gebhart/patrepeval huggingface dataset:
A Systems Biology View of Responses to Lignin Biosynthesis Perturbations inArabidopsis (2012)

Lignin engineering is an attractive strategy to improve lignocellulosic biomass quality for processing to biofuels and other bio-based products. However, lignin engineering also results in profound metabolic consequences in the plant. We used a systems biology approach to study the plant's response to lignin perturbations. To this end, inflorescence stems of 20 Arabidopsis thaliana mutants, each mutated in a single gene of the lignin biosynthetic pathway (phenylalanine ammonia-lyase1 [PAL1], PAL2, cinnamate 4-hydroxylase [C4H], 4-coumarate:CoA ligase1 [4CL1], 4CL2, caffeoyl-CoA O-methyltransferase1 [CCoAOMT1], cinnamoyl-CoA reductase1 [CCR1], ferulate 5-hydroxylase [F5H1], caffeic acid O-methyltransferase [COMT], and cinnamyl alcohol dehydrogenase6 [CAD6], two mutant alleles each), were analyzed by transcriptomics and metabolomics. A total of 566 compounds were detected, of which 187 could be tentatively identified based on mass spectrometry fragmentation and many were new for Arabidopsis. Up to 675 genes were differentially expressed in mutants that did not have any obvious visible phenotypes. Comparing the responses of all mutants indicated that c4h, 4cl1, ccoaomt1, and ccr1, mutants that produced less lignin, upregulated the shikimate, methyl-donor, and phenylpropanoid pathways (i.e., the pathways supplying the monolignols). By contrast, f5h1 and comt, mutants that provoked lignin compositional shifts, downregulated the very same pathways. Reductions in the flux to lignin were associated with the accumulation of various classes of 4-O- and 9-O-hexosylated phenylpropanoids. By combining metabolomic and transcriptomic data in a correlation network, system-wide consequences of the perturbations were revealed and genes with a putative role in phenolic metabolism were identified. Together, our data provide insight into lignin biosynthesis and the metabolic network it is embedded in and provide a systems view of the plant's response to pathway perturbations.
ChemInform Abstract: OXIDATION OF N‐HYDROXY‐AMINES BY SULFURYL CHLORIDE (1977)

Abstract Oxidation des Hydroxylamins (I) mit SOzClg in Äther bei ‐30°C ergibt das Salz (II), dessen KOH‐Hydrolyse das Nitron (III) liefert.
Phosphorus-Nitrogen Compounds. VII.1,2 Urea, Aziridinecarboxamide, and Semicarbazide Derivatives (1967)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhosphorus-Nitrogen Compounds. VII.1,2 Urea, Aziridinecarboxamide, and Semicarbazide DerivativesLindley A. CatesCite this: J. Med. Chem. 1967, 10, 5, 924–927Publication Date (Print):September 1, 1967Publication History Published online1 May 2002Published inissue 1 September 1967https://pubs.acs.org/doi/10.1021/jm00317a038https://doi.org/10.1021/jm00317a038research-articleACS PublicationsRequest reuse permissionsArticle Views81Altmetric-Citations10LEARN 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
A phase Ib/IIa, open‐label, multiple ascending‐dose trial of domagrozumab in fukutin‐related protein limb‐girdle muscular dystrophy (2021)

We conclude that, although domagrozumab was safe in patients in limb-girdle muscular dystrophy type 2I/R9, there was no clear evidence supporting its efficacy in improving muscle strength or function.
Partial purification and characterization of a growth factor for macrophage progenitor cells with high proliferative potential in mouse bone marrow (1982)

