gebhart/patrepeval huggingface dataset:
Revealing the Bacterial Butyrate Synthesis Pathways by Analyzing (Meta)genomic Data (2014)

Butyrate-producing bacteria have recently gained attention, since they are important for a healthy colon and when altered contribute to emerging diseases, such as ulcerative colitis and type II diabetes. This guild is polyphyletic and cannot be accurately detected by 16S rRNA gene sequencing. Consequently, approaches targeting the terminal genes of the main butyrate-producing pathway have been developed. However, since additional pathways exist and alternative, newly recognized enzymes catalyzing the terminal reaction have been described, previous investigations are often incomplete. We undertook a broad analysis of butyrate-producing pathways and individual genes by screening 3,184 sequenced bacterial genomes from the Integrated Microbial Genome database. Genomes of 225 bacteria with a potential to produce butyrate were identified, including many previously unknown candidates. The majority of candidates belong to distinct families within the Firmicutes, but members of nine other phyla, especially from Actinobacteria, Bacteroidetes, Fusobacteria, Proteobacteria, Spirochaetes, and Thermotogae, were also identified as potential butyrate producers. The established gene catalogue (3,055 entries) was used to screen for butyrate synthesis pathways in 15 metagenomes derived from stool samples of healthy individuals provided by the HMP (Human Microbiome Project) consortium. A high percentage of total genomes exhibited a butyrate-producing pathway (mean, 19.1%; range, 3.2% to 39.4%), where the acetyl-coenzyme A (CoA) pathway was the most prevalent (mean, 79.7% of all pathways), followed by the lysine pathway (mean, 11.2%). Diversity analysis for the acetyl-CoA pathway showed that the same few firmicute groups associated with several Lachnospiraceae and Ruminococcaceae were dominating in most individuals, whereas the other pathways were associated primarily with Bacteroidetes. IMPORTANCE Microbiome research has revealed new, important roles of our gut microbiota for maintaining health, but an understanding of effects of specific microbial functions on the host is in its infancy, partly because in-depth functional microbial analyses are rare and publicly available databases are often incomplete/misannotated. In this study, we focused on production of butyrate, the main energy source for colonocytes, which plays a critical role in health and disease. We have provided a complete database of genes from major known butyrate-producing pathways, using in-depth genomic analysis of publicly available genomes, filling an important gap to accurately assess the butyrate-producing potential of complex microbial communities from "-omics"-derived data. Furthermore, a reference data set containing the abundance and diversity of butyrate synthesis pathways from the healthy gut microbiota was established through a metagenomics-based assessment. This study will help in understanding the role of butyrate producers in health and disease and may assist the development of treatments for functional dysbiosis.
Increased exposure of anionic phospholipids on the surface of tumor blood vessels. (2002)

Anionic phospholipids are largely absent from the external leaflet of the plasma membrane of mammalian cells under normal conditions. Exposure of phosphatidylserine on the cell surface occurs during apoptosis, necrosis, cell injury, cell activation, and malignant transformation. In the present study, we determined whether anionic phospholipids become exposed on tumor vasculature. A monoclonal antibody, 9D2, which specifically recognizes anionic phospholipids, was injected into mice bearing a variety of orthotopic or ectopic tumors. Other mice received annexin V, a natural ligand that binds to anionic phospholipids. Both 9D2 and annexin V specifically localized to vascular endothelium in all of the tumors, and also to tumor cells in and around regions of necrosis. Between 15 and 40% of endothelial cells in tumor vessels were stained. No localization was detected on normal endothelium. Various factors and tumor-associated conditions known to be present in the tumor microenvironment were examined for their ability to cause exposure of anionic phospholipids in cultured endothelial cells, as judged by 9D2 and annexin V binding. Hypoxia/reoxygenation, acidity, thrombin, and inflammatory cytokines all induced exposure of anionic phospholipids. Hydrogen peroxide was also a strong inducer. Combined treatment with inflammatory cytokines and hypoxia/reoxygenation had greater than additive effects. Possibly, injury and activation of tumor endothelium by cytokines and reactive oxygen species induce exposure of anionic phospholipids, most likely phosphatidylserine. Anionic phospholipids on tumor vessels could potentially provide markers for tumor vessel targeting and imaging.
Five-Year Follow-Up Study of Iliofemoral Venous Thrombectomy (1968)

LANSING, ALLAN M. M.D., PH.D., F.R.C.S.(C), F.A.C.S.; DAVIS, WILLIAM M. M.D. Author Information
The effect of histocompatibility matching on canine frozen bone allografts. (1983)

