gebhart/patrepeval huggingface dataset:
Selective interactions between different species of mycorrhizal fungi and Rhizobium meliloti strains, and their effects on growth, N2‐fixation (15N) and nutrition of Medicago sativa L. (1991)

Three isolates of vesicular-arbuscular (VA) mycorrhizal fungi, belonging to the species Glomus mosseae (Nicol. and Gerd.) Gerd. and Trappe, G. fasciculatum (Taxter sensu Gerd.) Gerd, and Trappe, and G. caledonium (Nicol. and Gerd.) Trappe and Gerd, were inoculated in dual combinations with six strains of Rhizobium meliloti with the aim of testing these combinations for functional compatibility with their common host plant, the legume Medicago sativa L. Symbiotic efficiency (promotion of plant growth and N and P nutrition) was found to be dependent on the particular combination of Rhizobium strain and Glomus species indicating selective and specific compatibilities between strains and isolates of the two types of microsymbiont, but also between them and the common host plant. Observed effects on plant growth were in general, though not always, related to the extent of VA mycorrhizal colonization. Although the different mycorrhizal and/or rhizobial treatments produced different effects on plant growth, the rate of nodule formation on M. sativa roots remained constant. Most mycorrhizal treatments increased the concentration and/or content of N in plant shoots but effectiveness was in the order: G. fasciculatum > G. mosseae > G. caledonium. In some cases, this increase in N-content may be a consequence of a P-mediated stimulation of N<sub>2</sub> -fixation by VA mycorrhiza, as ascertained using <sup>15</sup> N. In other instances, however, the increase seems to reflect a VA mycorrhizal-mediated enhancement of N-uptake from soil. VA mycorrhizal inoculation decreased the concentration of Ca and Mg in plant shoots and a buffering effect of VA mycorrhiza in situations of nutrient excess in soil is proposed.
Caprine β-Mannosidosis (1983)

Beta-mannosidosis, an inherited defect of glycoprotein catabolism associated with deficiency of tissue β-mannosidase and accumulation of Man(β1–4)GlcNAc and Man(β1-4)GlcNAc(β1-4)GlcNAc, appeared in four of 13 offspring of a single pair of clinically normal, related Nubian goats. Neurological examinations revealed that all four affected goats were unable to rise or walk. All had facial dysmorphism, dome-shaped skulls, small palpebral fissures, carpal contractures, hyperextension of the pastern joints, proximal muscle atrophy, intermittent ocular oscillations resembling pendular nystagmus, marked intention tremor, and deafness. With intensive care, three affected kids were hand-reared and then killed at 1,7, and 21 days of age. Macroscopically, there were paucity of myelin in the cerebral and cerebellar hemispheres and ventricular dilatation. Microscopically, the extent and distribution of cytoplasmic vacuolation, myelin paucity, axonal spheroids, and filamentous expansions were evaluated in the cerebrum, cerebellum, brainstem, spinal cord. and peripheral nerves of the four affected kids and two age-matched, clinically normal kids. Widespread cytoplasmic vacuolation correlated with the previously reported accumulation of oligosaccharides in the brain and kidney and the deficiency of tissue β-mannosidase. β-Mannosidosis. not yet identified in man or other species, is characterized by distinctive neonatal clinical, pathological and biochemical features which differentiate it from the α-mannosidoses and other inherited diseases of glycoprotein catabolism.
Induction of tumour necrosis factor (TNF) receptor type p55 and p75 in patients with chronic hepatitis C virus (HCV) infection (1998)

There is evidence that TNF-alpha contributes to the pathogenesis of chronic viral hepatitis. The cellular effects of this cytokine are regulated by two specific receptors, and membranous shedding of these receptors reflects activation of the TNF system. We performed a study of TNF-alpha and functionally active soluble TNF-receptors (TNFR-p55 and -p75) in 105 patients with chronic HCV infection. In HCV RNA-positive patients a significant enhancement of TNF-alpha and both receptor types was observed compared with controls (TNF-alpha 83.8+/-91.7 pg/ml versus 18.8+/-8.4 pg/ml, P<0.001; TNFR-p55 1.4+/-0.4 ng/ml versus 0.9+/-0.2 ng/ml, P<0.0001; TNFR-p75 6.4+/-2.4 ng/ml versus 2.9+/-0.6 ng/ml, P<0.0001, respectively). The enhanced serum levels of TNF-alpha and TNFRs were reflected by a significant expression of TNFR-specific mRNA in peripheral mononuclear cells of HCV-infected patients (P<0.001). Serum aminotransferases correlated with soluble TNFR-p75 (P<0.001) but not with TNFR-p55 and TNF-alpha. We demonstrated an association of the degree of histological inflammation with both TNFRs (P<0.01). Furthermore, enhanced hepatocellular expression of TNF-alpha and TNFRs could be demonstrated by immunohistochemical staining in HCV-infected patients. Sixty-eight out of 105 patients were treated with interferon-alpha (IFN-alpha) (3x10(6)U x 3/week). Pretreatment levels of TNF-alpha and TNFRs did not differ between responders and non-responders. Our results demonstrate that TNF-alpha and TNFRs are enhanced in chronic HCV infection and reflect histological activity of the disease. This up-regulation of TNFRs might modify host response and potentially contribute to liver damage in chronic HCV infection.
Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome (2010)

