gebhart/patrepeval huggingface dataset:
Related Network and Differential Expression Analyses Identify Nuclear Genes and Pathways in the Hippocampus of Alzheimer Disease (2020)

BACKGROUND Alzheimer disease (AD) is a typical progressive and destructive neurodegenerative disease that has been studied extensively. However, genetic features and molecular mechanisms underlying AD remain unclear. Here we used bioinformatics to investigate the candidate nuclear genes involved in the molecular mechanisms of AD. MATERIAL AND METHODS First, we used Gene Expression Omnibus (GEO) database to obtain the expression profiles of the mRNAs from hippocampus microarray and identify differentially expressed genes (DEGs) the plier algorithm. Second, functional annotation and visualization of the DEGs were conducted by the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. Finally, BioGRID, IntAct, STRING, and Cytoscape were utilized to construct a protein-protein interaction (PPI) network. Hub genes were analytically obtained from the PPI network and the microRNA (miRNA)-target network. RESULTS Two hippocampus microarrays (GSE5281 and GSE48350) were obtained from the GEO database, comprising 161 and 253 cases separately. Among these, 118 upregulated genes and 694 downregulated genes were identified. The upregulated DEGs were mainly involved in positive regulation of transcription from RNA polymerase II promoter, positive regulation of cartilage development, and response to wounding. The downregulated DEGs were enriched in chemical synaptic transmission, neurotransmitter secretion, and learning. By combining the results of PPI and miRNA-target network, 8 genes and 2 hub miRNAs were identified, including YWHAZ, DLG4, AGAP2, EGFR, TGFBR3, PSD3, RDX, BRWD1, and hsa-miR-106b-5p and hsa-miR-93-5p. These target genes are highly enriched in various key pathways, such as amyloid-beta formation, regulation of cardiocyte differentiation, and actin cytoskeleton reorganization. CONCLUSIONS In this study, YWHAZ, DLG4, AGAP2, EGFR, TGFBR3, PSD3, RDX, and BRWD1 were identified as candidate genes for future molecular studies in AD, which is expected to improve our understanding of its cause and potential molecular mechanisms. Nuclear genes, DEGs, and related networks identified by integrated bioinformatics analysis may serve as diagnostic and therapeutic targets for AD.
Multifunctional Encoded Particles for High-Throughput Biomolecule Analysis (2007)

High-throughput screening for genetic analysis, combinatorial chemistry, and clinical diagnostics benefits from multiplexing, which allows for the simultaneous assay of several analytes but necessitates an encoding scheme for molecular identification. Current approaches for multiplexed analysis involve complicated or expensive processes for encoding, functionalizing, or decoding active substrates (particles or surfaces) and often yield a very limited number of analyte-specific codes. We present a method based on continuous-flow lithography that combines particle synthesis and encoding and probe incorporation into a single process to generate multifunctional particles bearing over a million unique codes. By using such particles, we demonstrate a multiplexed, single-fluorescence detection of DNA oligomers with encoded particle libraries that can be scanned rapidly in a flow-through microfluidic channel. Furthermore, we demonstrate with high specificity the same multiplexed detection using individual multiprobe particles.
Real-Time Glucose Sensing by Surface-Enhanced Raman Spectroscopy in Bovine Plasma Facilitated by a Mixed Decanethiol/Mercaptohexanol Partition Layer (2005)

