gebhart/patrepeval huggingface dataset:
Cys residues of the hepatitis B virus capsid protein are not essential for the assembly of viral core particles but can influence their stability (1992)

In the spherical capsid of hepatitis B virus (HBV), intermolecular disulfide bonds cross-link the approximately 180 p21.5 capsid protein subunits into a stable lattice. In this study, we used mutant capsid proteins to investigate the role that disulfide bonds and the four p21.5 Cys residues (positions 48, 61, 107, and 185) play in capsid assembly and/or stabilization. p21.5 Cys residues were either replaced by Ala or removed (Cys-185) by carboxyl-terminal truncation, creating Cys-minus mutants which were expressed in Xenopus oocytes via microinjected synthetic mRNAs. Fractionation of radiolabeled oocyte extracts on 10 to 60% sucrose gradients revealed that Cys-minus core proteins resolved into the nonparticulate and capsid forms seen for wild-type p21.5. On 5 to 30% sucrose gradients, nonparticulate Cys-minus core proteins sedimented as dimers of approximately 40 kDa. We conclude that Cys residues and disulfides are not required for the assembly of either HBV capsids or the dimers that provide the precursors for capsid assembly. Since assembly presumably demands an appropriate p21.5 tertiary structure, it is unlikely that Cys residues are required for proper p21.5 folding. However, Cys residues stabilize isolated p21.5 structures, as evidenced by the marked reduction in stability of Cys-minus dimers and capsids (i) in nonreducing sodium dodecyl sulfate-polyacrylamide gel electrophoresis and (ii) upon protease digestion. We discuss these results in the context of the HBV life cycle and the role of Cys residues in other proteins.
alpha-Ketoglutarate dehydrogenase complex of Escherichia coli. A hybrid complex containing pyruvate dehydrogenase subunits from pyruvate dehydrogenase complex. (1985)

The alpha-ketoglutarate dehydrogenase complex of Escherichia coli utilizes pyruvate as a poor substrate, with an activity of 0.082 units/mg of protein compared with 22 units/mg of protein for alpha-ketoglutarate. Pyruvate fully reduces the FAD in the complex and both alpha-keto[5-14C]glutarate and [2-14C]pyruvate fully [14C] acylate the lipoyl groups with approximately 10 nmol of 14C/mg of protein, corresponding to 24 lipoyl groups. NADH-dependent succinylation by [4-14C]succinyl-CoA also labels the enzyme with approximately 10 nmol of 14C/mg of protein. Therefore, pyruvate is a true substrate. However, the pyruvate and alpha-ketoglutarate activities exhibit different thiamin pyrophosphate dependencies. Moreover, 3-fluoropyruvate inhibits the pyruvate activity of the complex without affecting the alpha-ketoglutarate activity, and 2-oxo-3-fluoroglutarate inhibits the alpha-ketoglutarate activity without affecting the pyruvate activity. 3-Fluoro[1,2-14C]pyruvate labels about 10% of the E1 components (alpha-ketoacid dehydrogenases). The dihydrolipoyl transsuccinylase-dihydrolipoyl dehydrogenase subcomplex (E2E3) is activated as a pyruvate dehydrogenase complex by addition of E. coli pyruvate dehydrogenase, the E1 component of the pyruvate dehydrogenase complex. All evidence indicates that the alpha-ketoglutarate dehydrogenase complex purified from E. coli is a hybrid complex containing pyruvate dehydrogenase (approximately 10%) and alpha-ketoglutarate dehydrogenase (approximately 90%) as its E1 components.
Photoacoustic imaging of prostate brachytherapy seeds (2011)

Brachytherapy seed therapy is an increasingly common way to treat prostate cancer through localized radiation. The current standard of care relies on transrectal ultrasound (TRUS) for imaging guidance during the seed placement procedure. As visualization of individual metallic seeds tends to be difficult or inaccurate under TRUS guidance, guide needles are generally tracked to infer seed placement. In an effort to improve seed visualization and placement accuracy, the use of photoacoustic (PA) imaging, which is highly sensitive to metallic objects in soft tissue, was investigated for this clinical application. The PA imaging properties of bare (i.e., embedded in pure gelatin) and tissue-embedded (at depths of up to 13 mm) seeds were investigated with a multi-wavelength (750 to 1090 nm) PA imaging technique. Results indicate that, much like ultrasonic (US) imaging, an angular dependence (i.e., seed orientation relative to imaging transducer) of the PA signal exists. Despite this shortcoming, however, PA imaging offers improved contrast, over US imaging, of a seed in prostate tissue if sufficient local fluence is achieved. Additionally, although the PA signal of a bare seed is greatest for lower laser wavelengths (e.g., 750 nm), the scattering that results from tissue tends to favor the use of higher wavelengths (e.g., 1064 nm, which is the primary wavelength of Nd:YAG lasers) when the seed is located in tissue. A combined PA and US imaging approach (i.e., PAUS imaging) shows strong potential to visualize both the seed and the surrounding anatomical environment of the prostate during brachytherapy seed placement procedures.
Transcriptomic Architecture of the Adjacent Airway Field Cancerization in Non–Small Cell Lung Cancer (2014)

