gebhart/patrepeval huggingface dataset:
Full-Scale IFAS Investigation: Plant Data and Batch Testing to Assess Kinetics, Mass Transfer Effects and Population Dynamics (2010)

Full-Scale IFAS Investigation: Plant Data and Batch Testing to Assess Kinetics, Mass Transfer Effects and Population DynamicsA 2.0 MGD IFAS demonstration process was operated to evaluate nitrogen removal performance and to develop design criteria for a full plant upgrade. As part of this study, a number of additional sampling and analysis efforts were targeted at localizing AOB and NOB activity within the process, measuring the impacts of oxygen and substrate mass transfer limitations, and monitoring nitrifier kinetics...Author(s)Richard JonesCharles B. BottBob RutherfordRick BaumlerDavid WaltripSourceProceedings of the Water Environment FederationSubjectSession 61: Biofilm Processes IIDocument typeConference PaperPublisherWater Environment FederationPrint publication date Jan, 2010ISSN1938-6478SICI1938-6478(20100101)2010:12L.4221;1-DOI10.2175/193864710798182376Volume / Issue2010 / 12Content sourceWEFTECFirst / last page(s)4221 - 4247Copyright2010Word count167Subject keywordsIFASnitrificationdissolved oxygenmixingmodellingmass transfer
Chemiluminescent acridan phosphate labelling compounds for detection in gels (2001)

We have developed a chemiluminescent acridan phosphate labelling compound which produces a flash of light upon chemical triggering. Sequential treatment of the label with acid and a strong base, one of which contains a peroxide, initiates light emission as a rapid flash lasting 1--2 s. Labelling of analytes with these compounds permits their direct detection in a non-enzymatic assay format. Representative compounds have been linked to BSA as a model protein analyte and detected by chemiluminescence assay. Light intensity correlated with the amount of BSA over six orders of magnitude, permitting the detection of 50 amol of protein in solution. We have also demonstrated for the first time that labelled proteins can be separated by electrophoresis without destruction of the label and that chemiluminescence can be produced and detected directly in the gel. The ease, speed and sensitivity of detection by this new method should enable the development of simpler assays for a wide variety of analytes.
Pilus biogenesis by the chaperone-usher pathway. (2014)

<title>Abstract</title> Gram-negative bacteria display a variety of multi-subunit fibrillar structures on their cell surface called 'pili' or 'fimbriae'. Originally based on the filament morphology and the biogenesis machinery, pili are currently classified into five different families: (i) the curli, (ii) the type IV pili, (iii) the type III secretion system needle, (iv) the type IV secretion system pili, and (v) the chaperone-usher (CU) pili. This chapter reviews the biogenesis machinery of one of the most widespread and important microbial adhesion factor, the chaperone-usher (CU) pili, as well as its structure, function and polymerization. The CU pili are made of different subunits that polymerize to either thin flexible fibres or rigid long filaments. The main function of the CU pili is the adhesion to the host cells, mediated by a specialized pilus subunit, the adhesin, often containing a lectin domain that specifically recognizes the lining sugars of the target tissue, thereby defining the host tropism. Generally clustered under the same promoter, all the necessary components for the CU pili biogenesis are encoded within the same operon and it has been shown that multiple CU pathway clusters may be present within the same genome, extending the range of receptors the same bacterium might be able to adhere to.
Ex Vivo Expansion of Retrovirally Transduced Primate CD34+ Cells Results in Overrepresentation of Clones With MDS1/EVI1 Insertion Sites in the Myeloid Lineage After Transplantation (2010)

Activation of proto-oncogenes by retroviral insertion is an important issue delaying clinical development of gene therapy. We have reported the nonrandom persistence of hematopoietic clones with vector insertions within the MDS1/EVI1 locus following transplantation of rhesus macaques. We now ask whether prolonged culture of transduced CD34(+) cells before transplantation selects for clones with insertions in the MDS1/EVI11 or other proto-oncogene loci. CD34(+) cells were transduced with standard retroviral vectors for 4 days and then continued in culture for an additional 6 days before transplantation. A 15% of insertions identified in granulocytes 6 months post-transplant were in MDS1/EVI11, significantly increased compared to the frequency in animals transplanted with cells immediately following transduction. MDS1/EVI1 clones became more dominant over time post-transplantation in one animal that was followed long term, accompanied by an increased overall copy number of vector-containing granulocytes, with one MDS1/EVI1 clone eventually accounting for 100% of transduced granulocytes and marrow colony-forming unit (CFU). This vector insertion increased the expression of Evi1 mRNA. There was no overrepresentation of MDS1/EVI1 insertions contributing to lymphoid lineages. Strategies involving prolonged ex vivo expansion of transduced cells may increase the risk of genotoxicity.
Patient-reported experience of chemotherapy: Expectations versus reality (2008)

