gebhart/patrepeval huggingface dataset:
Silencing on the Spot. Induction and Suppression of RNA Silencing in the Agrobacterium-Mediated Transient Expression System (2001)

The Agrobacterium-mediated transient expression assay in intact tissues has emerged as a rapid and useful method to analyze genes and gene products in plants. In many cases, high levels of active protein can be produced without the need to produce transgenic plants. In this study, a series of tools were developed to enable strong or weak induction of RNA silencing and to suppress RNA silencing in the absence of stable transgenes. Transient delivery of a gene directing production of a double-stranded green fluorescent protein (GFP) transcript rapidly induced RNA silencing of a codelivered GFP reporter gene, effectively preventing accumulation of GFP protein and mRNA. RNA silencing triggered by the strong dsGFP inducer was partially inhibited by the tobacco etch virus silencing suppressor, P1/HC-Pro. In the absence of the strong double-stranded GFP inducer, the functional GFP gene served as a weak RNA silencing inducer in the transient assay, severely limiting accumulation of the GFP mRNA over time. The weak silencing induced by the GFP gene was suppressed by P1/HC-Pro. These results indicate RNA silencing can be triggered by a variety of inducers and analyzed entirely using transient gene delivery systems. They also indicate that RNA silencing may be a significant limitation to expression of genes in the Agrobacterium-mediated transient assay but that this limitation can be overcome by using RNA silencing suppressors.
Branhamella catarrhalis Respiratory Infections (1987)

Branhamella catarrhalis, a normal commensal of the oropharynx, is increasingly recognized as an important cause of bronchitis and bacterial pneumonia. Six patients with B. catarrhalis pneumonia documented by transtracheal aspirate or blood culture were studied, and 429 previously reported cases of B. catarrhalis bronchitis and pneumonia were reviewed. The mean age of patients with B. catarrhalis infection was 64.8 years, and preexisting chronic obstructive pulmonary disease was common. The typical clinical picture was that of purulent tracheobronchitis; patients with pneumonia were not severely ill and differed from those with bronchitis mainly by the presence of patchy lower-lobe infiltrates on chest roentgenogram. Fifty-three percent of reported strains produced beta-lactamase. Thirty-nine percent of the cultures were mixed, predominantly with Haemophilus influenzae and Streptococcus pneumoniae. The microbiologic, immunologic, and clinical features of B. catarrhalis infection, as well as the antimicrobial susceptibilities of this organism, were reviewed. The reasons for the lack of recognition of this common pathogen and possible solutions were considered.
Automatic speech recognition technique for voice command (2014)

In this paper, we represent a new method for robust speech recognition technique. Speech recognition is a process by which system is able to understand natural language. By the help of proposed method we will be able to give computer system the voice command to perform task. The first step is to take a single audio as an input. The second step is to eliminate the presence of noise. The third step is to match the patterns to recognize the input audio. The error tolerance mechanism is implemented so that it can be robust against human errors, environment noise. There is no requirement of storing the audio for matching, which leads to decrease the space and time complexity both compare to other systems. The database used in the experiment will only be consisting of various voice patterns. Patterns are hard coded in such a way that system is not needed to be trained by the end users.
Electrolysis of Gaseous CO2 to CO in a Flow Cell with a Bipolar Membrane (2017)

The conversion of CO2 to CO is demonstrated in an electrolyzer flow cell containing a bipolar membrane at current densities of 200 mA/cm2 with a Faradaic efficiency of 50%. Electrolysis was carried out by delivering gaseous CO2 at the cathode with a silver catalyst integrated in a carbon-based gas diffusion layer. Nonprecious nickel foam in a strongly alkaline electrolyte (1 M NaOH) was used to mediate the anode reaction. While a configuration where the anode and cathode were separated by only a bipolar membrane was found to be unfavorable for robust CO2 reduction, a modified configuration with a solid-supported aqueous layer inserted between the silver-based catalyst layer and the bipolar membrane enhanced the cathode selectivity for CO2 reduction to CO. We report higher current densities (200 mA/cm2) than previously reported for gas-phase CO2 to CO electrolysis and demonstrate the dependence of long-term stability on adequate hydration of the CO2 inlet stream.
Curing metastatic testicular cancer (2002)