The value of histocompatibility matching in frozen bone allografts was studied in a canine cancellous ulnar segmental-replacement model. Frozen bone that was exchanged across strong and weak transplantation barriers was evaluated histologically and radiographically at thirteen and twenty-six weeks after grafting. Histological grading criteria quantified the type of union at each end of the graft and the degree of remodeling of the marrow, spongiosa, and compacta. Radiographic grading criteria included the presence of union at each end of the graft and the degree of remodeling of the graft segment. In vitro studies for serum antibody and cell-mediated immunity were carried out by isotopic cytotoxicity methods at seven intervals during the twenty-six-week study period. Histologically, the strong-barrier allografts had fewer osseous unions and less reorganization of spongiosa and marrow when compared with autograft controls at both thirteen and twenty-six weeks. Radiographically, the strong-barrier allografts at thirteen weeks had fewer unions and marked resorption of grafts material when compared with autograft controls. There were no differences between weak transplantation-barrier grafts and control autografts radiographically or histologically at thirteen and twenty-six weeks after grafting. Frozen bone allografts did not elicit detectable serum antibody or lymphocytes that were cytotoxic for donor cells.
UCC3813 Dual Output Boost Converter (2003)

The traditional boost converter is modified to provide bipolar 25-V outputs from a 5-V supply. Using the UCC3813−3 low power economy BiCMOS current mode pulse width modulator to control the basic boost converter building block, the minus 25-V output is generated by capacitively coupling the switching node.
Luminescent Osmium(II) Complexes with Functionalized 2-Phenylpyridine Chelating Ligands: Preparation, Structural Analyses, and Photophysical Properties (2008)

Cyclometalated osmium complexes with the formulas [Os(ppy) 2(CO) 2] ( 1a, b), [Os(dfppy) 2(CO) 2] ( 2a, b), and [Os(btfppy) 2(CO) 2] ( 3a, b) have been synthesized, for which the chelating chromophores ppyH, dfppyH, and btfppyH denote 2-phenylpyridine, 2-(2,4-difluorophenyl)pyridine, and 2-(2,4-bis(trifluoromethyl)phenyl)pyridine, respectively. The isomers 1a- 3a, possessing an intrinsic C 2 rotational axis as determined by single-crystal X-ray diffraction analysis, underwent slow isomerization in solution at elevated temperature, giving the respective thermodynamic products 1b- 3b, which showed a distinctive coordination arrangement produced by a 180 degrees rotation of one cyclometalated ligand around the Os(II) metal center. In contrast to the case for 1a, b and 2a, which are inert to substitution, complexes 2b and 3b (or 3a) readily react with PPh 2Me to afford the products [Os(dfppy) 2(CO)(PPh 2Me)] ( 4) and [Os(btfppy) 2)(PPh 2Me)] ( 6), in which the incoming PPh 2Me replaced the CO located trans to the carbon atom of one cyclometalated ligand. UV-vis and emission spectra were measured, revealing the lowest excited state for all complexes as a nominally ligand-centered (3)pipi* state mixed with certain MLCT character. Introduction of the electron-withdrawing substituents on the cyclometalated chelates or replacement of one CO ligand with phosphine at the metal center increased the MLCT contribution in the first excited state, giving a broad and featureless emission with greatly enhanced quantum yields.
Surviving internet catastrophes (2005)

In this paper, we propose a new approach for designing distributed systems to survive Internet catastrophes called informed replication, and demonstrate this approach with the design and evaluation of a cooperative backup system called the Phoenix Recovery Service. Informed replication uses a model of correlated failures to exploit software diversity. The key observation that makes our approach both feasible and practical is that Internet catastrophes result from shared vulnerabilities. By replicating a system service on hosts that do not have the same vulnerabilities, an Internet pathogen that exploits a vulnerability is unlikely to cause all replicas to fail. To characterize software diversity in an Internet setting, we measure the software diversity of host operating systems and network services in a large organization. We then use insights from our measurement study to develop and evaluate heuristics for computing replica sets that have a number of attractive features. Our heuristics provide excellent reliability guarantees, result in low degree of replication, limit the storage burden on each host in the system, and lend themselves to a fully distributed implementation. We then present the design and prototype implementation of Phoenix, and evaluate it on the PlanetLab testbed. 1
Virulence in malaria: an evolutionary viewpoint (2004)

