gebhart/patrepeval huggingface dataset:
A global role for Fis in the transcriptional control of metabolism and type III secretion in Salmonella enterica serovar Typhimurium (2004)

Fis is a key DNA-binding protein involved in nucleoid organization and modulation of many DNA transactions, including transcription in enteric bacteria. The regulon of genes whose expression is influenced by Fis in Salmonella enterica serovar Typhimurium (S. typhimurium) has been defined by DNA microarray analysis. These data suggest that Fis plays a central role in coordinating the expression of both metabolic and type III secretion factors. The genes that were most strongly up-regulated by Fis were those involved in virulence and located in the pathogenicity islands SPI-1, SPI-2, SPI-3 and SPI-5. Similarly, motility and flagellar genes required Fis for full expression. This was shown to be a direct effect as purified Fis protein bound to the promoter regions of representative flagella and SPI-2 genes. Genes contributing to aspects of metabolism known to assist the bacterium during survival in the mammalian gut were also Fis-regulated, usually negatively. This category included components of metabolic pathways for propanediol utilization, biotin synthesis, vitamin B(12) transport, fatty acids and acetate metabolism, as well as genes for the glyoxylate bypass of the tricarboxylic acid cycle. Genes found to be positively regulated by Fis included those for ethanolamine utilization. The data reported reveal the central role played by Fis in coordinating the expression of both housekeeping and virulence factors required by S. typhimurium during life in the gut lumen or during systemic infection of host cells.
Molecular Dynamics Simulations of Template-Assisted Nucleation:  Alcohol Monolayers at the Air−Water Interface and Ice Formation (2001)

Perhaps the best characterized template nucleation systems are the alcohol monolayer assemblies at the air−water interface. These monolayers, consisting of aliphatic alcohols [CnH2n+1OH, n = 16−31) have been the subject of hexagonal ice (Ih) induction experiments over a range of temperatures. To learn more about the molecular basis of alcohol monolayer template−induced ice nucleation phenomena, we performed canonical molecular dynamics (MD) simulations (1 ns) of pure C29, C30, and C31 alcohol monolayer−water droplet systems, using the reversible reference system propagation algorithm (r-RESPA). We find that the MD-determined monolayer physical parameters (at 278.15 K) exhibit reasonable agreement with experimentally determined values for crystalline C30 and C31 monolayers at 278.15 K. More importantly, as the simulation temperatures approach monolayer-specific freezing points, the water layer immediately below the monolayer surfaces adopted “ice-like” lattice parameters and hexagonal or c-centered rectangular geometries that are characteristic of the (Ih) {001} plane. The analysis of monolayer −OH headgroup orientations and surface topologies reveal that odd-carbon monolayers, and C31 in particular, are more effective nucleation templates, due to the following factors: (1) ab-plane alcohol −OH headgroup geometries which provide a closer ab-plane lattice match to the {001} Ih interface and (2) the presence of smoother monolayer headgroup topologies (i.e., azimuthal positioning), which permit a larger percentage of water molecules to form hydrogen bonds with the monolayer alcohol headgroups.
A comparative study of anion-exchange membranes tethered with different hetero-cycloaliphatic quaternary ammonium hydroxides (2017)

Quaternary ammonium (QA) cations with high alkaline stability are crucial for the long term performance of anion-exchange membrane (AEM) fuel cells.
Molecular Cloning and Expression of Arabidopsis Fatty Acid Hydroperoxide Lyase (1999)

Fatty acid hydroperoxide lyase (HPOL), an enzyme of the octadecanoid pathway that forms carbon-6 aldehydes such as n-hexanal or (Z)-3-hexenal, was cloned from Arabidopsis thaliana as a full-length cDNA. The HPOL activity obtained by expressing the cDNA in Escherichia coli formed n-hexanal from linoleic acid 13-hydroperoxide, whereas linoleic acid 9-hydroperoxide was not a substrate for the enzyme. The HPOL mRNA is expressed at low level in leaves; however, its accumulation can be found in the inflorescence. Wounding or methyl jasmonate treatments increase the mRNA level in leaves. These results indicate that the HPOL gene is up-regulated in leaves in response to wounding and that the enzyme may be an active component of the octadecanoid defense response.
Involvement of Cholecystokinin/Gastrin‐Related Peptides and their Receptors in Clinical Gastrointestinal Disorders (2002)