Our initial studies with cisplatin + vinblastine + bleomycin began 27 years ago in 1974, changing the cure rate for disseminated disease from 5 to 60%. Subsequently, through random prospective clinical trials, we have modified the treatment regimen to reduce both the duration and dosages of the chemotherapy drugs. Cisplatin + etoposide was first used at Indiana University as salvage chemotherapy in 1978, representing the first time that a solid tumor had been cured with second-line chemotherapy. We next did a clinical trial comparing bleomycin + etoposide + cisplatin (BEP) to cisplatin + vinblastine + bleomycin. The BEP regimen was proven to have less toxicity and a higher cure rate and therefore, since 1984, has been standard chemotherapy. More recent studies have evaluated the use of lesser chemotherapy to maintain the same cure rate for patients with good-prognosis disease. Standard therapy for these patients is either three courses of BEP or four courses of EP, and over 90% of these patients will be cured of their disease. Patients who are not cured with their initial BEP chemotherapy are usually treated with salvage chemotherapy. Approximately 50% of these testicular cancer patients will subsequently be cured with salvage chemotherapy with tandem transplant of high-dose chemotherapy with peripheral stem cell rescue. Testicular cancer has become a model for a curable neoplasm. In the early 1970s, metastatic testicular cancer was associated with only 5% survival. Today, with modern chemotherapy and surgery techniques, 80% of patients will survive their disease.
Synthesis of N4-acylated N1,N8-bis(acyl)spermidines. An approach to the synthesis of siderophores (1980)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of N4-acylated N1,N8-bis(acyl)spermidines. An approach to the synthesis of siderophoresR. J. Bergeron, K. A. McGovern, M. A. Channing, and P. S. BurtonCite this: J. Org. Chem. 1980, 45, 9, 1589–1592Publication Date (Print):April 1, 1980Publication History Published online1 May 2002Published inissue 1 April 1980https://pubs.acs.org/doi/10.1021/jo01297a008https://doi.org/10.1021/jo01297a008research-articleACS PublicationsRequest reuse permissionsArticle Views386Altmetric-Citations43LEARN 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-Alertsclose Get e-Alerts
Identification and Characterization of the Escherichia coli -Expressed RNA-Dependent RNA Polymerase of Bamboo Mosaic Virus (1998)

Bamboo mosaic virus (BaMV), a member of the potexvirus group, infects primarily members of the Bambusoideae. The open reading frame 1 (ORF1) of BaMV encodes a 155-kDa polypeptide that was postulated to be involved in the replication and the formation of cap structure at the 5' end of the viral genome. To characterize the activities associated with the 155-kDa viral protein, it was expressed in Escherichia coli BL21(DE3) cells with thioredoxin, hexahistidine, and S. Tag fused consecutively at its amino terminus, and the fusion protein was purified by metal affinity chromatography. Several RNA fragments, prepared by in vitro transcription, were tested as substrates for the RNA-dependent RNA polymerase (RdRp) activity. Among them, the expressed fusion enzyme was able to generate a 32P-labeled RNA product when 3'-end RNA fragments of the positive strand or negative strand of BaMV were included in the assay mixture. Dot hybridization assay revealed that the reaction products are complementary to their RNA substrates. Taken together, the evidence suggests that the 155-kDa protein encoded by ORF1 of BaMV has an RdRp activity and should be involved in the replication of BaMV. Mutational analyses demonstrate the importance of the GDD motif in the polymerase activity, and deletion studies suggest that the polymerase activity resides in the carboxyl terminus of the 155-kDa viral protein.
High-Throughput Sequencing and Metagenomics: Moving Forward in the Culture-Independent Analysis of Food Microbial Ecology (2013)

