primarily on the development and application of using activation-state readouts of intracellular activity for phospho-epitopes. We present recent work on how a flow cytometric platform is used to obtain mechanistic insight into cellular processes as well as highlight the clinical applications that our laboratory has explored. Furthermore, this review discusses the challenges faced with processing high-content multidimensional and multivariate data sets. Flow cytometry, as a platform that is well situated in both the research and clinical settings, can contribute to drug discovery as well as having utility for both biomarker and patient-stratification.
Key management and distribution for secure multimedia multicast (2003)

The problem of controlling access to multimedia multicasts requires the distribution and maintenance of keying information. Typically, the problem of key management is considered separately from the problem of distributing the rekeying messages. Multimedia sources provide two approaches to distributing the rekeying messages associated with securing group communication. The first, and more conventional approach employs the use of a media-independent channel to convey rekeying messages. We propose, however, a second approach that involves the use of a media-dependent channel, and is achieved for multimedia by using data embedding techniques. Compared to a media-independent channel, the use of data embedding to convey rekeying messages provides enhanced security by masking the presence of rekeying operations. This covert communication makes it difficult for an adversary to gather information regarding the group membership and its dynamics. In addition to proposing a new mode of conveyance for the rekeying messages, we introduce a new message format that is suitable for multicast key management schemes. This new message format uses one-way functions to securely distribute new key material to subgroups of users. An advantage of this approach over the traditional message format is that no additional messages must be sent to flag the users which portion of the message is intended for them, thereby reducing communication overhead. We then show how to map the message to a tree structure in order to achieve desirable scalability in communication and computational overhead. Next, as an example of the interplay between the key management scheme and the mode of conveyance, we study the feasibility of embedding rekeying messages using a data embedding method that has been recently proposed for fractional-pel video coding standards such as H.263 and MPEG-2. Finally, since multimedia services will involve multiple layers or objects, we extend the tree-based key management schemes to include new operations needed to handle multilayer multimedia applications where group members may subscribe or cancel membership to some layers while maintaining membership to other layers.
A Low-complexity near-ML performance achieving algorithm for large MIMO detection (2008)

In this paper, we present a low-complexity, near maximum-likelihood (ML) performance achieving detector for large MIMO systems having tens of transmit and receive antennas. Such large MIMO systems are of interest because of the high spectral efficiencies possible in such systems. The proposed detection algorithm, termed as multistage likelihood-ascent search (M-LAS) algorithm, is rooted in Hopfield neural networks, and is shown to possess excellent performance as well as complexity attributes. In terms of performance, in a 64 × 64 V-BLAST system with 4-QAM, the proposed algorithm achieves an uncoded BER of 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">−3</sup> at an SNR of just about 1 dB away from AWGN-only SISO performance given by Q(√SNR). In terms of coded BER, with a rate-3/4 turbo code at a spectral efficiency of 96 bps/Hz the algorithm performs close to within about 4.5 dB from theoretical capacity, which is remarkable in terms of both high spectral efficiency as well as nearness to theoretical capacity. Our simulation results show that the above performance is achieved with a complexity of just O(N <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">t</inf> N <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">r</inf> ) per symbol, where N <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">t</inf> and N <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">r</inf> denote the number of transmit and receive antennas.
Immunohistochemical Localization of Nitric Oxide Synthase in the Autonomic Innervation of the Human Penis (1993)

An improved understanding of the physiology of penile erection has resulted from recent evidence that implicates nitric oxide as the principal mediator of erectile function. Previously, the neuroanatomy of erection in man was established with descriptions of the autonomic innervation of the pelvic organs and external genitalia. The basis upon which novel physiological concepts of erection relate to earlier neuroanatomical principles remains to be determined. In the present study these relationships were explored with nitric oxide synthase immunohistochemistry and reduced nicotinamide adenine dinucleotide phosphate (NADPH) diaphorase histochemistry of select pelvic tissue specimens obtained from 4 men (3 at radical prostatectomy and 1 at autopsy). Nitric oxide synthase, the enzyme that catalyzes nitric oxide production, was identified in discrete neuronal locations, including the pelvic plexus, cavernous nerves and their terminal endings within the corporeal erectile tissue, branches of the dorsal penile nerves and nerve plexuses in the adventitia of the deep cavernous arteries. This distribution of nitric oxide synthase-containing nerves suggests that nitric oxide neuronally modulates local vascular smooth musculature of the penis. On this basis, nitric oxide is identified as a neuronal mediator of penile erection in man.
Leadless Dual-Chamber Pacing (2018)