A population of macrophage progenitor cells, with high proliferative potential, has recently been demonstrated in postfluorouracil-treated and normal mouse bone marrow (BM) in vitro, when the newly discovered growth factor (synergistic activity, SA) is combined with a macrophage colony-stimulating factor (CSF) as a proliferative stimulus. SA, shown to be present in human spleen and placental conditioned media (HSCM and HPCM, respectively) have been studied and found to be unstable to trypsin digestion and to heating at 50 degrees C or above; stable between pH 4 and 9; nonadherent to Con-A-Sepharose; and to have an isoelectric point between pH 5 and 5.8 and a molecular weight of between 14,000 and 21,000 as indicated by gel filtration chromatography. SAs from both HSCM and HPCM have been purified 89- and 122-fold, respectively, by precipitation of extraneous proteins at pH 5 followed by chromatographing twice on Sephacryl S200. Neither of these partially purified SAs contain any CSF for mouse BM. These results indicate that the SAs from HSCM and HPCM may be closely related and that they are structurally different from CSFs derived from various murine sources that have been shown to be stable to proteolytic enzymes and heat.
A multiscale real-time navigation and communication satellite simulation model for OMNeT++ (2008)

This paper presents the first steps of developing the Galileo Satellite Communication Simulator (GSCS) based on the INET Framework [2] of OMNeT++ simulation engine [1]. We present our mobility model for the accurate prediction and modeling of satellite motion using NORAD's (North American Aerospace
Selection and Identification of a DNA Aptamer Targeted to Vibrio parahemolyticus (2012)

A whole-bacterium systemic evolution of ligands by exponential enrichment (SELEX) method was applied to a combinatorial library of FAM-labeled single-stranded DNA molecules to identify DNA aptamers demonstrating specific binding to Vibrio parahemolyticus . FAM-labeled aptamer sequences with high binding affinity to V. parahemolyticus were identified by flow cytometric analysis. Aptamer A3P, which showed a particularly high binding affinity in preliminary studies, was chosen for further characterization. This aptamer displayed a dissociation constant (K(d)) of 16.88 ± 1.92 nM. Binding assays to assess the specificity of aptamer A3P showed a high binding affinity (76%) for V. parahemolyticus and a low apparent binding affinity (4%) for other bacteria. Whole-bacterium SELEX is a promising technique for the design of aptamer-based molecular probes for microbial pathogens that does not require the labor-intensive steps of isolating and purifying complex markers or targets.
Microfluidics for multiscale studies of biomolecular condensates (2022)

Membraneless organelles formed through condensation of biomolecules in living cells have become the focus of sustained efforts to elucidate their mechanisms of formation and function. These condensates perform a range of vital functions in cells and are closely connected to key processes in functional and aberrant biology. Since these systems occupy a size scale intermediate between single proteins and conventional protein complexes on the one hand, and cellular length scales on the other hand, they have proved challenging to probe using conventional approaches from either protein science or cell biology. Additionally, condensate can form, solidify and perform functions on various time-scales. From a physical point of view, biomolecular condensates are colloidal soft matter systems, and microfluidic approaches, which originated in soft condensed matter research, have successfully been used to study biomolecular condensates. This review explores how microfluidics have aided condensate research into the thermodynamics, kinetics and other properties of condensates, by offering high-throughput and novel experimental setups.
Intersubunit movement is required for ribosomal translocation (2007)

Translocation of tRNA and mRNA during protein synthesis is believed to be coupled to structural changes in the ribosome. The "ratchet model," based on cryo-EM reconstructions of ribosome complexes, invokes relative movement of the 30S and 50S ribosomal subunits in this process; however, evidence that directly demonstrates a requirement for intersubunit movement during translocation is lacking. To address this problem, we created an intersubunit disulfide cross-link to restrict potential movement. The cross-linked ribosomes were unable to carry out polypeptide synthesis; this inhibition was completely reversed upon reduction of the disulfide bridge. In vitro assays showed that the cross-linked ribosomes were specifically blocked in elongation factor G-dependent translocation. These findings show that intersubunit movement is required for ribosomal translocation, accounting for the universal two-subunit architecture of ribosomes.
PERFORMANCEOFTHESLD WARM IRONCALORIMETER PRE-PROTOTYPEt (1986)

Theperformance ofa pre-prototype oftheSLD Warm IronCalorimeter (WIC)build withproportional tubecathodepadreadout hasbeenstudied. Thecalorimeter wasfound tohaveanaverage resolution of36.7±0.2%formuonsat2.0, 5.0and10.5GeVand81±2%/V'i- forpion showers at5.0and 10.5GeV.Themeanenergy foundforthepionshowers was consistent withalinear dependance onenergy within these standard deviations.
50 MHz bistatic wind profiling (2002)