The adjacent airway FC comprises both site-independent profiles as well as gradient and localized airway expression patterns. Profiling of the airway FC may provide new insights into NSCLC oncogenesis and molecular tools for detection of the disease.
Sharing (location) context to facilitate collaboration between city visitors (2000)

The sharing of contextual information between individuals is a notion that often sparks emotional debate. It is interesting to note that the majority of existing work on sharing contextual information, especially location, has focused on the privacy issues raised in the work domain. This paper describes our initial investigation into sharing context in the leisure domain. More specifically we investigate how location context may be usefully shared between city visitors. For example, visitors may benefit by i) knowing the whereabouts of family members, or, ii) determining the popularity of attractions based on the number of visits. Additionally the sharing of location might also encourage communication between visitors that are not exploring the city as part of a group. For example, noticing that a fellow GUIDE user is located at the city castle would be helpful if I could then contact the visitor to request his or her opinion of the castle. 1
Kraft Pulp and Papermaking Properties of Phanerochaete Chrysosporium Degraded Red Oak (1991)

The kraft pulp and papermaking properties of Phanerochaete chrysosporium degraded red oak ( Quercus rubra ) were investigated. Phanerochaete chrysosporium was grown on rye media, and the rye spawn was used to establish mycelia growth on glucose-supplemented red oak wood chips for 0-, 10-, 20- and 30 days, respectively. Kraft pulps were produced from biodegraded and nondegraded red oak wood chips and evaluated for pulp yield, pulp refinability, and handsheet properties. Results showed that as time (0, 10, 20, and 30 days) of vegetative mycelial growth on wood chips increased, significant changes in pulp yield, kappa number, water retention value, and handsheet properties occurred. At a given pulp kappa number, higher kraft pulp yields were obtained from wood chips fungally degraded for 30 days (3-5% yield advantage) compared to pulps obtained from non-degraded red oak wood chips. Data indicated that pulps prepared from P. chrysosporium degraded red oak wood chips were more hydrophylic, responded faster to beating, and at comparable freeness levels had higher tensile, burst, and fold properties than pulps prepared from nondegraded wood. Sheet opacity was not affected by fungal degradation. Handsheets made from fungally degraded wood, however, showed marked reductions in brightness as fungal incubation time increased.
Rapid Prototyping for Pervasive Applications (2007)

VisualRDK is a high-level programming language for prototyping pervasive applications. Context is tightly integrated into the language itself, so developers can attach functionality to locations, persons, or situations instead of the device. Pervasive computing appliances range from consumer devices over embedded sensor boards to PCs and large-scale context servers. Because these devices vary tremendously in their capabilities, application developers must create different programming models for every class of device. This makes rapid prototyping infeasible as soon as more than one class of devices is involved. Rapid prototyping therefore requires a programming model that hides the environment's heterogeneity.
Transmembrane assemblage of the photoreceptor connecting cilium and motile cilium transition zone contain a common immunologic epitope (1990)