Structural variation (SV) is a rich source of genetic diversity in mammals, but due to the challenges associated with mapping SV in complex genomes, basic questions regarding their genomic distribution and mechanistic origins remain unanswered. We have developed an algorithm (HYDRA) to localize SV breakpoints by paired-end mapping, and a general approach for the genome-wide assembly and interpretation of breakpoint sequences. We applied these methods to two inbred mouse strains: C57BL/6J and DBA/2J. We demonstrate that HYDRA accurately maps diverse classes of SV, including those involving repetitive elements such as transposons and segmental duplications; however, our analysis of the C57BL/6J reference strain shows that incomplete reference genome assemblies are a major source of noise. We report 7196 SVs between the two strains, more than two-thirds of which are due to transposon insertions. Of the remainder, 59% are deletions (relative to the reference), 26% are insertions of unlinked DNA, 9% are tandem duplications, and 6% are inversions. To investigate the origins of SV, we characterized 3316 breakpoint sequences at single-nucleotide resolution. We find that approximately 16% of non-transposon SVs have complex breakpoint patterns consistent with template switching during DNA replication or repair, and that this process appears to preferentially generate certain classes of complex variants. Moreover, we find that SVs are significantly enriched in regions of segmental duplication, but that this effect is largely independent of DNA sequence homology and thus cannot be explained by non-allelic homologous recombination (NAHR) alone. This result suggests that the genetic instability of such regions is often the cause rather than the consequence of duplicated genomic architecture.
Design and development of microemulsion drug delivery system of atorvastatin and study its intestinal permeability in rats. (2010)

The objective of this study was to design and develop microemulsion drug delivery system of Atorvastatin and to investigate its intestinal transport behavior using the single-pass intestinal perfusion method in rat. Microemulsion drug delivery system of Atorvastatin was prepared by water titration method and optimized formulation was characterized. The permeability behavior of Atorvastatin over three different concentrations (10, 20 and 40 μg/mL) was studied in each isolated region of intestine (i.e. duodenum, jejunum, ileum and colon) of rat by single-pass intestinal perfusion method in rat method at a flow rate of 0.2 ml/min. The concentration of the sample was determined by HPLC and the effective permeability coefficients were calculated. Considering the high correlation of rat permeability coefficient values with those of human, the human intestinal permeability was predicted using the Lawrence compartment absorption and transit model. The intestinal permeability of Atorvastatin in microemulsion, plain drug suspension and marketed formulation was also compared. The particle size and zeta potential of Atorvastatin microemulsion were (18.2±0.3) nm and (–9.19±0.8) mV respectively. There was no significant difference in permeability coefficient in jejunum, duodenum and ileum with same concentration but higher in colon was observed. The permeability coefficient in jejunum at 10 μg/mL was significantly higher than that at 40 μg/mL (p< 0.01). The estimated human intestinal permeability of Atorvastatin for the microemulsion was relatively higher. Based on the above results, it could be concluded that microemulsion formulation could enhance the intestinal permeability of Atorvastatin and thus could be presented as a possible alternative to traditional oral formulations for improving the oral absorption of Atorvastatin. Keywords: Microemulsion;, Zeta potential; Atorvastatin; Single-pass intestinal perfusion (SPIP) method; Compartment absorption and transit model (CAT)
Structural Correlates of an Anticarcinoma Antibody: Identification of Specificity-Determining Residues (SDRs) and Development of a Minimally Immunogenic Antibody Variant by Retention of SDRs Only (2000)

