gebhart/patrepeval huggingface dataset:
A proteomic view of the facultatively chemolithoautotrophic lifestyle of Ralstonia eutropha H16 (2009)

Ralstonia eutropha H16 is an H(2)-oxidizing, facultative chemolithoautotroph. Using 2-DE in conjunction with peptide mass spectrometry we have cataloged the soluble proteins of this bacterium during growth on different substrates: (i) H(2) and CO(2), (ii) succinate and (iii) glycerol. The first and second conditions represent purely lithoautotrophic and purely organoheterotrophic nutrition, respectively. The third growth regime permits formation of the H(2)-oxidizing and CO(2)-fixing systems concomitant to utilization of an organic substrate, thus enabling mixotrophic growth. The latter type of nutrition is probably the relevant one with respect to the situation faced by the organism in its natural habitats, i.e. soil and mud. Aside from the hydrogenase and Calvin-cycle enzymes, the protein inventories of the H(2)-CO(2)- and succinate-grown cells did not reveal major qualitative differences. The protein complement of the glycerol-grown cells resembled that of the lithoautotrophic cells. Phosphoenolpyruvate (PEP) carboxykinase was present under all three growth conditions, whereas PEP carboxylase was not detectable, supporting earlier findings that PEP carboxykinase is alone responsible for the anaplerotic production of oxaloacetate from PEP. The elevated levels of oxidative stress proteins in the glycerol-grown cells point to a significant challenge by ROS under these conditions. The results reported here are in agreement with earlier physiological and enzymological studies indicating that R. eutropha H16 has a heterotrophic core metabolism onto which the functions of lithoautotrophy have been grafted.
A Method for Selectively Enriching Microbial DNA from Contaminating Vertebrate Host DNA (2013)

DNA samples derived from vertebrate skin, bodily cavities and body fluids contain both host and microbial DNA; the latter often present as a minor component. Consequently, DNA sequencing of a microbiome sample frequently yields reads originating from the microbe(s) of interest, but with a vast excess of host genome-derived reads. In this study, we used a methyl-CpG binding domain (MBD) to separate methylated host DNA from microbial DNA based on differences in CpG methylation density. MBD fused to the Fc region of a human antibody (MBD-Fc) binds strongly to protein A paramagnetic beads, forming an effective one-step enrichment complex that was used to remove human or fish host DNA from bacterial and protistan DNA for subsequent sequencing and analysis. We report enrichment of DNA samples from human saliva, human blood, a mock malaria-infected blood sample and a black molly fish. When reads were mapped to reference genomes, sequence reads aligning to host genomes decreased 50-fold, while bacterial and Plasmodium DNA sequences reads increased 8-11.5-fold. The Shannon-Wiener diversity index was calculated for 149 bacterial species in saliva before and after enrichment. Unenriched saliva had an index of 4.72, while the enriched sample had an index of 4.80. The similarity of these indices demonstrates that bacterial species diversity and relative phylotype abundance remain conserved in enriched samples. Enrichment using the MBD-Fc method holds promise for targeted microbiome sequence analysis across a broad range of sample types.
Stability of Doped Transparent Carbon Nanotube Electrodes (2008)

Abstract This paper evaluates the effectiveness of p ‐doping transparent single‐walled carbon nanotube (SWNT) films via chemical treatment with HNO 3 and SOCl 2 . Stability of the improvement in electrical conductivity after doping is investigated for different doping treatments as a function of exposure time to air and as a function of temperature. Doped films were found to have a greater than twofold increase in conductivity with sheet resistance values as low as 105 Ω sq −1 with an optical transmittance of 80% at 550 nm. However, doping enhancements demonstrated limited stability in air and under thermal loading. The application of a thin capping layer of PEDOT/PSS is shown to stabilize the improvements in conductivity, evidenced by sustained lower sheet resistance in both air and under thermal loading.
SRAM bitline circuits on PD SOI: advantages and concerns (1997)

This paper presents a study of sub-0.25-/spl mu/m CMOS SRAM bitline circuitry on partially depleted (PD) silicon-on-insulator (SOI) technology. SOI implementations outperform conventional bulk ones due to significant reduction of collective device junction capacitance on the bitlines. Floating body effects are investigated for both read and write cycles. Array content dependent behaviors are identified for the first time and analyzed with worst-case temporal and spatial pattern combinations.
Prognostic value of circulating tumor cells in primary and metastatic breast cancer (2012)