Malaria parasites cause much morbidity and mortality to their human hosts. From our evolutionary perspective, this is because virulence is positively associated with parasite transmission rate. Natural selection therefore drives virulence upwards, but only to the point where the cost to transmission caused by host death begins to outweigh the transmission benefits. In this review, we summarize data from the laboratory rodent malaria model, Plasmodium chabaudi, and field data on the human malaria parasite, P. falciparum, in relation to this virulence trade-off hypothesis. The data from both species show strong positive correlations between asexual multiplication, transmission rate, infection length, morbidity and mortality, and therefore support the underlying assumptions of the hypothesis. Moreover, the P. falciparum data show that expected total lifetime transmission of the parasite is maximized in young children in whom the fitness cost of host mortality balances the fitness benefits of higher transmission rates and slower clearance rates, thus exhibiting the hypothesized virulence trade-off. This evolutionary explanation of virulence appears to accord well with the clinical and molecular explanations of pathogenesis that involve cytoadherence, red cell invasion and immune evasion, although direct evidence of the fitness advantages of these mechanisms is scarce. One implication of this evolutionary view of virulence is that parasite populations are expected to evolve new levels of virulence in response to medical interventions such as vaccines and drugs.
Autofluorescence characterisation of isolated whole crypts and primary cultured human epithelial cells from normal, hyperplastic, and adenomatous colonic mucosa (2005)

Short term primary cell cultures from endoscopic biopsies provide a novel model to understand differences in colonic tissue autofluorescence at the glandular (crypt) and cellular levels. The differences between normal, hyperplastic, and adenomatous epithelial cells are attributed in part to differences in the intrinsic numbers of mitochondria and lysosomes. This suggests that the detection of colonic epithelial fluorescence alone, if possible, may be sufficient to differentiate benign (hyperplastic) from preneoplastic and neoplastic (adenomatous) colonic intramucosal lesions during in vivo fluorescence endoscopy. Furthermore, highly orange/red autofluorescent intracellular granules found only in dysplastic epithelial cells may serve as a potential biomarker.
Preparation and Structure of Oligolides from (R)‐3‐Hydroxypentanoic Acid and comparison with the hydroxybutanoic‐acid derivatives: A small change with large consequences (1994)

Abstract Cyclic oligomers of ( R )‐3‐hydroxyvaleric acid (3‐HV) are prepared from the monomer by three different methods, giving various ratios of the oligomers. The macrocycles containing three to twelve 3‐HV units (12‐ to 48‐membered rings) are isolated in pure form by chromatography. The triolide 3 can be separated by distillation and isolated on large scale. Biopol , the copolymer of ( R )‐3‐hydroxybutanoic acid (3‐HB) and ( R )‐3‐hydroxyvaleric acid (3‐HV), is degraded to mixtures of Me‐ and Et‐substituted triolides (‘ mixolides ’) with high crystallization tendency. The X‐ray crystal structures of the tetrolide 4 , pentolide 5 , hexolide 6 , heptolide 7 , and of two ‘mixolides’ (with inclusions of solvent) have been determined ( Figs. 3–7, 10 , and 11 ) and are compared with those of the corresponding 3‐HB derivatives reported previously. From the structural data, a 3 1 and a 2 1 helix of 3‐HV can be modelled, and the latter one compared with helix structures of P9(3‐HB) and P(3‐HV) derived from stretch‐fibre X‐ray scattering. Crystals of a water‐containing NaSCN complex of the triethyl triolide 3 were obtained in good quality for X‐ray analysis. The structure ( Figs. 12, 13 , and Table 6 ) contains an interesting array of CO and H 2 O O‐atoms around the Na + ions along a channel‐type tube ( a ‐axis of the crystal) which may be relevant to the role of P(3‐HB) and P(3‐HV) as components of cellular ion channels.
Faster link-state IGP convergence and improved network scalability and stability (2002)

It is desirable to have fast detection of failures followed by fast restoration and recovery in data networks (IP, ATM, frame relay, etc.) using link-state interior gateway protocols (IGP). This requires faster hello exchanges (unless one relies on link level detection which is not always possible), fast flooding, and more frequent shortest-path-first calculations. However, through analysis and simulation we show that this compromises the scalability and stability of the network. This is mainly because hello packets received at a router are indistinguishable from other packets and may experience long queueing delays during a sudden burst of many LSA (link-state advertisement) updates and cause the associated link to be declared down. At a later instant the link would recover. Both the failure and recovery generate fresh LSA, in effect developing a feedback loop to sustain the LSA storm. We suggest that hello and potentially some other IGP packets, such as acknowledgments, be marked explicitly so that they may be distinguished and queued separately from other IGP and data packets at the line rate and provided prioritized treatment. This allows significant reduction in IGP convergence time while maintaining network stability.
Effect of Acetanilide and p-Hydroxyacetanilide on the Carcinogenicity of N-2-Fluorenylacetamide and N-Hydroxy-N-2-fluorenylacetamide in Mice, Hamsters, and Female Rats2 (1973)

