gebhart/patrepeval huggingface dataset:
Apolipoprotein CI enhances the biological response to LPS via the CD14/TLR4 pathway by LPS-binding elements in both its N- and C-terminal helix (2010)

Timely sensing of lipopolysaccharide (LPS) is critical for the host to fight invading Gram-negative bacteria. We recently showed that apolipoprotein CI (apoCI) (apoCI1-57) avidly binds to LPS, involving an LPS-binding motif (apoCI48-54), and thereby enhances the LPS-induced inflammatory response. Our current aim was to further elucidate the structure and function relationship of apoCI with respect to its LPS-modulating characteristics and to unravel the mechanism by which apoCI enhances the biological activity of LPS. We designed and generated N- and C-terminal apoCI-derived peptides containing varying numbers of alternating cationic/hydrophobic motifs. ApoCI1-38, apoCI1-30, and apoCI35-57 were able to bind LPS, whereas apoCI1-23 and apoCI46-57 did not bind LPS. In line with their LPS-binding characteristics, apoCI1-38, apoCI1-30, and apoCI35-57 prolonged the serum residence of 125I-LPS by reducing its association with the liver. Accordingly, both apoCI1-30 and apoCI35-57 enhanced the LPS-induced TNFalpha response in vitro (RAW 264.7 macrophages) and in vivo (C57Bl/6 mice). Additional in vitro studies showed that the stimulating effect of apoCI on the LPS response resembles that of LPS-binding protein (LBP) and depends on CD14/ Toll-like receptor 4 signaling. We conclude that apoCI contains structural elements in both its N-terminal and C-terminal helix to bind LPS and to enhance the proinflammatory response toward LPS via a mechanism similar to LBP.
ACYL-COENZYME A:CHOLESTEROL ACYLTRANSFERASE (1997)

Due to its presumed role in regulating cellular cholesterol homeostasis, and in various pathophysiological conditions, acyl-coenzyme A:cholesterol acyltransferase (ACAT) has attracted much attention. Cloning the ACAT gene provides the necessary tool to advance molecular studies of this enzyme. The topics reviewed in this chapter include the pathophysiological roles of ACAT, the biochemistry and molecular biology of the ACAT protein and the ACAT gene, and the mode of regulation by sterol or nonsterol agents in mammalian cells. In addition, we present a working model linking the presumed allosteric property of ACAT with cholesterol trafficking into and out of the endoplasmic reticulum.
Investigations into the Robustness of Secondary and Tertiary Architecture of Hydrogen-Bonded Crystalline Tapes (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTInvestigations into the Robustness of Secondary and Tertiary Architecture of Hydrogen-Bonded Crystalline TapesJonathan A. Zerkowski, John C. MacDonald, and George M. WhitesidesCite this: Chem. Mater. 1994, 6, 8, 1250–1257Publication Date (Print):August 1, 1994Publication History Published online1 May 2002Published inissue 1 August 1994https://pubs.acs.org/doi/10.1021/cm00044a024https://doi.org/10.1021/cm00044a024research-articleACS PublicationsRequest reuse permissionsArticle Views349Altmetric-Citations74LEARN 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 InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
PRE-1, a cis element sufficient to enhance cone- and rod- specific expression in differentiating zebrafish photoreceptors (2011)

PRE-1 is a novel cis-regulatory module that is sufficient to enhance the initiation of photoreceptor-specific gene expression in differentiating rod and cone photoreceptors.
Describing and prescribing the constitutive response of yield stress fluids using large amplitude oscillatory shear stress (LAOStress) (2012)

