gebhart/patrepeval huggingface dataset:
Clonal Analysis of Colonizing Group B Streptococcus , Serotype IV, an Emerging Pathogen in the United States (2010)

Colonizing group B Streptococcus (GBS) capsular polysaccharide (CPS) type IV isolates were recovered from vaginal and rectal samples obtained from 97 (8.4%) nonpregnant women of 1,160 women enrolled in a U.S. multicenter GBS vaccine study from 2004 to 2008. Since this rate was much higher than the rate of prevalence of 0.4 to 0.6% that we found in previous studies, the isolates were analyzed by using surface protein profile identification, pulsed-field gel electrophoresis (PFGE), and multilocus sequence typing (MLST) to characterize them and identify trends in DNA clonality and divergence. Of the 101 type IV isolates studied, 53 expressed alpha and group B protective surface (BPS) proteins, 27 expressed BPS only, 20 expressed alpha only, and 1 had no detectable surface proteins. The isolates spanned three PFGE macrorestriction profile groups, groups 37, 38, and 39, of which group 37 was predominant. The isolates in group 37 expressed the alpha and BPS proteins, while those in groups 38 and 39 expressed the alpha protein only, with two exceptions. MLST studies of selective isolates from the four protein profile groups showed that isolates expressing alpha,BPS or BPS only were of a new sequence type, sequence type 452, while those expressing alpha only or no proteins were mainly of a new sequence type, sequence type 459. Overall, our study revealed a limited diversity in surface proteins, MLST types, and DNA macrorestriction profiles for type IV GBS. There appeared to be an association between the MLST types and protein expression profiles. The increased prevalence of type IV GBS colonization suggested the possibility that this serotype may emerge as a GBS pathogen.
Diffuse calcification in human coronary arteries. Association of osteopontin with atherosclerosis. (1994)

Coronary atherosclerosis is frequently associated with calcification of arterial plaque. To understand the mechanisms responsible for the formation of atherosclerotic calcification, we examined human coronary arteries for the presence and extent of mineral. In sections stained specifically for mineral, staining was diffuse and present in all atherosclerotic plaques. Hydroxyapatite was not detected in normal coronary artery sections. Distribution of hydroxyapatite coincided with a similar distribution of calcium detected by a radiodense pattern using contact microradiography of the same sections before cytochemical staining. By energy-dispersive x-ray microanalysis, the chemical composition of calcified sites was identical to hydroxyapatite (Ca10[PO4]6[OH]2), the major inorganic component of bone. Osteopontin is a phosphorylated glycoprotein with known involvement in the formation and calcification of bone and is regulated by local cytokines. Human coronary artery segments (14 normal and 34 atherosclerotic) obtained at autopsy were evaluated immunohistochemically using polyclonal antibodies generated against human osteopontin. Immunohistochemistry for osteopontin indicated intense, highly specific staining in the outer margins of all diseased segments at each calcification front; staining was evident throughout the entire plaque. Conversely, arterial segments free of atheroma and calcification and sections treated with nonimmune serum had no evidence of positive staining. Osteopontin, a protein involved in mineralization is specifically associated with calcific coronary atheroma and may play an important role in the onset and progression of this disease in human coronary arteries. The deposition of noncollagenous proteins such as osteopontin may regulate the presence or absence of calcification and ultimately alter vessel compliance.
Aberrant Eukaryotic Translation Initiation Factor 4E-Dependent mRNA Transport Impedes Hematopoietic Differentiation and Contributes to Leukemogenesis (2003)

