gebhart/patrepeval huggingface dataset:
De novo biosynthesis of defense root exudates in response to Fusarium attack in barley (2009)

Summary *Despite recent advances in elucidation of natural products in root exudates, there are significant gaps in our understanding of the ecological significance of products in the rhizosphere. *Here, we investigated the potential of barley (Hordeum vulgare) to secrete defense root exudates when challenged by the soilborne pathogen Fusarium graminearum. *Liquid chromatography with photodiode array detection (LC-DAD) was used to profile induced small-molecular-weight exudates. Thus, t-cinnamic, p-coumaric, ferulic, syringic and vanillic acids were assigned to plant metabolism and were induced within 2 d after Fusarium inoculation. Biological tests demonstrated the ability of those induced root exudates to inhibit the germination of F. graminearum macroconidia. In vivo labeling experiments with (13)CO(2) revealed that the secreted t-cinnamic acid was synthesized de novo within 2 d of fungal infection. Simultaneously to its root exudation, t-cinnamic acid was accumulated in the roots. Microscopic analysis showed that nonlignin cell wall phenolics were induced not only in necrosed zones but in all root tissues. *Results suggest that barley plants under attack respond by de novo biosynthesis and secretion of compounds with antimicrobial functions that may mediate natural disease resistance.
Molecular Basis for the Interaction of the Hepatitis B Virus Core Antigen with the Surface Immunoglobulin Receptor on Naive B Cells (2001)

The nucleocapsid of the hepatitis B virus (HBV) is composed of 180 to 240 copies of the HBV core (HBc) protein. HBc antigen (HBcAg) capsids are extremely immunogenic and can activate naive B cells by cross-linking their surface receptors. The molecular basis for the interaction between HBcAg and naive B cells is not known. The functionality of this activation was evidenced in that low concentrations of HBcAg, but not the nonparticulate homologue HBV envelope antigen (HBeAg), could prime naive B cells to produce anti-HBc in vitro with splenocytes from HBcAg- and HBeAg-specific T-cell receptor transgenic mice. The frequency of these HBcAg-binding B cells was estimated by both hybridoma techniques and flow cytometry (B7-2 induction and direct HBcAg binding) to be approximately 4 to 8% of the B cells in a naive spleen. Cloning and sequence analysis of the immunoglobulin heavy- and light-chain variable (VH and VL) domains of seven primary HBcAg-binding hybridomas revealed that six (86%) were related to the murine and human VH1 germ line gene families and one was related to the murine VH3 family. By using synthetic peptides spanning three VH1 sequences, one VH3 sequence, and one VLkappaV sequence, a linear motif in the framework region 1 (FR1)complementarity-determining region 1 (CDR1) junction of the VH1 sequence was identified that bound HBcAg. Interestingly, the HBcAg-binding motif was present in the VL domain of the HBcAg-binding VH3-encoded antibody. Finally, two monoclonal antibodies containing linear HBcAg-binding motifs blocked HBcAg presentation by purified naive B cells to purified HBcAg-primed CD4(+) T cells. Thus, the ability of HBcAg to bind and activate a high frequency of naive B cells seems to be mediated through a linear motif present in the FR1-CDR1 junction of the heavy or light chain of the B-cell surface receptor.
Monitoring the Biodegradation of Dendritic Near-Infrared Nanoprobes by in Vivo Fluorescence Imaging (2008)

Synthetic polymers and dendrimers have been widely used by the medical community to overcome biological barriers and enhance in vivo biomedical applications. Despite the widespread use of biomaterials it has been generally extremely difficult to monitor noninvasively their fate in vivo. Here we report multilayered nanoprobes, consisting of a near-infrared core, nanoencapsulated in a biodegradable dendrimer, and surrounded by a shell of polyethylene oxide. Covalent encapsulation of the near-infrared fluorophores in the dendritic scaffold conferred enhanced stability to the nanoprobe with added resistance to enzymatic oxidation and prolonged blood residence time. Insight into the time course of biodegradation of the dendritic aliphatic polyester nanoprobe was gained using noninvasive whole body in vivo fluorescence lifetime imaging. As the dendritic shell biodegrades the NIR probe becomes exposed, enabling monitoring of fluorescence lifetime changes in vivo.
Cross-Sectional Analysis of Clinical and Environmental Isolates of Pseudomonas aeruginosa : Biofilm Formation, Virulence, and Genome Diversity (2003)