A new, mixed decanethiol (DT)/mercaptohexanol (MH) partition layer with dramatically improved properties has been developed for glucose sensing by surface-enhanced Raman spectroscopy. This work represents significant progress toward our long-term goal of a minimally invasive, continuous, reusable glucose sensor. The DT/MH-functionalized surface has greater temporal stability, demonstrates rapid, reversible partitioning and departitioning, and is simpler to control compared to the tri(ethylene glycol) monolayer used previously. The data herein show that this DT/MH-functionalized surface is stable for at least 10 days in bovine plasma. Reversibility is demonstrated by exposing the sensor alternately to 0 and 100 mM aqueous glucose solutions (pH approximately 7). The difference spectra show that complete partitioning and departitioning occur. Furthermore, physiological levels of glucose in two complex media were quantified using multivariate analysis. In the first system, the sensor is exposed to a solution consisting of water with 1 mM lactate and 2.5 mM urea. The root-mean-squared error of prediction (RMSEP) is 92.17 mg/dL (5.12 mM) with 87% of the validation points falling within the A and B range of the Clarke error grid. In the second, more complex system, glucose is measured in the presence of bovine plasma. The RMSEP is 83.16 mg/dL (4.62 mM) with 85% of the validation points falling within the A and B range of the Clarke error grid. Finally, to evaluate the real-time response of the sensor, the 1/e time constant for glucose partitioning and departitioning in the bovine plasma environment was calculated. The time constant is 28 s for partitioning and 25 s for departitioning, indicating the rapid interaction between the SAM and glucose that is essential for continuous sensing.
Detection of Gene Expression in Genetically Engineered Microorganisms and Natural Phytoplankton Populations in the Marine Environment by mRNA Analysis (1991)

A simple method that combines guanidinium isothiocyanate RNA extraction and probing with antisense and sense RNA probes is described for analysis of microbial gene expression in planktonic populations. Probing of RNA sample extracts with sense-strand RNA probes was used as a control for nonspecific hybridization or contamination of mRNA with target DNA. This method enabled detection of expression of a plasmid-encoded neomycin phosphotransferase gene (nptII) in as few as 10Vibrio cells per ml in 100 ml of seawater. We have used this method to detect expression of the ribulose-1,5-bisphosphate carboxylase large-subunit gene (rbcL) in Synechococcus cultures and natural phytoplankton populations in the Dry Tortugas, Florida. During a 36-h diel study, rbcL expression of the indigenous phytoplankton was greatest in the day, least at night (1100, 0300, and 0100 h), and variable at dawn or dusk (0700 and 1900 h). These results are the first report of gene expression in natural populations by mRNA isolation and probing. This methodology should be useful for the study of gene expression in microorganisms released into the environment for agricultural or bioremediation purposes and indigenous populations containing highly conserved target gene sequences.
Dynamic instability of microtubules (1987)

Abstract Recent evidence shows that dynamic instability is the dominant mechanism for the assembly of pure tubulin in vitro and for the great majority of microtubules in the mitotic spindle and the interphase cytoplasmic microtubule complex. The basic concepts of this model provide a framework for future characterization of the molecular basis of spatial and temporal regulation of microtubule dynamics in the cell and the function of microtubule dynamics in motile processes such as chromosome movement.
Exchange of iron by gallium in siderophores (1986)

Siderophores are iron transport compounds produced by numerous microorganisms and which strongly chelate Fe(III), but not Fe(II). Other trivalent metals, such as Al(III), Cr(III), or Ga(III), are not capable of significantly displacing iron from siderophores. However, I demonstrate here that Ga(III) can effectively displace iron under reducing conditions. With ascorbate as reductant and ferrozine as Fe(II) trapping agent, the kinetics of reductive displacement of iron by Ga(III) were followed spectroscopically by the increase of absorbance at 562 nm due to formation of the Fe(II)-ferrozine complex. No significant reduction of siderophore occurred in the absence of Ga(III). With excess Ga(III), the displacement was quantitative and very rapid. The rate of metal exchange was pseudo first order with respect to Ga(III) concentration and highly pH dependent, suggesting that siderophore ligands are displaced from the iron in a concerted mechanism by Ga(III) and protonation to expose the Fe(III) to reduction by ascorbate. Reaction rates were dependent upon the structure of the siderophore, being greatest for ferric rhodotorulic acid and slowest for ferrichrome A at pH 5.4. The pH profile for ferric rhodotorulic acid was unusual in that it showed a maximum at pH 6.5, while all other siderophores examined showed an increase in rate as pH was lowered from 7.0. The physiological significance of this reaction to the clinical use of gallium is discussed.
Light-coupling masks for lensless, sub-wavelength optical lithography (1998)