The eukaryotic translation initiation factor 4E (eIF4E) acts as both a key translation factor and as a promoter of nucleocytoplasmic transport of specific transcripts. Traditionally, its transformation capacity in vivo is attributed to its role in translation initiation in the cytoplasm. Here, we demonstrate that elevated eIF4E impedes granulocytic and monocytic differentiation. Our subsequent mutagenesis studies indicate that this block is a result of dysregulated eIF4E-dependent mRNA transport. These studies indicate that the RNA transport function of eIF4E could contribute to leukemogenesis. We extended our studies to provide the first evidence that the nuclear transport function of eIF4E contributes to human malignancy, specifically in a subset of acute and chronic myelogenous leukemia patients. We observe an increase in eIF4E-dependent cyclin D1 mRNA transport and a concomitant increase in cyclin D1 protein levels. The aberrant nuclear function of eIF4E is due to abnormally large eIF4E bodies and the loss of regulation by the proline-rich homeodomain PRH. We developed a novel tool to modulate this transport activity. The introduction of IkappaB, the repressor of NF-kappaB, leads to suppression of eIF4E, elevation of PRH, reorganization of eIF4E nuclear bodies, and subsequent downregulation of eIF4E-dependent mRNA transport. Thus, our findings indicate that this nuclear function of eIF4E can contribute to leukemogenesis by promoting growth and by impeding differentiation.
Polysialic acid and N-CAM localisation in embryonic rat kidney: mesenchymal and epithelial elements show different patterns of expression (1990)

The expression of polysialic acid (PSA) and the neural cell adhesion molecule (N-CAM) during the embryonic development of rat kidney was investigated using immunocytochemistry and immunoblotting. A monoclonal antibody (mAb 735), which recognised only long chain PSA, and polyclonal antibodies specific for N-CAM were employed. At the earliest stages of metanephros formation, PSA and N-CAM immunostaining was found in both embryonic anlagen, namely the uretic bud and the metanephrogenic mesenchyme. Reactivity in uretic bud derivatives declined during embryonic development and was generally absent in the collecting duct system by embryonic day 18 (E18). Uninduced metanephrogenic mesenchyme was immunostained throughout development while induced mesenchymal cells showed greatly increased PSA and N-CAM immunoreactivity during their transformation into epithelium. This staining declined rapidly as nephrons differentiated. These processes were preceded by sorting of PSA and N-CAM to the basolateral plasma membrane. Similar N-CAM and PSA patterns were observed in mesonephros development. In adult kidney parenchyma both PSA and N-CAM were undetectable. Immunoblotting of samples of embryonic kidney with mAb 735 revealed a broad band ranging from 140 to greater than 200 x 10(3) Mr. N-CAM antibodies revealed reactivity in a band of 140 x 10(3) Mr after removal of PSA by endoneuraminidase treatment. Expression of N-CAM and PSA in both embryonic anlagen indicates that neither molecular species acts primarily as an inductive signal. These molecules were localised in areas where changes in cell adhesion during organogenesis might be important and thus may be involved in the grouping of developing cells.
Ensembl's 10th year (2009)

Ensembl (http://www.ensembl.org) integrates genomic information for a comprehensive set of chordate genomes with a particular focus on resources for human, mouse, rat, zebrafish and other high-value sequenced genomes. We provide complete gene annotations for all supported species in addition to specific resources that target genome variation, function and evolution. Ensembl data is accessible in a variety of formats including via our genome browser, API and BioMart. This year marks the tenth anniversary of Ensembl and in that time the project has grown with advances in genome technology. As of release 56 (September 2009), Ensembl supports 51 species including marmoset, pig, zebra finch, lizard, gorilla and wallaby, which were added in the past year. Major additions and improvements to Ensembl since our previous report include the incorporation of the human GRCh37 assembly, enhanced visualisation and data-mining options for the Ensembl regulatory features and continued development of our software infrastructure.
Cytotoxicity of the V ibrio vulnificus MARTX toxin Effector DUF5 is linked to the C2A Subdomain (2014)

