gebhart/patrepeval huggingface dataset:
Improvements for comparative analysis of changes in diversity of microbial communities using internal standards in PCR-DGGE (2005)

The use of internal standards both during DNA extraction and PCR-DGGE procedure gives the opportunity to analyse the relative abundance of individual species back to the original sample, thereby facilitating relative comparative analysis of diversity. Internal standards were used throughout the DNA extraction and PCR-DGGE to compensate for experimental variability. Such variability causes decreased reproducibility among replicate samples as well as compromise comparisons between samples, since experimental errors cannot be differentiated from actual changes in the community abundance and structure. The use of internal standards during DNA extraction and PCR-DGGE is suitable for ecological and ecotoxicological experiments with microbial communities, where relative changes in the community abundance and structure are studied. We have developed a protocol Internal Standards in Molecular Analysis of Diversity (ISMAD) that is simple to use, inexpensive, rapid to perform and it does not require additional samples to be processed. The internal standard for DNA extraction (ExtrIS) is a fluorescent 510-basepair PCR product which is added to the samples prior to DNA extraction, recovered together with the extracted DNA from the samples and analysed with fluorescence spectrophotometry. The use of ExtrIS during isolation of sample DNA significantly reduced variation among replicate samples. The PCR internal standard (PCR(IS)) originates from the Drosophila melanogaster genome and is a 140-basepair long PCR product, which is amplified by non-competitive primers in the same PCR reaction tubes as the target DNA and analysed together with the target PCR product on the same DGGE gel. The use of PCR(IS) during PCR significantly reduced variation among replicate samples both when assessing total PCR product and when comparing bands representing species on a DGGE gel. The entire ISMAD protocol was shown to accurately describe changes in relative abundance in an environmental sample using PCR-DGGE. It should, however, be mentioned that despite the use of ISMAD some inherent biases still exist in DNA extraction and PCR-DGGE and these should be taken into consideration when interpreting the diversity in a sample based on a DGGE gel.
Humidification practices in the Adult Intensive Care Unit, Prince of Wales Hospital. (1998)

In the Adult Intensive Care Unit of The Prince of Wales Hospital, Sydney, Australia, inspiratory gas is humidified to saturation at 37 degrees C. This stops the buildup of dried sputum within the endotracheal tubes and thus prevents blocked tubes and the increased resistance caused by partial obstruction. Inspiratory and expiratory hose heater wires are used to produce a completely dry circuit, allowing the elimination of water traps and circuit support arms without the resistance of a heat and moisture exchanger.
High Incidence of p53 Gene Mutation in Human Ovarian Cancer and Its Association with Nuclear Accumulation of p53 Protein and Tumor DNA Aneuploidy (1992)

Using the polymerase chain reaction and single-strand conformation polymorphism analysis, p53 gene mutations were examined in 24 cases of ovarian tumor including 14 ovarian carcinomas and 2 borderline cases of common epithelial type, 7 germ cell tumors, and one stromal tumor. Abnormal bands indicating mutations were detected in 12 (50%) of the cases examined, being present most frequently in common "epithelial" ovarian carcinoma (71%, 10/14). One case each of squamous cell carcinoma originating in a dermoid cyst and anaplastic dysgerminoma were positive for mutation. Direct sequencing confirmed 12 mutations and revealed G-->A and G-->C nucleotide changes in 5 and 3 cases (42% and 25%), respectively. The mutation was localized at the CpG site of the gene in 3 cases. Immunohistochemical examination of p53 protein in 21 cases and DNA flow-cytometrical analysis in 17 cases were also performed. Nuclear accumulation of the p53 protein and DNA aneuploidy pattern were detected in 11 (52%) and 9 (53%) cases, respectively. These were significantly correlated with p53 gene mutation (P < 0.01 and P < 0.05, respectively; Fisher's exact test). Neither mutation of the p53 gene, nuclear accumulation of p53 protein nor DNA aneuploidy was detected in borderline cases of common "epithelial" type, typical dysgerminoma and immature teratoma. These results suggest that p53 gene mutation, nuclear accumulation of the protein and the DNA aneuploidy pattern are events occurring almost simultaneously in the progression of ovarian tumors, and that p53 abnormalities seem to be correlated with a high grade of malignancy.
Hydrogen Transfer from Supercritical Methanol over a Solid Base Catalyst: A Model for Lignin Depolymerization (2009)