The photoreceptor connecting cilium bears a unique transmembrane assemblage which stably links cell surface glycoconjugates with the underlying axonemal cytoskeleton. Structural similarities between the photoreceptor connecting cilium and the transition zone of motile cilia suggests that this assemblage may also be present in motile cilia. Using a subcellular fraction enriched in detergent-extracted photoreceptor axonemes, three high molecular mass glycoconjugates (425, 600, and 700 kD) were previously identified as potential components of the assemblage. Through oligosaccharide characterization and binding of a specific monoclonal antibody, we have verified the localization of the 425 kD glycoconjugate to the transmembrane assemblage. Binding of the lectin peanut agglutinin (PNA) to the 425 kD glycoconjugate on nitrocellulose blots, and to isolated detergent-extracted axonemes, was assessed following treatment with the enzymes neuraminidase and O-glycanase. Changes in binding to the 425 kD glycoconjugate precisely paralleled changes in binding to intact axonemes, supporting the hypothesis that the 425 kD glycoconjugate is a component of the transmembrane assemblage. Furthermore, the results suggest that the 425 kD glycoconjugate contains sialated galactose-N-acetylgalactosamine oligosaccharides which are O-linked to the protein backbone. To directly assess the distribution of the 425 kD glycoconjugate, we produced a monoclonal antibody directed against this glycoconjugate. The antibody, K26, recognizes only the 425 kD on transblots of the axoneme fraction. K26 immunoreactivity of intact axonemes is identical to that seen by PNA staining. K26 staining of isolated photoreceptors and whole retina is uniquely localized to the region of the connecting cilium. Thus, in the photoreceptor, the 425 kD is not only a component of the transmembrane assemblage but is also completely restricted to the connecting cilium. Based on morphological similarities, the photoreceptor connecting cilium is thought to be homologous to the transition zone of the motile cilium. As such, we have stained oviduct epithelium with the K26 monoclonal antibody. Immunoreactivity is restricted to the region of the transition zone at the base of motile cilia.
GDNF fusion protein for targeted‐drug delivery across the human blood–brain barrier (2007)

Glial-derived neurotrophic factor (GDNF) is a neurotrophin that could be developed as a neurotherapeutic for Parkinson's disease, stroke, and motor neuron disease. However, GDNF does not cross the blood-brain barrier (BBB). Human GDNF was re-engineered by fusion of the mature GDNF protein to the carboxyl terminus of the chimeric monoclonal antibody (MAb) to the human insulin receptor (HIR). The HIRMAb-GDNF fusion protein is bi-functional, and both binds the HIR, to trigger receptor-mediated transport across the BBB, and binds the GDNF receptor (GFR)-alpha1, to activate GDNF neuroprotection pathways behind the BBB. COS cells were dual transfected with the heavy chain (HC) and light chain fusion protein expression plasmids, and the HC of the fusion protein was immunoreactive with antibodies to both human IgG and GDNF. The HIRMAb-GDNF fusion protein bound with high affinity to the extracellular domain of both the HIR, ED(50) = 0.87 +/- 0.13 nM, and the GFRalpha1, ED(50) = 1.68 +/- 0.17 nM. The HIRMAb-GDNF fusion protein activated luciferase gene expression in human neural SK-N-MC cells dual transfected with the c-ret kinase and a luciferase reporter gene under the influence of the rat tyrosine hydroxylase promoter, and the ED(50), 1.68 +/- 0.45 nM, was identical to the ED(50) in the GFRalpha1 binding assay. The fusion protein was active in vivo in a rat middle cerebral artery occlusion model, where the stroke volume was reduced 77% (P < 0.001). In conclusion, these studies describe the re-engineering of GDNF, to make this neurotrophin transportable across the human BBB.
Common γ-chain blocking peptide reduces in vitro immune activation markers in HTLV-1-associated myelopathy/tropical spastic paraparesis (2015)

Human T-cell lymphotropic virus type 1 (HTLV-1)-associated myelopathy/tropical spastic paraparesis (HAM/TSP) is a progressive inflammatory myelopathy occurring in a subset of HTLV-1-infected individuals. Despite advances in understanding its immunopathogenesis, an effective treatment remains to be found. IL-2 and IL-15, members of the gamma chain (γc) family of cytokines, are prominently deregulated in HAM/TSP and underlie many of the characteristic immune abnormalities, such as spontaneous lymphocyte proliferation (SP), increased STAT5 phosphorylation in the lymphocytes, and increased frequency and cytotoxicity of virus-specific cytotoxic CD8(+) T lymphocytes (CTLs). In this study, we describe a novel immunomodulatory strategy consisting of selective blockade of certain γc family cytokines, including IL-2 and IL-15, with a γc antagonistic peptide. In vitro, a PEGylated form of the peptide, named BNZ132-1-40, reduced multiple immune activation markers such as SP, STAT5 phosphorylation, spontaneous degranulation of CD8(+) T cells, and the frequency of transactivator protein (Tax)-specific CD8(+) CTLs, thought to be major players in the immunopathogenesis of the disease. This strategy is thus a promising therapeutic approach to HAM/TSP with the potential of being more effective than single monoclonal antibodies targeting either IL-2 or IL-15 receptors and safer than inhibitors of downstream signaling molecules such as JAK1 inhibitors. Finally, selective cytokine blockade with antagonistic peptides might be applicable to multiple other conditions in which cytokines are pathogenic.
Clinical review: The liver in sepsis (2012)