The multifunctional-autoprocessing repeats-in-toxin (MARTX) toxins are bacterial protein toxins that serve as delivery platforms for cytotoxic effector domains. The domain of unknown function in position 5 (DUF5) effector domain is present in at least six different species' MARTX toxins and as a hypothetical protein in Photorhabdus spp. Its presence increases the potency of the Vibrio vulnificus MARTX toxin in mouse virulence studies, indicating DUF5 directly contributes to pathogenesis. In this work, DUF5 is shown to be cytotoxic when transiently expressed in HeLa cells. DUF5 localized to the plasma membrane dependent upon its C1 domain and the cells become rounded dependent upon its C2 domain. Both full-length DUF5 and the C2 domain caused growth inhibition when expressed in Saccharomyces cerevisiae. A structural model of DUF5 was generated based on the structure of Pasteurella multocida toxin facilitating localization of the cytotoxic activity to a 186 amino acid subdomain termed C2A. Within this subdomain, an alanine scanning mutagenesis revealed aspartate-3721 and arginine-3841 as residues critical for cytotoxicity. These residues were also essential for HeLa cell intoxication when purified DUF5 fused to anthrax toxin lethal factor was delivered cytosolically. Thermal shift experiments indicated that these conserved residues are important to maintain protein structure, rather than for catalysis. The Aeromonas hydrophila MARTX toxin DUF5(Ah) domain was also cytotoxic, while the weakly conserved C1-C2 domains from P. multocida toxin were not. Overall, this study is the first demonstration that DUF5 as found in MARTX toxins has cytotoxic activity that depends on conserved residues in the C2A subdomain.
Safety and Efficacy of a Lipid Emulsion Containing a Mixture of Soybean Oil, Medium‐chain Triglycerides, Olive Oil, and Fish Oil: A Randomised, Double‐blind Clinical Trial in Premature Infants Requiring Parenteral Nutrition (2010)

Parenteral infusion of SMOFlipid was safe and well tolerated and showed a potential beneficial influence on cholestasis, n-3 FA, and vitamin E status in premature infants requiring PN.
Expression of the SOS genes of Escherichia coli in Salmonella typhimurium. (1985)

To lysogenize Salmonella typhimurium by Lambda phage, a region of 10.2 kb of Escherichia coli DNA carrying the nusA gene was cloned in a S. typhimurium strain containing a F'112 plasmid which codifies for the lamB region of E. coli. The strain of S. typhimurium obtained in this way, was lysogenized by lambda c IndO- bacteriophage harboring either a fusion between recA1 or sfiA genes of E. coli with lacZ gene. Likewise, pSE143 plasmid with a umu C::lacZ fusion was introduced in S. typhimurium. Afterwards, induction of these SOS genes was studied. Results obtained show that the basal transcription of both recA and sfiA genes of E. coli was higher in S. typhimurium than in E. coli. Nevertheless, induction of recA and sfiA genes by UV-irradiation and mitomycin C was higher in E. coli than in S. typhimurium. On the other hand, umuC gene of E. coli presents the same basal level of transcription in both E. coli and S. typhimurium species, although induction of this gene by UV-irradiation and mitomycin C was higher in S. typhimurium than in E. coli. Therefore, the plasmid pUA25 constructed in this work may be used to introduce, using the Lambda phage as a vector, the SOS genes of E. coli in other bacterial species which may be useful to study the relationship between their respective SOS systems.
Atmospheric-pressure plasma sources for biomedical applications (2012)

Atmospheric-pressure plasmas (APPs) have attracted great interest and have been widely applied in biomedical applications, as due to their non-thermal and reactive properties, they interact with living tissues, cells and bacteria. Various types of plasma sources generated at atmospheric pressure have been developed to achieve better performance in specific applications. This article presents an overview of the general characteristics of APPs and a brief summary of their biomedical applications, and reviews a wide range of these sources developed for biomedical applications. The plasma sources are classified according to their power sources and cover a wide frequency spectrum from dc to microwaves. The configurations and characteristics of plasma sources are outlined and their biomedical applications are presented.
A Nucleoside Transporter from Trypanosoma brucei Involved in Drug Resistance (1999)

Drug resistance of pathogens is an increasing problem whose underlying mechanisms are not fully understood. Cellular uptake of the major drugs against Trypanosoma brucei spp., the causative agents of sleeping sickness, is thought to occur through an unusual, so far unidentified adenosine transporter. Saccharomyces cerevisiae was used in a functional screen to clone a gene (TbAT1) from Trypanosoma brucei brucei that encodes a nucleoside transporter. When expressed in yeast, TbAT1 enabled adenosine uptake and conferred susceptibility to melaminophenyl arsenicals. Drug-resistant trypanosomes harbor a defective TbAT1 variant. The molecular identification of the entry route of trypanocides opens the way to approaches for diagnosis and treatment of drug-resistant sleeping sickness.
The Parkinson's disease sleep scale: a new instrument for assessing sleep and nocturnal disability in Parkinson's disease (2002)

