gebhart/patrepeval huggingface dataset:
Pectin Enhances Bio-Control Efficacy by Inducing Colonization and Secretion of Secondary Metabolites by Bacillus amyloliquefaciens SQY 162 in the Rhizosphere of Tobacco (2015)

Bacillus amyloliquefaciens is a plant-beneficial Gram-positive bacterium involved in suppressing soil-borne pathogens through the secretion of secondary metabolites and high rhizosphere competence. Biofilm formation is regarded as a prerequisite for high rhizosphere competence. In this work, we show that plant extracts affect the chemotaxis and biofilm formation of B. amyloliquefaciens SQY 162 (SQY 162). All carbohydrates tested induced the chemotaxis and biofilm formation of the SQY 162 strain; however, the bacterial growth rate was not influenced by the addition of carbohydrates. A strong chemotactic response and biofilm formation of SQY 162 were both induced by pectin through stimulation of surfactin synthesis and transcriptional expression of biofilm formation related matrix genes. These results suggested that pectin might serve as an environmental factor in the stimulation of the biofilm formation of SQY 162. Furthermore, in pot experiments the surfactin production and the population of SQY 162 in the rhizosphere significantly increased with the addition of sucrose or pectin, whereas the abundance of the bacterial pathogen Ralstonia decreased. With increased production of secondary metabolites in the rhizosphere of tobacco by SQY 162 and improved colonization density of SQY 162 in the pectin treatment, the disease incidences of bacterial wilt were efficiently suppressed. The present study revealed that certain plant extracts might serve as energy sources or environmental cues for SQY 162 to enhance the population density on tobacco root and bio-control efficacy of tobacco bacterial wilt.
On Ligand Design for Catalytic Outer Sphere Reactions: A Simple Asymmetric Synthesis of Vinylglycinol (1996)

A quantitative synthesis with an enantiomeric ratio of 99:1 has been achieved for the important building block vinylglycinol. The crucial concept lay in sculpting the chiral pocket in catalyst 1 by restricting bond rotations in its chiral-inducing ligand.
Slip at polymer–polymer interfaces: Rheological measurements on coextruded multilayers (2002)

Polypropylene (PP) and polystyrene (PS), with closely matched viscosity, were coextruded into 8, 32, and 64 alternating layers. The apparent steady shear viscosity of these multilayer samples was measured with an in-line slit rheometer and with a parallel-plate rheometer. In both cases the apparent viscosity decreased with the number of layers providing strong evidence for interfacial slip. The velocity difference across the interface (interfacial slip velocity) versus shear stress, ΔVI(τ) was calculated from the apparent viscosity measurements. ΔVI(τ) showed sigmoidal behavior: a region of very low slip (&lt; 10−3 μm) at low shear stress, a strongly increasing region at τ &gt; 103 Pa followed by a linear region ΔVI=τ/β∞. These data could be fit with a modified Ellis model. The same function fit the different number of layers and both slit and parallel-plate data indicating ΔVI(τ) is a material property of the PP/PS pair. Slip was also observed in PS/PMMA (polymethyl methacrylate) and PP/aPA (amorphous nylon) pairs. Addition of a premade P(S-b-EE) diblock copolymer to the PP/PS pair was able to suppress the interfacial slip but only after enough time for sufficient block copolymers to diffuse to the interfaces. The in situ formed graft copolymer of maleated PP with aPA at the interface of the PP/aPA pair directly suppressed the slip. Our results are in qualitative agreement with the theory of Furukawa (1989) and de Gennes (1992), which predicts fewer chain entanglements near the interface between two immiscible polymers, and thus a narrow region (∼ interfacial width) with lower viscosity. This lower viscosity is the cause of apparent interfacial slip. Goveas and Fredrickson (1998) extended these ideas to calculate the slip in a symmetric bilayer where both bulk and interface are Newtonian. Their results are in qualitative agreement with our observation but predict a stronger slip. Our results also indicate that the anomalously low viscosity reported by a number of researchers for immiscible polymer blends is due to interfacial slip. Blends of PP and PS show similar negative viscosity deviations to those reported but only at τ &gt; 2000 Pa. No negative deviations were found for linear viscoelastic (low-stress) measurements.
MRI-Guided 9-Gauge Vacuum-Assisted Breast Biopsy: Initial Clinical Experience (2005)