Clinical utility of murine mAbs is limited because many elicit Abs to murine Ig constant and variable regions in patients. An Ab humanized by the current procedure of grafting all the complementarity determining regions (CDRs) of a murine Ab onto the human Ab frameworks is likely to be less immunogenic, except that its murine CDRs could still evoke an anti-variable region response. Previous studies with anticarcinoma mAb CC49 showed that light chain LCDR1 and LCDR2 of humanized CC49 could be replaced with the corresponding CDRs of a human Ab with minimal loss of Ag-binding activity. The studies reported in this paper were undertaken to dissect the CC49 Ag-binding site to identify 1) specificity determining residues (SDRs), the residues of the hypervariable region that are most critical in Ag-Ab interaction, and 2) those residues that contribute to the idiotopes that are potential targets of patients' immune responses. A panel of variants generated by genetic manipulation of the murine CC49 hypervariable regions were evaluated for their relative Ag-binding affinity and reactivity to sera from several patients who had been immunized with murine CC49. One variant, designated HuCC49V10, retained only the SDRs of CC49 and does not react with the anti-variable region Abs of the sera from the murine CC49-treated patients. These studies thus demonstrate that the genetic manipulation of Ab variable regions can be accomplished by grafting only the SDRs of a xenogeneic Ab onto human Ab frameworks. This approach may reduce the immunogenicity of Abs to a minimum.
13.56 MHz High Density DC–DC Converter With PCB Inductors (2014)

This paper presents the design and implementation of a high density 150-200 V to 28 V, 200-400 W resonant dc-dc converter with embedded inductors. The converter has a switching frequency of 13.56 MHz and uses air-core toroidal inductors fabricated with printed circuit board (PCB) technology. Implementing toroidal inductors with the PCB reduces inductance variation. Hence, the tuning and implementation of the converter are simplified while achieving high levels of performance and power density. By not using magnetic cores, the inductors also maintain stable values over a wide temperature range. Moreover, the paper discusses the tradeoffs between simplicity and performance of implementing a hard-switched gate drive at megahertz switching frequencies. We describe the advantages of resonant power converter topologies in applications requiring high density and high performance in demanding environmental conditions.
Wastewater treatment with complementary filter feeders: A new method to control excessive suspended solids and nutrients in stabilization ponds (1993)

ABSTRACT: Zooplankton filter feed small suspended solids (SS) while filter‐feeding fish ( Hypophthalmichthys molitrix ) feed on large suspended particles. The combination should control SS and nutrients in wastewater stabilization ponds. The technique proposed herein maintains coexistence of zooplankton and filter‐feeding fish by excluding the fish from part of the water column. A series of 1‐m 3 tanks was stocked with channel catfish ( Ictalurus punctatus ) alone, catfish and silver carp, or catfish and silver carp that were excluded from one‐half of the water column. The refuge permitted coexistence of high densities of zooplankton with the silver carp, and the combination of filter feeders reduced algal biomass by as much as 99% compared to controls. SS and nutrients were presumably likewise controlled. Application to stabilization ponds in series would be straightforward.
Attenuation correction for a combined 3D PET/CT scanner (1998)

In this work we demonstrate the proof of principle of CT-based attenuation correction of 3D positron emission tomography (PET) data by using scans of bone and soft tissue equivalent phantoms and scans of humans. This method of attenuation correction is intended for use in a single scanner that combines volume-imaging (3D) PET with x-ray computed tomography (CT) for the purpose of providing accurately registered anatomical localization of structures seen in the PET image. The goal of this work is to determine if we can perform attenuation correction of the PET emission data using accurately aligned CT attenuation information. We discuss possible methods of calculating the PET attenuation map at 511 keV based on CT transmission information acquired from 40 keV through 140 keV. Data were acquired on separate CT and PET scanners and were aligned using standard image registration procedures. Results are presented on three of the attenuation calculation methods: segmentation, scaling, and our proposed hybrid segmentation/scaling method. The results are compared with those using the standard 3D PET attenuation correction method as a gold standard. We demonstrate the efficacy of our proposed hybrid method for converting the CT attenuation map from an effective CT photon energy of 70 keV to the PET photon energy of 511 keV. We conclude that using CT information is a feasible way to obtain attenuation correction factors for 3D PET.
Synthesis of Biologically Active Portions of an Intercistronic Region by Use of a New 3′‐Phosphate Incorporation Method to Protect 3′‐OH and Their Binding to Ribosomes (1979)