A (super)critical transfer: The consecutive hydrogenolysis and hydrogenation of the lignin model compound dihydrobenzofuran was studied in supercritical methanolic solutions using porous metal oxide catalysts. These catalysts promote H(2) production from methanol followed by hydrogenolysis of the ether linkages and reduction of the aromatic rings, leading principally to a mixture of cyclohexanols.
Enzymatic Synthesis of (S‐(−)‐3‐(3,4‐Dihydroxyphenyl)lactic Acid (1988)

Abstract The first enzymatic synthesis of ( S )‐(−)‐3‐(3,4‐dihydroxyphenyl)lactic acid, a DOPA metabolite and naturally occurring compound with a broad spectrum of pharmacological activities, is described. L‐Hydroxyisocaproate dehydrogenase was used as enzyme.
Formation and decompositions of chloride adduct ions, [M + Cl]−, in negative ion electrospray ionization mass spectrometry (2000)

The ability to promote chloride-attachment ions of the form [M + Cl]- in negative ion electrospray ionization mass spectrometry (ESI-MS) has been developed using chlorinated solvents such as chloroform and carbon tetrachloride. This approach expands the current capabilities of negative ion ESI-MS by enabling detection of analytes that lack acidic sites and thus exhibit weak [M - H]- signals. In contrast to the remote-site collision-induced dissociation (CID) often observed in positive ion ESI-MS/MS for alkali metal cation adducts, the decomposition of chloride adducts usually proceeds via competitive dissociations to form Cl-, which is not structurally informative, or [M - H]-. The latter can provide structural information via consecutive decompositions. For compounds having higher gas-phase acidities than HCl, a low CID collision energy can promote the formation of [M - H]-, whereas for the majority of compounds with lower gas phase acidities than HCl, higher collision energies generally improve the relative yield of [M- H] . Because chloride attachment occurs primarily at electrophilic hydrogens, the daughter ion ratio, Cl-/[M - H]-, depends primarily upon the difference in gas phase acidity between the analyte molecule and HCl. At higher collision energies, entropic factors take on increased importance in determining the product ratio. The difference between the deltaS(0) terms for formation of Cl and formation of [M - H]- has been estimated for a series of substituted phenols and a series of acetic acid analogs. Finally, a novel neutral loss of CH3Cl from glycerophosphocholine and from ganglioside GM3 methyl ester is reported.
Slow protein evolutionary rates are dictated by surface–core association (2011)

Why do certain proteins evolve much slower than others? We compared not only rates per protein, but also rates per position within individual proteins. For ∼90% of proteins, the distribution of positional rates exhibits three peaks: a peak of slow evolving residues, with average log(2)[normalized rate], log(2)μ, of ca. -2, corresponding primarily to core residues; a peak of fast evolving residues (log(2)μ ∼ 0.5) largely corresponding to surface residues; and a very fast peak (log(2)μ ∼ 2) associated with disordered segments. However, a unique fraction of proteins that evolve very slowly exhibit not only a negligible fast peak, but also a peak with a log(2)μ ∼ -4, rather than the standard core peak of -2. Thus, a "freeze" of a protein's surface seems to stop core evolution as well. We also observed a much higher fraction of substitutions in potentially interacting residues than expected by chance, including substitutions in pairs of contacting surface-core residues. Overall, the data suggest that accumulation of surface substitutions enables the acceptance of substitutions in core positions. The underlying reason for slow evolution might therefore be a highly constrained surface due to protein-protein interactions or the need to prevent misfolding or aggregation. If the surface is inaccessible to substitutions, so becomes the core, thus resulting in very slow overall rates.
Genomics of Ovarian Cancer Progression Reveals Diverse Metastatic Trajectories Including Intraepithelial Metastasis to the Fallopian Tube (2016)