Contemporary leadless pacemakers only feature single-chamber pacing capability. This study presents a prototype of a leadless dual-chamber pacemaker. Highly energy-efficient intrabody communication was implemented for wireless pacemaker synchronization. Optimal communication parameters were obtained by in vivo and ex vivo measurements in the heart and blood. The prototype successfully performed dual-chamber pacing in vivo. The presented wireless communication method may in the future also enable leadless cardiac resynchronization therapy.
Improved axial resolution of FINCH fluorescence microscopy when combined with spinning disk confocal microscopy (2014)

FINCH holographic fluorescence microscopy creates super-resolved images with enhanced depth of focus. Addition of a Nipkow disk real-time confocal image scanner is shown to reduce the FINCH depth of focus while improving transverse confocal resolution in a combined method called "CINCH".
De Novo Enzyme Design Using Rosetta3 (2011)

The Rosetta de novo enzyme design protocol has been used to design enzyme catalysts for a variety of chemical reactions, and in principle can be applied to any arbitrary chemical reaction of interest. The process has four stages: 1) choice of a catalytic mechanism and corresponding minimal model active site, 2) identification of sites in a set of scaffold proteins where this minimal active site can be realized, 3) optimization of the identities of the surrounding residues for stabilizing interactions with the transition state and primary catalytic residues, and 4) evaluation and ranking the resulting designed sequences. Stages two through four of this process can be carried out with the Rosetta package, while stage one needs to be done externally. Here, we demonstrate how to carry out the Rosetta enzyme design protocol from start to end in detail using for illustration the triosephosphate isomerase reaction.
Epigenetics in the perioperative period (2014)

The perioperative period is characterized by profound changes in the body's homoeostatic processes. This review seeks to address whether epigenetic mechanisms may influence an individual's reaction to surgery and anaesthesia. Evidence from animal and human studies suggests that epigenetic mechanisms can explain many facets of susceptibility to acute and chronic pain, making them potential therapeutic targets. Modern pain management is still based upon opiates, and both the developmental expression of opioid receptors and opioid-induced hyperalgesia have been linked to epigenetic mechanisms. In general, opiates seem to increase global DNA methylation levels. This is in contrast to local anaesthetics, which have been ascribed a global demethylating effect. Even though no direct investigations have been carried out, the potential influence of epigenetics on the inflammatory response that follows surgery seems a promising area for research. There is a considerable body of evidence that supports the involvement of epigenetics in the complex process of wound healing. Epigenetics is an important emerging research topic in perioperative medicine, with a huge potential to positively influence patient outcome.
Design and Synthesis of Potential Anticancer Agents (2010)

Most cancers mainly rely on glucose as a source of biosynthesis material and energy for their fast growth and proliferation.We proposed inhibiting glucose uptake might kill cancer cells by restricting their energy supply.Based on this hypothesis, we designed and synthesized small molecules which can inhibit the glucose uptake and cell growth in lung cancer line H1299.These small molecules acted as potential novel anticancer agents.First, we designed and synthesized phenolic benzoate esters, from which most compounds displayed mild to good inhibitory activity in glucose uptake and cell growth.The Structure-Activity-Relationship (SAR) was studied by changing different substituents on the core aromatic ring and the pendant aromatic rings, as well as changing the number of hydroxyl groups on the pendant aromatic rings.SAR showed the meta-hydroxyl group played an important role in both inhibitory activity.Due to the instability of the benzoate esters, we designed and synthesized hydrolytically more stable analogs-phenolic ethers, N-linked and S-linked phenolic derivatives.The phenolic ethers showed better inhibitory activity than the N-linked and S-linked phenolic analogs.Finally, the nitro phenolic ether WZB-173 was selected as the lead compound.
Increased presence of dendritic cells and dendritic cell chemokines in the sinus mucosa of chronic rhinosinusitis with nasal polyps and allergic fungal rhinosinusitis (2011)

AFRS and CRSwNP have increased numbers of DCs displaying costimulatory molecules, DC chemoattractants, and their corresponding receptors in the sinus mucosa compared to controls. These differences represent a possible mechanism for increased numbers of DCs with a T helper 2 (Th2)-skewed profile seen in CRSwNP and AFRS.