Light-coupling masks (LCMs) based on structured organic polymers that make conformal contact with a substrate can constitute an amplitude mask for light-based lithographies. The LCM is exposed through its backside, from where the light is differentially guided by the structures towards the substrate. Images of arbitrarily shaped features having dimensions much smaller than that of the vacuum wavelength of the exposing light are formed in the resist in a 1:1 correspondence to their size in light-guiding portions of the mask. LCMs allow pattern replication at high resolution and densities over large areas in photoresist without the need for elaborate projection optics.
Phenazine antibiotic biosynthesis in Pseudomonas aureofaciens 30-84 is regulated by PhzR in response to cell density (1994)

We have identified a gene that acts in trans to activate the expression of the phenazine biosynthetic genes in the biological control organism Pseudomonas aureofaciens 30-84. This gene, phzR (phenazine regulator), is located upstream of and divergently transcribed from the phenazine biosynthetic genes. Thus, the phenazine biosynthetic locus consists of at least two divergently transcribed operons. A functional phzR gene is required for phenazine production. The nucleotide sequence of phzR revealed an open reading frame of 723 nucleotides encoding a protein of ca. 27 kDa. The predicted amino acid sequence of PhzR has homology with other bacterial positive transcriptional activators, including LasR of Pseudomonas aeruginosa, LuxR of Vibrio fischerii, and TraR of Agrobacterium tumefaciens. The addition of cell-free supernatants from late-exponential-phase cultures of strain 30-84 resulted in expression of a genomic phzB:lacZ reporter strain at a lower cell density than normal, indicating the possible presence of an autoinducer. These results indicate that PhzR is a member of a two-component sensor-regulator family with known or predicted carboxy-terminal DNA-binding domains which regulates gene expression in response to environmental and cell density signals.
The two faces of transforming growth factor β in carcinogenesis (2003)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Simple but Effective Way to Sense Pyrophosphate and Inorganic Phosphate by Fluorescence Changes (2006)

A new fluorescent chemosensor based on the acridine-Zn(II) derivative effectively recognizes pyrophosphate and inorganic phosphate at pH 7.4. Acridine derivative 1 displayed a fluorescent quenching effect with pyrophosphate; on the other hand, a large fluorescent enhancement was observed with inorganic phosphate. [structure: see text].
Structural Studies of the Transmembrane C-Terminal Domain of the Amyloid Precursor Protein (APP): Does APP Function as a Cholesterol Sensor? (2008)

The amyloid precursor protein (APP) is subject to alternative pathways of proteolytic processing, leading either to production of the amyloid-beta (Abeta) peptides or to non-amyloidogenic fragments. Here, we report the first structural study of C99, the 99-residue transmembrane C-terminal domain of APP liberated by beta-secretase cleavage. We also show that cholesterol, an agent that promotes the amyloidogenic pathway, specifically binds to this protein. C99 was purified into model membranes where it was observed to homodimerize. NMR data show that the transmembrane domain of C99 is an alpha-helix that is flanked on both sides by mostly disordered extramembrane domains, with two exceptions. First, there is a short extracellular surface-associated helix located just after the site of alpha-secretase cleavage that helps to organize the connecting loop to the transmembrane domain, which is known to be essential for Abeta production. Second, there is a surface-associated helix located at the cytosolic C-terminus, adjacent to the YENPTY motif that plays critical roles in APP trafficking and protein-protein interactions. Cholesterol was seen to participate in saturable interactions with C99 that are centered at the critical loop connecting the extracellular helix to the transmembrane domain. Binding of cholesterol to C99 and, most likely, to APP may be critical for the trafficking of these proteins to cholesterol-rich membrane domains, which leads to cleavage by beta- and gamma-secretase and resulting amyloid-beta production. It is proposed that APP may serve as a cellular cholesterol sensor that is linked to mechanisms for suppressing cellular cholesterol uptake.
Low frequency oscillations in cephalic vessels assessed by near infrared spectroscopy (2012)