MRI-guided vacuum-assisted biopsy is a fast and safe alternative to surgical biopsy for MRI-detected breast lesions. Imaging-histologic correlation is necessary to ensure lesion sampling.
High Resolution Printing of DNA Feature on Poly(methyl methacrylate) Substrates Using Supramolecular Nano-Stamping (2005)

In recent years, a large number of devices based on organic and biological materials have been developed. To scale-up the production of these systems to industrially acceptable standards, there is a need to develop soft-material stamping approaches with the needed resolution, complexity, and versatility. We have recently developed a DNA-based stamping method (supramolecular nano-stamping, SuNS) that has superior resolution and can print multiple molecules at the same time. A similar technique was independently developed by Crooks and co-workers. Here we show that SuNS can be used to efficiently print DNA features on a polymeric substrate (poly(methyl methacrylate), PMMA) with a 40 nm point resolution and a coverage that exceeds 100 mum2. The stamped PMMA substrate was also used as a master to print on a gold substrate. With PMMA being optically clear and electrically insulating, future applications of SuNS to print DNA micro- and nanoarrays are envisioned.
Mass drug administration under the programme to eliminate lymphatic filariasis in Orissa, India: a mixed-methods study to identify factors associated with compliance and non-compliance (2008)

The present study aimed to identify the factors responsible for compliance and non-compliance of mass drug administration (MDA) under the programme to eliminate lymphatic filariasis (LF) from Orissa, India. It was based on both quantitative (through household MDA coverage survey) and qualitative data (through semi-structured interviews with heads of compliant and non-compliant households) collected during an MDA held in November 2005 in two districts of Orissa. In these districts, 83% of the eligible population received the drug (coverage) and only 49.5% people actually consumed the drug (compliance). Seventeen percent of the population did not even receive the drug. The predominant reason for not receiving the drug at household level was that the drug distributor did not visit the household, while the fear of adverse reactions is the predominant reason for not consuming it. The qualitative data revealed that the major contributor to taking the drug was the awareness that drug protects them from LF. Motivation by health workers was another reason for compliance. In many endemic areas, the issues related to non-compliance were taken casually during implementation. Hence, it is imperative to make the programme more efficient by addressing the issues linked to low compliance.
Optical Traps as Force Transducers:  The Effects of Focusing the Trapping Beam through a Dielectric Interface (2000)

The use of optical forces generated by a focused laser beam for manipulating single polymer chains and colloidal particles has begun to receive increasing attention in polymer and colloid science and in biophysics. Devices based on such optical traps are increasingly used for probing the elasticity of single polymer chains and for studying the structure and mechanical behavior of biopolymers and their relation to biological activity. Colloidal forces and viscoelastic behavior of the suspending fluids can also be examined through the use of optical traps as force transducers and from the dynamics of optically bound probe particles. Such applications require a precise understanding of the trap potential and its dependence on the distance between the trap center and the glass/liquid interfaces that exist in experimental arrangements. This paper addresses some of the issues relevant to the above class of applications of optical traps using wave optics calculations. It is shown that the use of simple geometric optics corrections for the change in focus caused by a dielectric interface could lead to errors in the estimation of the measured forces. The occurrence of secondary traps and corresponding deviations from the commonly assumed harmonicity of trap potentials are also identified.
Association of Circulating Sclerostin With Bone Mineral Mass, Microstructure, and Turnover Biochemical Markers in Healthy Elderly Men and Women (2013)

Sclerostin levels are markedly different according to the immunoassay used. Detection of an association with calcitropic hormones or turnover markers relies on the epitope recognized by the immunoassay and adjustment for bone mass.
Radiation hardness of silicon detectors: current status (1997)

Silicon detectors are used or going to be used as tracking devices in many high energy physics experiments. Therefore they are located close to the interaction point, where the detectors are exposed to very high particle fluxes and ionization doses, especially in future experiments with very high energies and luminosities. Ongoing investigations concerning the radiation damage, started already several years ago, include bulk and surface damage related questions. The two main objectives of these studies are: (1) predict the radiation induced change in the detector parameters expected for any application, and (2) improve the radiation hardness of the detectors. A general overview of the current progress of the radiation hardness studies towards these goals is given here.
Colorimetric Assay for Antifungal Susceptibility Testing of <i>Aspergillus</i> Species (2001)