This appears to be the first description of a simple bedside screening instrument for evaluation of sleep disturbances in Parkinson's disease. A combination of subitems may help identify specific aspects of sleep disturbance, which in turn may help target treatment.
The Antidiabetic Action of Somatostatin-28 as Assessed by the Artificial Endocrine Pancreas: Greater Potency than Somatostatin-14 (1987)

In order to investigate the action of somatostatin-28 (SS-28) on the metabolic homeostasis of insulin-dependent diabetics, we compared its effects to those of somatostatin-14 (SS-14) in terms of insulin sparing, changes in dextrose demands, glucose fluctuations and behavior of growth hormone and glucagon secretion. Eight insulin-dependent subjects were connected to Artificial Endocrine Pancreas (Biostator) for 84 hours during which they received intravenous infusions of either SS-14, SS-28 or isotonic saline in a randomized order, after a steady state of metabolism had been achieved. Five of the patients received SS-28 100 micrograms/h and SS-14 250 micrograms/h for 10 hours and three of them SS-28, 50 micrograms/h and SS-14 250 micrograms/h for 12 hours. Identical doses of both peptides were administered as bolus infusions prior to the continuous ones. Under SS-28 100 micrograms/h and SS-14 250 micrograms/h patients required 13.5 +/- 2.3 and 14.5 +/- 1.9 U of insulin respectively vs 40 +/- 5.6 U under isotonic saline infusion (mean +/- SEM, P less than 0.005 and P less than 0.01). At the same period the apparatus delivered 15 times more dextrose under SS-28 and 20 times more under SS-14. The magnitude of glucose fluctuations diminished from 64.6 +/- 2.47 mg% without to 41.4 +/- 2 mg% under SS-14 (P less than 0.01) and 46 +/- 3.8 mg% under SS-28 (P less than 0.02). Similar changes were observed in the remaining three patients who received SS-28 in the dose of 50 micrograms/h.(ABSTRACT TRUNCATED AT 250 WORDS)
IgG subclass-associated affinity differences of specific antibodies in humans. (1988)

Human IgG subclasses differ in their biologic functions and are restricted as specific antibodies to certain Ag. The basis for this restriction is unknown but in order to characterize it further, we obtained serum preparations containing one single subclass by using subclass-specific mAb in affinity chromatography. Subsequently we determined the affinity of antibodies in the four IgG subclasses for gp30/p25, a hepatitis B surface Ag (HBsAg) complex, for a nine-amino acid cyclical peptide representing residues 139 to 147 of HBsAg, and for a peptide representing residues 126 to 140 of the hepatitis B virus pre-S2 region and the relative avidity of IgG1 and IgG2 antibodies for purified pneumococcal polysaccharide type 3. Affinities to the HBsAg showed a clear pattern of decreasing affinity in the order IgG1 greater than IgG2 greater than IgG3 greater than IgG4 both in sera from vaccinated and from naturally infected individuals. The relative avidities of antibodies to the polysaccharide Ag had a reverse pattern, IgG2 greater than IgG1. In individuals with or without Ig H chain gene deletions where the anti-HBsAg response was restricted to one subclass, the affinity was similar to that observed for the same subclass in sera from individuals who in addition possessed high or low affinity antibodies of other subclasses.
Fourier-Based Imaging for Multistatic Radar Systems (2014)

Fourier-based methods for monostatic and bistatic setups have been widely used for high-accuracy radar imaging. However, the multistatic configuration has several characteristics that make Fourier processing more challenging: 1) a nonuniform grid in k-space, which requires multidimensional interpolation methods, and 2) image distortion when the incident spherical wave is approximated by a plane wave. This contribution presents a Fourier-based imaging method for multistatic systems, solving the aforementioned limitations: the first, by using k-space partitioning and applying interpolation in each domain; the second, by approximating the spherical wave with multiple plane waves. Both solutions are fully parallelizable, thus allowing calculation time savings. Validation and benchmarking with a synthetic aperture radar backpropagation algorithm have been performed through 2-D and 3-D simulation-based examples. Imaging results from radar measurements have been assessed.
Reductive Amination of Aldehydes and Amines with an Efficient Pd/NiO Catalyst (2013)