In patients with breast cancer, there is evidence correlating the presence of circulating tumor cells (CTCs) with disease-free survival, progression-free survival and overall survival. The detection of CTCs may be useful in gaining a better understanding of the mechanisms of tumor growth and in the improvement of patient management. This review analyzes the prognostic and predictive relevance of CTCs through the principal published studies, cytometric techniques and nucleic acid-based approaches to detect CTCs, phenotypic expression of specific receptors, molecular pathways and genetic signatures for potential tailored therapies.
Angiotensin II Type 2 Receptor Is Upregulated in Human Heart With Interstitial Fibrosis, and Cardiac Fibroblasts Are the Major Cell Type for Its Expression (1998)

The expression pattern of angiotensin (Ang) II type 2 receptor (AT2-R) in the remodeling process of human left ventricles (LVs) remains poorly defined. We analyzed its expression at protein, mRNA, and cellular levels using autopsy, biopsy, or operation LV samples from patients with failing hearts caused by acute (AMI) or old (OMI) myocardial infarction and idiopathic dilated cardiomyopathy (DCM) and also examined functional biochemical responses of failing hearts to Ang II. In autopsy samples from the nonfailing heart group, the ratio of AT1-R and AT2-R was 59% and 41%, respectively. The expression of AT2-R was markedly increased in DCM hearts at protein (3.5-fold) and mRNA (3.1-fold) levels compared with AMI or OMI. AT1-R protein and mRNA levels in AMI hearts showed 1.5- and 2.1-fold increases, respectively, whereas in OMI and DCM hearts, AT1-R expression was significantly downregulated. AT1-R-mediated response in inositol phosphate production was significantly attenuated in LV homogenate from failing hearts compared with nonfailing hearts. AT2-R sites were highly localized in the interstitial region in either nonfailing or failing heart, whereas AT1-R was evenly distributed over myocardium at lower densities. Mitogen-activated protein kinase (MAPK) activation by Ang II was significantly decreased in fibroblast compartment from the failing hearts, and pretreatment with AT2-R antagonist caused an additional significant increase in Ang II-induced MAPK activity (36%). Cardiac hypertrophy suggested by atrial and brain natriuretic peptide levels was comparably increased in OMI and DCM, whereas accumulation of matrix proteins such as collagen type 1 and fibronectin was much more prominent in DCM than in OMI. These findings demonstrate that (1) AT2-R expression is upregulated in failing hearts, and fibroblasts present in the interstitial regions are the major cell type responsible for its expression, (2) AT2-R present in the fibroblasts exerts an inhibitory effect on Ang II-induced mitogen signals, and (3) AT1-R in atrial and LV tissues was downregulated during chronic heart failure, and AT1-R-mediated functional biochemical responsiveness was decreased in the failing hearts. Thus, the expression level of AT2-R is likely determined by the extent of interstitial fibrosis associated with heart failure, and the expression and function of AT1-R and AT2-R are differentially regulated in failing human hearts.
Analysis of single nucleotide polymorphisms in genes in the chromosome 12Q24.31 region points to P2RX7 as a susceptibility gene to bipolar affective disorder (2006)

Previous results from our genetic analyses using pedigrees from a French Canadian population suggested that the interval delimited by markers on chromosome 12, D12S86 and D12S378, was the most probable genomic region to contain a susceptibility gene for affective disorders. Association studies with microsatellite markers using a case/control sample from the same population (n = 427) revealed significant allelic associations between the bipolar phenotype and marker NBG6. Since this marker is located in intron 9 of the P2RX7 gene, we analyzed the surrounding genomic region for the presence of polymorphisms in regulatory, coding and intron/exon junction sequences. Twenty four (24) SNPs were genotyped in a case/control sample and 12 SNPs in all pedigrees used for linkage analysis. Allelic, genotypic or family-based association studies suggest the presence of two susceptibility loci, the P2RX7 and CaMKK2 genes. The strongest association was observed in bipolar families at the non-synonymous SNP P2RX7-E13A (rs2230912, P-value = 0.000708), which results from an over-transmission of the mutant G-allele to affected offspring. This Gln460Arg polymorphism occurs at an amino acid that is conserved between humans and rodents and is located in the C-terminal domain of the P2X7 receptor, known to be essential for normal P2RX7 function.
Next Generation DNA Sequencing and the Future of Genomic Medicine (2010)