Following recent trends in environmental microbiology, food microbiology has benefited from the advances in molecular biology and adopted novel strategies to detect, identify, and monitor microbes in food. An in-depth study of the microbial diversity in food can now be achieved by using high-throughput sequencing (HTS) approaches after direct nucleic acid extraction from the sample to be studied. In this review, the workflow of applying culture-independent HTS to food matrices is described. The current scenario and future perspectives of HTS uses to study food microbiota are presented, and the decision-making process leading to the best choice of working conditions to fulfill the specific needs of food research is described.
CK2α, over-expressed in human malignant pleural mesothelioma, regulates the Hedgehog signaling pathway in mesothelioma cells (2014)

Thus, we report for the first time that over-expressed CK2α positively regulate Hh/Gli1 signaling in human mesothelioma.
Adding casein phosphopeptide-amorphous calcium phosphate to sports drinks to eliminate in vitro erosion. (2005)

Adding casein phosphopeptide-stabilized amorphous calcium phosphate to the sports drink Powerade significantly reduced the beverage's erosivity without affecting the product's taste.
Purification and Characterization of Diacylglycerol Acyltransferase from the Lipid Body Fraction of an Oleaginous Fungus (1997)

Diacylglycerol acyltransferase (DGAT) [EC 2.3.1.20] was purified to apparent homogeneity from the lipid body fraction of an oleaginous fungus, Mortierella ramanniana var. angulispora. The enzyme was solubilized from the lipid body fraction with 0.1% Triton X-100, and purified by subsequent column chromatography on Yellow 86 agarose, Superdex-200, Heparin-Sepharose, second Superdex-200, and second Yellow 86 agarose. The enzyme activity was finally enriched 4,802-fold over that of the starting 1,500X g supernatant. The apparent molecular mass of the enzyme was 53 kDa on SDS polyacrylamide gel electrophoresis. The purified enzyme did not exhibit glycerol-3-phosphate acyltransferase, lysophosphatidic acid acyltransferase, lipase, transacylase, or acyl-CoA hydrolase activities, although 2-monoolein was acylated with about a half of the enzyme activity toward 1,2-diolein. The purified DGAT depended on exogenous sn-1,2-diolein and oleoyl-CoA, with the highest activity at about 200 and 20 microM, respectively. Purified DGAT utilized a broad range of molecular species of both diacylglycerol and acyl-CoA as substrates. The highest activity was observed with sn-1,2-diolein and lauroyl-CoA. Anionic phospholipids such as phosphatidic acid (PA) activated the purified enzyme, as found for the Triton X-100 extract. Sphingosine dose-dependently inhibited DGAT activity activated by PA and basal activity without PA. These results provide a basis for further studies on the molecular mechanism of triacylglycerol biosynthesis and lipid body formation, in which DGAT plays an important role.
Superantigens and Chronic Rhinosinusitis: Detection of Staphylococcal Exotoxins in Nasal Polyps (2005)

The current study demonstrates the presence of superantigen toxins in 14 of 29 patients with CRSwNP, with SEB and TSST-1 being the most common. Further studies are necessary to correlate the presence of toxin with the pathological changes present in polyp tissue.
Clinical Application of Volatile Organic Compound Analysis for Detecting Infectious Diseases (2013)

This review article introduces the significance of testing of volatile organic compounds (VOCs) in clinical samples and summarizes important features of some of the technologies. Compared to other human diseases such as cancer, studies on VOC analysis in cases of infectious diseases are limited. Here, we have described results of studies which have used some of the appropriate technologies to evaluate VOC biomarkers and biomarker profiles associated with infections. The publications reviewed include important infections of the respiratory tract, gastrointestinal tract, urinary tract, and nasal cavity. The results highlight the use of VOC biomarker profiles resulting from certain infectious diseases in discriminating between infected and healthy subjects. Infection-related VOC profiles measured in exhaled breath as well as from headspaces of feces or urine samples are a source of information with respect to disease detection. The volatiles emitted in clinical matrices may on the one hand represent metabolites of the infecting pathogen or on the other hand reflect pathogen-induced host responses or, indeed, a combination of both. Because exhaled-breath samples are easy to collect and online instruments are commercially available, VOC analysis in exhaled breath appears to be a promising tool for noninvasive detection and monitoring of infectious diseases.
Selective oxidation of the exonuclease domain of bacteriophage T7 DNA polymerase. (1987)