Conceptual designs are presented for an improved Doppler wind profiler system to support space shuttle launches from NASA Kennedy Space Center. This system is based upon extending KSC's current monostatic wind profiler to the bistatic configuration. Results are presented for several bistatic antenna sub-systems that produced acceptable wind profiler performance.
Supplementary Figure from Tadalafil Enhances Immune Signatures in Response to Neoadjuvant Nivolumab in Resectable Head and Neck Squamous Cell Carcinoma (2023)

Supplementary Figure from Tadalafil Enhances Immune Signatures in Response to Neoadjuvant Nivolumab in Resectable Head and Neck Squamous Cell Carcinoma
Blocked or Broken? Automatically Detecting When Privacy Interventions Break Websites (2022)

A core problem in the development and maintenance of crowd-sourced filter lists is that their maintainers cannot confidently predict whether (and where) a new filter list rule will break websites. This is a result of enormity of the Web, which prevents filter list authors from broadly understanding the impact of a new blocking rule before they ship it to millions of users. The inability of filter list authors to evaluate the Web compatibility impact of a new rule before shipping it severely reduces the benefits of filter-list-based content blocking: filter lists are both overly-conservative (i.e. rules are tailored narrowly to reduce the risk of breaking things) and error-prone (i.e. blocking tools still break large numbers of sites). To scale to the size and scope of the Web, filter list authors need an automated system to detect when a new filter rule breaks websites, before that breakage has a chance to make it to end users. In this work, we design and implement the first automated system for predicting when a filter list rule breaks a website. We build a classifier, trained on a dataset generated by a combination of compatibility data from the EasyList project and novel browser instrumentation, and find it is accurate to practical levels (AUC 0.88). Our open source system requires no human interaction when assessing the compatibility risk of a proposed privacy intervention. We also present the 40 page behaviors that most predict breakage in observed websites.
Cloning, sequencing and expression of the glutamine synthetase structural gene (glnA) from the obligate methanotroph Methylococcus capsulatus (Bath) (1990)

The structural gene (glnA) encoding the ammonia-assimulation enzyme glutamine synthetase (GS) has been cloned from the obligate methanotroph Methylococcus capsulatus (Bath). Complementation of Escherichia coli glnA mutants was demonstrated. In vitro expression analysis revealed that the cloned glnA gene coded for a polypeptide of apparent Mr 60,000, as determined by PAGE. Expression of the M. capsulatus (Bath) glnA gene in E. coli was regulated by nitrogen levels in an Ntr+ but not an Ntr- background. The nucleotide sequence of the M. capsulatus (Bath) glnA gene and flanking sequences was determined. This gene, of 1407 bp, encoded a polypeptide of Mr 51717 containing 468 amino acids. The 5' leader region contained three putative promoters. Promoters P1 and P3 resembled the canonical -10 -35 E. coli-type promoter. Promoter P2, which was located between P1 and P3, resembled the NtrA-dependent promoters of enteric organisms. A potential NtrC-binding site was also determined, flanking the Pribnow box at P1. Comparisons of nucleotide-derived amino acid sequences of GS enzymes from prokaryotes and eukaryotes with GS from M. capsulatus are made.
Optical detection of ammonia inside a stack: Comparison of different techniques (2020)

The quantitative detection of pollutants in industrial emissions, in particular the emissions of biomass burners, requires different types of analyzers. Optical devices are usually sensitive to the transparency and dirtiness of the exhaust gases, so optical measurements are normally carried out by extracting the samples from the stacks. This paper has a twofold aim. First, we will prove that the molecular composition of the exhaust mixture (in particular the concentration of water and carbon dioxide) can deeply affect the outcome of optical analyzers, depending on the adopted detection technique. This is a critical issue, in particular with a view to the necessity of providing suitable reference methods for monitoring biomass burners emissions. Second, we will show how it is possible to measure inside an artificial stack by using an optical multipass cell located across the gas flow, even at 140 °C, or in presence of soot.
Prediction of missense mutation functionality depends on both the algorithm and sequence alignment employed (2011)