Chronic lung infections with Pseudomonas aeruginosa biofilms are associated with refractory and fatal pneumonia in cystic fibrosis (CF). In this study, a group of genomically diverse P. aeruginosa isolates were compared with the reference strain PAO1 to assess the roles of motility, twitching, growth rate, and overproduction of a capsular polysaccharide (alginate) in biofilm formation. In an in vitro biofilm assay system, P. aeruginosa displayed strain-specific biofilm formation that was not solely dependent on these parameters. Compared with non-CF isolates, CF isolates expressed two opposing growth modes: reduced planktonic growth versus efficient biofilm formation. Planktonic cells of CF isolates showed elevated sensitivity to hydrogen peroxide, a reactive oxygen intermediate, and decreased lung colonization in an aerosol infection mouse model. Despite having identical genomic profiles, CF sequential isolates produced different amounts of biofilm. While P. aeruginosa isolates exhibited genomic diversity, the genome size of these isolates was estimated to be 0.4 to 19% (27 to 1,184 kb) larger than that of PAO1. To identify these extra genetic materials, random amplification of polymorphic DNA was coupled with PAO1-subtractive hybridization. Three loci were found within the genomes of two CF isolates encoding one novel homolog involved in retaining a Shigella virulence plasmid (mvpTA) and two divergent genes that function in removing negative supercoiling (topA) and biosynthesis of pyoverdine (PA2402). Together, P. aeruginosa biodiversity could provide one cause for the variation of morbidity and mortality in CF. P. aeruginosa may possess undefined biofilm adhesins that are important to the development of an antibiofilm therapeutic target.
Cloning of multiple cellulase cDNAs fromVolvariella volvaceaand their differential expression during substrate colonization and fruiting (2006)

We used PCR-based methods to clone and sequence four previously unidentified cellulase cDNAs: cbhI-I, cbhI-II, cbhII-I and egII. CbhI-I, cbhI-II and cbhII-I consist of 1710, 1610 and 1453 bp, respectively, and encode for 512, 458 and 442 amino acids, respectively. EgII consists of 1180 bp encoding for 310 amino acids, and belongs to family 61 of the glycosyl hydrolases. CbhI-I, cbhII-I and egII all have a modular structure, with the catalytic domain (CD) and cellulose-binding domain (CBD) located at the C-terminus in cbhI-I and egII, and at the N-terminus in cbhII-I. CbhI-II shows high homology to cbhI-I but lacks a CBD. Northern blotting revealed that cbhI-I, cbhI-II and cbhII-I were coordinately expressed at various stages of the mushroom developmental cycle (substrate colonization to mature fruit body), although the number of cbhI-I transcripts was much smaller. No egII expression was detectable during the substrate colonization phase but transcription levels increased as fruit body morphogenesis progressed.
Multi-dimensional Density Estimation (2004)

Modern data analysis requires a number of tools to undercover hidden structure. For initial exploration of data, animated scatter diagrams and nonparametric density estimation in many forms and varieties are the techniques of choice. This article focuses on the application of histograms and nonparametric kernel methods to explore data. The details of theory, computation, visualization, and presentation are all described.
Enrichment of Integral Membrane Proteins for Proteomic Analysis Using Liquid Chromatography−Tandem Mass Spectrometry (2002)

An increasing number of proteomic strategies rely on liquid chromatography-tandem mass spectrometry (LC-MS/MS) to detect and identify constituent peptides of enzymatically digested proteins obtained from various organisms and cell types. However, sample preparation methods for isolating membrane proteins typically involve the use of detergents and chaotropes that often interfere with chromatographic separation and/or electrospray ionization. To address this problem, a sample preparation method combining carbonate extraction, surfactant-free organic solvent-assisted solubilization, and proteolysis was developed and demonstrated to target the membrane subproteome of Deinococcus radiodurans. Out of 503 proteins identified, 135 were recognized as hydrophobic on the basis of their calculated hydropathy values (GRAVY index), corresponding to coverage of 15% of the predicted hydrophobic proteome. Using the PSORT algorithm, 53 of the proteins identified were classified as integral outer membrane proteins and 215 were classified as integral cytoplasmic membrane proteins. All identified integral cytoplasmic membrane proteins had from 1 to 16 mapped transmembrane domains (TMDs), and 65% of those containing four or more mapped TMDs were identified by at least one hydrophobic membrane spanning peptide. The extensive coverage of the membrane subproteome (24%) by identification of highly hydrophobic proteins containing multiple TMDs validates the efficacy of the described sample preparation technique to isolate and solubilize hydrophobic integral membrane proteins from complex protein mixtures.
PLUXter: Rapid Discovery of Metal-Organic Framework Structures Using PCA and HCA of High Throughput Synchrotron Powder Diffraction Data (2011)