Simultaneous dietary administration of acetanilide (AA) or p-hydroxyacetanilide (p-OHAA) with the carcinogen N-2-fluorenylacetamide (FAA) inhibited mammary tumor formation in female Sprague-Dawley-derived rats. p-OHAA had no effect on the mammary tumor incidence from N-hydroxy-2-fluorenylacetamide (N-OHFAA). In male mice on similar regimens, AA was more effective than p-OHAA in reducing the liver cancer incidence from FAA. Neither AA nor p-OHAA altered the yield of bladder tumors induced by FAA in mice. p-OHAA decreased the bladder but not the liver tumor incidence caused by N-OHFAA in male mice. Either AA or p-OHAA reduced the number of liver tumors in female mice fed FAA, and p-OHAA had a similar action with N-OHFAA. Either AA or p-OHAA inhibited liver tumors in male or female hamsters fed FAA, and p-OHAA did likewise with N-OHFAA. The incidence of gastric papillomas and carcinomas From N-OHFAA was not markedly decreased by p-OHAA.
Mouse Glucose Transporter 9 Splice Variants Are Expressed in Adult Liver and Kidney and Are Up-Regulated in Diabetes (2005)

A novel glucose transporter (GLUT), mouse GLUT9 (mGLUT9), was recently cloned from mouse 7-d embryonic cDNA. Several splice variants of mGLUT9 were described, two of which were cloned (mGLUT9a and mGLUT9a Delta 209-316). This study describes the cloning and characterization of another splice variant, mGLUT9b. Cloned from adult liver, mGLUT9b is identical to mGLUT9a except at the amino terminus. Based on analysis of the genomic structure, the different amino termini result from alternative transcriptional/translational start sites. Expression and localization of these two mGLUT9 splice variants were examined in control and diabetic adult mouse tissues and in cell lines. RT-PCR analysis demonstrated expression of mGLUT9a in several tissues whereas mGLUT9b was observed primarily in liver and kidney. Using a mGLUT9-specific antibody, Western blot analysis of total membrane fractions from liver and kidney detected a single, wide band, migrating at approximately 55 kDa. This band shifted to a lower molecular mass when deglycosylated with peptide-N-glycosidase F. Both forms were present in liver and kidney. Immunohistochemical localization demonstrated basolateral distribution of mGLUT9 in liver hepatocytes and the expression of mGLUT9 in specific tubules in the outer cortex of the kidney. To investigate the alternative amino termini, mGLUT9a and mGLUT9b were overexpressed in kidney epithelium cell lines. Subcellular fractions localized both forms to the plasma membrane. Immunofluorescent staining of polarized Madin Darby canine kidney cells overexpressing mGLUT9 depicted a basolateral distribution for both splice variants. Finally, mGLUT9 protein expression was significantly increased in the kidney and liver from streptozotocin-induced diabetic mice compared with nondiabetic animals.
Facile Synthesis of Monodisperse Superparamagnetic Fe3O4 Core@hybrid@Au Shell Nanocomposite for Bimodal Imaging and Photothermal Therapy (2011)

A simple seed-mediated growth route is developed to fabricate monodisperse, uniform superparamagnetic Fe(3)O(4) core/gold shell structured nanocomposites with tunable sizes and optical properties, in which gold seed formation and attachment onto the core surface via S-Au covalent bonding proceeds almost simultaneously in the one-pot synthesis. The as-prepared nanocomposite is demonstrated to have a great potential for magnetic resonance imaging (MRI)-guided, focused photothermal tumor therapy under near-IR laser radiation.
Photochemistry of Roussin's Red Salt, Na2[Fe2S2(NO)4], and of Roussin's Black Salt, NH4[Fe4S3(NO)7]. In Situ Nitric Oxide Generation To Sensitize γ-Radiation Induced Cell Death1 (1997)

