gebhart/patrepeval huggingface dataset:
Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities (2013)

Next-generation sequencing has dramatically changed the landscape of microbial ecology, large-scale and in-depth diversity studies being now widely accessible. However, determining the accuracy of taxonomic and quantitative inferences and comparing results obtained with different approaches are complicated by incongruence of experimental and computational data types and also by lack of knowledge of the true ecological diversity. Here we used highly diverse bacterial and archaeal synthetic communities assembled from pure genomic DNAs to compare inferences from metagenomic and SSU rRNA amplicon sequencing. Both Illumina and 454 metagenomic data outperformed amplicon sequencing in quantifying the community composition, but the outcome was dependent on analysis parameters and platform. New approaches in processing and classifying amplicons can reconstruct the taxonomic composition of the community with high reproducibility within primer sets, but all tested primers sets lead to significant taxon-specific biases. Controlled synthetic communities assembled to broadly mimic the phylogenetic richness in target environments can provide important validation for fine-tuning experimental and computational parameters used to characterize natural communities.
Direct Fixation of Atmospheric CO2 towards Chemical Synthesis of Fuel Hydrocarbon (2021)

We have reported that fuel hydrocarbon was chemically synthesized from CO2 and activated water. In this report, we show the direct evidence of CO2 fixation from air. CO2 in the air is composed of about 99 % 12C, about 1% 13C, and about one trillionth radioisotope 14C. The extremely trace amount of 14C was measured with liquid scintillation counter by following beta-decay. The newly synthesized hydrocarbon revealed 14.6 dpm/gC. These facts clearly demonstrate direct fixation of atmospheric CO2 toward hydrocarbon synthesis.
Net Analyte Signal Calculation in Multivariate Calibration (1997)

Net analyte signal plays an important role in the calculation of figures of merit for characterizing a calibration model. Until now, its computation has only been feasible for the direct calibration model, which requires knowledge of pure spectra or concentrations of all contributing species in the calibration samples. An increasingly important calibration model is the inverse calibration model, which also allows for quantitation if the knowledge about the interferents is incomplete. This paper shows that net analyte signal computation is possible for the inverse calibration case. Application to the determination of protein content in wheat samples by near-infrared spectrometry is presented. Net analyte signal calculation was used to estimate selectivities (ratio of signal available for quantitation to the total measured signal). The selectivities were found to range between 0 and 2% of the measured reflectance signal. A new measure for outlier diagnosis based on the correlation of the net analyte signal to the regression coefficients vector is introduced and tested on the same data.
Discovery and Biological Evaluation of 5-Aryl-2-furfuramides, Potent and Selective Blockers of the Nav1.8 Sodium Channel with Efficacy in Models of Neuropathic and Inflammatory Pain (2008)

Nav1.8 (also known as PN3) is a tetrodotoxin-resistant (TTx-r) voltage-gated sodium channel (VGSC) that is highly expressed on small diameter sensory neurons and has been implicated in the pathophysiology of inflammatory and neuropathic pain. Recent studies using an Nav1.8 antisense oligonucleotide in an animal model of chronic pain indicated that selective blockade of Nav1.8 was analgesic and could provide effective analgesia with a reduction in the adverse events associated with nonselective VGSC blocking therapeutic agents. Herein, we describe the preparation and characterization of a series of 5-substituted 2-furfuramides, which are potent, voltage-dependent blockers (IC50 < 10 nM) of the human Nav1.8 channel. Selected derivatives, such as 7 and 27, also blocked TTx-r sodium currents in rat dorsal root ganglia (DRG) neurons with comparable potency and displayed >100-fold selectivity versus human sodium (Nav1.2, Nav1.5, Nav1.7) and human ether-a-go-go (hERG) channels. Following systemic administration, compounds 7 and 27 dose-dependently reduced neuropathic and inflammatory pain in experimental rodent models.
ON AIR ENTRAINING PERFORMANCE OF POLYCARBOXYLATE TYPE WATER REDUCER (2009)