Multiple algorithms are used to predict the impact of missense mutations on protein structure and function using algorithm-generated sequence alignments or manually curated alignments. We compared the accuracy with native alignment of SIFT, Align-GVGD, PolyPhen-2, and Xvar when generating functionality predictions of well-characterized missense mutations (n = 267) within the BRCA1, MSH2, MLH1, and TP53 genes. We also evaluated the impact of the alignment employed on predictions from these algorithms (except Xvar) when supplied the same four alignments including alignments automatically generated by (1) SIFT, (2) Polyphen-2, (3) Uniprot, and (4) a manually curated alignment tuned for Align-GVGD. Alignments differ in sequence composition and evolutionary depth. Data-based receiver operating characteristic curves employing the native alignment for each algorithm result in area under the curve of 78-79% for all four algorithms. Predictions from the PolyPhen-2 algorithm were least dependent on the alignment employed. In contrast, Align-GVGD predicts all variants neutral when provided alignments with a large number of sequences. Of note, algorithms make different predictions of variants even when provided the same alignment and do not necessarily perform best using their own alignment. Thus, researchers should consider optimizing both the algorithm and sequence alignment employed in missense prediction.
ELECTROMAGNETIC IMAGING METHOD BASED ON TIME REVERSAL PROCESSING APPLIED TO THROUGH-THE-WALL TARGET LOCALIZATION (2008)

A time reversal method is studied and adapted to throughthe-wall detection and localization of moving targets. Tests are realised on experimental data in a synthetic aperture radar configuration. The efficiency of the method to extract a moving target from a cluttered environment is proved on experimental data.
Multimedia adaptation in ubiquitous environments (2008)

This paper demonstrates the advantages of using structured multimedia documents for session management and media distribution in ubiquitous environments. We show how document manipulations can be used to perform powerful operations such as content to context adaptation and presentation continuity. When consuming media in ubiquitous environments, where the set of devices surrounding a user may change, dynamic media adaptation and session transfer become primary requirements. This paper presents a working system, based on a representative scenario, in which multimedia content is distributed and adapted to a movable user to best suit his/her contextual situation. The implemented scenario includes the following scenes: content selection using a personal mobile phone, content distribution to the most suitable device according to the user's context, and presentation continuity when the user moves to another location. This paper introduces the underlying document manipulations that turn the scenario into a working system.
Feedback Effects of the Testis on Pituitary Responsiveness to Luteinizing Hormone-Releasing Hormone Infusions in the Ram* (1980)

The present studies examined the effects of both short term and long term alterations in testicular hormone levels on pituitary gonadotropin responses during 4–6 h of constant infusions of LHRH (0.5 μg/min) in the ram. Short term changes in testicular hormone levels were produced either by testosterone (T) infusions [three animals (6.7 μg/min) and 3 animals (83 /xg/min)] beginning 4 h before the LHRH infusion or by castration (n = 4) 2 h before the LHRH infusions. Long term alterations in testicular hormone levels were induced by T injections (T enanthate, 250 mg im twice weekly for 2 weeks) or castration (n = 4) performed 3–4 months before the LHRH infusion. Control LHRH infusions were performed in the same animals 2 weeks before the T studies. For the acute castrations, control studies were undertaken in four animals acutely sham castrated; for chronic castration normal animals were used as controls (n = 5). Acute changes in testicular feedback induced either by castration 2 h before LHRH administration or by several hours of T infusion did not alter the normal patterns of LH and FSH increase and decrease during LHRH infusions. The normal biphasic pattern of increase in plasma LH levels and the monophasic pattern of FSH increase persisted, as did the development of pituitary refractoriness to LHRH stimulation in the last 2–3 h of LHRH administration. In contrast, more chronic changes in testicular feedback induced either by T injections for 2 weeks or by castration 3–4 months before LHRH administration produced definite alterations in pituitary responsiveness. LH secretion from the immediately releasable pool was markedly increased in the chronically castrated animals and decreased by 2 weeks of T administration. LH secretion from the second pool was less affected by 2 weeks of T therapy and was apparently unaffected by chronic castration. Chronic castration led to markedly increased basal FSH levels, but no further increase was seen during LHRH administration. These results demonstrate that in the ram 1) alterations in testicular hormone production require longer than 2–4 h to affect pituitary responsiveness to LHRH, 2) testicular feedback exerts a greater effect on the immediately releasable pool of pituitary LH than on the pool requiring longer LHRH stimulation for release, and 3) the pituitary refractoriness that develops after 2–3 h of LHRH stimulation in normal rams is not caused by the increasing plasma T levels but is an intrinsic pituitary phenomenon that could be due to an adverse effect of LHRH on its own receptors. (Endocrinology106: 329, 1980)
Culture of human fetal B-cell precursors on bone marrow stroma maintains highly proliferative CD20dim cells (1993)