The quantitative photoreactivities in solution of Roussin's red salt (RRS, Na2[Fe2S2(NO)4]) and of Roussin's black salt (RBS, NH4[Fe4S3(NO)7]) are described. Photolysis of the red Roussinate anion Fe2S2(NO)42- in aerobic aqueous solution leads to quantitative formation of the black Roussinate anion Fe4S3(NO)7-. The quantum yield for disappearance of Fe2S2(NO)42- (ΦI = 0.14) is independent of excitation wavelength over a broad range (313−546 nm). Real time detection of nitric oxide by electrochemical sensors in the photolysis solution demonstrated the release of NO with a quantum yield of 0.07. The black Roussinate anion is much less photoactive (ΦII = 1.1 × 10-3) but does undergo photodecomposition in aerobic solution to give, eventually, ferric precipitates plus NO. These studies were initiated with the goal of developing photochemical strategies for delivering NO to biological targets on demand. In this context, the photolability of Fe2S2(NO)42- was examined as a possible candidate for exploiting the known nitric oxide sensitization of γ-radiation induced cell killing in V79 cell cultures (Mitchell, J. B.; et al. Cancer Res. 1993, 53, 5845−5848). Hypoxic cell cultures treated with RRS solution (1.0 mM) and then subjected to γ-radiation (15 Gy) demonstrated strikingly lower survival rates when simultaneously exposed to white light irradiation than did control systems treated identically but in the dark. The black salt was similarly probed, but its greater toxicity and lower quantum yields for NO release make this a less likely candidate for such photochemically induced radiation sensitization.
Growth factor requirements of childhood acute leukemia: establishment of GM-CSF-dependent cell lines (1987)

Abstract Eight permanent cell lines were established from cells of 50 consecutive patients with childhood acute leukemia. Three cell lines required growth factor-containing conditioned media. Analysis using blocking antisera and recombinant granulocytic macrophage (GM) colony- stimulating factor (CSF) identified GM-CSF as a growth factor required to establish the latter three cell lines and necessary for their continuous proliferation in chemically defined medium. Two of the GM- CSF-dependent cell lines were derived from patients with undifferentiated T- and a biphenotypic B-myelomonocytic leukemia, which suggests that GM-CSF might maintain proliferation of leukemias originating from immature progenitor cells. Cytogenetic analysis indicated that all established leukemic cell lines were aneuploid, with six lines containing chromosomal alterations related to those observed in the leukemic cells of the patient. Two patients did not have an abnormal clone identified in the marrow but did yield an aneuploid cell line. These studies indicate that GM-CSF-dependent leukemic cell lines can be established in a fraction of childhood leukemia. These cell lines lend themselves to studies aimed at the evaluation in vitro of the role of growth factors in controlling proliferation and differentiation of leukemic cells.
Chemical Sensors Based on Cyclodextrin Derivatives (2008)

This review focuses on chemical sensors based on cyclodextrin (CD) derivatives. This has been a field of classical interest, and is now of current interest for numerous scientists. First, typical chemical sensors using chromophore appended CDs are mentioned. Various "turn-off" and "turn-on" fluorescent chemical sensors, in which fluorescence intensity was decreased or increased by complexation with guest molecules, respectively, were synthesized. Dye modified CDs and photoactive metal ion-ligand complex appended CDs, metallocyclodextrins, were also applied for chemical sensors. Furthermore, recent novel approaches to chemical sensing systems using supramolecular structures such as CD dimers, trimers and cooperative binding systems of CDs with the other macrocycle [2]rotaxane and supramolecular polymers consisting of CD units are mentioned. New chemical sensors using hybrids of CDs with p-conjugated polymers, peptides, DNA, nanocarbons and nanoparticles are also described in this review.
Syntheses and anti-inflammatory and analgesic activities of hydroxamic acids and acid hydrazides. (1983)

On the basis of the generally accepted view that copper ions take part in the occurrence of inflammation, hydroxamic acids and acid hydrazides derived from various substituted cinnamic acids and hydrocinnamic acids, which were expected to chelate with copper ions, were synthesized and evaluated for anti-inflammatory activity by the carrageenin-induced rat paw edema assay and for analgesic activity by the phenylquinone writhing method in mice. Some of the synthesized compounds exhibited both activities, and 3-(3, 4-dimethoxyphenyl)propiohydroxamic acid and its Zn complex were more active than aspirin. The Cu (II) complexes of hydroxamic acid derivatives were synthesized and were assumed to have polymeric structures from the results of elemental analysis, molecular weight measurement and determination of magnetic susceptibility.