This paper describes the air entraining performance of polycarboxylate type water reducer. From the results obtained in this study, it is concluded that Methoxypoly (n=10) ethyleneglycol methacrylate - methacrylic acid copolymer (PC-10) can be purified by utilizing its cloud point; The purified polymer obtained from PC-10 through using its cloud point shows the lower air entraining performance than that of PC-10, and the ingredient that displays the strongest air entraining effect for PC-10 is methoxypoly (n=10) ethylene glycol, which remains in PC-10 as a raw material or an elimination product generated by an alkaline hydrolysis of PC-10 in the cement-water system; In order to decrease the air entraining performance of PC, the side chains of it should be sufficiently hydrophilic: we reached the preliminary conclusion that as the end group of side chains, -H or -CH3 group should be required and the side chains' length should be more than 30 moles in the additional number of ethylene oxide when the end group is -CH3 group.
Chemical stabilities of fluoro compounds for lubricants to AlCl3. (1985)

The fluoro compounds for lubricants, such as hexakis ( 1,1,5-trihydroperfluoropentyloxy )cyclotriphosphazene ( I ) and perfluoropolyether ( II), were examined comparatively concerning their chemical stabilities toward AlC13 at various *
Angular oversampling with temporally offset layers on multilayer detectors in computed tomography (2016)

The presented oversampling method is easy to implement in today's multilayer detectors and has the potential to reduce aliasing artifacts in the reconstructed images.
Thérapie génique: intérêt et limites des outils (2011)

Les développements spectaculaires de la biologie et de la biotechnologie, durant ces dernières décennies, ont bouleversé le paysage de la recherche biomédicale et offrent des possibilités thérapeutiques sans précédent. À coté des méthodes désormais classiques de la génomique/ post-génomique, citons le phénomène d’ARN interférence, l’établissement de réseaux gènes/protéines, le transfert de gènes ex vivo etin vivo et la construction de modèles de maladies humaines chez différentes espèces animales. Un exemple emprunté au domaine de l’obésité illustre avec force ces nouvelles possibilités et la puissance des approches de transfert de gène. De nombreuses maladies peuvent bénéficier de la thérapie génique, en particulier les maladies neurodégénératives (cerveau et oeil), pour lesquelles il n’existe pratiquement pas, à l’heure actuelle, d’alternatives satisfaisantes. De nombreuses preuves de principe ont été établies et des essais chez l’homme ont été couronnés de succès. Toutefois, la majorité des protocoles de thérapie génique font appel à des vecteurs dérivés de virus. Bien que «désarmés» , ces vecteurs présentent encore des risques pour le patient, en particulier de recombinaison, qu’il est impératif d’analyser et de prendre en compte. Seuls cette prise de conscience et le développement de recherches appropriées permettront l’utilisation clinique, en routine, des outils de la thérapie génique et ainsi d’exploiter pleinement leur remarquable potentiel thérapeutique.
Peripheral Treatment with Enoxaparin, a Low Molecular Weight Heparin, Reduces Plaques and β-Amyloid Accumulation in a Mouse Model of Alzheimer's Disease (2004)

We investigated the effect of long-term, peripheral treatment with enoxaparin, a low molecular weight heparin, in transgenic mice overexpressing human amyloid precursor protein(751). Enoxaparin (6 IU per mouse intraperitoneally, three times a week for 6 months) significantly lowered the number and the area occupied by cortical beta-amyloid deposits and the total beta-amyloid (1-40) cortical concentration. Immunocytochemical analysis of glial fibrillary acid protein-positive cells showed that enoxaparin markedly reduced the number of activated astrocytes surrounding beta-amyloid deposits. In vitro, the drug dose-dependently attenuated the toxic effect of beta-amyloid on neuronal cells. Enoxaparin dose-dependently reduced the ability of beta-amyloid to activate complement and contact systems, two powerful effectors of inflammatory response in AD brain. By reducing the beta-amyloid load and cytotoxicity and proinflammatory activity, enoxaparin offers promise as a tool for slowing the progression of Alzheimer's disease.
Transcription factor MBF-I interacts with metal regulatory elements of higher eucaryotic metallothionein genes. (1989)