During sepsis, the liver plays a key role. It is implicated in the host response, participating in the clearance of the infectious agents/products. Sepsis also induces liver damage through hemodynamic alterations or through direct or indirect assault on the hepatocytes or through both. Accordingly, liver dysfunction induced by sepsis is recognized as one of the components that contribute to the severity of the disease. Nevertheless, the incidence of liver dysfunction remains imprecise, probably because current diagnostic tools are lacking, notably those that can detect the early liver insult. In this review, we discuss the epidemiology, diagnostic tools, and impact on outcome as well as the pathophysiological aspects, including the cellular events and clinical picture leading to liver dysfunction. Finally, therapeutic considerations with regard to the weakness of the pertinent specific approach are examined.
Surface Plasmon Resonance Spectroscopy of Gold Nanoparticle-Coated Substrates: Use as an Indicator of Exposure to Chemical Warfare Simulants (2005)

Gold nanoparticles with diameters of 9 +or- 6 nm have been synthesized, using the citrate reduction method, and deposited onto quartz substrates. The responsiveness of the resulting gold nanoparticle films to gas-phase warfare agent simulant exposures has been examined using 2-chloroethyl ethyl sulfide and paraoxon. Significant shifts in the peak position of the surface plasmon resonance associated with the nanoparticles were observed in both cases. This shift was reversible and the peak positions returned to their pre-exposure values once the simulants were removed. The response to the exposure events was also found to be faster than ^10 s, the rate at which data was acquired in the experiments. A larger shift was observed upon exposure of the films to formaldehyde, a highly hazardous toxic industrial chemical. Unlike 2-chloroethyl ethyl sulfide and paraoxon, the shift was not readily reversible and extensive heating and pumping under vacuum was required to shift the peak position back to pre-exposure values. Through analysis of the 2-chloroethyl ethyl sulfide and paraoxon data, ^600 pM and ^2 nM are estimated as lower detection limits for the two simulants, respectively.
Design of secondary optics for IRED in active night vision systems (2013)

An effective optical design method is proposed to solve the problem of adjustable view angle for infrared illuminator in active night vision systems. A novel total internal reflection (TIR) lens with three segments of the side surface is designed as the secondary optics of infrared emitting diode (IRED). It can provide three modes with different view angles to achieve a complete coverage of the monitored area. As an example, a novel TIR lens is designed for SONY FCB-EX 480CP camera. Optical performance of the novel TIR lens is investigated by both numerical simulation and experiments. The results demonstrate that it can meet the requirements of different irradiation distances quit well with view angles of 7.5°, 22° and 50°. The mean optical efficiency is improved from 62% to 75% and the mean irradiance uniformity is improved from 65% to 85% compared with the traditional structure.
Identification of CCR8: A Human Monocyte and Thymus Receptor for the CC Chemokine I-309 (1997)

The human CC chemokine I-309 is a potent monocyte chemoattractant and inhibits apoptosis in thymic cell lines. Here, we identify a specific human I-309 receptor, and name it CCR8 according to an accepted nomenclature system. The receptor has seven predicted transmembrane domains, is expressed constitutively in monocytes and thymus, and is encoded by a previously reported gene of previously unknown function named, alternatively, CY6, TER1, and CKR-L1. After transfection with the CY6 open reading frame, a mouse pre-B cell line exhibited calcium flux and chemotaxis in response to I-309 (EC50 = 2 nM for each), whereas 20 other chemokines were inactive. Signaling was sensitive to pertussis toxin, suggesting coupling to a Gi-type G protein. These properties parallel those of endogenous I-309 receptors expressed in an HL-60 clone 15 cell line model. The apparent monogamous relationship between I-309 and CCR8 is unusual among known CC chemokines and known CC chemokine receptors. CCR8 may regulate monocyte chemotaxis and thymic cell line apoptosis.
Influence of Mint and Peppermint on Tetranychus urticae and Some Predacious Mites of the Family Phytoseiidae (Acari: Tetranychidae: Phytoseiidae) (2001)