Our results show that LFO phase shift ABP-oxyHb may be used as a robust measurement of differences in autoregulation between hemispheres and over time. In addition, we found a strong relation between oxyHb and Vmca during paced breathing. Gain showed too large variation for clinical use, as the SD was up to 100-fold of mean values.
Peer Reviewed: Genomics technologies for environmental science (2001)

The ongoing explosion of nucleotide sequence data from prokaryotic and eukaryotic organisms is creating a vast information resource. Potential applications range fromunderstanding and combating human disease to characterizing naturally occurring microbial communities, whose combined biomass is the singlemost important biological force influencing global elemental cycles and the balance of atmospheric gases. Although the health sector is moving rapidly into the postgenomics era, environmental genomics, the use of genomics to address environmental issues and problems, remains in its infancy. For example, although specific nucleotide sequence information has been available for some time, whole genome sequences for environmentally relevant microorganisms are only now beginning to appear in databases. Presently, ecological studies ofmicrobial communities remain largely process-oriented. Measurable metabolic parameters, like nitrogen fixation and substrate biodegradation, are determined as a function of the whole community. The contribution of individual bacterial species to these parameters is nearly impossible to determine becausemany organisms cannot be cultivated in vitro. The use of genomics-based tools to augment these traditional methods promises to accelerate our understanding of the complexities of species diversity, population dynamics, andmetabolic pathways withinmicrobial communities in soil and water. Their use should markedly improve the reliability and accuracy of remediation activities and of predictions of adverse environmental impacts before they happen.
High-throughput fluorescent-based optimization of eukaryotic membrane protein overexpression and purification in Saccharomyces cerevisiae (2007)

Eukaryotic membrane proteins are often difficult to produce in large quantities, which is a significant obstacle for further structural and biochemical investigation. Based on the analysis of 43 eukaryotic membrane proteins, we present a cost-effective high-throughput approach for rapidly screening membrane proteins that can be overproduced to levels of >1 mg per liter in Saccharomyces cerevisiae. We find that 70% of the well expressed membrane proteins tested in this system are stable, targeted to the correct organelle, and monodisperse in either Fos-choline 12 (FC-12) or n-dodecyl-beta-D-maltoside. We illustrate the advantage of such an approach, with the purification of monodisperse human and yeast nucleotide-sugar transporters to unprecedented levels. We estimate that our approach should be able to provide milligram quantities for at least one-quarter of all membrane proteins from both yeast and higher eukaryotic organisms.
No Association Between the Common MTHFR 677C→T Polymorphism and Venous Thrombosis (2007)

In a single large study, MTHFR 677C-->T was not associated with the risk of venous thrombosis, and the narrow confidence interval excludes even a small effect. Therefore, mildly elevated homocysteine levels as a result of MTHFR 677TT do not seem to cause venous thrombosis. There is no rationale for measuring the MTHFR 677C-->T variant for clinical purposes.
Hybrid vanadate waveguiding configurations for extreme optical confinement and efficient polarization management in the near-infrared (2018)

Vanadate materials such as CaVO3 and SrVO3 were recently proposed as promising alternatives to their conventional transparent conducting oxide counterparts owing to the superior capability for simultaneous realization of high optical transparency and high electrical conductivity originating from strong electron-electron interactions. Here we show that, in addition to their remarkable optoelectronic properties as conducting materials, their incorporation into planar waveguiding configurations could enable outstanding optical performance that is otherwise difficult to achieve with conventional material building blocks, especially metals. Starting from the guided wave at a single CaVO3/dielectric interface, the unique dispersion relationship and propagation property of the fundamental mode are revealed and compared to the conventional surface plasmon polariton associated with a silver/dielectric planar configuration. The superior confinement capability and the unique modal attenuation of the CaVO3-based waveguiding platform are further demonstrated via investigating silicon-based hybrid guiding schemes integrated with a CaVO3 nanostructure. By leveraging the pronounced polarization dependent loss in the hybrid configuration, an ultra-compact TE-pass polarizer is numerically demonstrated at telecommunication wavelengths. This transformative design features a reduced footprint and enhanced optical performance when benchmarked against the current state-of-the-art in hybrid silicon polarizers. The combination of these vanadate materials with traditional waveguiding platforms thereby opens new avenues towards miniaturized functional integrated photonic devices, and potentially enables a variety of intriguing applications at the sub-diffraction-limited scale.
<title>Development and performance of a diamond-film polishing apparatus with hot metals</title> (1990)