In this paper the possible roles of cholecystokinin (CCK), gastrin, or gastrin-related peptides and their receptors in human gastrointestinal diseases are reviewed. For CCK/CCK(A) receptors (CCK(A)-R), the evidence for their proposed involvement in diseases caused by impaired CCK release or CCK(A)-R mutations, pancreatic disorders (acute/chronic pancreatitis), gastrointestinal motility disorders (gallbladder disease, irritable bowel syndrome), pancreatic tumor growth and satiety disorders, is briefly reviewed. The evidence that has established the involvement of gastrin/CCK(B)-R in mediating the action of hypergastrinaemic disorders, mediating hypergastrinaemic effects on the gastric mucosa (ECL hyperplasia, carcinoids, parietal cell mass), and acid-peptic diseases, is reviewed. The evidence for their possible involvement in mediating growth of gastric and pancreatic tumours and possible involvement of gastrin-related peptides in colon cancers, is reviewed briefly.
Duration of Nocturnal Hypoglycemia Before Seizures (2008)

Even with a subcutaneous glucose lag of 18 min when compared with blood glucose measurements, glucose sensors have time to provide clinically meaningful alarms. Current nocturnal hypoglycemic alarms need to be improved, however, since patients can sleep through the current alarm systems.
Glucose-Containing Oligosaccharides in the Urine of Patients with Glycogen Storage Disease Type II and Type III (1978)

Patients with glycogen storage disease type II and type III were recently found to excrete increased amounts of a glucose-containing tetrasaccharide DGlcp(alpha1 leads to 6)DGlcp(alpha1 leads to 4)DGlcp(alpha1 leads to 4)DGlc [Lennartson, G., Lundblad, A., Sjöblad, S., Svensson, S. and Ockerman, P.A. (1976) Biomed. Mass Spectrom. 3, 51--54]. In addition to this tetrasaccharide, urine from these patients also contains larger oligosaccharides containing only glucose. From urine of patients with glycogen storage disease type II and type III, three and four oligosaccharides respectively have been isolated. Structural studies including sugar analyses, methylation analyses, partial acid hydrolysis and optical rotation revealed that three compounds were present in the urine of both patients. Their proposed structures or partial structures are as follows: DGlcp(alpha1--6)DGlcp(alpha1--6)DGlcp(alpha1--4)DGlcp(alpha1--4)DGlcp(alpha1--4)DGlc, DGlcp(alpha1--4)DGlcp(alpha1--6)DGlcp(alpha1--6)DGlcp(alpha1--4)DGlcp(alpha1--4)DGlc, and DGlcp(alpha1--6)DGlcp(alpha1--4)DGlcp(alpha1--4)DGlcp(alpha1--4)DGlcp(alpha1--6)DGlcp(alpha1--4)DGlcp(alpha1--4)DGlc. A fourth compound has been partially characterized as a branched heptasaccharide with four (1 leads to 4) linkages and two (1 lead to 6) linkages. Glycogen is possibly the origin of these compounds. However, the number of (1 leads to 6) linkages is higher than expected and may indicate a shorter distance between branches in glycogen than has been generally assumed.
Thermal barrier coatings technology: critical review, progress update, remaining challenges and prospects (2013)

A comprehensive and integrated review of thermal barrier coatings (TBCs) applied to turbine components is provided. Materials systems, processes, applications, durability issues, technical approaches and progress for improved TBC, and our understanding of the science and technology are discussed. Thermal barrier coating prime reliance and further advances have been hampered by TBC loss by particle impact and erosion in certain locations of the turbine blades. Accumulation of low melting eutectic containing calcia, magnesia, alumina and silica resulting in TBC spallation limits maximum surface temperature. Design methodologies to address durability and data scatter issues are discussed. Compositions, morphology, characteristics and performance data for new bonds to achieve longer TBC life are described. Further reduction in the thermal conductivity of the top layer to minimise the parasitic mass of the coating on the component is being sought via top layer composition and processing modifications as well as by alternate ceramic compositions. The progress in these areas is critically reviewed including processing, stability and durability limitations. The paper also describes effort to understand various failure mechanisms including modelling and simulation.
A low power, wide dynamic range multigain signal processor for the SNAP CCD (2004)