In the years since the first complete human genome sequence was reported, there has been a rapid development of technologies to facilitate high-throughput sequence analysis of DNA (termed "next-generation" sequencing). These novel approaches to DNA sequencing offer the promise of complete genomic analysis at a cost feasible for routine clinical diagnostics. However, the ability to more thoroughly interrogate genomic sequence raises a number of important issues with regard to result interpretation, laboratory workflow, data storage, and ethical considerations. This review describes the current high-throughput sequencing platforms commercially available, and compares the inherent advantages and disadvantages of each. The potential applications for clinical diagnostics are considered, as well as the need for software and analysis tools to interpret the vast amount of data generated. Finally, we discuss the clinical and ethical implications of the wealth of genetic information generated by these methods. Despite the challenges, we anticipate that the evolution and refinement of high-throughput DNA sequencing technologies will catalyze a new era of personalized medicine based on individualized genomic analysis.
Ribozyme-mediated RNA degradation in nuclei suspension (1995)

Ribozymes containing 2'-fluoro- and 2'-amino-modified pyrimidine nucleosides in combination with terminal phosphorothioate linkages were targeted against HTLV-I tax RNA. In order to examine the activity of such chemically modified ribozymes in the nuclear environment, they were incubated with nuclei of a Tax-transformed mouse fibroblast cell line. Ribozyme cleavage of tax RNA was analyzed by the RNase protection assay. Comparison of the cleavage of tax RNA isolated nuclei with that of tax RNA present in nuclei suspension revealed a 30 times more efficient cleavage of the latter one. Pre-treatment with proteinase K and SDS abolished the enhancement of the ribozyme-mediated RNA cleavage. Catalytically inactive ribozymes did not yield any cleavage products. These results demonstrate an augmenting effect of nuclear proteins on the ribozyme-mediated RNA cleavage.
Manipulation of Self-Renewal in Human Embryonic Stem Cells Through a Novel Pharmacological GSK-3 Inhibitor (2006)

This chapter introduces a new method of maintaining human embryonic stem cells (hESCs) in the undifferentiated state through treatment with a GSK-3 inhibitor, BIO, under a feeder-free condition. Additionally, methods are introduced that determine multidifferentiation potential of hESCs by differentiating into a specific type or random heterogenous cell populations in vitro. These approaches will become a fundamental platform to identify molecular networks regulating cell fate determination in hESCs and mouse embryonic stem cells.
Covalent attachment of metal chelates to proteins:the stability in vivo and in vitro of the conjugate of albumin with a chelate of 111indium. (1976)

Human serum albumin has been conjugated to 1-(p-bnezenediazonium)-(ethylenedinitrilo)tetraacetic acid, a powerful chelating agent, and radioactive 111indium ions have been added specifically to the chelating groups. The product, with a specific radioactivity of about 1 mCi/mg of protein, was employed as a radiotracer in scintillation scanning studies with human volunteers. Results show that 48 hr after injection, practically all of the label remains attached to albumin. This is confirmed by electrophoresis of serum proteins; 7 days after injection, 85% of the radioactivity in the serum is still in the albumin fraction. These observations agree with in vitro studies of the labeled albumin in human serum, where loss of the metal ion from the chelating group to the protein transferrin amounts to less than 3% after 1 week and less than 5% after 2 weeks. Measurements of the distribution of label in mice up to 23 days after injection suggest that metabolism of the labeled protein does not lead to binding of indium ions by transferrin. The binding of indium and other metal ions by transferrin has previously posed a major impediment to the use of metal chelates for in vivo diagnostic procedures. Demonstration of the kinetic inertness of the chelate in these experiments suggests the use of related chelates as physical probes of biological systems.
Cancer immunotherapy with mRNA‐transfected dendritic cells (2004)