The diamond film polishing apparatus with hot metals has been presented . Diamond films deposited by both microwave plasma CVD and arc discharge plasma jet CVD are used as workpieces . As a diamond film sways on a polishing plate made of an iron or a nickel heated to 75O''95O C it is finished to flat and glass-like surfaces without any exfoliation. Not only swaying speed but also polishing pressure in this apparatus are extremely low in comparison to a conventional mechanical polishing method. When a cast iron and a molybdenum are used as a polishing plate polishing is not advanced . The polishing rate is highest in a vacuum atmosphere . Among gas atmospheres the rate is highes t in a hydrogen atmosphere . These result show that a diamond film is polished by the diffusion of carbon into a polishing plate. When a diamond film surface is too rough to polish by this apparatus the surface planing with YAG laser is applied then polishing is conducted on the planed surface. 1 .
Red Wine Ingredient Resveratrol Protects from β-Amyloid Neurotoxicity (2003)

Our findings suggest that red wine may be neuroprotective through the actions of resveratrol.
Enterprise data management in mixed workload environments (2009)

Enterprise applications are presently built on a 20year old data management infrastructure that was designed to meet a specific set of requirements for OLTP systems. In the meantime, enterprise applications have become more sophisticated, data set sizes have increased, requirements on the freshness of input data have been strengthened, and the time allotted for completing business processes has been reduced. To meet these challenges, enterprise applications have become increasingly complicated to make up for short-comings in the data management infrastructure. This paper outlines the characteristics of enterprise application with regards to the underlying data management layer. We also propose a database design perfectly fit to the demanded requirements of enterprise applications.
Antibody-Mediated Protection against Mucosal Simian-Human Immunodeficiency Virus Challenge of Macaques Immunized with Alphavirus Replicon Particles and Boosted with Trimeric Envelope Glycoprotein in MF59 Adjuvant (2010)

We have previously shown that rhesus macaques were partially protected against high-dose intravenous challenge with simian-human immunodeficiency virus SHIV(SF162P4) following sequential immunization with alphavirus replicon particles (VRP) of a chimeric recombinant VEE/SIN alphavirus (derived from Venezuelan equine encephalitis virus [VEE] and the Sindbis virus [SIN]) encoding human immunodeficiency virus type 1 HIV-1(SF162) gp140DeltaV2 envelope (Env) and trimeric Env protein in MF59 adjuvant (R. Xu, I. K. Srivastava, C. E. Greer, I. Zarkikh, Z. Kraft, L. Kuller, J. M. Polo, S. W. Barnett, and L. Stamatatos, AIDS Res. Hum. Retroviruses 22:1022-1030, 2006). The protection did not require T-cell immune responses directed toward simian immunodeficiency virus (SIV) Gag. We extend those findings here to demonstrate antibody-mediated protection against mucosal challenge in macaques using prime-boost regimens incorporating both intramuscular and mucosal routes of delivery. The macaques in the vaccination groups were primed with VRP and then boosted with Env protein in MF59 adjuvant, or they were given VRP intramuscular immunizations alone and then challenged with SHIV(SF162P4) (intrarectal challenge). The results demonstrated that these vaccines were able to effectively protect the macaques to different degrees against subsequent mucosal SHIV challenge, but most noteworthy, all macaques that received the intramuscular VRP prime plus Env protein boost were completely protected. A statistically significant association was observed between the titer of virus neutralizing and binding antibodies as well as the avidity of anti-Env antibodies measured prechallenge and protection from infection. These results highlight the merit of the alphavirus replicon vector prime plus Env protein boost vaccine approach for the induction of protective antibody responses and are of particular relevance to advancing our understanding of the potential correlates of immune protection against HIV infection at a relevant mucosal portal of entry.