20686 Background: Patients’ pretreatment expectations regarding chemotherapy are framed significantly by counseling provided by the treating oncologist during the consent process. The clinician’s proficiency in this regard, and the extent to which patients’ experience with chemotherapy matches their pre-treatment expectations, has never been formally evaluated. This is an exploratory study, to determine to what degree variance between expectations and actual experience occurs, and to identify predictors of this divergence. Method: Patients who had completed a first course of chemotherapy at Thomas Jefferson University Hospital, and who were clinically in remission, were asked to fill out an anonymous and voluntary survey. Results: 50 patients responded. All had completed their planned chemotherapy, and 16 had experienced predefined complications. In response to the statement “my therapy proceeded as expected”, 74% agreed, 20% were ‘neutral’, and 6% disagreed. The majority (58%) stated that their chemotherapy experience was ‘better than I expected’, 17% said ‘about what I expected’, and 8% said ‘worse than I expected’. All patients (100%) indicated that, with the benefit of hindsight, they would still have chosen to proceed with the chemotherapy they received. There was no correlation between patients’ reported experience with chemotherapy and any of the following parameters; type of chemotherapy, presence of complications, patient’s satisfaction with consenting process, and patients’ expectation of cure from disease. (The sample size limits the statistical power to detect the above correlations.) Conclusion: In this single-institution study, an overwhelming majority of patients indicated that their experience with chemotherapy was either as, or better, than expected. No patients regretted their decision to receive chemotherapy, despite the presence of complications in a sizable proportion. To attribute this unexpected (and satisfying) result to the proficiency of clinicians at our institution in consenting patients would probably be an oversimplification; among other factors, we note that the prevalence of negative misconceptions about the rigor of chemotherapy in the lay population may equally have accounted for our result. No significant financial relationships to disclose.
Tricarbonylbis(trichlorosilyl)nickel. An unusual carbonyl complex of nickel(II) (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTricarbonylbis(trichlorosilyl)nickel. An unusual carbonyl complex of nickel(II)Stuart K. Janikowski, Lewis J. Radonovich, Thomas J. Groshens, and Kenneth J. KlabundeCite this: Organometallics 1985, 4, 2, 396–398Publication Date (Print):February 1, 1985Publication History Published online1 May 2002Published inissue 1 February 1985https://pubs.acs.org/doi/10.1021/om00121a036https://doi.org/10.1021/om00121a036research-articleACS PublicationsRequest reuse permissionsArticle Views116Altmetric-Citations28LEARN 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
Regulation of Inducible Enzyme Synthesis in Escherichia coli by Cyclic Adenosine 3',5'-Monophosphate (1969)

Abstract Cyclic adenosine 3',5'-monophosphate (cyclic AMP) overcomes the repression by glucose of the synthesis of the following inducible enzymes and proteins in Escherichia coli: β-galactosidase, lac permease, galactokinase, glycerokinase, l-α-glycerophosphate permease, Enzyme II for fructose of the phosphoenolpyruvate phosphotransferase system, l-arabinose permease, tryptophanase, d-serine deaminase, and thymidine phosphorylase. Cyclic AMP overcomes the repression by glucose of the synthesis of β-galactosidase in Serratia marcescens F lac, Salmonella typhimurium F lac, Proteus inconstans P lac, and Aerobacter aerogenes; it also overcomes the repression by glucose of galactokinase synthesis in S. typhimurium. A number of analogues of cyclic AMP failed to mimic or inhibit the action of the cyclic nucleotide on β-galactosidase synthesis. Since glucose lowers the intracellular concentration of cyclic AMP in E. coli, we propose that the intracellular level of cyclic AMP regulates the rate of synthesis of many inducible enzymes in E. coli and other microorganisms and that glucose lowers the rate of synthesis of these enzymes by decreasing the intracellular level of cyclic AMP.
Identification of a novel class of covalent modifiers of hemoglobin as potential antisickling agents (2015)