We find that the putative precursor lesions for HGSOC, STIC, possess most of the genomic aberrations present in advanced cancers. In addition, a proportion of STIC represent intraepithelial metastases to the fallopian tube rather than the origin of HGSOC. Cancer Discov; 6(12); 1342-51. ©2016 AACR.See related commentary by Swisher et al., p. 1309This article is highlighted in the In This Issue feature, p. 1293.
Metabolism of Pentose Sugars in the Hyperthermophilic Archaea Sulfolobus solfataricus and Sulfolobus acidocaldarius (2010)

We have previously shown that the hyperthermophilic archaeon, Sulfolobus solfataricus, catabolizes d-glucose and d-galactose to pyruvate and glyceraldehyde via a non-phosphorylative version of the Entner-Doudoroff pathway. At each step, one enzyme is active with both C6 epimers, leading to a metabolically promiscuous pathway. On further investigation, the catalytic promiscuity of the first enzyme in this pathway, glucose dehydrogenase, has been shown to extend to the C5 sugars, D-xylose and L-arabinose. In the current paper we establish that this promiscuity for C6 and C5 metabolites is also exhibited by the third enzyme in the pathway, 2-keto-3-deoxygluconate aldolase, but that the second step requires a specific C5-dehydratase, the gluconate dehydratase being active only with C6 metabolites. The products of this pathway for the catabolism of D-xylose and L-arabinose are pyruvate and glycolaldehyde, pyruvate entering the citric acid cycle after oxidative decarboxylation to acetyl-coenzyme A. We have identified and characterized the enzymes, both native and recombinant, that catalyze the conversion of glycolaldehyde to glycolate and then to glyoxylate, which can enter the citric acid cycle via the action of malate synthase. Evidence is also presented that similar enzymes for this pentose sugar pathway are present in Sulfolobus acidocaldarius, and metabolic tracer studies in this archaeon demonstrate its in vivo operation in parallel with a route involving no aldol cleavage of the 2-keto-3-deoxy-pentanoates but direct conversion to the citric acid cycle C5-metabolite, 2-oxoglutarate.
Use of Defibrotide in Renal Transplantation in Man (1986)

In transplanted patients graft rejection is the most frequent complication in the first year after surgery. Vascular lesions (necrosis, intimal proliferation, thrombosis) are signs of poor prognosis and lead to irreversible loss of renal function and graft removal in most cases. The problem of vascular rejection is still not solved and the results of therapy unsatisfactory, both because of inadequacy of diagnosis and/or inadequacy of available therapy. The role of prevention, very likely the best approach, is still sub judice. In an attempt to explore the validity of prevention, 22 transplanted patients (group A) were given a new antithrombotic agent (defibrotide) immediately after surgery, and the results were compared with those of a well-matched group of 30 patients on dipyridamole (group B). Follow-up lasted 6-19 months (mean 9.9) for group A; 5-21 months (mean 12) for group B. In group A, 8 patients (36%) had rejection episodes. Antirejection therapy was followed by recovery of renal function in all cases. In group B, 9 patients (29%) had rejection crises and graft removal was necessary in 7 instances due to severe vascular lesions. At the end of follow-up, all patients treated with defibrotide had normally functioning grafts: among the 30 patients on dipyridamole, 22 (73%) had satisfactory graft function.
Mitochondrial Respiratory Chain and NAD(P)H Oxidase Are Targets for theAntiproliferative Effect of Carbon Monoxide in Human Airway SmoothMuscle (2005)