To examine the influence of bases contiguous to a starter codon, a rapid means of assembling biologically active regions corresponding to portions, or to analogues of portions of intercistronic regions is desirable. To do this, a chemical method for the specific insertion of 3′‐monophosphate groups on to chemically synthesized trinucleotides, tetranucleotides and hexanucleotides of defined sequence bearing different bases at the 3′ terminus has been devised. The method involved phosphorylation of blocked oligoribonucleotides synthesized by a phosphotriester method. The deblocked oligoribonucleotides were phosphorylated at the 5′ end with T4‐induced polynucleotide kinase. The products of this kinase reaction served as“donors” in RNA ligase reactions. The [ 32 P]pC‐A‐U‐A‐U‐Gp, [ 32 P]pA‐U‐Gp, [ 32 P]pU‐A‐A, [ 32 P]pA‐G‐G‐Ap, [ 32 P]pC‐U‐U‐Ap and [ 32 P]pU‐C‐C‐Up “donors” were used to synthesize A‐G‐G‐A[ 32 P]pC‐A‐U‐A‐U‐Gp, U‐C‐C‐U[ 32 P]pC‐A‐U‐A‐U‐Gp, U‐A‐A[ 32 P]pA‐U‐G, A‐U‐G[ 32 P]pU‐A‐A, U‐A‐A‐G[ 32 P]pA‐G‐G‐Ap, U‐C‐C‐U[ 32 P]pC‐U‐U‐Ap and A‐U‐U‐C[ 32 P]pU‐C‐C‐Up indicating that the method functions with all bases. A‐U‐Gp, PA‐U‐Gp and pC‐A‐U‐A‐U‐Gp were isolated free of reactants and, along with PA‐U‐G, were all shown to promote the formation of translational initiation complexes. A‐G‐G‐A[ 32 P]pC‐A‐U‐A‐U‐Gp, which corresponds to the 5′‐terminal portion of the intracistronic region of the maturation protein of bacteriophage Qβ, bound more efficiently to Escherichia coli ribosomes than the U‐C‐C‐U[ 32 P]pC‐A‐U‐A‐U‐Gp, [ 32 P]pC‐A‐U‐A‐U‐Gp, [ 32 P]pA‐U‐G‐U‐A‐A or [ 32 P]pU‐A‐A‐A‐U‐G controls. The results suggested that the content and number of residues at the 5′ terminus attached to A‐U‐G affect binding of oligonucleotides to ribosomes; purine nucleosides appear to be more effective than pyrimidine nucleosides in this regard.
A Film Detection Method for Tritium‐Labelled Proteins and Nucleic Acids in Polyacrylamide Gels (1974)

A simple method is described for detecting 3 H in polyacrylamide gels by scintillation autography (fluorography) using X‐ray film. The gel is dehydrated in dimethyl sulphoxide, soaked in a solution of 2,5‐diphenyloxazole (PPO) in dimethylsulphoxide, dried and exposed to RP Royal “X‐Omat” film at ‐70 °C. Optimal conditions for each step are described. β‐particles from 3 H interact with the 2,5‐diphenyloxazole emitting light which causes local blackening of an X‐ray film. The image produced resembles that obtained by conventional autoradiography of isotopes with higher emission energies such as 14 C. 3000 dis. 3 H/min in a band in a gel can be detected in a 24‐h exposure. Similarly 500 dis./min can be detected in one week. When applied to the detection of 35 S and 14 C in polyacrylamide gels, this method is ten times more sensitive than conventional autoradiography. 130 dis. 35 S or 14 C/min in a band in a gel can be detected in 24 h.
Structure of halomicin B (1974)

A. K. Ganguly, S. Szmulewicz, O. Z. Sarre, D. Greeves, J. Morton and J. McGlotten, J. Chem. Soc., Chem. Commun., 1974, 395 DOI: 10.1039/C39740000395
Realization of conductive InAs nanotubes based on lattice-mismatched InP∕InAs core-shell nanowires (2006)

We report the realization of ordered arrays of single-crystalline InAs nanotubes by a simple pure-eptiaxial approach. The process involved the fabrication of lattice-mismatched InP∕InAs core-shell nanowires using selective area metalorganic vapor phase epitaxy on InP (111)A substrates. The subsequent removal of the InP core resulted in vertically aligned InAs nanotubes which were highly uniform with well-defined features and controllable dimensions. Transmission electron microscopy studies confirmed that the nanotubes were single-crystalline with wurtzite crystal structure and temperature-dependent transport measurements revealed that they were conductive without any intentional doping. The realization of such conductive InAs nanotubes opens up new possibilities for both fundamental studies and future device applications.
The Interaction of Specific Peptide Aptamers With the DNA Binding Domain and the Dimerization Domain of the Transcription Factor Stat3 Inhibits Transactivation and Induces Apoptosis in Tumor Cells (2004)