Abstract By applying a simple Pd/NiO catalyst, the reductive amination of amines and aldehydes can progress efficiently under mild reaction conditions, and 24 substituted amines with different structures were synthesized with up to 98% isolated yields.
Insecticidal toxicities of glucosinolate-containing extracts from crambe seeds. (1996)

Glucosinolate components were extracted from defatted cTambe (Crambe abyssinica Hochst ex. R. E. Fries) seed meal by using four different extraction solvents. These extracts containing naturally occurring glucosinolnt.es were tested in bioassays against some selected agricultural and public health insect pests. The results showed that continuous aqueous exposure to dilutions of the extracts caused acute mortality to mosquito (Aedes aegypti (L.ll larvae. Crambe seed meal (containing intact glucosinolates) showed toxicity against house fly larvae (Musca domestica L.) when incorporated into the regular fly diet. Neither extracts nor seed meal were acutely toxic to the red flour beetle [Tribolium castaneum (Herbst» or the sawtoothed grain beetle [Oryzeaphilus surinamensis (L.U within 24 h; however, longer observation demonstrated a high mortality and antifeedanl effect toward these insects. The two species of grain beetles began dying 10 d after exposure. The glucosjnolate extracts also were effective on western corn rootworm [Diabrotica uirgi{era uirgi{cra (LeConte)1 larvae. No observable behavioral changes were found on German cockroaches IBlattella germanica (L.)]. The results showed that crambe glucosinolatcs have potential as a possible control agent for certain agricultural and public health insect pests.
Measurement by holographic interferometry of the deformation of the eye accompanying changes in intraocular pressure (1978)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text T. Matsumoto, R. Nagata, M. Saishin, T. Matsuda, and S. Nakao, "Measurement by holographic interferometry of the deformation of the eye accompanying changes in intraocular pressure," Appl. Opt. 17, 3538-3539 (1978) Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
VGluT2 expression in painful Achilles and patellar tendinosis: Evidence of local glutamate release by tenocytes (2007)

The pathogenesis of chronic tendinopathy is unclear. We have previously measured high intratendinous levels of glutamate in patients with tendinosis, suggesting potential roles of glutamate in the modulation of pain, vascular function, and degenerative changes including apoptosis of tenocytes. However, the origin of free glutamate found in tendon tissue is completely unknown. Surgical biopsies of pain-free normal tendons and tendinosis tendons (Achilles and patellar) were examined immunohistochemically using antibodies against vesicular glutamate transporters (VGluT1 and VGluT2), as indirect markers of glutamate release. In situ hybridization for VGluT2 mRNA was also conducted. Specific immunoreactions for VGluT2, but not VGluT1, could be consistently detected in tenocytes. However, there were interindividual variations in the levels of immunoreactivity. The level of immunoreaction for VGluT2 was higher in tendinosis tendons compared to normal tendons (p < 0.05). In situ hybridization of VGluT2 demonstrated that mRNA was localized in a similar pattern as the protein, with marked expression by certain tenocytes, particularly those showing abnormal appearances. Reactivity for VGluT1 and -2 was absent from nerves and vessel structures in both normal and painful tendons. The current data demonstrate that tenocytes may be involved in the regulation of extracellular glutamate levels in tendons. Specifically, the observations suggest that free glutamate may be locally produced and released by tenocytes, rather than by peripheral neurons. Excessive free glutamate is expected to impact a variety of autocrine and paracrine functions important in the development of tendinosis, including tenocyte proliferation and apoptosis, extracellular matrix metabolism, nociception, and blood flow.
Simulating the structure and effect of the electrical double layer at nanometre electrodes (2007)

A computer simulation of the structure and effect of an electrical double layer (EDL) is presented. Without applying electroneutrality and Boltzmann distributions, the problem is solved based on the Poisson, Nernst–Plank and Butler–Volmer equations along with a continuous function depicting the relative permittivity of the compact layer. The results show that the EDL will alter electron transfer and current response at nanometre electrodes. This effect will be magnified either as the reactant charge valence increases or when no supporting electrolyte is present in the solution, and it will be influenced by changes in both the relative permittivity and the thickness of the compact layer. This work will help pave the way for future investigation of the effect of the EDL on electron transfer at nanometre electrodes (single or in arrays) in complex systems such as fuel cells and biosensors.