gebhart/patrepeval huggingface dataset:
The Arabidopsis HOBBIT gene encodes a CDC27 homolog that links the plant cell cycle to progression of cell differentiation (2002)

In plant meristems, dividing cells interpret positional information and translate it into patterned cell differentiation. Here we report the molecular identification of the Arabidopsis HOBBIT gene that is required for cell division and cell differentiation in meristems. We show that it encodes a homolog of the CDC27 subunit of the anaphase-promoting complex (APC). HOBBIT partially complements a yeast nuc2/cdc27 mutant. Unlike other CDC27 homologs in Arabidopsis, its transcription is cell cycle regulated. Furthermore, hobbit mutants show a reduction in DR5 :: GUS auxin reporter gene expression and accumulate the AXR3/IAA17 repressor of auxin responses. HOBBIT activity may thus couple cell division to cell differentiation by regulating cell cycle progression in the meristem or by restricting the response to differentiation cues, such as auxin, to dividing cells.
STUDY OF ENZYMATIC HYDROLYSIS OF PRETREATED BIOMASS AT INCREASED SOLIDS LOADING (2012)

The effect of biomass loading from 50 to 200 g/L on enzymatic hydrolysis was studied using switchgrass samples pretreated by dilute acid and hypochlorite-alkaline methods. It was confirmed that an increase of initial loading of the pretreated biomass leads to a decrease of enzymatic digestibility, probably due to difficulty of mass transfer of cellulolytic enzymes in the high-viscous substrate slurry and also because of an inhibiting effect of the formed sugars. An additional sharp problem connected with enzymatic hydrolysis at the high-solids loading is absorption and retention of liquid hydrolysate by residual non-hydrolyzed biomass that causes diminution of the available volume (V a ) of the sugar solution and decreases productivity of the saccharification process. To optimize the high-solids enzymatic hydrolysis, the maximal amount of the formed sugars was determined A m = C m x V a,m , where C m is maximal concentration of the sugar solution and V a,m is maximal available volume. Such an approach makes it possible to find the optimal conditions for the hydrolysis: optimal biomass loading and hydrolysis time. After enzymatic hydrolysis at these optimal conditions, the low-lignified biomass pretreated by hypochlorite-alkaline method displayed much more available volume of sugar solution and higher digestibility characteristics than the cellolignin obtained by acidic pretreatment of the initial biomass sample.
Amino‐terminal sequence of ethylene‐induced bean leaf chitinase reveals similarities to sugar‐binding domains of wheat germ agglutinin (1985)

Chitinase has been reported for many plant species. A role in plant defense has been suggested for plant chitinases, due to their ability to degrade fungal cell wall chitin. Increased levels of chitinase are induced in bean plants by the plant hormone ethylene [(1983) Planta 157, 22‐31]. The amino acid sequence of positions 1–30 of ethylene‐induced bean leaf chitinase was determined and found to possess considerable sequence homology to wheat germ agglutinin and hevein. The implication of a lectin‐related structure for the enzymatic specificity of chitinase is discussed.
Twin studies reveal specific imbalances in the mucosa-associated microbiota of patients with ileal Crohnʼs disease (2008)

Large interindividual variation in the composition of the intestinal microbiota between unrelated individuals has made it challenging to identify specific aspects of dysbiosis that lead to Crohn's disease (CD). To reduce variations in exposure during establishment of the gut flora and the influence of genotype, we studied the mucosa-associated microbiota of monozygotic twin pairs that were discordant (n = 6) or concordant (n = 4) for CD. DNA was extracted from biopsies collected from 5 locations between the ileum and rectum. Bacterial 16S ribosomal RNA genes were amplified and community composition assessed by terminal-restriction fragment length polymorphism, cloning and sequencing, and quantitative real-time polymerase chain reaction (PCR). The microbial compositions at all biopsy locations for each individual were similar, regardless of disease state, but there were differences between individuals. In particular, individuals with predominantly ileal CD had a dramatically lower abundance (P < 0.001) of Faecalibacterium prausnitzii and increased abundance (P < 0.03) of Escherichia coli compared to healthy co-twins and those with CD localized in the colon. This dysbiosis was significantly correlated to the disease phenotype rather than genotype. The reduced abundance of F. prausnitzii and increased abundance of E. coli are indicative of an ileal CD phenotype, distinct from colonic CD, and the relative abundances of these specific bacterial populations are promising biomarker candidates for differential diagnosis of CD and eventually customized treatment.
Codon-Optimized Genes that Enable Increased Heterologous Expression in Mammalian Cells and Elicit Efficient Immune Responses in Mice after Vaccination of Naked DNA (2004)