A four-channel custom chip designed for reading out the CCDs of the proposed SNAP satellite visible imager is presented. Each channel consists of a single-ended to differential converter followed by a correlated double sampler and a novel multislope integrator. The output signal is differentially brought out of the chip by an output buffer. This circuit is designed to operate at room temperature for test purpose and at 140 K, which will be the operating temperature. The readout speed is 100 kHz. The 16-bit dynamic range is covered using 3 gains each with a 12-bit signal to noise ratio. The prototype chip, implemented in a 0.25 /spl mu/m CMOS technology, has a measured readout noise of 7 /spl mu/V rms at 100 kHz readout speed, a measured nonlinearity of /spl plusmn/0.0025% and a power consumption of 6.5 mW, with a 3.3 V supply voltage.
Use of phononic materials in microfluidic & lab-on-a-chip manipulations (2012)

The development of microfluidic systems is often constrained both by difficulties associated with the chip interconnection to other instruments, and by mechanisms that can enable fluid movement and processing. Surface acoustic wave (SAW) devices have previously shown promise in allowing samples to be manipulated, although designing complex fluid manipulations involves the generation of mixed signals at multiple electrode transducers. We now demonstrate a new and simple interface between a piezoelectric SAW device and a disposable microfluidic chip, involving the use of phononic structures, to shape the acoustic field. Such phononic structures can be designed in such a way that the interaction of the fluid within the chip structure is dependent upon the acoustic frequency, providing a new method to programme complex fluidic functions into a microchip. We demonstrate applications in biological sensing involving enrichment enrichment of cells, lysis, PCR and sensing, exploring the application of this chip based technology to Developing World Diganostics.
Model studies on multiple channel analysis of free magnesium, calcium, sodium, and potassium at physiological concentration levels with ion-selective electrodes (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTModel studies on multiple channel analysis of free magnesium, calcium, sodium, and potassium at physiological concentration levels with ion-selective electrodesMatthias. Otto and J. D. R. ThomasCite this: Anal. Chem. 1985, 57, 13, 2647–2651Publication Date (Print):November 1, 1985Publication History Published online1 May 2002Published inissue 1 November 1985https://pubs.acs.org/doi/10.1021/ac00290a049https://doi.org/10.1021/ac00290a049research-articleACS PublicationsRequest reuse permissionsArticle Views696Altmetric-Citations111LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Topological Fisheye Views for Visualizing Large Graphs (2004)

Graph drawing is a basic visualization tool. For graphs of up to hundreds of nodes and edges, there are many effective techniques available. At greater scale, data density and occlusion problems often negate its effectiveness. Conventional pan-and-zoom, and multiscale and geometric fisheye views are not fully satisfactory solutions to this problem. As an alternative, we describe a topological zooming method. It is based on the precomputation of a hierarchy of coarsened graphs, which are combined on the fly into renderings with the level of detail dependent on the distance from one or more foci. We also discuss a related distortion method that allows our technique to achieve constant information density displays
Biocompatibility of a polyether urethane, polypropylene oxide, and a polyether polyester copolymer. A qualitative and quantitative study of three alloplastic tympanic membrane materials in the rat middle ear (1990)