Metallothionein (MT) gene promoters in higher eucaryotes contain multiple metal regulatory elements (MREs) that are responsible for the metal induction of MT gene transcription. We identified and purified to near homogeneity a 74-kilodalton mouse nuclear protein that specifically binds to certain MRE sequences. This protein, MBF-I, was purified employing as an affinity reagent a trout MRE that is shown to be functional in mouse cells but which lacks the G+C-rich and SP1-like sequences found in many mammalian MT gene promoters. Using point-mutated MREs, we showed that there is a strong correlation between DNA binding in vitro and MT gene regulation in vivo, suggesting a direct role of MBF-I in MT gene transcription. We also showed that MBF-I can induce MT gene transcription in vitro in a mouse extract and that this stimulation requires zinc.
Tea Polyphenols in Promotion of Human Health (2018)

Tea is the most widely used beverage worldwide. Japanese and Chinese people have been drinking tea for centuries and in Asia, it is the most consumed beverage besides water. It is a rich source of pharmacologically active molecules which have been implicated to provide diverse health benefits. The three major forms of tea are green, black and oolong tea based on the degree of fermentation. The composition of tea differs with the species, season, leaves, climate, and horticultural practices. Polyphenols are the major active compounds present in teas. The catechins are the major polyphenolic compounds in green tea, which include epigallocatechin-3-gallate (EGCG), epigallocatechin, epicatechin-3-gallate and epicatechin, gallocatechins and gallocatechin gallate. EGCG is the predominant and most studied catechin in green tea. There are numerous evidences from cell culture and animal studies that tea polyphenols have beneficial effects against several pathological diseases including cancer, diabetes and cardiovascular diseases. The polyphenolic compounds present in black tea include theaflavins and thearubigins. In this review article, we will summarize recent studies documenting the role of tea polyphenols in the prevention of cancer, diabetes, cardiovascular and neurological diseases.
The Metric Average of 1D Compact Sets (2002)

We study properties of a binary operation between two compact sets depending on a weight in [0,1], termed metric average. The metric average is used in spline subdivision schemes for compact sets in |R^n, instead of the Minkowski convex combination of sets, to retain non-convexity, see N. Dyn, E. Farkhi, ``Spline subdivision schemes for compact sets with metric averages", Trends in Approximation Theory (2001). Some properties of the metric average of sets in |R, like the cancellation property and the linear behavior of the Lebesgue measure of the metric average with respect to the weight, are proven. We present an algorithm for computing the metric average of two compact sets in |R, which are finite unions of intervals, as well as an algorithm for reconstructing one of the metric average's operands, given the second operand, the metric average and the weight.
Identification of novel carrier peptides for the specific delivery of therapeutics into cancer cells (2002)

Cancer therapy is currently limited by the difficulty of achieving efficient delivery into target cells. To investigate whether therapeutics can be delivered specifically to cancer cells, we have explored the possibility of selecting small peptides that bind specifically, or preferentially, to breast cancer cell lines. By using random peptide phage libraries and an experimental approach that allows the selection of internalized peptides, cell-specific binding peptides have been identified. The peptides define a major core motif (LTVXPWY) that was not found in negative phages. Phage displaying LTVSPWY peptide sequence exhibited a specific binding to breast cancer cells. None of the selected peptides bound to human primary cells from different tissue origin (e.g., epithelial, endothelial, hematopoetic). The potential of the selected peptides to mediate cellular internalization in the context of phages and recombinant GFP-peptide fusions was demonstrated. By linking the LTVSPWY peptide to an antisense phosphorothioate oligonucleotide against the ErbB2 receptor, specific delivery to cancer cells was achieved. In contrast to free antisense, the peptide-antisense conjugates inhibited ErbB2 gene expression. Thus, efficient delivery of antisense oligonucleotides can be achieved by coupling them to cancer cell-specific peptides, identified by a method that did not require any knowledge about their corresponding receptors.
Clinical translation of cell transplantation in the brain (2011)

In spite of rapid progress, the conditions for reliable, well tolerated and effective cell therapies in brain disease are not yet fully established.
Therapy of polycythemia vera with radiotytrium (Y-90). (1962)

BS>Nine patients with polycythemia vera were treated from 5-l7 months ago with a single intravenous injection of chelated radioactive yttrium (Y-90) in dosages ranging from 0.l0 to 0.25 mc/kg of body weight. An excellent response, both clinical and hematologic, was obtained in all the patients. This includes relief of symptoms, regression of organomegaly, and normalization of the hematologic picture. Two of these patients, treated l6 and 9 months ago, may possibly be going into relapse. The others are continuing in essentially complete remission. Toxicity was limtted to transient petechiosis and epistaxis, from which recovery was spontaneous. (auth)
Biosynthesis of plant polyketides in yeast (2019)