A colorimetric assay for antifungal susceptibility testing of Aspergillus species (Aspergillus fumigatus, Aspergillus flavus, Aspergillus terreus, Aspergillus nidulans, and Aspergillus ustus) is described based on the reduction of the tetrazolium salt 2,3-bis(2-methoxy-4-nitro-5-[(sulphenylamino)carbonyl]-2H-tetrazolium-hydroxide (XTT) in the presence of menadione as an electron-coupling agent. The combination of 200 microg of XTT/ml with 25 microM menadione resulted in a high production of formazan within 2 h of exposure, allowing the detection of hyphae formed by low inocula of 10(2) CFU/ml after 24 h of incubation. Under these settings, the formazan production correlated linearly with the fungal biomass and less-variable concentration effect curves for amphotericin B and itraconazole were obtained.
Multi-box: An Updated Box Beam Analysis Program (1989)

Computers have become an integral part of the engineers 'toolbox' for design and analysis. No where is this more true than in aeronautical engineering. For structural analysis of airframes the modern methods based on Finite Element Analysis have become very important, however the traditional procedures involving the stressed-skin concept still have a useful role in the aircraft structural design cycle. In this work we examine box-beam analysis using the stressed-skin/shear flow conventions and establish an analysis procedure with fewer assumptions, principally that the skin carries its proper share of bending stress and consequently the shear flow variation is quadratic. This improved formulation has been coded into a microcomputer program called MULTI-BOX which has been subjected to benchmark testing for a whole range of structural situations, from determining the shear flow round strange cross-sections to doing a total wing analysis including root warping constraints. The paper describes the theory behind MULTI-BOX and presents some applications.
Reconstruction of the immunogenic peptide RNase(43-56) by identification and transfer of the critical residues into an unrelated peptide backbone. (1989)

The involvement of each of the amino acid residues of the I-Ak-restricted T cell determinant RNase(43-56) was examined in detail using a series of peptides containing single amino acid substitutions. Four positions were identified as being essential for the formation of the determinant, Phe-46, Val-47, His-48, and Leu-51. When these four residues were substituted into the backbone of the unrelated peptide HA(130-144), a nonstimulatory peptide was obtained. The inclusion of an additional residue, Val-54, resulted in a chimeric peptide, RN/HA2, which was nearly as active as the native molecule. The peptide RN/HA2 was able to prime in vivo for RNase reactivity, confirming that these five residues contained all of the specificity of the RNase(43-56) determinant. The role of three of these critical residues was examined using both a functional competition assay and an in vivo priming assay. It was ascertained that the Phe-46 was directly involved in contacting the TCR, while the His-48 and Leu-51 were either involved in binding to the I-Ak molecule or in determining the conformation of the peptide. Thus, by critically evaluating the contribution of each of the amino acid residues in a T cell determinant, we were able to generate a chimeric peptide only containing 5 of 15 residues from the RNase(43-56) sequence that was functionally identical to the native RNase(43-56) molecule both in vitro and in vivo.
The Protein Information Resource (PIR) (2000)

The Protein Information Resource (PIR) produces the largest, most comprehensive, annotated protein sequence database in the public domain, the PIR-International Protein Sequence Database, in collaboration with the Munich Information Center for Protein Sequences (MIPS) and the Japan International Protein Sequence Database (JIPID). The expanded PIR WWW site allows sequence similarity and text searching of the Protein Sequence Database and auxiliary databases. Several new web-based search engines combine searches of sequence similarity and database annotation to facilitate the analysis and functional identification of proteins. New capabilities for searching the PIR sequence databases include annotation-sorted search, domain search, combined global and domain search, and interactive text searches. The PIR-International databases and search tools are accessible on the PIR WWW site at http://pir.georgetown.edu and at the MIPS WWW site at http://www. mips.biochem.mpg.de. The PIR-International Protein Sequence Database and other files are also available by FTP.
Effect of Porcine Small Intestinal Submucosa on Acute Full‐Thickness Wounds in Dogs (2008)

Acute, full-thickness wounds in dogs do not benefit from treatment with PSIS.
Analog timing recovery architectures for PRML detectors (2002)