Many of the problems related with mammalian gene expression, such as low translation efficiency and mRNA halflife, can be solved by means of a rational gene design, based on modern bioinformatics, followed by the de novo generation of a synthetic gene. Moreover, high expression rates and prolonged mRNA stability are not only crucial for heterologous mammalian expression, but, in particular, are important for the generation of effective DNA vaccines. In this chapter we show that an optimized synthetic gene encoding the HIV-1 Pr55gag outperforms wild-type gene driven expression by several orders of magnitude. RNA analysis revealed that this positive effect was mostly due to increased mRNA stability of the optimized transcripts. Moreover, mice vaccinated with the optimized gag gene elicited a much stronger immune response against Pr55gag than the control groups immunized with the respective wild-type gene.
Serum soluble CD27 level is associated with outcome in patients with diffuse large B-cell lymphoma treated with rituximab, cyclophosphamide, doxorubicin, vincristine and prednisolone (2012)

Since the introduction of rituximab (R), the prognosis for diffuse large B-cell lymphoma (DLBCL) has markedly improved. We evaluated the prognostic significance of serum soluble CD27 (sCD27) in 143 patients with DLBCL treated with cyclophosphamide, doxorubicin, vincristine and prednisolone plus rituximab (R-CHOP). Five-year overall survival rates for patients with sCD27≥213 U/mL or <213 U/mL were 38.7% and 76.8%, respectively (p =0.0005). Multivariate analysis revealed that serum sCD27 was significantly correlated with OS (p =0.047). Immunohistochemical staining for CD27 in lymphoma tissues revealed positive lymphoma cells in 22 cases (18.5%) and positive microenvironment T-cells in 62 cases (52.1%) and was negative in the remaining patients. In these three subgroups, median sCD27 levels were 336 U/mL, 242.6 U/mL and 109.9 U/mL, respectively (p =0.004). Thus, serum sCD27 level is associated with CD27 expression on lymphoma cells, and may be a powerful prognostic factor for DLBCL.
Specific inhibition of type I and type II collagen fibrillogenesis by the small proteoglycan of tendon (1984)

The small dermatan sulphate proteoglycan of bovine tendon demonstrated a unique ability to inhibit fibrillogenesis of both type I and type II collagen from bovine tendon and cartilage respectively in an assay performed in vitro. None of the other proteoglycan populations from cartilage, tendon or aorta, even those similar in size and chemical structure, had this effect. Alkali treatment of the small proteoglycan of tendon eliminated its ability to inhibit fibrillogenesis, whereas chondroitinase digestion did not. This indicates that its interaction with collagen depends on the core protein. Fibrillogenesis of pepsin-digested collagens was affected similarly, indicating that interaction with the collagen telopeptides is not involved. The results suggest that interactions between collagen and proteoglycans may be quite specific both for the type of proteoglycan and its tissue of origin.
Transmembrane TNF- : structure, function and interaction with anti-TNF agents (2010)

Transmembrane TNF-alpha, a precursor of the soluble form of TNF-alpha, is expressed on activated macrophages and lymphocytes as well as other cell types. After processing by TNF-alpha-converting enzyme (TACE), the soluble form of TNF-alpha is cleaved from transmembrane TNF-alpha and mediates its biological activities through binding to Types 1 and 2 TNF receptors (TNF-R1 and -R2) of remote tissues. Accumulating evidence suggests that not only soluble TNF-alpha, but also transmembrane TNF-alpha is involved in the inflammatory response. Transmembrane TNF-alpha acts as a bipolar molecule that transmits signals both as a ligand and as a receptor in a cell-to-cell contact fashion. Transmembrane TNF-alpha on TNF-alpha-producing cells binds to TNF-R1 and -R2, and transmits signals to the target cells as a ligand, whereas transmembrane TNF-alpha also acts as a receptor that transmits outside-to-inside (reverse) signals back to the cells after binding to its native receptors. Anti-TNF agents infliximab, adalimumab and etanercept bind to and neutralize soluble TNF-alpha, but exert different effects on transmembrane TNF-alpha-expressing cells (TNF-alpha-producing cells). In the clinical settings, these three anti-TNF agents are equally effective for RA, but etanercept is not effective for granulomatous diseases. Moreover, infliximab induces granulomatous infections more frequently than etanercept. Considering the important role of transmembrane TNF-alpha in granulomatous inflammation, reviewing the biology of transmembrane TNF-alpha and its interaction with anti-TNF agents will contribute to understanding the bases of differential clinical efficacy of these promising treatment modalities.
A Chronic Obstructive Pulmonary Disease Susceptibility Gene, FAM13A , Regulates Protein Stability of β-Catenin (2016)