Bacteriophage T7 DNA polymerase, the product of gene 5 of the phage, has both polymerase and single-and double-stranded DNA 3'-to 5'-exonuclease activities. The exonuclease activities can be inactivated selectively by an oxidation reaction that requires molecular oxygen, a reducing agent, and iron at a concentration less than or equimolar to that of the gene 5 protein. Both exonuclease activities can be diminished by several thousandfold, with only a small decline in the polymerase activity. Escherichia coli thioredoxin, an accessory protein that binds tightly to the gene 5 protein and increases the processivity of the polymerization reaction, has no effect on the rate of oxidation. We propose that iron binds specifically to the exonuclease domain and, in the presence of molecular oxygen and a reducing agent, generates reactive oxygen species that selectively modify amino acid residues essential for the exonuclease activities.
Investigation into the Effects of PEGylation on the Thermodynamic Stability of the WW Domain (2013)

The covalent attachment of poly(ethylene glycol) (PEG) to a protein surface (known as PEGylation), has been demonstrated to increase the serum half-life of therapeutic proteins by reducing kidney clearance and immunogenicity and by protecting against proteolysis. Theses beneficial effects could be further enhanced if PEGylation consistently increased protein conformational stability (i.e. the difference in free energy between the folded and unfolded states). However, the effects of PEGylation on protein conformational stability are unpredictable; PEGylation has been reported to increase, decrease, or have no effect on the conformational stability of medicinal proteins.This thesis details the results of two studies aimed at discovering the structural determinants which influence the thermodynamic impact of PEGylation on the WW domain, a small model protein. Chapter 1 is a brief introduction to protein therapeutics and protein PEGylation. Chapter 2 describes a study which demonstrates that the thermodynamic impact of PEGylation is strongly dependent on the site to which PEG is conjugated. The studies described in Chapter 3 elaborate on this site dependence, and demonstrate that PEG stabilizes the WW domain through interactions with the surface of the folded peptide, and that two factors – the orientation of the PEG chain (relative to the protein surface) and the identity of nearby side chains – play a critical role in determining the thermodynamic impact of PEGylation.
Mannose hyperbranched dendritic polymers interact with clustered organization of DC‐SIGN and inhibit gp120 binding (2006)

DC-SIGN (dendritic cell-specific ICAM-3 grabbing non-integrin) is a C-type lectin receptor of dendritic cells and is involved in the initial steps of numerous infectious diseases. Surface plasmon resonance has been used to study the affinity of a glycodendritic polymer with 32 mannoses, to DC-SIGN. This glycodendrimer binds to DC-SIGN surfaces in the submicromolar range. This binding depends on a clustered organization of DC-SIGN mimicking its natural organization as microdomain in the dendritic cells plasma membrane. Moreover, this compound inhibits DC-SIGN binding to the HIV glycoprotein gp120 with an IC50 in the micromolar range and therefore can be considered as a potential antiviral drug.
Sex, Gender, and Pain: An Overview of a Complex Field (2008)

Traditionally, biomedical research in the field of pain has been conducted with male animals and subjects. Over the past 20-30 yr, it has been increasingly recognized that this narrow approach has missed an important variable: sex. An ever-increasing number of studies have established sex differences in response to pain and analgesics. These studies have demonstrated that the differences between the sexes appear to have a biological and psychological basis. We will provide brief review of the epidemiology, rodent, and human experimental findings. The controversies and widespread disagreement in the literature highlight the need for a progressive approach to the questions involving collaborative efforts between those trained in the basic and clinical biomedical sciences and those in the epidemiological and social sciences. In order for patients suffering from acute and/or chronic pain to benefit from this work, the approach has to involve the use or development of clinically relevant models of nociception or pain to answer the basic, but complex, question. The present state of the literature allows no translation of the work to our clinical decision-making.
Optical devices from AlGaAs-GaAs HBTs heavily doped with amphoteric Si (1995)