Large amplitude oscillatory shear (LAOS) is used as a tool to probe the nonlinear rheological response of a model elasto-viscoplastic material (a Carbopol microgel). In contrast to most recent studies, these large amplitude measurements are carried out in a stress-controlled manner. We outline a descriptive framework of characterization measures for nonlinear rheology under stress-controlled LAOS, and this is contrasted experimentally to the strain-controlled framework that is more commonly used. We show that this stress-controlled methodology allows for a physically intuitive interpretation of the yielding behavior of elasto-viscoplastic materials. The insight gained into the material behavior through these nonlinear measures is then used to develop two constitutive models that prescribe the rheological response of the Carbopol microgel. We show that these two successively more sophisticated constitutive models, which are based on the idea of strain decomposition, capture in a compact manner the important features of the nonlinear rheology of the microgel. The second constitutive model, which incorporates the concept of kinematic hardening, embodies all of the essential behaviors exhibited by Carbopol. These include elasto-viscoplastic creep and time-dependent viscosity plateaus below a critical stress, a viscosity bifurcation at the critical stress, and Herschel–Bulkley flow behavior at large stresses.
Nanostructure of Polyplexes Formed between Cationic Diblock Copolymer and Antisense Oligodeoxynucleotide and Its Influence on Cell Transfection Efficiency (2007)

Although various cationic polymers have been used to condense anionically charged DNA to improve their transfection efficiency, there is still a lack of fundamental understanding about how to control the nanostructure and charge of the polyplexes formed and how to relate such information to cell transfection efficiency. In this work, we have synthesized a weak cationic and phosphorylcholine-containing diblock copolymer and used it as a model vector to deliver an antisense oligodeoxynucleotide (ODN) into HeLa cells. Small angle neutron scattering (SANS) was used to determine the copolymer/ODN polyplex structure. The SANS data revealed the formation of polyplex nanocylinders at high copolymer (N)/ODN (P) charge ratios, where N symbolizes the amine groups on the copolymer and P symbolizes the phosphate groups. However, the cylindrical lengths remained constant, indicating that the ODN binding over this region did not alter the cylindrical shape of the copolymer in solution. As the N/P ratio decreased and became close to unity the polyplex diameters remained constant, but their lengths increased substantially, suggesting the end-to-end bridging by ODN binding between copolymer cylinders. As the N/P ratios went below unity (with ODN in excess), the polyplex diameters increased substantially, indicating different ODN bridging to bundle the small polyplexes together. Transfection studies from HeLa cells indicated a steady increase in transfection efficiency with increasing cationic charge and decreasing polyplex size. Cell growth inhibition assay showed significant growth inhibition by the polyplexes coupled with weak cytotoxicity, indicating effective ODN delivery. While this study has confirmed the overall charge effect, it has also revealed progressive structural changes of the polyplexes against varying charge ratio, thereby providing useful insight into the mechanistic process behind the ODN delivery.
The intestinal stem cell (2008)

The epithelium of the adult mammalian intestine is in a constant dialog with its underlying mesenchyme to direct progenitor proliferation, lineage commitment, terminal differentiation, and, ultimately, cell death. The epithelium is shaped into spatially distinct compartments that are dedicated to each of these events. While the intestinal epithelium represents the most vigorously renewing adult tissue in mammals, the stem cells that fuel this self-renewal process have been identified only recently. The unique epithelial anatomy makes the intestinal crypt one of the most accessible models for the study of adult stem cell biology. This review attempts to provide a comprehensive overview of four decades of research on crypt stem cells.
Improvement of neurobehavioral disorders in children supplemented with magnesium-vitamin B6. I. Attention deficit hyperactivity disorders. (2006)

Some previous studies have reported the involvement of magnesium (Mg) deficiency in children with ADHD syndrome. In this work, 40 children with clinical symptoms of ADHD were followed clinically and biologically during a magnesium-vitamin B6 (Mg-B6) regimen (6 mg/kg/d Mg, 0.6 mg/kg/d vit-B6) which was set up for at least 8 weeks. Symptoms of ADHD (hyperactivity, hyperemotivity/ aggressiveness, lack of attention at school) were scored (0-4) at different times; in parallel, intraerythrocyte Mg2+ (Erc-Mg) and blood ionized Ca2+ (i-Ca) were measured. Children from the ADHD group showed significantly lower Erc-Mg values than control children (n = 36). In almost all cases of ADHD, Mg-B6 regimen for at least two months significantly modified the clinical symptoms of the disease: namely, hyperactivity and hyperemotivity/aggressiveness were reduced, school attention was improved. In parallel, the Mg-B6 regimen led to a significant increase in Erc-Mg values. When the Mg-B6 treatment was stopped, clinical symptoms of the disease reappeared in few weeks together with a decrease in Erc-Mg values. This study brings additional information about the therapeutic role of a Mg-B6 regimen in children with ADHD symptoms.
Performance evaluation of a TOA-based trilateration method to locate terminals in WLAN (2006)