Bone marrow-derived dendritic cells (DCs) are the most potent antigen-presenting cells capable of activating naïve T cells. Loading DCs ex vivo with tumor antigens can stimulate potent antitumor immunity in tumor-bearing mice. This review describes the use of mRNA-encoded tumor antigens as a form of antigen loaded onto DCs, including our early experience from clinical trials in urological cancers. Transfection of DCs with mRNA is simple and effective. Comparative studies suggest that mRNA transfection is superior to other antigen-loading techniques in generating immunopotent DCs. The ability to amplify RNA from microscopic amounts of tumor tissue extends the use of DC vaccination to virtually every cancer patient. The striking observation from two phase I clinical trials, in patients with prostate cancer immunized with prostate-specific antigen mRNA-transfected DCs and patients with renal cancer immunized with autologous tumor RNA-transfected DCs, was that the majority of patients exhibited a vaccine-induced T-cell response. Suggestive evidence of clinically related responses was seen in both the trials. Immunization with mRNA-transfected DCs is a promising strategy to stimulate potent antitumor immunity and could serve as a foundation for developing effective treatments for cancer.
Cell proliferation during fibre growth initiation in ferret hair follicles (1992)

The commencement and course of cell proliferation is described in proanagen hair follicles of ferrets. Initiation of autumn fur growth was synchronised in 32 animals using melatonin implants. Skin samples containing S-phase cells labelled in vivo with bromodeoxyuridine were collected fiomgroups of four animals up until the time of development of metanagen follicles at 14 days postimplant. Cells were visualised by an indirect immunocytcchemical method and counts made of proliferating cells in the hair germ, epithelial strand/outer root sheath, connective tissue sheath and dermal papilla. Telogen follicles showed no labelling in all four tissues until 4 days after melatonln implant. The largest number of proliferating cells were in the hair germ, which formed the new fibre and innerroot sheath. Thecell labellingindexforthls tissueremainedhighat 14dayspost-implant. Inothertissues, cellproliferationreached peaks during mid to late proanagen, then declined as the metanagen state was reached. These results indicate that some key signalling events controlling ferret hair growth occur between 0 and 4 days after the melatonin implant, and illustrate the separate processes of follicular regeneration and fibre growth occurring in proanagen follicles.
P/Q-type voltage-gated calcium channel antibodies in paraneoplastic disorders of the central nervous system (1999)

Whether P/Q-type voltage-gated calcium channel (VGCC) antibodies are present in the serum of patients with paraneoplastic syndromes other than the Lambert-Eaton myasthenic syndrome (LEMS) and tumors other than small-cell lung cancer (SCLC) is controversial. Using a commercially available radioimmunoprecipitation assay kit, we examined the sera of 93 patients with paraneoplastic syndromes of the central nervous system (CNS), including 27 patients with paraneoplastic cerebellar degeneration (PCD) associated with tumors other than SCLC and 66 SCLC patients with paraneoplastic encephalomyelitis and sensory neuronopathy (PEM/SN). All PCD sera from patients with tumors other than SCLC were negative for P/Q-type VGCC antibodies. Eight of 66 (12%) SCLC patients with PEM/SN had P/Q-type VGCC antibodies; 4 had LEMS and the other 4 had no symptoms of LEMS or they were overlooked and, therefore, not examined electrophysiologically. In patients with paraneoplastic syndromes of the CNS, the detection of P/Q-type VGCC antibodies supports the diagnosis of LEMS; in our series, only 6% of patients with SCLC and PEM/SN may have had a false positive antibody result, or undiagnosed LEMS.
Digital Microfluidic Platform for Multiplexing Enzyme Assays: Implications for Lysosomal Storage Disease Screening in Newborns (2011)

A digital microfluidic platform compared favorably with a clinical reference laboratory to perform enzymatic analysis in DBSs for Pompe and Fabry disorders. This platform presents a new technology for a newborn screening laboratory to screen LSDs by fully automating all the liquid-handling operations in an inexpensive system, providing rapid results.
Up regulation of GW112 Gene by NFκB promotes an antiapoptotic property in gastric cancer cells (2009)