A new optoelectronic multifunctional device, having triple function of light emission, detection and amplification have been developed and some preliminary integrated circuits are demonstrated. The devices consist of N-p-n or N-P-n AlGaAs-GaAs HBT utilizing amphoteric Si heavily-doped GaAs or AlGaAs p-type base layer. Maximum current gain of 3600, and light output power of about 0.17 /spl mu/W with 100 /spl mu/A base current (I/sub b/) in transistor mode operation and of about 10 /spl mu/W with I/sub b/=40 mA in diode mode operation are obtained. The optical emission wavelengths in both are about 0.85-0.86 /spl mu/m. Optical gain of about 130 was obtained near the 0.86 /spl mu/m wavelength as a detection transistor. Spectrum matching between emission and detection wavelength range is achieved. Some monolithic integrated circuits constituted of the transistors are proposed and demonstrated successfully. The relationship between current gain and radiative quantum efficiency at the transistor operation is also discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Interweaving mobile games with everyday life (2006)

We introduce a location--based game called Feeding Yoshi that provides an example of seamful design, in which key characteristics of its underlying technologies-the coverage and security characteristics of WiFi-are exposed as a core element of gameplay. Feeding Yoshi is also a long--term, wide--area game, being played over a week between three different cities during an initial user study. The study, drawing on participant diaries and interviews, supported by observation and analysis of system logs, reveals players' reactions to the game. We see the different ways in which they embedded play into the patterns of their daily lives, augmenting existing practices and creating new ones, and observe the impact of varying location on both the ease and feel of play. We identify potential design extensions to Feeding Yoshi and conclude that seamful design provides a route to creating engaging experiences that are well adapted to their underlying technologies.
Human microvascular endothelial cells use beta 1 and beta 3 integrin receptor complexes to attach to laminin. (1990)

Microvascular endothelial cells (MEC) use a set of surface receptors to adhere not only to the vascular basement membrane but, during angiogenic stimulation, to the interstitium. We examined how cultured human MEC interact with laminin-rich basement membranes. By using a panel of monoclonal antibodies, we found that MEC cells express a number of integrin-related receptor complexes, including alpha 1 beta 1, alpha 2 beta 1, alpha 3 beta 1, alpha 5 beta 1, alpha 6 beta 1, alpha V beta 3. Attachment to laminin, a major adhesive protein in basement membranes, was studied in detail. Blocking monoclonal antibodies specific to different integrin receptor complexes showed that the alpha 6 beta 1 complex was important for MEC adhesion to laminin. In addition, blocking antibody also implicated the vitronectin receptor (alpha V beta 3) in laminin adhesion. We used ligand affinity chromatography of detergent-solubilized receptor complexes to further define receptor specificity. On laminin-Sepharose columns, we identified several integrin receptor complexes whose affinity for the ligand was dependent on the type of divalent cation present. Several beta 1 complexes, including alpha 1 beta 1, alpha 2 beta 1, and alpha 6 beta 1 bound strongly to laminin. In agreement with the antibody blocking experiments, alpha V beta 3 was found to bind well to laminin. However, unlike binding to its other ligands (e.g., vitronectin, fibrinogen, von Willebrand factor), alpha V beta 3 interaction with laminin did not appear to be Arg-Gly-Asp (RGD) sensitive. Finally, immunofluorescent staining demonstrated both beta 1 and beta 3 complexes in vinculin-positive focal adhesion plaques on the basal surface of MEC adhering to laminin-coated substrates. The results indicate that both these subfamilies of integrin heterodimers are involved in promoting MEC adhesion to laminin and the vascular basement membrane.