Aromatic aldehydes and ethacrynic acid (ECA) exhibit antipolymerization properties that are beneficial for sickle cell disease therapy. Based on the ECA pharmacophore and its atomic interaction with hemoglobin, we designed and synthesized several compounds - designated as KAUS (imidazolylacryloyl derivatives) - that we hypothesized would bind covalently to βCys93 of hemoglobin and inhibit sickling. The compounds surprisingly showed weak allosteric and antisickling properties. X-ray studies of hemoglobin in complex with representative KAUS compounds revealed an unanticipated mode of Michael addition between the β-unsaturated carbon and the N-terminal αVal1 nitrogen at the α-cleft of hemoglobin, with no observable interaction with βCys93. Interestingly, the compounds exhibited almost no reactivity with the free amino acids, L-Val, L-His and L-Lys, but showed some reactivity with both glutathione and L-Cys. Our findings provide a molecular level explanation for the compounds biological activities and an important framework for targeted modifications that would yield novel potent antisickling agents.
Implementation of Accurate Per-Flow Packet Loss Monitoring in Segment Routing over IPv6 Networks (2020)

Segment Routing over IPv6 (SRv6 in short) is a networking solution for IP backbones and datacenters, which has been recently adopted in several of large scale network deployments. The SRv6 research, standardization and implementation activities are going on at a remarkable pace. In particular, a number of Internet Drafts have been submitted related to the Performance Monitoring (PM) of flows in an SRv6 network. In this paper we discuss the proposed PM approaches, considering both data plane and control plane aspects and focusing on loss monitoring. Then we describe the implementation of a per-flow packet loss measurement (PF-PLM) solution based on the “alternate marking” method. Our implementation is based on Linux kernel networking and it is open source. We describe a platform that can be used to validate the standardization proposals from a functional perspective and the implemented solution from the performance point of view. We analyze two different design choices for the implementation of PF-PLM and evaluate their impact on the maximum forwarding throughput of a software based (Linux) router.
Isolation and Characterization of a Sex-Specific Lectin in a Marine Red Alga, Aglaothamnion oosumiense Itono (2012)

In red algae, spermatial binding to female trichogynes is mediated by a lectin-carbohydrate complementary system. Aglaothamnion oosumiense is a microscopic filamentous red alga. The gamete recognition and binding occur at the surface of the hairlike trichogyne on the female carpogonium. Male spermatia are nonmotile. Previous studies suggested the presence of a lectin responsible for gamete recognition on the surface of female trychogynes. A novel N-acetyl-D-galactosamine-specific protein was isolated from female plants of A. oosumiense by affinity chromatography and named AOL1. The lectin was monomeric and did not agglutinate horse blood or human erythrocytes. The N-terminal amino acid sequence of the protein was analyzed, and degenerate primers were designed. A full-length cDNA encoding the lectin was obtained using rapid amplification of cDNA ends-PCR (RACE-PCR). The cDNA was 1,095 bp in length and coded for a protein of 259 amino acids with a deduced molecular mass of 21.4 kDa, which agreed well with the protein data. PCR analysis using genomic DNA showed that both male and female plants have this gene. However, Northern blotting and two-dimensional electrophoresis showed that this protein was expressed 12 to 15 times more in female plants. The lectin inhibited spermatial binding to the trichogynes when preincubated with spermatia, suggesting its involvement in gamete binding.
Supplementary Figures S3-S6 from Real-time, Near-Infrared Fluorescence Imaging with an Optimized Dye/Light Source/Camera Combination for Surgical Guidance of Prostate Cancer (2023)

&lt;p&gt;Supplementary Figures S3-S6. S3. PSMA expression in LMD-PSMA cells. S4. PSMA expression has no effect on cell growth. S5. Cell migration is similar between LMD and LMD-PSMA cells. S6. LMD and LMD-PSMA cells both are capable of forming xenografts.&lt;/p&gt;
Alternative Computational Protocols for Supercharging Protein Surfaces for Reversible Unfolding and Retention of Stability (2020)