To clarify the regulatory mechanism of GW112 gene expression, 5'-flanking region of the human GW112 gene was isolated and characterized in the present study. 5'-RACE analysis showed a single transcription start site, which is located 142 nucleotides upstream of the translation initiation site. Transient transfection studies with serial deletion constructs and close examination of the sequences identified a putative NF kappaB binding sequence between -442 and -430, which could be responsible for efficient expression of the GW112 gene. Indeed, GW112 gene was found to be regulated by NF kappaB signals including overexpressed p65 and I kappaB alpha, IKK inhibitor, and proteasome inhibitor. Binding of NF kappaB to its putative site was confirmed by EMSA and ChIP assays. These results suggest that NF kappaB is an essential regulatory factor for GW112 transcription. Based on this finding, we next confirmed that inhibition of GW112 expression could induce apoptosis in the presence of cytotoxic agent in gastric cancer cells. Furthermore, knocking-down or overexpression of GW112 gene in gastric cancer cells demonstrated that GW112 has an antiapoptotic property against the cytotoxic agents-induced apoptosis. Taken together, these results suggest that GW112 could be an important mediator in NF kappaB-dependent tumorigenesis of digestive tract tissues.
Amphiphilic peptides enhance the efficiency of liposome-mediated DNA transfection (1994)

Recently, synthetic amphiphilic peptides composed of 20 amino acids, E5 (GLFEAIAEFIEGGWEGLIEG) and K5 (GLFKAIAKFIKGGWKGLIKG), derived from an influenza virus hemagglutinin have been revealed to induce the membrane fusion (1). The peptide E5 contains 5 Glu residues to be anionic and the peptide K5 contains 5 Lys residues to be cationic, and both have the same sequence except for these charged amino acids. Furthermore, both peptides can form alfa-helical structure, in which the charged amino acids (E or K) aligned on one side of the helix while the other side of the helix is very hydrophobic, which is favorable for interacting with lipid bilayers. At neutral pH's, E5 or K5 alone failed to induce the liposome fusion, however, an equimolar mixture of E5 and K5 rapidly and efficiently induced the liposome fusion. This might be due to an electrostatic interaction between the reversely charged amino acid residues (glutamic acids and lysines) on these peptides resulting in the fusion among two liposome populations (1).
Crystallographic textures (1991)

Abstract To material scientists the term texture means the crystallographic orientation of grains in a polycrystal. In contrast, geologists use the term more generally to refer to the spatial arrangement or association of mineral grains in a rock. In this contribution we are concerned with the materials science definition. There are several established techniques available for the determination of crystallographic textures in rocks. It has also been realised that the scanning electron microscope (SEM) is applicable to the study of crystallographic textures via the electron channelling (EC) effect. This provides an image of mineral/rock microstructure (via orientation contrast), as well as a means of accurately indexing their crystal orientations (via electron channelling patterns, ECP). Both types of EC image result from the relationship between incident electron beam and crystal structure, and the subsequent modulation of the backscattered electron (BSE) emission signal according to Bragg's Law. It is a simple matter to switch between the two imaging modes. A related effect, electron backscattering, provides only the diffraction patterns, but has superior spatial resolution and pattern angles. Due to crystal symmetry restrictions, there is only a limited range of ECP configurations possible for any mineral. Individual patterns can therefore be identified by comparison with the complete ‘ECP-map’. The location of an individual pattern within the map area is determined by spherical angles, the exact definition of which depends on the type of fabric diagram (e.g. inverse pole figure, pole figure or orientation distribution function). Originally, these angles were measured manually. A computer program (CHANNEL) has been developed which uses a digitisation approach to pattern recognition, derives the required fabric diagrams and also constructs ECP-maps from standard crystal data (i.e. unit cell parameters etc.). The combination of SEM/EC and CHANNEL dramatically facilitates the study of crystal textures in minerals and rocks, making statistical crystallographic analysis from individual orientations a practicality. The following example applications are considered: (1) crystal structure representation of the Al 2 SiO 5 polymorph system; (2) local crystal texture relationships (epitaxial nucleation) between andalusite and sillimanite grains; (3) bulk rock crystal textures of quartzites; and (4) physical properties (e.g. elastic constants and seismic velocities) determined from bulk rock texture.