This paper reports on a systematic method--called PLUXter--developed for screening and data mining of large numbers of potential metal-organic framework compounds that have been synthesized then subsequently analyzed with high throughput synchrotron radiation X-ray powder diffraction. The first part of the method utilizes principal components analysis (PCA), which allows materials to be ranked in order of crystallinity so that undesirable amorphous materials may be identified and eliminated. The second part allows structural grouping within and between samples to be observed using hierarchical cluster analysis (HCA). Classification using a single linkage distance produced unsatisfactory clusters however the dendrogram's structural relationships were used to establish and guide the boundaries of groups. The resultant grouping identities allowed further structure-property studies to be undertaken on representative structures from the clusters, significantly reducing time and the use of resources.
Study of the molecular orientation in a chiral smectic liquid crystal mixture using infrared dichroism (1996)

Abstract The molecular reorientation of a ferroelectric liquid crystal mixture, has been investigated as a function of applied voltage using polarised Fourier transform infrared spectroscopy. For a cell with chevron structure, a rapid decrease in the order parameter on applied voltage has been found for voltages in the range 10–30 V. The correlation between the dependence of the order parameter and the optical contrast ratio has also been found.
The Reproductive Cycle of Microtus ochrogaster in Eastern Kansas (1978)

About 800 Microtus ochrogaster were live—trapped at biweekly intervals from May 1971 through March 1973 in 3 grassland study areas in eastern Kansas, USA. Details of reproduction were determined by autopsy. Population density increased through the first winter, reached a peak in April 1972, then declined sharply during that summer and beyond. Body length, but not body mass, tended to be positively related to density. Both sexes matured at about the same weight; development was somewhat prolonged during the winter months, especially in the winter preceding the population peak. Pregnancy rates were high, approaching maximal iteroparity, throughout the study, with intervals of nonbreeding in both Julys, and in August and December of the population decline. Embryo counts increased significantly during the months of peak density but did not diminish in the period of the population decline. There was no association between either maternal weight or parity and number of embryos. Corpora counts were not higher in heavy or multiparious ♀ ♀, nor did the level of prenatal mortality increase during the period of greatest density. Except for a few individuals taken in July and August 1971, ♂ ♂ with a mass 30 g or more were judged to be fertile, as were a majority of the 20 to 29—g ♂ ♂. Body weight and testes weight were significantly correlated in fertile ♂ ♂ but not in nonfertile ♂ ♂. These reproductive findings were applied to a model of population regulation of microtine cycles. The pattern of reproduction of Kansas and Indiana prairie voles was compared. Three concordant lines of evidence seem to indicate that Kansas and possibly other geographical populations of prairie voles have adjusted the breeding schedule to accommodate both hot and dry summers and cold, snowy winters. Pregnancy rate, litter size, and adjusted testes weight all show a significant increase in March–April and September–October and a decrease in midsummer and midwinter. Thus the pattern of reproduction of Kansas prairie voles may represent a composite of the patterns shown by the dry—adapted species, such as Microtus californicus, and the cold—adapted microtines, such as Microtus pennsylvanicus. Based on the observations of this study, Kansas prairie voles seem to have adjusted to both harsh seasons by breeding more or less continuously, with the midsummer depression possibly reflecting the Great Plains origin of the species, and the winter depression being a facultative response to weather, density, or quality of habitat.
Tuning spectral properties of fullerenes by substitutional doping (2004)