Reengineering protein surfaces to exhibit high net charge, referred to as “supercharging”, can improve reversibility of unfolding by preventing aggregation of partially unfolded states. Incorporation of charged side chains should be optimized while considering structural and energetic consequences, as numerous mutations and accumulation of like-charges can also destabilize the native state. A previously demonstrated approach deterministically mutates flexible polar residues (amino acids DERKNQ) with the fewest average neighboring atoms per side chain atom (AvNAPSA). Our approach uses Rosetta-based energy calculations to choose the surface mutations. Both protocols are available for use through the ROSIE web server. The automated Rosetta and AvNAPSA approaches for supercharging choose dissimilar mutations, raising an interesting division in surface charging strategy. Rosetta-supercharged variants of GFP (RscG) ranging from −11 to −61 and +7 to +58 were experimentally tested, and for comparison, we re-tested the previously developed AvNAPSA-supercharged variants of GFP (AscG) with +36 and −30 net charge. Mid-charge variants demonstrated ∼3-fold improvement in refolding with retention of stability. However, as we pushed to higher net charges, expression and soluble yield decreased, indicating that net charge or mutational load may be limiting factors. Interestingly, the two different approaches resulted in GFP variants with similar refolding properties. Our results show that there are multiple sets of residues that can be mutated to successfully supercharge a protein, and combining alternative supercharge protocols with experimental testing can be an effective approach for charge-based improvement to refolding.
Enhancement of indium-based organic photovoltaics (2012)

We report on the optimization of poly(3-hexylthiopene) and [6,6]-phenyl C61 butyric acid methyl ester bulk heterojunction photovoltaics using indium tin oxide anode and metallic indium cathode. The devices are fabricated, tested, and stored at ambient atmosphere, without encapsulation. By tuning the spin coating conditions for the hole-transport and the photoactive layers, along with a combination of mechanical pressure and annealing conditions during the cathode deposition, a 3-fold improvement is achieved, while maintaining devices stability. Consequently, the cells undergo a less than 10% loss in power conversion efficiency after 200 days.
The synthesis of a series of 7‐amino‐1‐cyclopropyl‐8‐fluoro‐1,4‐dihydro‐4‐oxo‐1,6‐naphthyridine‐3‐carboxylic acids as potential antibacterial agents (1993)

Abstract A series of 7‐amino‐1‐cyclopropyl‐1,4‐dihydro‐8‐fluoro‐4‐oxo‐1,6‐naphthyridine‐3‐carboxylic acids has been prepared and evaluated for antibacterial activity. These compounds were prepared by the displacement of the chloro substituent from 7‐chloro‐1‐cyclopropyl‐1,4‐dihydro‐8‐fluoro‐4‐oxo‐1,6‐naphthyridine‐3‐carboxylic acid employing the requisite nitrogen nucleophile to produce the title compounds. The naphthyridine acid was synthesized in ten steps from ethyl 2,4‐dihydroxy‐3‐nitro‐5‐pyridinecarboxylate. The key step in the sequence was a Schiemann reaction carried out using the hexafluorophosphate salt of the diazonium ion derived from ethyl 3‐amino‐2,4‐dichloro‐5‐pyridinecarboxylate.
Optical coherence tomography for medical diagnostics (1993)

Techniques for non-invasive biomedical imaging include nuclear magnetic resonance, ultrasound, positron emission tomography, x-ray computed to- mography, and optical transillumination. Each of these methods has dif- ferent advantages and limitations and has found particular applications in medicine. Optical imaging of tissue offers the potential of a non-invasive diagnostic with non-ionizing radiation and the possibility of using spectro- scopic properties to distinguish tissue type and probe metabolic function.
The induction of secondary cytolytic T lymphocytes by solubilized membrane proteins. (1978)

Membrane-bound antigens responsible for induction of a secondary allogeneic murine cytolytic T-cell (CTL) response have been obtained in a soluble, biologically active form by deoxycholate solubilization of tumor cell plasma membranes. The active proteins are soluble by the criteria of both ultracentrifugation and gel filtration. The immunological specificity of the induced CTL and removal of the activity from solution by treatment with B6 anti-P815 (anti-H-2d) antiserum and Protein A-Sepharose demonstrate that the CTL-inducing activity is dependent upon solubilized major histocompatibility complex antigens.
Gene structure and promoter functional analysis of the marmoset type II GnRH receptor (2007)