Carbon monoxide (CO), one of the end products of heme oxygenase activity, inhibits smooth muscle proliferation by decreasing ERK1/2 phosphorylation and cyclin D1 expression, a signaling pathway that is known to be modulated by reactive oxygen species (ROS) in airway smooth muscle cells (ASMCs). Two important sources of ROS involved in cell signaling are the membrane NAD(P)H oxidase and the mitochondrial respiratory chain. Thus, that CO could modulate redox signaling in ASMCs by interacting with the heme moiety of NAD(P)H oxidase and/or the respiratory chain is a plausible hypothesis. Here we show that a recently identified carbon monoxide-releasing molecule, [Ru(CO)3Cl2]2 (or CORM-2) 1) inhibits NAD(P)H oxidase cytochrome b558 activity, 2) increases oxidant production by the mitochondria, and 3) inhibits ASMC proliferation and phosphorylation of the ERK1/2 mitogen-activated protein kinase and expression of cyclin D1, two critical pathways involved in muscle proliferation. No such effects were observed with the negative control (Ru(Me2SO)4Cl2), which does not contain CO groups. Because both diphenylene iodinium or apocynin (inhibitors of NAD(P)H oxidase) and rotenone (a molecule that increases mitochondrial ROS production by blocking the respiratory chain) mimicked the effect of CORM-2 on cyclin D1 expression and ASMC proliferation, the antiproliferative effect of CORM-2 is probably related to inhibition of cytochromes on both NAD(P)H oxidase and the respiratory chain. The involvement of increased mitochondria-derived oxidants is substantiated by the findings showing that the antioxidant N-acetylcysteine partially inhibited the effects of CORM-2. This study provides a new mechanism to explain redox signaling by CO.
Cerebrospinal fluid pulse waveform as an indicator of cerebral autoregulation (1982)

Systems analysis of the systemic arterial (SAPW), cerebrospinal fluid (CSFPW), and sagittal sinus (SSPW) pulse waves was carried out in 13 dogs during hypercapnia (5% CO2), intracranial normotension (inhalation of 100% O2), and intracranial hypertension (inhalation of 100% O2 plus an intraventricular infusion). Power amplitude and phase spectra were determined for each wave, and the power amplitude and phase transfer functions calculated between the cerebrospinal fluid (CSF) pressure and systemic arterial pressures, and between the sagittal sinus pressure and CSF pressure. The study indicates that the CSFPW and SSPW were virtually identical when impedance between the cerebral veins and sagittal sinus was minimal, which argues that the CSF pulse was derived from the cerebral venous bed. During inhalation of 100% O2, transmission of the SAPW across the precapillary resistance vessels into the cerebral venous pulse (as represented by the CSFPW) was nonlinear, while transmission across the lateral lacunae into the sagittal sinus was linear. During intracranial hypertension, wave transmission across the precapillary resistance vessels was linear, and across the lateral lacunae was nonlinear. During hypercapnia, wave transmission across the precapillary resistance vessels and the lateral lacunae was linear. When the wave transmission was nonlinear, there was also suppression in transmission of the lower harmonics, particularly the fundamental frequency, and a more positive phase transfer function, suggesting an inertial effect or decrease in acceleration of the pulse. Conversion from a nonlinear to linear transmission across the precapillary resistance vessels is evidence of loss of vasomotor tone, and is accompanied by rounding of the CSFPW. A vascular model which encompasses the above data and is based on flow in collapsible tubes and changes in vasomotor tone is posited to explain control of pulsatile flow and pulse waveform changes in the cerebrovascular bed. The model helps to clarify the strong interrelationship between intracranial pressure, cerebral blood flow, and cerebral autoregulation.
The erbB Family: Targets for Therapeutic Development Against Cancer and Therapeutic Strategies Using Monoclonal Antibodies and Tyrosine Kinase Inhibitors (2004)

