gebhart/patrepeval huggingface dataset:
Conditional Osmotic Stress in Yeast (2004)

The accumulation and transport of solutes are hallmarks of osmoadaptation. In this study we have employed the inability of the Saccharomyces cerevisiae gpd1Delta gpd2Delta mutant both to produce glycerol and to adapt to high osmolarity to study solute transport through aquaglyceroporins and the control of osmostress-induced signaling. High levels of different polyols, including glycerol, inhibited growth of the gpd1Delta gpd2Delta mutant. This growth inhibition was suppressed by expression of the hyperactive allele Fps1-Delta1 of the osmogated yeast aquaglyceroporin, Fps1. The degree of suppression correlated with the relative rate of transport of the different polyols tested. Transport studies in secretory vesicles confirmed that Fps1-Delta1 transports polyols at increased rates compared with wild type Fps1. Importantly, wild type Fps1 and Fps1-Delta1 showed similarly low permeability for water. The growth defect on polyols in the gpd1Delta gpd2Delta mutant was also suppressed by expression of a heterologous aquaglyceroporin, rat AQP9. We surmised that this suppression was due to polyol influx, causing the cells to passively adapt to the stress. Indeed, when aquaglyceroporin-expressing gpd1Delta gpd2Delta mutants were treated with glycerol, xylitol, or sorbitol, the osmosensing HOG pathway was activated, and the period of activation correlated with the apparent rate of polyol uptake. This observation supports the notion that deactivation of the HOG pathway is closely coupled to osmotic adaptation. Taken together, our "conditional" osmotic stress system facilitates studies on aquaglyceroporin function and reveals features of the osmosensing and signaling system.
A novel passive protected SONET bi-directional self-healing ring architecture (2002)

The authors present a cost-effective implementation for a four-fiber bidirectional self-healing ring architecture (BSHR/4) which uses a totally passive ring as the protection ring of the BSHR/4. The proposed passive protected SONET BSHR/4 uses a SONET ring to carry working traffic, and a passive ring to carry protection traffic in case of network component failures. The passive protection ring, which is composed of optical switches and optical amplifiers, is essentially an optical add-drop protection ring, where optical switches of two ends of the failed facility act as optical add-drop components and optical switches of intermediate ring nodes are used as optical pass-through components. The optical sign add-drop is controlled by SONET add-drop multiplexers. A SONET control scheme for this implementation is discussed. The proposed BSHR/4 is attractive not only because it has a significant cost advantage over conventional BSHR/4 implementations, but also because it can easily evolve from any two-fiber ring, including the two-fiber bidirectional ring, with a minimum capital investment but gaining twice the capacity of the two-fiber ring.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Prostaglandin transporter PGT is expressed in cell types that synthesize and release prostanoids (2002)

PGT is a broadly expressed transporter of prostaglandins (PGs) and thromboxane that is energetically poised to take up prostanoids across the plasma membrane. To gain insight into the function of PGT, we generated mouse monoclonal antibody 20 against a portion of putative extracellular loop 5 of rat PGT. Immunoblots of endogenous PGT in rat kidney revealed a 65-kDa protein in a zonal pattern corresponding to PG synthesis rates (papilla congruent with medulla > cortex). Immunocytochemically, PGT in rat kidneys was expressed in glomerular endothelial and mesangial cells, arteriolar endothelial and muscularis cells, principal cells of the collecting duct, medullary interstitial cells, medullary vasa rectae endothelia, and papillary surface epithelium. Proximal tubules, which are known to take up and metabolize PGs, were negative. Immunoblotting and immunocytochemistry revealed that rat platelets also express abundant PGT. Coexpression of the PG synthesis apparatus (cyclooxygenase) and PGT by the same cell suggests that prostanoids may undergo release and reuptake.
Synthesis and Pharmacological Testing of Dequalinium Analogues as Blockers of the Apamin-Sensitive Ca2+-Activated K+ Channel:  Variation of the Length of the Alkylene Chain (1996)