The biocompatibility of porous implants made of Estane 5714 F1 polyether urethane, polypropylene oxide, and a poly(ethylene oxide hydantoin) and poly(tetramethylene terephthalate) segmented polyether polyester copolymer (HPOE/PBT copolymer), which were selected as candidates for an alloplastic tympanic membrane, was assessed after implantation in rat middle ears for periods of up to 1 year. Implantation of the materials led to tissue reactions initially associated with the wound-healing process, whereas after 1 month not only the presence of macrophages and foreign-body giant cells surrounding the implant materials but also implant degradation were characteristic for a foreign-body reaction. Macrophages and foreign-body giant cells dominated the picture of the tissue surrounding polypropylene oxide. The altered morphology of these cells, the persistent infiltration of the implantation sites by exudate cells, and the premature death of five rats in the 1-year group suggest that polypropylene oxide degradation was accompanied by the release of toxic substances. Estane and copolymer degradation did not induce tissue responses reflecting implant toxicity, and tympanic membranes given these alloplasts showed a normal healing pattern. Inclusions in the cytoplasm of macrophages associated with degradation and phagocytosis of all of the polymers under study were found to contain iron, silicon, titanium, and aluminum. Growth of fibrous tissue and bone, the latter into Estane and HPOE/PBT copolymer implants, indicated appropriate implant fixation by tissue, although macrophages and foreign-body giant cells were present as well. Especially the fixation of copolymer by ingrowth of bone seems promising in terms of the amount of bone in the pores and the electron-dense bone/copolymer interface. The latter is indicative for bonding osteogenesis. The HPOE/PBT copolymer is a better candidate for alloplastic tympanic membrane than Estane, and the use of polypropylene oxide cannot be recommended.
Pictures Are Not Taken in a Vacuum (2006)

onsiderable research has been devoted to the problem of multimedia indexing and retrieval in the past decade. However, limited by the state of the art in image understanding, the majority of the existing con-tent-based image retrieval (CBIR) systems have taken a relatively low-level approach and fallen short of higher-level interpretation and knowledge. Recent research has begun to focus on bridging the semantic and conceptual gap that exists between man and computer by integrating knowledge-based techniques, human perception, scene content understanding, psychology, and linguistics. In this article, we provide an overview of exploiting context for semantic scene content understanding. Context is critical in humans ’ recognition process, where the human visual system makes extensive use of the envi-ronment to facilitate object detection (e.g., where are the pedestrians? should we look around sidewalks?) [1]. Likewise, it can be used to improve the performance of automated systems for semantic indexing and retrieval of mul-timedia data. In this article, we intend to present a unique perspective on systematically exploiting a broad array of
An accurate relativistic effective core potential for excited states of Ag atom: An application for studying the absorption spectra of Agn and Agn+ clusters (1999)

A new 11-electron relativistic effective core potential (11e-RECP) for Ag atom based on correlated level of theory and the associated atomic orbital (AO) basis set have been derived which allows for an accurate determination of excited states. This has been verified by comparing the calculated excited states of the dimer with experimental data. Therefore, we applied the new 11e-RECP in the framework of the linear response equation-of-motion coupled-cluster (EOM-CC) method to determine absorption spectra of small Agn=2−4 and Agn=2−4+ clusters. The correlation treatment of 11 electrons per atom and calculations of transition energies and oscillator strengths in a large energy interval allowed us to investigate the influence of d-electrons on the spectroscopic patterns. We have found that d-electrons play a crucial role for accurate predictions of absorption spectra in spite of the fact that they are not always directly involved in the leading excitations contributing to the intense transitions. The calculated spectroscopic patterns for the stable structures are compared with available experimental data.
Optical Interconnects Using Single-Mode and Multi-Mode VCSEL and Multi-Mode Fiber (2020)

Single mode (SM) VCSELs, produced in industrial 4” technology, are suitable for 100Gb/s PAM2 and >160Gb/s PAM4 data transmission. >107Gb/s transmission over 1km of multimode (MM) fiber at 850nm and 910nm is realized.
Triggering DNAzymes with Light:  A Photoactive C8 Thioether-Linked Adenosine (2004)