We propose a substitutional doping approach to achieve tunable optical properties from fullerenes. Taking ${\mathrm{C}}_{60}$ as an example and using time-dependent density functional theory, we compute the absorption spectra of heterofullerenes ${\mathrm{C}}_{60\ensuremath{-}n\ensuremath{-}m}{\mathrm{N}}_{n}{\mathrm{B}}_{m},$ and demonstrate that their optical gaps and first triplet energies can be tuned from the near-infrared up to the ultraviolet by tailoring the dopant numbers n and m. This is supported by experiment and suggests heterofullerenes as single-molecule fluorescent probes and as building blocks for the bottom-up assembly of tunable luminescent devices. For the example of ${\mathrm{C}}_{59}\mathrm{HN},$ we discuss the effect of organic functionalization, which is needed for device fabrication, on optical properties.
Interaction of peroxidized cardiolipin with rat‐heart mitochondrial membranes: Induction of permeability transition and cytochrome c release (2006)

Cardiolipin peroxidation plays a critical role in mitochondrial cytochrome c release and subsequent apoptotic process. Mitochondrial pore transition (MPT) is considered as an important step in this process. In this work, the effect of peroxidized cardiolipin on MPT induction and cytochrome c release in rat heart mitochondria was investigated. Treatment of mitochondria with micromolar concentrations of cardiolipin hydroperoxide (CLOOH) resulted in a dose-dependent matrix swelling, DeltaPsi collapse, release of preaccumulated Ca2+ and release of cytochrome c. All these events were inhibited by cyclosporin A and bongkrekic acid, indicating that peroxidized cardiolipin behaves as an inducer of MPT. Ca2+ accumulation by mitochondria was required for this effect. ANT (ADP/ATP translocator) appears to be involved in the CLOOH-dependent MPT induction, as suggested by the modulation by ligands and inhibitors of adenine nucleotide translocator (ANT). Together, these results indicate that peroxidized cardiolipin lowers the threshold of Ca2+ for MPT induction and cytochrome c release. This synergistic effect of Ca2+ and peroxidized cardiolipin on MPT induction and cytochrome c release in mitochondria, might be important in regulating the initial phase of apoptosis and also may have important implications in those physiopathological situations, characterized by both Ca2+ and peroxidized cardiolipin accumulation in mitochondria, such as aging, ischemia/reperfusion and other degenerative diseases.
η6-Cycloparaphenylene Transition Metal Complexes: Synthesis, Structure, Photophysical Properties, and Application to the Selective Monofunctionalization of Cycloparaphenylenes (2015)

The synthesis, structure, photophysical properties, and reactivity of cycloparaphenylenes (CPPs) coordinated to group 6 transition metal fragments are described. The η(6)-coordination of [9]CPP or [12]CPP with M(CO)6 (M = Cr, Mo, W) afforded the corresponding [n]CPP-M(CO)3 complexes (n = 9, 12; M = Cr, Mo, W). In the (1)H NMR spectra of these complexes, characteristic upfield-shifted singlet signals corresponding to the four hydrogen atoms attached to the coordinated C6H4 ring of the CPPs were observed at 5.4-5.9 ppm. The complex [9]CPP-Cr(CO)3 could be successfully isolated in spite of its instability. X-ray crystallographic analysis and computational studies of [9]CPP-Cr(CO)3 revealed that chromium-CPP coordination occurs at the convex surface of [9]CPP both in the solid state and in solution. TD-DFT calculations suggested that the emerging high-wavenumber absorption peak upon coordination of [9]CPP to Cr(CO)3 should be assigned to a weak HOMO-LUMO transition. Moreover, by using the complex [9]CPP-Cr(CO)3, a rapid and highly monoselective CPP functionalization has been achieved. The established one-pot method, consisting of complexation, deprotonation, nucleophilic substitution, and decomplexation steps, yielded silyl-, boryl-, and methoxycarbonyl-substituted CPPs in up to 93% yield relative to reacted starting material.
Reversal of normal ovarian function in experimental autoimmune ovarian failure mouse model post-dexamethasone treatment (51.10) (2012)