We show that FAM13A may influence COPD susceptibility by promoting β-catenin degradation.
Theory of variable-ratio power splitters using multimode interference couplers (1999)

In this letter, we analyze the integrated optical N/spl times/N generalized Mach-Zehnder interferometer (GMZI) employing multimode interference (MMI) couplers. A transfer matrix is used to derive analytic expressions for the intensity distribution at the output ports of the GMZI as a function of the phase shifts applied to the arms. These expressions form a system of nonlinear equations which are numerically solved for the phase shifts, enabling a new interpretation of the GMZI as a variable-ratio power splitter. The performance of the GMZI has been simulated, and it is found that the power splitting ratio is tolerant to both the accuracy of the applied phase shifts and to fluctuations in wavelength.
An homogeneous radioimmunoassay for abscisic acid using a scintillation proximity assay technique (1991)

Abstract An homogeneous radioimmunoassay (RIA) for the plant growth regulator abscisic acid (ABA) has been developed by modifying an established heterogeneous assay. The introduction of a scintillation proximity reagent has enabled the production of a one‐step RIA in which radioactivity associated with antibody‐bound ABA can be counted in the presence of the unbound radiolabelled ABA and without the addition of a liquid scintillation cocktail. The assay has been validated by comparing the results with those obtained by combined gas chromatography/mass spectrometry and the precision of each method determined. The homogeneous RIA has a working range of 0.165–13.2 ng ABA and has been used to determine ABA concentration in extracts of leaves of tomato, Lycopersicon esculentum Mill. cv. Ailsa Craig (wild type) and three wilty mutants, notabilis, flacca and sitiens .
Regio- and Stereoselective Functionalization of an Optically Active Tetrahydroindolizine Derivative. Catalytic Asymmetric Syntheses of Lentiginosine, 1,2-Diepilentiginosine, and Gephyrotoxin 209D (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRegio- and Stereoselective Functionalization of an Optically Active Tetrahydroindolizine Derivative. Catalytic Asymmetric Syntheses of Lentiginosine, 1,2-Diepilentiginosine, and Gephyrotoxin 209DSeiji Nukui, Mikiko Sodeoka, Hiroaki Sasai, and Masakatsu ShibasakiCite this: J. Org. Chem. 1995, 60, 2, 398–404Publication Date (Print):January 1, 1995Publication History Published online1 May 2002Published inissue 1 January 1995https://doi.org/10.1021/jo00107a019RIGHTS & PERMISSIONSArticle Views673Altmetric-Citations112LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (2 MB) Get e-AlertsSupporting Info (2)»Supporting Information Supporting Information Get e-Alerts
parkin counteracts symptoms in a Drosophila model of Parkinson's disease (2004)

The highly conserved parkin E3 ubiquitin ligase can suppress the damaging effects of human alpha-synuclein. These results are consistent with a role for parkin in targeting alpha-synuclein to the proteasome. If this relationship is conserved in humans, this suggests that up-regulation of parkin should suppress alpha-synucleinopathic PD. The development of therapies that regulate parkin activity may be crucial in the treatment of PD.
Dose-dependent effects of perindopril on blood pressure and small-artery structure. (1994)