The marmoset type II GnRH receptor (GnRH-R) gene has the same structure and genomic organisation as the human and other type II GnRH-R genes. The gene consists of three exons and two introns and overlaps in the antisense orientation on its 5' end with peroxisomal membrane protein 11beta and on its 3' end with the RNA-binding motif protein 8A. However, these genes occur only at one locus in the marmoset genome, while in the human at two loci. Employing 5' rapid amplification of cDNA ends demonstrated that the marmoset type II GnRH-R gene has two transcriptional start sites at -341 and -567 nucleotides relative to the translational start codon and both start sites lack TATA and CAAT consensus sequences. A luciferase reporter construct with a 2.3 kb 5' flanking region of the type II GnRH-R gene was active in a wide variety of cell lines tested, consistent with the wide tissue expression of the receptor. Progressive 5' and 3' deletions were employed to identify sequences required for basal expression of the type II GnRH-R gene. This analysis identified negative regulatory elements in the regions -2342/-1995, -1679/-1084 and -458/-1 and positive regulatory elements in the regions -1995/-1679, -1084/-458 and -458/-1 relative to the translational start site. The strongest of the positive regions located between -766/-665 has enhancer activity when cloned in front of a heterologous minimal promoter and is critical for basal expression of the type II GnRH-R.
Recycling for Electric Home Appliances. Measures and Future Problems Manufactures. (1999)

20世紀型の文化生活では, より多くの物を消費する者が裕福な者であった。それは物質とエネルギーを大量に消費し廃棄する文明であった。使い捨て文化の先に, 持続的な豊かさはない。この生活スタイルと価値観を変えずに来世紀の地球環境問題は解決できない。消費と廃棄を出来うる限り小さくした「循環型社会」の構築が緊急の課題となってきた。家電製品の普及でこの文化的生活の向上を目指してきた日本の家電製品業界は, 2001年4月に施行される「特定家庭用機器再商品化法」 (家電リサイクル法) を通じ, この循環型社会の構築に取り組む。エアコン, テレビ, 冷蔵庫, 洗濯機は個々の企業が, 消費者から使用済み製品を引き取り, その素材の一定量を再商品化する資源循環型の企業に変身せねばならない。これまでの取り組み, 課題と予想される業界と社会の変化を紹介する。
A Network Coding Approach to Network Tomography (2009)

Network tomography aims at inferring internal network characteristics based on measurements at the edge of the network. In loss tomography, in particular, the characteristic of interest is the loss rate of individual links. There is a signiï¬cant body of work dedicated to this problem using multicast and/or unicast end-to-end probes. Independently, recent advances in network coding have shown that there are several advantages from allowing intermediate nodes to process and combine, in addition to just forward, packets. In this paper, we re-visit the problem of loss tomography in networks that have network coding capabilities. We design a novel framework for estimating link loss rates, which leverages network coding capabilities to improve several aspects of the tomography problem, including the identiï¬ability of links, the tradeoff between accuracy of estimation and bandwidth efï¬ciency, and the complexity of probe path selection. We present ï¬rst the case of tree topologies and then the case of general graphs. In the latter case, the beneï¬ts of our approach are even more pronounced compared to standard techniques but we also face novel challenges, such as dealing with cycles and multiple paths between sources and receivers.
The U6 small nuclear RNA fromTrypanosoma brucei (1988)

Journal Article The U6 small nuclear RNA from Trypanosoma brucei Get access Christian Tschudi, Christian Tschudi Yale MacArthur Center for Molecular Parasitology, Department of Internal Medicine, Yale University School of Medicine333 Ceder Street New Haven, CT 06510, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Adrian R. Krainer, Adrian R. Krainer 1Cold Spring Harbor LaboratoryP0 Box 100, Cold Spring Harbor, NY 11724, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Elisabetta Ullu Elisabetta Ullu Yale MacArthur Center for Molecular Parasitology, Department of Internal Medicine, Yale University School of Medicine333 Ceder Street New Haven, CT 06510, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 16, Issue 23, 9 December 1988, Page 11375, https://doi.org/10.1093/nar/16.23.11375 Published: 09 December 1988 Article history Accepted: 24 October 1988 Published: 09 December 1988