The overexpression and aberrant function of members of the erbB family of receptors, particularly erbB1 (also known as epidermal growth factor receptor), and its ligands in many human cancers have provided a rationale for targeting this signaling network with novel approaches. erbB1 is a selective target for inhibiting cancers because its activation often confers a proliferative advantage. Activation of the erbB1 tyrosine kinase provides signals that drive dysregulated proliferation, invasion, metastasis, angiogenesis, and cell survival, and its inhibition has potential in both the treatment and prevention of these malignancies. Based on the structure and function of erbB1, two therapeutic strategies have been developed. The first uses human monoclonal antibodies (MAbs) generated against the receptor's ligand-binding extracellular domain. These MAbs block binding of receptor-activating ligands, and, in some cases, can induce receptor endocytosis and downregulation. The second uses small molecules that compete with adenosine triphosphate (ATP) for binding to the receptor's kinase pocket, thereby blocking receptor activation and the transduction of postreceptor signals. Early clinical studies suggest that both approaches are well tolerated and can induce clinical activity in many common malignancies.
Bi- and Trinuclear Ruthenium Alkylidene Triggered Cyclopolymerization of 1,6-Heptadiynes:  Access to An−X−An Block and (An)3X Tristar Copolymers (2006)

Benzoic acid (4-(2-propoxy)-3-vinylphenyl) ester (1), the divinyl compounds terephthalic acid bis(4-(2-propoxy)-3-vinylphenyl) ester (2) and bis(4-(2-propoxy)-3-vinylphenoxy)diphenylsilane (3), and the trivinyl compound benzene-1,3,5-tricarboxylic acid tris(4-(2-propoxy)-3-vinylphenyl) ester (4) were used for the synthesis of a series of ruthenium-based mono-, bi-, and trinuclear metathesis catalysts, i.e., RuX2(IMesH2)(CH-2-(2-PrO)-C6H3-5-OOCC6H5) (X = Cl, I1a; X = OOCCF3, I1b), 1,4-[RuX2(IMesH2)(CH-2-(2-PrO)-C6H3-5-OOC)]2C6H4 (X = Cl, I2a; X = OOCCF3, I2b), [RuX2(IMesH2)(CH-2-(2-PrO)-C6H3-5-O)]2SiPh2 (X = Cl, I3a; X = OOCCF3, I3b), and 1,3,5-[RuX2(IMesH2)(CH-2-(2-PrO)-C6H3-5-OOC)]3C6H3 (X = Cl, I4a; X = OOCCF3, I4b) (IMesH2 = 1,3-dimesityl-4,5-dihydroimidazol-2-ylidene), where the corresponding trifluoroacetate-derived systems were prepared from the parent dichloro-substituted initiators via reaction with CF3COOAg. Initiators I1a−I4a and I1b−I4b were used for the cyclopolymerization of a series of 1,6-heptadiynes, i.e., dimethyl dipropargylmalonate (M1), diethyl dipropargylmalonate (M2), di-tert-butyl dipropargylmalonate (M3), 4-(ethoxycarbonyl)-1,6-heptadiyne (M4), 4,4-(bishydroxymethyl)-1,6-heptadiyne (M5), and 4-(hydroxymethyl)-1,6-heptadiyne (M6), to yield the corresponding An−X−An type block and (An)3X type tristar copolymers. Cleavage of the An−X−An type block copolymer M225−CH-[2-(2-PrO)-1,5-C6H3]-O-SiPh2-O-[2-(2-PrO)-1,5-C6H3]-CH-M225 with tetrabutylammonium fluoride resulted in the formation of the low-PDI telechelic homopolymer M225-CH-[2-(2-PrO)-1,5-C6H3]-OH with half the molecular weight of the parent block copolymer, indicative for an equal activity of both initiator sites in I3b. An interesting finding was the fact that monomers with reduced steric demands in the 4-position (M1, M4, M5, and M6) could even be polymerized with chlorine-based initiators; however, values for Mn were in general lower than the calculated ones. In contrast to Mo-based initiators, no influence of monomer size on the structure of the final polymer in terms of the ratio of 1,2-(cyclopent-1-ene)vinylene and 1,3-(cyclohex-1-ene)methylidene units, respectively, was observed.
Improving Tumor Uptake and Pharmacokinetics of 64Cu-Labeled Cyclic RGD Peptide Dimers with Gly3 and PEG4 Linkers (2009)