Nowadays, several systems are available for outdoor localization, such as GPS, assisted GPS and other systems working on cellular networks. However, there is no proper location system for indoor scenarios. Research into designing location systems for 802.11 networks is being carried out, so locating mobile devices on global networks (GSM/cellular + GPS + WLAN) finally seems feasible. The technique presented in this paper uses existing wireless LAN infrastructure with minor changes to provide an accurate estimation of the location of mobile devices in indoor environments. This technique is based on round-trip time (RTT) measurements, which are used to estimate distances between the device to be located and WLAN access points. Each RTT measurement estimates the time elapsed between the RTS (Request-to-Send) and the CTS (Clear-to-Send) frame of the 802.11 standard. By applying trilateration algorithms, an accurate estimation of the mobile position is calculated.
The pathophysiology of bronchiectasis (2009)

Bronchiectasis is defined by permanent and abnormal widening of the bronchi. This process occurs in the context of chronic airway infection and inflammation. It is usually diagnosed using computed tomography scanning to visualize the larger bronchi. Bronchiectasis is also characterized by mild to moderate airflow obstruction. This review will describe the pathophysiology of noncystic fibrosis bronchiectasis. Studies have demonstrated that the small airways in bronchiectasis are obstructed from an inflammatory infiltrate in the wall. As most of the bronchial tree is composed of small airways, the net effect is obstruction. The bronchial wall is typically thickened by an inflammatory infiltrate of lymphocytes and macrophages which may form lymphoid follicles. It has recently been demonstrated that patients with bronchiectasis have a progressive decline in lung function. There are a large number of etiologic risk factors associated with bronchiectasis. As there is generally a long-term retrospective history, it may be difficult to determine the exact role of such factors in the pathogenesis. Extremes of age and smoking/chronic obstructive pulmonary disease may be important considerations. There are a variety of different pathogens involved in bronchiectasis, but a common finding despite the presence of purulent sputum is failure to identify any pathogenic microorganisms. The bacterial flora appears to change with progression of disease.
PipeRench: a co/processor for streaming multimedia acceleration (1999)

Future computing workloads will emphasize an architecture's ability to perform relatively simple calculations on massive quantities of mixed-width data. This paper describes a novel reconfigurable fabric architecture, PipeRench, optimized to accelerate these types of computations. PipeRench enables fast, robust compilers, supports forward compatibility, and virtualizes configurations, thus removing the fixed size constraint present in other fabrics. For the first time we explore how the bit-width of processing elements affects performance and show how the PipeRench architecture has been optimized to balance the needs of the compiler against the realities of silicon. Finally, we demonstrate extreme performance speedup on certain computing kernels (up to 190x versus a modern RISC processor), and analyze how this acceleration translates to application speedup.
IFN‐γ enhances TRAIL‐induced apoptosis through IRF‐1 (2004)

Tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL) is a member of the TNF family and a potent inducer of apoptosis. TRAIL has been shown to effectively limit tumor growth in vivo without detectable cytotoxic side-effects. Interferon (IFN)-gamma often modulates the anticancer activities of TNF family members including TRAIL. However, little is known about the mechanism. To explore the mechanism, A549, HeLa, LNCaP, Hep3B and HepG2 cells were pretreated with IFN-gamma, and then exposed to TRAIL. IFN-gamma pretreatment augmented TRAIL-induced apoptosis in all these cell lines. A549 cells were selected and further characterized for IFN-gamma action in TRAIL-induced apoptosis. Western blotting analyses revealed that IFN-gamma dramatically increased the protein levels of interferon regulatory factor (IRF)-1, but not TRAIL receptors (DR4 and DR5) and pro-apoptotic (FADD and Bax) and anti-apoptotic factors (Bcl-2, Bcl-XL, cIAP-1, cIAP-2 and XIAP). To elucidate the functional role of IRF-1 in IFN-gamma-enhanced TRAIL-induced apoptosis, IRF-1 was first overexpressed by using an adenoviral vector AdIRF-1. IRF-1 overexpression minimally increased apoptotic cell death, but significantly enhanced apoptotic cell death induced by TRAIL when infected cells were treated with TRAIL. In further experiments using an antisense oligonucleotide, a specific repression of IRF-1 expression abolished enhancer activity of IFN-gamma for TRAIL-induced apoptosis. Therefore, our data indicate that IFN-gamma enhances TRAIL-induced apoptosis through IRF-1.
The translation elongation factor eEF2 is a novel tumor-associated antigen overexpressed in various types of cancers (2014)