Abstract Growth of human B-cell precursors (BCP) was achieved by plating fetal CD10+ surface-mu (s mu)- cells in liquid medium onto bone marrow- derived fibroblastic stromal cell layers deprived of hematopoietic cells. Proliferation of the fetal BCP was strongly potentiated by the addition of interleukin-7 (IL-7) to the cultures. Cultures included both a stroma-adherent and -nonadherent fraction of lymphoid cells, allowing us to expand the number of input BCP to 13-fold. In the presence of exogenous IL-7, proliferation was dose-dependent relative to the number of stromal cells, demonstrating that soluble IL-7 does not act alone to promote optimal growth. We further showed that the lymphoid cells recovered remain CD10+ sIg- BCP and that most cells expressed the maturation-associated CD20 antigen when IL-7 was added to the cultures. Whereas both freshly isolated CD20- and CD20bright BCP proliferated in the presence of stroma, we observed that high- proliferative capacity CD20dim cells were maintained in the cultures. Finally, CD20dim sorted cells were shown to subsequently acquire high levels of CD20 expression in culture, thus demonstrating a partial maturation sequence. The present culture system thus represents a useful model for studying the regulatory signals in early human B lymphopoiesis.
Introduction (2016)

Abstract Waste is a general outcome of processes of formation, but it assumes a distinct character in North American modernity. If forms can last only by releasing transient materials, then their relative durability is reliant on the constitutive absence of wastes. North American moderns manage wastes in a way that further transforms their imaginations and social relations. Mass waste is the anonymous and indeterminate by-product of modern life that requires management by someone else somewhere else. Landfilling disposes of mass waste so efficiently and cheaply that more disposability is introduced and bigger landfills are required at greater distances from our everyday lives. Examining how people live with the mass waste of other people and places at one landfill makes this clear.
Using CQIM{trademark} to evaluate the performance and economic impacts of gas co-firing at Conesville Unit 3 (1996)

The Coal Quality Impact Model (CQIM{trademark}) was used to perform a case study on the performance and economic impacts of natural gas co-firing at American Electric Power`s Conesville Unit 3, a unit that was originally designed to burn coal. CQIM offers a quick, cost-effective solution to the performance and economic issues not normally considered when the interrelationships between performance improvements and penalties and busbar generation costs are examined. For this case study, gas co-firing was found to be economically advantageous over coal firing for Conesville Unit 3. The design coal was evaluated at 0, 10, 25, 50, and 75 percent gas co-firing at full-load conditions. The effect of gas co-firing on unit performance was a decrease in auxiliary power requirements and boiler efficiency as the amount of gas co-firing increased. Due to the reduction in boiler efficiency, the net unit heat rate increased as the amount of gas co-firing increased. The worsening of the net unit heat rate was offset by an improvement in availability, auxiliary power, and SO{sub 2} emissions as the percentage of gas co-firing was increased. On the basis of the performance improvements and penalties predicted by CQIM, the total fuel-related costs were reduced as the percentagemore » of gas co-firing increased. The annual fuel cost component increased as a result of slightly higher natural gas prices and an increase in the net unit heat rate; however, waste disposal, O and M, and replacement energy costs decreased as the percentage of gas co-firing increased. Most of the O and M cost elements (SO{sub 2} emissions and maintenance) and replacement energy cost elements (availability and auxiliary power) decreased as the amount of gas co-firing increased.« less