Dequalinium is a potent and selective blocker of the small conductance Ca(2+)-activated K+ (SKCa) channel in rat sympathetic neurones. Analogues of dequalinium possessing 3-6, 8, 10, and 12 methylene groups in the linking chain have been synthesized and tested for inhibition of the afterhyperpolarization in rat sympathetic neurones. The compounds having a 5-12-carbon chain showed very little variation in their activity as SKCa channel blockers. The analogues possessing four and three methylenes exhibited 3- and 8-fold lower potency, respectively, compared with dequalinium. These results are discussed in the context of possible modes of binding of the compounds to the SKCa channel.
Antigen‐induced arthritis in mice (1977)

Antigen-induced arthritis was established in the mouse by immunizaiton with methylated bovine serum albumin (mBSA) in complete Freund's adjuvant with B pertusis vaccine. The knee joint was injected after 21 days with mBSA in saline. The arthritis was chronic, antigen-specific, and T-cell dependent in hypothmic nu/nu mice. C57BL and balb/c mice were susceptible, whereas CBA mice were relatively resistant. Susceptibility was dominant; one gene was loosely linked to the "b" allele of the H-2 complex of C57BL mice.
The International Protein Index: An integrated database for proteomics experiments (2004)

Despite the complete determination of the genome sequence of several higher eukaryotes, their proteomes remain relatively poorly defined. Information about proteins identified by different experimental and computational methods is stored in different databases, meaning that no single resource offers full coverage of known and predicted proteins. IPI (the International Protein Index) has been developed to address these issues and offers complete nonredundant data sets representing the human, mouse and rat proteomes, built from the Swiss-Prot, TrEMBL, Ensembl and RefSeq databases.
Eucalyptus: intelligent infrastructure enabled participatory design studio (2006)

A new notion of participation is at stake with advances in technologically mediated work environments. Insufficient bandwidth and insufficiently powerful, crudely coordinated tools resulted in distributed task-based modes of collaboration that did not allow full participation by members of distributed design teams. The emergence of Service Oriented Architectures (SOA) and User-Controlled Light-Paths (UCLP) herald the beginning of a new age where fully participatory multi-site design may become possible. While most service-oriented solutions are developed for gluing systems or data together, the Participatory Design Studio (PDS) Eucalyptus is developed to manage and configure the resources needed by users engaging in a participatory design session, such as a videoconference application, and a visualization server. Harnessing the power of UCLP, Eucalyptus strives to provide a set of upper layer services for non-technical users to provision devices and applications running on high-speed broadband networks, in addition to conventional TCP/IP networks.
Estimating Crop Area at County Level on the North China Plain with an Indirect Sampling of Segments and an Adapted Regression Estimator (2017)

Image classifications, including sub-pixel analysis, are often used to estimate crop acreage directly. However, this type of assessment often leads to a biased estimation, because commission and omission errors generally do not compensate for each other. Regression estimators combine remote sensing information with more accurate ground data on a field sample, and can result in more accurate and cost-effective assessments of crop acreage. In this pilot study, which aims to produce crop statistics in Guoyang County, the area frame sampling approach is adapted to a strip-like cropping pattern on the North China Plain. Remote sensing information is also used to perform a stratification in which non-agricultural areas are excluded from the ground survey. In order to compute crop statistics, 202 ground points in the agriculture stratum were surveyed. Image classification was included as an auxiliary variable in the subsequent analysis to obtain a regression estimator. The results of this pilot study showed that the integration of remote sensing information as an auxiliary variable can improve the accuracy of estimation by reducing the variance of the estimates, as well as the cost effectiveness of an operational application at the county level in the region.
Effects of intermodulation, AM-PM conversion, and additive noise in multicarrier TWT systems (1971)

The intermodulation due to the traveling-wave tube (TWT) is analyzed for the case where arbitrarily modulated carriers and Gaussian noise are amplified through the TWT. Both AM-PM conversion effects and nonlinear amplification in the TWT are considered. The possibility of reducing intermodulation for system improvement is also discussed.
K4[Fe(CN)6]/Glycerol—A New Liquid Matrix System for Matrix‐assisted Laser Desorption/Ionization Mass Spectrometry of Hydrophobic Compounds (1996)