Long-term treatment of young spontaneously hypertensive rats (SHR) with angiotensin-converting enzyme (ACE) inhibitors has a persistent effect on blood pressure when treatment is withdrawn. The aim of the present study was to determine whether this effect could be mediated by the effect of treatment on resistance-artery structure. We determined the dose dependence of ACE-inhibitor therapy on blood pressure and small-artery structure during treatment and on the recovery of blood pressure when treatment was withdrawn. SHR (40 per group) were treated from age 4 to 24 weeks with one of three doses of perindopril (0.4, 0.8, or 1.5 mg/kg per day). Control groups were untreated SHR and Wistar-Kyoto rats. At 24 weeks, treatment was stopped and small arteries were taken from half of the rats from the mesenteric, femoral, cerebral, and coronary vascular beds for morphological and functional measurements. The blood pressure of the other half of the rats was followed until 36 weeks of age. During treatment, perindopril caused a dose-dependent reduction in blood pressure and in the media-lumen ratio and media area of the small arteries, whereas there was a dose-dependent increase in lumen diameter. The effect of treatment on the structure of arteries from the different vascular beds was homogeneous. Compared with values from Wistar-Kyoto rats, blood pressure normalization in SHR was not associated with full normalization of structure. After withdrawal of treatment, there was an inverse relation between perindopril dose and the persistent effect.(ABSTRACT TRUNCATED AT 250 WORDS)
Phosphorylation of linker histone is associated with transcriptional activation in a normally silent nucleus. (1996)

Previous studies have suggested that micronuclear linker histones are phosphorylated by cAMP-dependent protein kinase (PKA) in Tetrahymena (Sweet, M.T., and C.D. Allis. 1993. Chromosoma. 102: 637-647). In this study, we report that a rapid and dramatic phosphorylation of the micronuclear linker histone, delta, occurs early in the sexual pathway, conjugation. Phosphorylated isoforms of delta are detected as early as 30 min after mixing cells of different mating types; blocking pair formation abolishes this induction completely. Phosphorylation of delta is stimulated by the addition of N6-benzoyladenosine 3':5' cyclic monophosphate to starved (nonmating) cells, suggesting that a PKA/cAMP signal transduction pathway is involved. Maximal phosphorylation of delta is observed during meiotic prophase, a period when micronuclei become transcriptionally active. In situ staining, using phospho-delta-specific antibodies combined with [3H]uridine autoradiography, shows that decondensed micronuclear chromatin undergoing active transcription is enriched in phosphorylated delta isoforms. In contrast, condensed inactive micronuclear chromatin is enriched in dephosphorylated delta. These results strongly suggest that phosphorylation of linker histone plays an important and previously unsuspected role in establishing transcriptional competence in micronuclei.
Optimal Synthetic Glycosylation of a Therapeutic Antibody (2016)

Glycosylation patterns in antibodies critically determine biological and physical properties but their precise control is a significant challenge in biology and biotechnology. We describe herein the optimization of an endoglycosidase-catalyzed glycosylation of the best-selling biotherapeutic Herceptin, an anti-HER2 antibody. Precise MS analysis of the intact four-chain Ab heteromultimer reveals nonspecific, non-enzymatic reactions (glycation), which are not detected under standard denaturing conditions. This competing reaction, which has hitherto been underestimated as a source of side products, can now be minimized. Optimization allowed access to the purest natural form of Herceptin to date (≥90 %). Moreover, through the use of a small library of sugars containing non-natural functional groups, Ab variants containing defined numbers of selectively addressable chemical tags (reaction handles at Sia C1) in specific positions (for attachment of cargo molecules or "glycorandomization") were readily generated.
Inhibition of Collagen Synthesis With Prolyl 4-Hydroxylase Inhibitor Improves Left Ventricular Function and Alters the Pattern of Left Ventricular Dilatation After Myocardial Infarction (2001)