The transcription factor signal transducer and activator of transcription (Stat) 3 is activated through the interleukin-6 family of cytokines and by binding of growth factors to the epidermal growth factor (EGF) receptor. It plays an essential role in embryonic development and assumes specialized tasks in many differentiated tissues. Constitutively activated Stat3 has been found in tumor cell lines and primary tumors and plays a crucial role in tumor cell survival and proliferation. To inhibit the oncogenic action of Stat3 in tumor cells, we have selected short peptides, so-called peptide aptamers, which specifically interact with defined functional domains of this transcription factor. The peptide aptamers were selected from a peptide library of high complexity by an adaptation of the yeast two-hybrid procedure. Peptide aptamers specifically interacting with the Stat3 dimerization domain caused inhibition of DNA binding activity and suppression of transactivation by Stat3 in EGF-responsive cells. Similarly, a peptide aptamer selected for its ability to recognize the Stat3 DNA binding domain inhibited DNA binding and transactivation by Stat3 following EGF stimulation of cells. Peptide aptamers were expressed in bacteria as fusion proteins with a protein transduction domain and introduced into human myeloma cells. This resulted in dose-dependent growth inhibition, down-regulation of Bcl-x(L) expression, and induction of apoptosis. The inhibition of Stat3 functions through the interaction with peptide aptamers counteracts the transformed phenotype and could become useful in targeted tumor therapy.
Formation of a Diffractional Grating by Magnetic Lithograph (1990)

A new method to make an optical diffraction grating has been developed using the Bitter method. A periodic magnetic pattern like 0101 ... is written in a magnetic memory medium, and a magnetic fluid is used as magnetic toner to visualize this pattern. To enhance the contrast of the grating, an interfacial active agent in the magnetic fluid is destroyed by a certain organic solvent, and a DC magnetic bias field is applied to the memory medium to thicken the pattern. When a transparent grating is required, Au film is deposited on it as a parting agent after the formation of a magnetic toner pattern. After separation of the epoxy resin film from the memory medium, Au film is chemically etched. A sharp diffraction image is observed by projecting a laser diode onto the diffraction grating. Using this method, an optical grating can easily be made even on a convex or concave surface.
Serp-1, a Viral Anti-inflammatory Serpin, Regulates Cellular Serine Proteinase and Serpin Responses to Vascular Injury (2003)

Complex DNA viruses have tapped into cellular serpin responses that act as key regulatory steps in coagulation and inflammatory cascades. Serp-1 is one such viral serpin that effectively protects virus-infected tissues from host inflammatory responses. When given as purified protein, Serp-1 markedly inhibits vascular monocyte invasion and plaque growth in animal models. We have investigated mechanisms of viral serpin inhibition of vascular inflammatory responses. In vascular injury models, Serp-1 altered early cellular plasminogen activator (tissue plasminogen activator), inhibitor (PAI-1), and receptor (urokinase-type plasminogen activator) expression (p < 0.01). Serp-1, but not a reactive center loop mutant, up-regulated PAI-1 serpin expression in human endothelial cells. Treatment of endothelial cells with antibody to urokinase-type plasminogen activator and vitronectin blocked Serp-1-induced changes. Significantly, Serp-1 blocked intimal hyperplasia (p < 0.0001) after aortic allograft transplant (p < 0.0001) in PAI-1-deficient mice. Serp-1 also blocked plaque growth after aortic isograft transplant and after wire-induced injury (p < 0.05) in PAI-1-deficient mice indicating that increase in PAI-1 expression is not required for Serp-1 to block vasculopathy development. Serp-1 did not inhibit plaque growth in uPAR-deficient mice after aortic allograft transplant. We conclude that the poxviral serpin, Serp-1, attenuates vascular inflammatory responses to injury through a pathway mediated by native uPA receptors and vitronectin.
Growth Control Under Stress: mTOR Regulation through the REDD1-TSC Pathway (2005)

Dysregulated signaling by the checkpoint kinase TOR (target of rapamycin) has been linked to numerous human cancers. The tuberous sclerosis tumor suppressors TSC1 and TSC2 form a protein complex that integrates and transmits cellular growth factor and stress signals to negatively regulate TOR activity. Several recent reports have identified the stress response gene REDD1 as an essential regulator of TOR activity through the TSC1/2 complex in both Drosophila and mammalian cells. REDD1 is induced in response both to hypoxia and energy stress, and cells that lack REDD1 exhibit highly defective TOR regulation in response to either of these stress signals. While the precise mechanism of REDD1 function remains to be determined, the finding that REDD1-dependent TOR regulation contributes to cell growth/cell size control in flies and mammals suggests that abnormalities of REDD1-mediated signaling might disrupt energy homeostasis and/or promote tumorigenesis.