Since the introduction of MALDI mass spectrometry, only a few liquid matrix systems have been proposed. This paper reports a new liquid matrix system consisting of glycerol and K4[Fe(CN)6]. With this binary system, best results are achieved for hydrophobic compounds like triacylglycerols, galactosyl diacylglycerols, phosphatidylcholines, phosphatidylethanolamines, ceramides and several chloroform soluble, synthetic polymers. Only amounts of analyte in the femtomol range have been required to obtain good results with satisfactory mass resolution, mass accuracy and excellent shot-to-shot reproducibility. In all cases, only potassium adducts are formed. No protonated molecular ions could be detected. Potassium adducts of small peptides (up to approx. 3000 Da) and carbohydrates can also be generated with this matrix system but with lower sensitivity than in the case of hydrophobic compounds (picomol to nanomol range). Additionally, sample preparation in the case of hydrophilic compounds is critical and hard to reproduce. This is presumably caused by the destruction of the thin UV absorbing matrix layer by aqueous sample solutions.
Effects of Oral L‐Carnitine on Liver Functions after Transarterial Chemoembolization in Intermediate‐Stage HCC Patients (2015)

Transarterial chemoembolization (TACE) is usually followed by hepatic dysfunction. We evaluated the effects of L-carnitine on post-TACE impaired liver functions. Methods. 53 cirrhotic hepatocellular carcinoma patients at Osaka Medical College were enrolled in this study and assigned into either L-carnitine group receiving 600 mg oral L-carnitine daily or control group. Liver functions were evaluated at pre-TACE and 1, 4, and 12 weeks after TACE. Results. The L-carnitine group maintained Child-Pugh (CP) score at 1 week after TACE and exhibited significant improvement at 4 weeks after TACE (P < 0.01). Conversely, the control group reported a significant CP score deterioration at 1 week (P < 0.05) and 12 weeks after TACE (P < 0.05). L-carnitine suppressed serum albumin deterioration at 1 week after TACE. There were significant differences between L-carnitine and control groups regarding mean serum albumin changes from baseline to 1 week (P < 0.05) and 4 weeks after TACE (P < 0.05). L-carnitine caused prothrombin time improvement from baseline to 1, 4 (P < 0.05), and 12 weeks after TACE. Total bilirubin mean changes from baseline to 1 week after TACE exhibited significant differences between L-carnitine and control groups (P < 0.05). The hepatoprotective effects of L-carnitine were enhanced by branched chain amino acids combination. Conclusion. L-carnitine maintained and improved liver functions after TACE.
Measurement of 10-fs laser pulses (1996)

We report full characterization of the intensity and phase of /spl sim/10-fs optical pulses using second-harmonic-generation frequency-resolved-optical-gating (SHG FROG). We summarize the subtleties in such measurements, compare these measurements with predicted pulse shapes, and describe the implications of these measurements for the creation of even shorter pulses. We also discuss the problem of validating these measurements. Previous measurements of such short pulses using techniques such as autocorrelation have been difficult to validate because at best incomplete information is obtained and internal self-consistency checks are lacking. FROG measurements of these pulses, in contrast, can be validated, for several reasons. First, the complete pulse-shape information provided by FROG allows significantly better comparison of experimental data with theoretical models than do measurements of the autocorrelation trace of a pulse. Second, there exist internal self-consistency checks in FROG that are not present in other pulse-measurement techniques. Indeed, we show how to correct a FROG trace with systematic error using one of these checks.
Security threats to mobile multimedia applications: Camera-based attacks on mobile phones (2014)

Today's mobile smartphones are very powerful, and many smartphone applications use wireless multimedia communications. Mobile phone security has become an important aspect of security issues in wireless multimedia communications. As the most popular mobile operating system, Android security has been extensively studied by researchers. However, few works have studied mobile phone multimedia security. In this article, we focus on security issues related to mobile phone cameras. Specifically, we discover several new attacks that are based on the use of phone cameras. We implement the attacks on real phones, and demonstrate the feasibility and effectiveness of the attacks. Furthermore, we propose a lightweight defense scheme that can effectively detect these attacks.
Prognosis and Clinical Trial Design in Traumatic Brain Injury: The IMPACT Study (2007)