Industrial biotechnology aims to replace production processes based on petrochemicals with more sustainable biological processes based on renewable raw materials. With the rise of metabolic engineering and synthetic biology in the last decades, the range of products attainable by this technology has widened substantially. This thesis explores the potential of Saccharomyces cerevisiae for the production of two commercially interesting compound classes within the plant polyphenols. The first part demonstrates heterologous production of various dihydrochalcones. A side activity of the native ScTsc13, the reduction of p-coumaroyl-CoA to p- dihydrocoumaroyl-CoA, was used for de novo production of phloretin, the first committed dihydrochalcone. By further extension of the pathway from phloretin, by employing decorating enzymes with known specificities for dihydrochalcones, and by exploiting substrate flexibility of enzymes involved in flavonoid biosynthesis, de novo production of the antioxidant molecule nothofagin, the antidiabetic molecule phlorizin, the sweet molecule naringin dihydrochalcone, and 3-hydroxyphloretin was achieved. In the second part, yeast was engineered for de novo production of anthocyanins, molecules that are used in the food and beverage industries as natural colorants. Enzymes from different plant sources were screened and efficient variants were found for most steps of the pathways to the three main anthocyanins. However, as previously shown in vitro and in Escherichia coli, the shunt flavonol production by the anthocyanidin synthase was a major limitation. In the third part, this flavonol by-product formation was eliminated by co- expression of glutathione-S-transferases. These enzymes, previously thought to be involved in vacuolar transport of anthocyanins in plants, were shown to be required for correct product formation by anthocyanidin synthases. By additional co-expression of glycosyltransferases and a malonyltransferase, the pathway was extended to various decorated anthocyanins with a range of different colors. This thesis uncovers and describes important steps towards a sustainable biotechnological process for production of dihydrochalcones and anthocyanins. However, further optimization to increase titers will be required before such processes become commercially viable.
Aminoacetyl Moiety as a Potential Surrogate for Diacylhydrazine Group of SC-51089, a Potent PGE2 Antagonist, and Its Analogs (1996)

8-Chlorodibenz[b,f][1,4]oxazepine-10(11H)-carboxylic acid, 2-[1-oxo-3-(4-pyridinyl)propyl]hydrazide, monohydrochloride (1, SC-51089) is a functional PGE2 antagonist selective for the EP1 receptor subtype with antinociceptive activity. During metabolism in cultured rat hepatocytes, SC-51089, which contains a diacylhydrazine moiety, has been shown to release hydrazine. Analogs of SC-51089, in which the diacylhydrazine functionality has been replaced by isosteric and isoelectronic groups, have been synthesized and have been shown to be analgesics and PGE2 antagonists of the EP1 subtype. This report discusses the structure-activity relationships within these series.
Incorporation of Alkoxysilanes into Model Latex Systems:  Vinyl Copolymerization of Vinyltriethoxysilane and n-Butyl Acrylate (2002)

The increase in industrial interest in the incorporation of alkoxysilanes in organic polymer coatings arises from their ability to form self-cross-linkable films at room temperature. In the past few years, many patents were published, offering solutions for avoiding premature cross-linking of alkoxysilane-containing latexes and for obtaining good film-forming properties without using organic solvents. The present paper proposes a miniemulsion approach for the incorporation of alkoxysilanes into acrylate latex systems in order to protect the silane moieties from hydrolysis and premature cross-linking by reducing their contact with water. Vinyltriethoxysilane (VTES)/n-butyl acrylate (BA) copolymer latexes were synthesized by both conventional emulsion and miniemulsion procedures. The amount of coagulum and conversion were determined by gravimetry. Differences in coagulum levels were observed with respect to the copolymerization procedure (1.1−32.7 wt % based on monomers in conventional systems vs 1.2−5.5 wt % on monomers in miniemulsion systems for a VTES feed of 1−50 mol %) and acrylate/alkoxysilane molar ratio. Gas chromatography was used to determine the reactivity ratios of VTES/BA pairs by analyzing the evolution of unreacted comonomers during copolymerization. The reactivity ratios between the alkoxysilane and acrylate differed by 2 orders of magnitude for VTES (monomer 1) and BA (monomer 2), where r1 = 0.044 and r2 = 8.56. These results were confirmed by FT-IR analysis of the copolymer composition (r1 = 0.086, r2 = 8.51).
G protein coupling of human platelet V1 vascular vasopressin receptors (1993)