Herein we report evidence for a light-inducible DNAzyme. In so doing, we also disclose the synthesis and photochemical properties of a novel nucleoside: 8-(2-(4-imidazolyl)ethyl-1-thio)-2'-deoxyriboadenosine (d1). The light sensitivity of (d1) was evaluated via an examination of the photoinduced reactivation of DNAzyme 8-17E from an inactive form that contained a single nucleotide (d1) modification. Restoration of DNAzyme activity results from a photoinduced reversion of (d1) to unmodified deoxyadenosine. Deuterium studies indicate that water is the source of hydrogen in the C8-H product and not the alkylthio group, suggesting that reversion of (1) to adenosine is not a consequence of simple homolysis of the C8-S bond but of an unprecedented photochemical conversion. This adenosine, which affords significant control of catalytic reactivation of a DNAzyme, may find general use in photodecaging other biological systems.
KIF5C, a Novel Neuronal Kinesin Enriched in Motor Neurons (2000)

Kinesin superfamily proteins (KIFs) are the molecular motors conveying cargos along microtubules. KIF5s, the heavy chains of conventional kinesin (KHC), are originally identified members of KIFs, and neuronal KIF5A and ubiquitous KIF5B have been identified so far. In the present work, we cloned a novel member of KIF5, KIF5C, and generated specific antibodies against three KIF5s to investigate their distribution and functions. KIF5A showed pan-neuronal distribution in the nervous system. KIF5B showed a glial cell distribution pattern in general; however, interestingly, its expression was strongly upregulated in axon-elongating neurons, such as olfactory primary neurons and mossy fibers. KIF5C was also a neuronal KIF5 like KIF5A but was highly expressed in lower motor neurons in 2-week-old or older mice, suggesting its important roles in the maintenance of motor neurons rather than in their formation, such as axonal elongation. Because a large part of KIF5s in adult motor neurons were expected to be KIF5C, we generated mice lacking the kif5C gene to investigate the functions of KIF5C in neurons in living animals. The mutant mice showed smaller brain size but were viable and did not show gross changes in the nervous system. Closer examinations revealed the relative loss of motor neurons to sensory neurons. Because three KIF5s showed high similarity in the amino acid sequence, could rescue the KIF5B mutant cells, and could form heterodimers, we think that there are functional redundancy among the three KIF5s and that KIF5A and KIF5B prevented the KIF5C null mice from the severe phenotype.
Fully Automated One-Step Synthesis of Single-Transcript TALEN Pairs Using a Biological Foundry (2017)

Transcription activator-like effector nuclease (TALEN) is a programmable genome editing tool with wide applications. Since TALENs perform cleavage of DNA as heterodimers, a pair of TALENs must be synthesized for each target genome locus. Conventionally, TALEN pairs are either expressed on separate vectors or synthesized separately and then subcloned to the same vector. Neither approach allows high-throughput construction of TALEN libraries for large-scale applications. Here we present a single-step assembly scheme to synthesize and express a pair of TALENs in a single-transcript format with the help of a P2A self-cleavage sequence. Furthermore, we developed a fully automated platform to custom manufacture TALENs in a versatile biological foundry. 400 pairs of TALENs can be synthesized with over 96.2% success rate at a material cost of $2.1/pair. This platform opens the door to TALEN-based genome-wide studies.
Ring waveguides for gigahertz acoustic waves on silicon (2014)

We demonstrate a ring resonator for gigahertz surface acoustic waves (SAWs) consisting of a Ge waveguide on a silicon chip. SAWs generated by interdigital transducers on a section of the waveguide are guided over a curved path and detected by a second interdigital transducers. The structure of the GHz waveguide modes mapped using high resolution interferometry compares well with elastic calculations. The acoustic propagation properties as well as the potential applications of these semiconductor-based resonators are discussed.
ChemInform Abstract: Preparation of N‐Acetyl‐2‐arylglycin Esters by N—H Insertion Reaction of Aryldiazoacetates with Acetamide. (2010)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Two Lactobacillus strains, isolated from breast milk, differently modulate the immune response (2006)

The results of this study show that two Lactobacillus strains isolated from breast milk can exert different and even opposing effects on immune response demonstrating the specificity of each strain.
Myeloid-related protein (MRP)-8 from cervico-vaginal secretions activates HIV replication (2001)

MRP-8 in cervico-vaginal secretions stimulates HIV production. Strategies aimed at blocking MRP-8 activity in the genital tract could reduce risk of sexual as well as maternal--infant transmission of HIV.