Traumatic brain injury (TBI) is a major health and socio-economic problem throughout the world. Many randomized controlled trials (RCTs) have been performed to investigate the effectiveness of new therapies, but none have convincingly demonstrated benefit. Clinical trials in TBI pose complex methodological challenges and meeting these requires new approaches. The challenges are related to the heterogeneity of head injuries, to optimum analysis of outcome and to aspects of the design of trials. To address these, we have created the IMPACT database on TBI through merging individual patient data from eight RCTs and three observational surveys. This database forms a culture medium in which innovative approaches to improving trial design and analysis are being explored. We hypothesize that the statistical power of TBI trials may be increased by adjusting for heterogeneity with covariate adjustment and/or prognostic targeting, by exploiting the ordinal nature of the Glasgow Outcome Scale and by relating the outcome obtained in individual patients to their baseline prognostic risk. Extensive prognostic analysis was required as a first step towards our aim of optimizing the chance of demonstrating benefit of new therapies in future trials. The fruits of this analysis are reported in detail in the subsequent reports in this issue of the Journal of Neurotrauma. The results will lead to the development and validation of new prognostic models, which will be applied to deal with heterogeneity. The findings will be synthesized into recommendations for the design and analysis of future RCTs, with the expectation of increasing the likelihood of demonstrating the benefit of a truly effective new therapy or therapeutic agent in victims of a head injury.
Structural Basis of TLR5-Flagellin Recognition and Signaling (2012)

Toll-like receptor 5 (TLR5) binding to bacterial flagellin activates signaling through the transcription factor NF-κB and triggers an innate immune response to the invading pathogen. To elucidate the structural basis and mechanistic implications of TLR5-flagellin recognition, we determined the crystal structure of zebrafish TLR5 (as a variable lymphocyte receptor hybrid protein) in complex with the D1/D2/D3 fragment of Salmonella flagellin, FliC, at 2.47 angstrom resolution. TLR5 interacts primarily with the three helices of the FliC D1 domain using its lateral side. Two TLR5-FliC 1:1 heterodimers assemble into a 2:2 tail-to-tail signaling complex that is stabilized by quaternary contacts of the FliC D1 domain with the convex surface of the opposing TLR5. The proposed signaling mechanism is supported by structure-guided mutagenesis and deletion analyses on CBLB502, a therapeutic protein derived from FliC.
μManager: Open Source Software for Light Microscope Imaging (2007)

Abstract No longer are biologists content to peer through the oculars of a microscope. Eyes have been replaced by digital cameras. Instead of manual control of microscope stages, filters and light sources, modern microscopes have become fully robotic. Image acquisition and robotic movements require computer control. With such equipment it is possible to automatically record images at multiple wavelengths, carry out time-lapse recordings of living cells using very short exposure times and low light doses, and even to record images at multiple positions (e.g. from a multi-well plate) without operator intervention. Clearly, computer control of light microscope image acquisition is making many new experimental imaging strategies possible in the biological sciences.
Displacement Measurement and Its Application in Interframe Image Coding (1981)

A new technique for estimating interframe displacement of small blocks with minimum mean square error is presented. An efficient algorithm for searching the direction of displacement has been described. The results of applying the technique to two sets of images are presented which show 8-10 dB improvement in interframe variance reduction due to motion compensation. The motion compensation is applied for analysis and design of a hybrid coding scheme and the results show a factor of two gain at low bit rates.
Lectin receptors as markers for Trypanosoma cruzi. Developmental stages and a study of the interaction of wheat germ agglutinin with sialic acid residues on epimastigote cells. (1980)