Background- Left ventricular (LV) remodeling after myocardial infarction (MI) is associated with fibrosis, dilatation, and dysfunction. We postulated that prevention of fibrosis after MI with a prolyl 4-hydroxylase inhibitor (P4HI) would preserve LV function and attenuate LV enlargement. Methods and Results- Adult female rats (200 to 250 g) had experimental MI and were then randomized to treatment with P4HI (MI-FG041, n=29) or vehicle (MI-control, n=29) 48 hours after MI for 4 weeks in 2 phases. Echocardiograms were performed weekly with a 15-MHz linear transducer, and at 4 weeks, collagen isoform determinations and in vivo hemodynamics were performed. At randomization, the infarct size and LV function and size were similar in MI-FG041 and MI-control but significantly different from shams (n=9). At week 4, the LV function in MI-FG041 was significantly better than in MI-controls (fractional shortening 21% versus 16%, P=0.01; fractional area change 30% versus 19%, P=0.002; ejection fraction 35% versus 23%, P=0.001). In the FG041 group, LV area in systole was less (P<0.05), the dP/dt(max) after isoproterenol was higher (P<0.05), and types I and III collagen in noninfarcted LV were less than in MI-control. The hydroxyproline/proline ratio was increased by 64% in MI-control and reduced to the sham value in MI-FG041 rats. In the scar tissue, it was reduced by 24% in MI-FG041. Conclusions- This study demonstrates that prevention of interstitial fibrosis with a P4H inhibitor alters the pattern of LV enlargement and produces partial recovery of LV function after MI.
Neurotoxic Organophosphate Degradation with Polyvinyl Alcohol Gel-Immobilized Microbial Cells (1998)

A genetically engineered strain of Escherichia coli that expresses organophosphorus hydrolase (OPH) was immobilized in a polyvinyl alcohol (PVA) cryogel to form a porous biocatalyst that successfully degrades organophosphorus (OP) neurotoxins. The impacts of both diffusion and reaction on biocatalyst efficiency were determined to enable prediction and optimization of the biocatalyst performance. The kinetic rate parameters and activation energies of pure OPH, free cell suspensions, and the immobilized cell biocatalyst were compared. Diffusion was a determining factor for paraoxon hydrolysis because of the very rapid OPH kinetics for its model substrate. Both the paraoxon diffusion through the PVA matrix and the diffusion associated with microbial transport of paraoxon were shown to impact the biocatalyst reaction. However, the enhancement in storage stability resulting from diffusional limitations provides an advantage to diffusion-limited operation. This research may serve as a guide to define the influence of diffusion in biological reaction systems. The broad substrate specificity and hydrolytic efficiency of OPH coupled with the ability to genetically engineer the enzyme for specific target OP neurotoxins enhance the suitability of OPH-based technologies for detoxification of these compounds. Cryoimmobilization provides a suitable vehicle as a cost-effective, efficient technology for bioremediation of environmental media contaminated with OP compounds.
Vibro-impacting power harvester (2010)

The certification of retro-fitted structural health monitoring (SHM) systems for use on aircraft raises a number of challenges. One critical issue is determining the optimal means of supplying power to these systems, given that access to the existing aircraft power-system is often problematic. Previously, the DSTO has shown that a structural-strain based energy harvesting approach can be used to power a device for SHM of aircraft structure. Acceleration-based power harvesting from airframes can be more demanding than a strain based approach because the vibration spectrum of an aircraft structure can vary dynamically with flight conditions. A vibration spectrum with varying frequency may severely limit the power harvested by a single-degree-of-freedom resonance-based device, and hence a frequency agile or (relatively) broadband device is often required to maximize the energy harvested. This paper reports on an investigation into the use of a vibro-impact approach to construct an acceleration-based power harvester that can operate in the frequency range 29-41 Hz.
Testosterone Replacement Therapy for Hypogonadal Men With Major Depressive Disorder (2001)

In this clinical trial with depressed, hypogonadal men, antidepressant effects of testosterone replacement could not be differentiated from those of placebo.
Novel Modulator for Endothelial Adhesion Molecules (1999)

These observations suggest that adiponectin modulates endothelial inflammatory response and that the measurement of plasma adiponectin levels may be helpful in assessment of CAD risk.
Linkages between glucosaminoglycan and glucan determine alkali-insolubility of the glucan in walls ofSaccharomyces cerevisiae (1987)

Glucosaminoglycans in the alkali-insoluble wall fraction of the yeast Saccharomyces cerevisiae could be partly degraded by treatment with nitrous acid, indicating the presence of non-acetylated glucosamine residues, and almost completely degraded by treatment with chitinase. The latter treatment, solubilising 95% of the glucosaminoglycan, converted 92% of the alkali-insoluble glucan in the complex into an alkali-soluble form. It is suggested that the small amount of alkali-insoluble glucosaminoglycan in the yeast cell wall (less than 2% of the dry weight) is covalently linked to the β-glucan (about 28% of the dry weight), keeping the latter in an alkali-insoluble form.