Recent studies have shown that cancer immunotherapy could be a promising therapeutic approach for the treatment of cancer. In the present study, to identify novel tumor-associated antigens (TAAs), the proteins expressed in a panel of cancer cells were serologically screened by immunoblot analysis and the eukaryotic elongation factor 2 (eEF2) was identified as an antigen that was recognized by IgG autoantibody in sera from a group of patients with head and neck squamous cell carcinoma (HNSCC) or colon cancer. Enzyme-linked immunosorbent assay showed that serum eEF2 IgG Ab levels were significantly higher in colorectal and gastric cancer patients compared to healthy individuals. Immunohistochemistry experiments showed that the eEF2 protein was overexpressed in the majority of lung, esophageal, pancreatic, breast and prostate cancers, HNSCC, glioblastoma multiforme and non-Hodgkin's lymphoma (NHL). Knockdown of eEF2 by short hairpin RNA (shRNA) significantly inhibited the growth in four eEF2-expressing cell lines, PC14 lung cancer, PCI6 pancreatic cancer, HT1080 fibrosarcoma and A172 glioblastoma cells, but not in eEF2-undetectable MCF7 cells. Furthermore, eEF2-derived 9-mer peptides, EF786 (eEF2 786-794 aa) and EF292 (eEF2 292-300 aa), elicited cytotoxic T lymphocyte (CTL) responses in peripheral blood mononuclear cells (PBMCs) from an HLA-A*24:02- and an HLA-A*02:01-positive healthy donor, respectively, in an HLA-A-restricted manner. These results indicated that the eEF2 gene is overexpressed in the majority of several types of cancers and plays an oncogenic role in cancer cell growth. Moreover, the eEF2 gene product is immunogenic and a promising target molecule of cancer immunotherapy for several types of cancers.
Halitosis: A review (2011)

Halitosis or bad breath is a problem faced by many and can limit their potential to even interact with the society in a positive manner. It is very subjective in that for many this malady is “A perception rather than a real thing, everybody's breath smells to a certain extent”. However real halitosis is an unpleasant condition which creates huge embarrassment with potentially grave consequences. Most of the individuals suffering from halitosis seek help from general practioners initially, not the dentist.
Promoter and Enhancer Elements from the Rat Elastase I Gene Function Independently of each other and of Heterologous Enhancers (1987)

An elastase-human growth hormone (hGH) fusion gene containing 205 base pairs of elastase 5' flanking region is expressed exclusively in pancreatic acinar cells of transgenic mice. This paper shows that the promoter region (-72 to +8) and the enhancer (-205 to -73) function independently of each other. The elastase enhancer can activate the heterologous mouse metallothionein gene and the hGH gene promoters; conversely, enhancers from the thymocyte-specific murine leukemia virus MCF13 and the metal regulatory elements from the metallothionein gene can activate the elastase promoter in a variety of cell types. Combinations of immunoglobulin and elastase enhancers with a heterologous promoter and the hGH gene result in expression in all of the tissues predicted by the sum of each enhancer acting alone. Thus these enhancer elements act independently of each other, suggesting that they do not have silencing activity in cells in which they are normally inactive.
Smart Autopilot Drone System for Surface Surveillance and Anomaly Detection via Customizable Deep Neural Network (2020)