Trypanosoma cruzi at various stages of maturation and differentiation have been isolated by conventional cellular fractionation procedures and characterized by cell surface markers using 30 highly purified lectins encompassing all known sugar specificities. Cell surface carbohydrates of the various T. cruzi stages were analyzed by agglutination and lectin-binding assays. Specific receptors for wheat germ agglutinin (WGA), Helix pomatia, Sophora japonica, and Bandeiraea simplicifolia lectin II were found only in culture epimastigotes, whereas peanut agglutinin (PNA) sites were present exclusively in amastigotes, those for Phaseolus vulgaris in bloodstream trypomastigotes and amastigotes, and for Wistaria floribunda hemagglutinin predominantly in culture forms of T. cruzi. The N-acetylgalactosamine (DGalNAc)-binding lectin from Bauhinia purpurea agglutinated and inhibited the movement of epimastigotes and bloodstream trypomastigotes, but it only inhibited--without agglutinating--culture trypomastigotes. Because both the agglutination and inhibition of movement were reversed by specific sugar haptens, Bauhinia purpurea sites were present in all the flagellated parasites. On the other hand, PNA sites were detectable on epimastigotes after the cells were treated with sialidase, whereas, at the same time, WGA receptors were completely removed and those for the other sialic acid-binding proteins, Aaptos papillata lectin II and Limulus polyphemus, were partially eliminated; moreover, the activity of Wistaria floribunda hemagglutinin, a DGalNAc-binding lectin, increased 4,000 times. Trypsinization and lyzozyme treatment of epimastigote cells did not significantly affect lectin agglutination or lectin binding. WGA reacted solely with sialic acid residues on epimastigote cell surface with an apparent association constant of 2 x 10(6) M-1, each epimastigote having an estimated average of 3 x 10(6) WGA sites, as determined by binding experiments and a minimum of 7.7 x 10(6) sialic acid residues, as calculated by colorimetric method after sialidase digestion. Evidences are presented that the sialyl residues are rapidly regenerated (in approximately 4 h) and that they, at least for the most part, are not adsorbed from the culture medium. The receptor for the D-mannose-binding lectins (concanavalin A [Con A] and Lens culinaris) must either be on the same carbohydrate moiety having the WGA site, or, if in a distinct molecule, both carrier molecules of Con A and WGA sites must be located close to each other in the plasma membrane of the parasite.
A fluorouridine‐anti‐CEA immunoconjugate is therapeutically effective in a human colonic cancer xenograft model (1990)

5-fluorouridine (FUR), an antineoplastic agent, was site-specifically conjugated to the carbohydrate moiety of a anticarcinoembryonic antigen (CEA) monoclonal antibody (MAb) by using amino-dextran as the intermediate carrier. The final immunoconjugate contains approximately 30-35 molecules of FUR per molecule of immunoglobulin, has immunoreactivity retained as examined by flow cytometry, and is cytotoxic to the target cells as examined by 75selenomethionine incorporation studies. In the GW-39/nude mouse model, the conjugate remained efficient in targeting the human colonic tumor and possessed greater inhibitory growth effects on the subcutaneous tumor than free FUR or an irrelevant antibody conjugate. In addition, the reduced host toxicity of the conjugate may permit the use of this agent in a high-dose therapy of this tumor system.
Peptide‐Embedded Heterocycles by Mild Single and Multiple Aza‐Wittig Ring Closures (2007)

Ring a ring o'azoles: The aza-Wittig cyclization of amino acids and peptides is extremely mild, selective, and versatile. The reaction of amino acid esters and amino acid thioester azides delivers peptidic 1,3-azolines and 1,3-azoles with unsurpassed functional-group tolerance. This method allows multiple ring closures and tolerates aqueous solvents. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2007/z604507_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
mTOR regulation of autophagy (2010)

Nutrient starvation induces autophagy in eukaryotic cells through inhibition of TOR (target of rapamycin), an evolutionarily-conserved protein kinase. TOR, as a central regulator of cell growth, plays a key role at the interface of the pathways that coordinately regulate the balance between cell growth and autophagy in response to nutritional status, growth factor and stress signals. Although TOR has been known as a key regulator of autophagy for more than a decade, the underlying regulatory mechanisms have not been clearly understood. This review discusses the recent advances in understanding of the mechanism by which TOR regulates autophagy with focus on mammalian TOR (mTOR) and its regulation of the autophagy machinery.