Radiolabeled cyclic RGD (Arg-Gly-Asp) peptides represent a new class of radiotracers with potential for early tumor detection and noninvasive monitoring of tumor metastasis and therapeutic response in cancer patients. This article describes the synthesis of two cyclic RGD peptide dimer conjugates, DOTA-PEG(4)-E[PEG(4)-c(RGDfK)](2) (DOTA-3PEG(4)-dimer: DOTA = 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid; PEG(4) = 15-amino-4,7,10,13-tetraoxapentadecanoic acid) and DOTA-G(3)-E[G(3)-c(RGDfK)](2) (DOTA-3G(3)-dimer: G(3) = Gly-Gly-Gly). Integrin alpha(v)beta(3) binding affinities of cyclic RGD peptides were determined by competitive displacement of (125)I-echistatin bound to U87MG human glioma cells and follow the order of DOTA-E{E[c(RGDfK)](2)}(2) (DOTA-tetramer: IC(50) = 10 +/- 2 nM) > DOTA-3G(3)-dimer (IC(50) = 62 +/- 6 nM) approximately DOTA-3PEG(4)-dimer (IC(50) = 74 +/- 3 nM) > DOTA-E[c(RGDfK)](2) (DOTA-dimer: IC(50) = 102 +/- 5 nM). The addition of PEG(4) and G(3) linkers between two cyclic RGD motifs in DOTA-3G(3)-dimer and DOTA-3PEG(4)-dimer makes it possible for them to achieve the simultaneous integrin alpha(v)beta(3) binding in a bivalent fashion. Both (64)Cu(DOTA-3PEG(4)-dimer) and (64)Cu(DOTA-3G(3)-dimer) were prepared in high yield with specific activity being >50 Ci/mmol. Biodistribution and imaging studies were performed in athymic nude mice bearing U87MG human glioma xenografts. The results from those studies show that PEG(4) and G(3) linkers are particularly useful for improving tumor uptake and clearance kinetics of (64)Cu radiotracers from the nontumor organs, such as kidneys, liver, and lungs. There is a linear relationship between the tumor size and %ID tumor uptake, suggesting that (64)Cu(DOTA-3PEG(4)-dimer) and (64)Cu(DOTA-3PEG(4)-dimer) might be useful for noninvasive monitoring of tumor growth or shrinkage during antiangiogenic therapy. MicroPET imaging data clearly demonstrate the utility of (64)Cu(DOTA-3G(3)-dimer) as a new PET radiotracer for imaging integrin alpha(v)beta(3)-positive tumors.
Visual SPARQL querying based on extended filter/flow graphs (2014)

SPARQL is currently the major query language for the Semantic Web. However, writing SPARQL queries is not an easy task and requires some understanding of technologies like RDF. In order to enable users without this knowledge to query linked data, visual interfaces are required that hide the SPARQL syntax and provide graphical support for query building. Based on the concept of extended filter/flow graphs, we present a novel approach for visual querying that addresses the unique specifics of SPARQL and RDF. In particular, it enables the creation of SELECT and ASK queries, though it can also be used for other query forms. In contrast to related work, the users do not need to provide any structured text input but can create the queries entirely with graphical elements. Our approach supports most features of SPARQL and hence also the construction of complex query expressions. It has been implemented in a visual querying framework and tested on different RDF datasets, including DBpedia that is used as an example in this paper. Since the filter/flow concept is empirically well-founded, we expect our approach to be very usable, which is additionally supported by the results of a qualitative user study we conducted.