Copter-based unmanned aerial vehicle (drone) systems are being utilized for surveillance, inspection and security purposes for well sites, gathering centers, pipelines, refineries, and other surface facilities. However, most of the practices largely rely on humans, including drone operation, data transfer, image analysis, etc. In this paper, we present a comprehensive, cloud-enabled, human-free autopilot drone system and its application in field surveillance and anomaly detection powered by customizable deep neural network and computer vision models. The proposed system consists of customized quadcopter drones equipped with high-definition cameras, thermal imaging and gas sensing devices, autopiloted by cloud-connected onboard computers. A series of advanced algorithms are developed and deployed onboard and over the Cloud for processing and diagnosing the image/thermal/gas sensing data collected by the drones in real-time or near real-time, including accurate 2D geospatial aerial mapping, anomaly detection and classification for events like oil leak, gas leak, facility failure, human activities, etc. Object detection deep learning models are customized and parallelized for low-profile multi-core single board computers. In our case study, a pre-configured drone flew along the same path twice at a 6-month gap. A robust, iterative image registering algorithm is developed to precisely align and overlay images taken at different days at the same or similar GPS locations, even with significant changes to the environment due to season shift, human activities, camera angles or height variations. Local changes are filtered and selected based on their sizes and magnitudes in the residual images by subtracting pairs of perfectly overlaid scenes. Pre-trained Residual Convolutional Neural network (He et al. 2015) is rapidly re-trained to further classify the type of changes using the techniques of transfer learning and data augmentation. An ROC of 99% was achieved in the multi-task binary classification, wherein the detected changes are divided into positive anomalies (such as oil/gas leak, facility failures, unauthored human activities) and negative (natural/insignificant) signals. Comparing against a support vector machine baseline with a ROC=92%, the ResNet model demonstrates significant, more promising detection accuracy at a faster training time. This innovative integrated platform is presented that combines physical drone, onboard imaging/sensing devices, cloud connectivity, onboard and back-end control system, deep learning and computer vision architecture for situational awareness of oil &amp; gas fields and the mining industry. It achieves full automation of mass surveillance, data acquisition and storage, diagnostics and asset situational understanding. The system architecture, especially the onboard and cloud computation engines, can be readily transferred and applied to other common drone platforms.
Relative contributions of hyaluronic acid capsule and M protein to virulence in a mucoid strain of the group A Streptococcus (1997)

The antiphagocytic effect of M protein has been considered a critical element in virulence of the group A streptococcus. The hyaluronic acid capsule also appears to play an important role: studies of an acapsular mutant derived from the mucoid or highly encapsulated M protein type 18 group A streptococcal strain 282 indicated that loss of capsule expression was associated with decreased resistance to phagocytic killing and with reduced virulence in mice. To study directly the relative contributions to virulence of M protein and the hyaluronic acid capsule in strain 282, we inactivated the gene encoding the M protein (emm18) both in wild-type strain 282 and in its acapsular mutant, strain TX72. Inactivation of emm18 was accomplished by integrational plasmid mutagenesis, using the temperature-sensitive shuttle vector pJRS233 harboring a 5' DNA segment of emm18. As reported previously, wild-type strain 282 was resistant to phagocytic killing in vitro, both in whole human blood and in 10% serum. The capsule mutant TX72 was highly susceptible to phagocytic killing in 10% serum and moderately sensitive in whole blood. The M protein mutant 282KZ was highly susceptible to phagocytic killing in blood but only moderately sensitive in 10% serum. The double mutant TX74 was sensitive to killing in both conditions. In a mouse infection model, the 50% lethal dose was increased by 60- and 80-fold for the capsule and double mutants, respectively, compared with that of strain 282, but only by 6-fold for the M protein mutant. Integration of the strain 282 capsule genes into the chromosome of a nonmucoid M1 strain resulted in high-level capsule production and rendered the transformed strain resistant to phagocytic killing in 10% serum. These results provide further evidence that the hyaluronic acid capsule confers resistance to phagocytosis and enhances group A streptococcal virulence. The results suggest also that assessment of in vitro resistance to phagocytosis in 10% serum rather than in whole blood may be a more accurate reflection of virulence in vivo of group A streptococci.