Abstract Glucocorticoids (GCs) are in widespread clinical use for treatment of autoimmune diseases including Premature Ovarian Failure and In Vitro fertilization-Embryo Transfer failures. Immunosuppression by GCs in these patients inhibits potential adverse effects of Anti-Ovarian Antibodies (AOAs) on oocyte quality, gamete interaction, implantation and embryo development. The present study highlights the restoration of normal follicular development and fertility in experimental autoimmune ovarian failure mouse model after dexamethasone treatment, thus establishing the significance of corticosteroids in human autoimmune ovarian failures. However, their mode of action in these cases remains unknown. Female mice were immunized with immunodominant epitopes of three dominant human ovarian autoantigens and monitored for various ovarian parameters. Immunized female mice showed high AOA titers and specific reactivity to different ovarian cell types. Adverse effects on cyclicity, pregnancy, pre-implantation embryos and fertility were noticed. Ovaries from these mice exhibited fewer healthy corpora lutea (CL) and growing follicles and increased atretic follicles. However, the number of healthy follicles, CL, pre-implantation embryos and fertility was restored to normal in dexamethasone treated mice in a dose dependent manner, thereby establishing that the three putative autoimmune ovarian antigens can be used for developing targeted therapies in human autoimmune ovarian pathologies.
Compliance in clinical trials of two nonbronchodilator, antiasthma medications. (1991)

An electronic monitoring device was used to assess patient compliance during clinical trials of two new aerosolized nonbronchodilator, antiasthma drugs. Compliance was poor, but similar, in both trials. Patients took the study drug as instructed on a mean of 37.3% days (range 10% to 77%) in one trial and 37.4% days (range 0% to 63%) in the other. Both underuse and overuse were observed. Underuse was seen on a mean of 38.9% days (range 9% to 81%) and 46.0% (range 15% to 80%) respectively; overuse on a mean of 23.5% days (range 6% to 54%) and 16.6% days (range 0% to 41%). In some patients ten or more activations of the device were recorded at the same time. In six patients such multiple simultaneous activations were recorded on two or more separate days. These patients were among the most noncompliant in the study. Multiple simultaneous activations frequently followed underuse days or preceded followup visits, suggesting the possibility of duplicity. Overall compliance was such that valid conclusions about efficacy of the drugs could only have been drawn in six of 34 patients.
Recent molecular discoveries in angiogenesis and antiangiogenic therapies in cancer (2013)

Four decades ago, angiogenesis was recognized as a therapeutic target for blocking cancer growth. Because of its importance, VEGF has been at the center stage of antiangiogenic therapy. Now, several years after FDA approval of an anti-VEGF antibody as the first antiangiogenic agent, many patients with cancer and ocular neovascularization have benefited from VEGF-targeted therapy; however, this anticancer strategy is challenged by insufficient efficacy, intrinsic refractoriness, and resistance. Here, we examine recent discoveries of new mechanisms underlying angiogenesis, discuss successes and challenges of current antiangiogenic therapy, and highlight emerging antiangiogenic paradigms.
v-Src activates the expression of 92-kDa type IV collagenase gene through the AP-1 site and the GT box homologous to retinoblastoma control elements. A mechanism regulating gene expression independent of that by inflammatory cytokines. (1993)

The 92-kDa type IV collagenase (matrix metalloproteinase-9; MMP-9) is frequently expressed in cells showing an invasive nature during physiological and pathological processes, and the expression is strictly controlled by a variety of trans-membrane signals. Binding sites for NF-kB, Sp-1, and AP-1 are reportedly required for induction of MMP-9 gene expression by tumor necrosis factor-alpha or 12-O-tetradecanoylphorbol-13-acetate. Comparison of the sequence of the newly cloned mouse MMP-9 promoter region with our previous human isolate revealed that, in addition to the above mentioned elements, four units of GGGG(T/A)GGGG sequence (GT box) were conserved between the two species. In this study, we have demonstrated that one of the GT boxes located downstream of the AP-1 site is essential along with the AP-1 site for the activation of the promoter by v-Src but not by tumor necrosis factor-alpha or 12-O-tetradecanoylphorbol-13-acetate. Gel mobility-shift assays revealed that binding proteins for retinoblastoma control element, including Sp-1 family protein, can bind specifically to GT boxes. Thus, the v-Src signals to the AP-1 site and to the GT box homologous to retinoblastoma control element acted synergistically in transcriptional activation. These results suggest that certain v-Src-mediated signals are propagated along pathways that are independent of inflammatory cytokines.
TALENoffer: genome-wide TALEN off-target prediction (2013)

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