We used several approaches to identify the G protein coupled to V1 vascular arginine vasopressin (AVP) receptors of human platelets. In purified platelet membranes, high-affinity specific binding of [3H]AVP but not that of the V1 vascular antagonist [3H]d(CH2)5Tyr(Me)AVP was modulated by guanosine 5'-O-(3-thiotriphosphate) or sodium fluoride both in the presence and absence of MgCl2. AVP failed to modify the [alpha-32P]GTP labeling pattern or the cytosolic translocation of the 24- to 27-kDa GTP-binding proteins. AVP-stimulated GTPase activity of platelet membranes was blocked by antibodies specific for the COOH-terminal of the Gq alpha protein. AVP increased labeling of a 42-kDa platelet membrane protein by the photoreactive GTP analogue [alpha-32P]azidoanilido GTP. Immunoblotting of platelet proteins with various G protein-specific antibodies revealed that the 42-kDa protein labeled with [alpha-32P]azidoanilido GTP was immunoblotted only by antibodies specific for the alpha-subunit of GQ-11. Thus V1 vascular AVP receptors of human platelets are coupled in a divalent cation-dependent manner to a G protein belonging to the Gq-11 family.
Does cardio-hepatic communication contribute to pregnancy-induced cardiac growth and its reversal? (2023)

Introduction: During pregnancy, the maternal heart undergoes physiological cardiac growth, which reverses following parturition; however, the underlying processes that contribute are largely unknown. Changes in both systemic and cardiac metabolism appear to be associated with cardiac growth, which could also contribute during pregnancy. We have shown that several cardiac metabolic transcripts and proteins and liver-derived metabolites are elevated during pregnancy and postpartum and are associated with cardiac growth. Therefore, the goal of this study was to examine the extent to which the cardio-hepatic signaling axis contributes to pregnancy-induced cardiac growth and reversal. Methods and Results: Timed pregnancy studies in 12-week-old FVB/NJ mice revealed that both heart weight (HW:TL; p &lt; 0.0001) and liver weight (LIV:TL; p &lt;0.0001) were highest in lactating 1-week post-birth (PB) mice versus mid-pregnant (8 d), late-pregnant (LP; 16 d), and non-pregnant (NP) mice. Interestingly, we also found that HW:TL ( p &lt; 0.01) and LIV:TL ( p &lt; 0.0001) were significantly reduced in non-lactating 1-week post-birth mice (PBNL) compared with PB mice. Hearts and livers both remained significantly larger, irrespective of lactation status, following parturition through 6 weeks post birth (PB) versus NP. Plasma proteomics revealed significant increases in prolactin at LP in addition to increases in liver-derived proteins including hepatocyte growth factors; however, these levels returned to NP levels by PB. Examination of the liver proteome from the same mice revealed significant increases in fatty acid and ketone body metabolism proteins. Cardiac and liver immunoblot analysis revealed significant reductions in Pdk4 between 1- and 3-week PB and PBNL groups that was reversed by 6-weeks postpartum and a significant increase in Pdk4 expression at 6 weeks postpartum, respectively. Interestingly, we see a sustained increase in cardiac Bdh1 expression that persisted at 6-weeks postpartum which could contribute to the sustained increases in HW:TL versus NP. Conclusion: Changes in both lactation status and metabolism are likely contributing to similar patterns of growth seen in the heart and liver during and following pregnancy. NIGMS COBRE Pilot project grant P30 GM127607; NIH R01 HL147844 (Hill/ Jones); Jewish Heritage Fund for Excellence Faculty Support; Jewish Heritage Fund for Excellence Research Enhancement Award; UofL School of Medicine Basic Science award; NIGMS IDeA state funded proteomics voucher. This is the full abstract presented at the American Physiology Summit 2023 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.