The deterrent and toxicity effects of mint, Mentha virdis L. and peppermint, Mentha piperita L. on Tetranychus urticae Koch were studied under laboratory conditions. M. virdis was more potent for T. urticae than M. piperita, with a significant increase in repellency. Leaf discs treated with increasing concentrations of both materials showed reduction in the total numbers of eggs laid. A high percentage of T. urticae mortality was recorded in case of M. virdis. The direct toxicity of both essential oils to the female of the predacious mites namely Typhlodromus athiase Porath and Swirski Phytoseius finitimus Ribaga, Amblyseius barkeri (Hughes), Amblyseius zaheri Yousef and El-Borolossy, Amblyseius yousefi Zaher and El-Borolossy and Amblyseius deleoni (Muma and Denmark) were tested. At LC 50 level, M. virdis was the most toxic to females A. yousefi and the least to females T. athiasae. With the exception of A. zaheri, M. piperita proved to be more toxic to the predacious mites tested than M. virdis. The results obtained chemically and biologically, may suggest that the higher percentage of the hydrocarbons of M. virdis were responsible for the toxic effect.
Multi-objective Optimization Design of Wing Structure with the Model Management Framework (2006)

Evolutionary algorithm is time-consuming because of the large number of evolutions and much times of finite element analysis, when it is used to optimize the wing structure of a certain high attitude long endurance unmanned aviation vehicle(UAV). In order to improve efficiency it is proposed to construct a model management framework to perform the multi-objective optimization design of wing structure. The sufficient accurate approximation models of objective and constraint functions in the wing structure optimization model are built when using the model management framework, therefore in the evolutionary algorithm a number of finite element analyses can be avoided and the satisfactory multi-objective optimization results of the wing structure of the high altitude long endurance UAV are obtained.
Dynamic Documents: Mobile Wireless Access to the WWW (1994)

We propose dynamic documents as an approach to extending and customizing the WWW/Mosaic for mobile computing plaforms. Dynamic documents are programs executed on a mobile platform to generate a document; they are implemented as Tcl scripts. We have modified the NCSA Mosaic web client to run the dynamic documents it retrieves through a modfied Tcl interpreter The interpreter is designed to execute only commands that do not violate safety. To hide the latencies of slow links we have modified the Mosaic client to perform caching and prefetching. The policies for caching and prefetching can be under control of dynamic documents, allowing the strategies to be document specific. Using dynamic documents, we have built an adaptive email browser that employs application-specific caching and prefetching strategies. Both the browser and the displayed email messages are dynamically customized to the mobile computing environment in which they run.
Relative Chemical Stability of Imidazolium-Based Alkaline Anion Exchange Polymerized Ionic Liquids (2011)

We thoroughly investigate and quantify the chemical stability of an imidazolium-based alkaline anion exchange polymerized ionic liquid (PIL), poly(1-[(2-methacryloyloxy)ethyl]-3-butylimidazolium hydroxide) (poly(MEBIm-OH), over a broad range of humidities, temperatures, and alkaline concentrations using the combined techniques of electrochemical impedance spectroscopy and nuclear magnetic resonance spectroscopy. High chemical stability was observed under dry conditions (10% RH) at 30 °C, humid and saturated conditions up to 80 °C, and even in mild alkaline conditions ([KOH] < 1 M) at 25 °C. Degradation was only observed under more vigorous conditions: dry conditions (10% RH) at 80 °C or at higher alkaline concentrations ([KOH] > 1 M). Under these conditions, we suggest an imidazolium ring-opening mechanism as the primary degradation pathway, based on a detailed analysis of the 1H NMR spectra. Similar to poly(MEBIm-OH), other alkaline anion (carbonate (CO32–) and bicarbonate (HCO3–)) exchange PILs were also synthesized in this study via salt metathesis of the PIL precursor, poly(1-[(2-methacryloyloxy)ethyl]-3-butylimidazolium bromide) (poly(MEBIm-Br)). The thermal and ion conductive properties of each PIL in this study were characterized. The ionic conductivity of the hydroxide conducting PIL, poly(MEBIm-OH), was the highest of these PILs investigated at 9.6 mS cm–1 at 90% RH and 30 °C with an Arrhenius activation energy of 17.1 kJ mol–1 at 90% RH.
Absence of p350 Subunit of DNA-Activated Protein Kinase from a Radiosensitive Human Cell Line (1995)

The radiosensitive rodent mutant cell line xrs-5 is defective in DNA double-strand break repair and lacks the Ku component of the DNA-activated protein kinase, DNA-PK. Here radiosensitive human cell lines were analyzed for DNA-PK activity and for the presence of related proteins. The radiosensitive human malignant glioma M059J cell line was found to be defective in DNA double-strand break repair, but fails to express the p350 subunit of DNA-PK. These results suggest that DNA-PK kinase activity is involved in DNA double-strand break repair.