Analog circuit implementations of decision-directed timing recovery for partial response maximum likelihood (PRML) detectors for disk drives are investigated. First, the basic equations and block diagrams are examined. The parts of the behavioral simulations of the analog system that have significant impact on choosing a topology are discussed. Our results indicate that analog implementations of decision-directed LMS timing recovery are feasible. We anticipate that these implementations will provide higher speed operation at lower power than digital implementations in a comparable technology.
Regulatory RNA as Mediator in GacA/RsmA-Dependent Global Control of Exoproduct Formation in<i>Pseudomonas fluorescens</i>CHA0 (2002)

In Pseudomonas fluorescens CHA0, an antagonist of root-pathogenic fungi, the GacS/GacA two-component system tightly controls the expression of antifungal secondary metabolites and exoenzymes at a posttranscriptional level, involving the RNA-binding protein and global regulator of secondary metabolism RsmA. This protein was purified from P. fluorescens, and RNA bound to it was converted to cDNA, which served as a probe to isolate the corresponding chromosomal locus, rsmZ. This gene encoded a regulatory RNA of 127 nucleotides and a truncated form lacking 35 nucleotides at the 3' end. Expression of rsmZ depended on GacA, increased with increasing population density, and was stimulated by the addition of a solvent-extractable extracellular signal produced by strain CHA0 at the end of exponential growth. This signal appeared to be unrelated to N-acyl-homoserine lactones. A conserved upstream element in the rsmZ promoter, but not the stress sigma factor RpoS, was involved in rsmZ expression. Overexpression of rsmZ effectively suppressed the negative effect of gacS and gacA mutations on target genes, i.e., hcnA (for hydrogen cyanide synthase) and aprA (for the major exoprotease). Mutational inactivation of rsmZ resulted in reduced expression of these target genes in the presence of added signal. Overexpression of rsmA had a similar, albeit stronger negative effect. These results support a model in which GacA upregulates the expression of regulatory RNAs, such as RsmZ of strain CHA0, in response to a bacterial signal. By a titration effect, RsmZ may then alleviate the repressing activity of RsmA on the expression of target mRNAs.
Grundlagen und Entwicklung des Verfahrens zur Trennung der Elemente Zirkonium und Hafnium durch Verteilen ihrer Thiocyanate (1966)

Abstract Die Verteilungsgleichgewichte von Zirkonium‐ und Hafniumthiocyanat zwischen Wasser und Methyl‐isobutyl‐keton werden in Abhängigkeit von verschiedenen Versuchsbedingungen untersucht. Da das System in extremer Weise vom Nernstschen Verteilungssatz abweicht, ist eine weitgehende Trennung der beiden Elemente durch vielstufige Verteilung in einem Arbeitsgang nicht ohne weiteres möglich. Durch geeignete Zusätze und eine neue Art der Phasenführung gelang es jedoch, ein kontinuierliches Verfahren für präparative und technische Zwecke zu entwickeln, mit dem sich mit 23 Mischer‐Absetzern aus einem Zirkonium‐Hafnium‐Gemisch (Hafnium‐Gehalt: 1 bis 2%) ein ZrO 2 ‐Präparat mit < 10 ppm HfO 2 und gleichzeitig ein HfO 2 ‐Präparat mit 0,3% ZrO 2 gewinnen läßt.
Next-Generation Sequence Analysis of Cancer Xenograft Models (2013)

Next-generation sequencing (NGS) studies in cancer are limited by the amount, quality and purity of tissue samples. In this situation, primary xenografts have proven useful preclinical models. However, the presence of mouse-derived stromal cells represents a technical challenge to their use in NGS studies. We examined this problem in an established primary xenograft model of small cell lung cancer (SCLC), a malignancy often diagnosed from small biopsy or needle aspirate samples. Using an in silico strategy that assign reads according to species-of-origin, we prospectively compared NGS data from primary xenograft models with matched cell lines and with published datasets. We show here that low-coverage whole-genome analysis demonstrated remarkable concordance between published genome data and internal controls, despite the presence of mouse genomic DNA. Exome capture sequencing revealed that this enrichment procedure was highly species-specific, with less than 4% of reads aligning to the mouse genome. Human-specific expression profiling with RNA-Seq replicated array-based gene expression experiments, whereas mouse-specific transcript profiles correlated with published datasets from human cancer stroma. We conclude that primary xenografts represent a useful platform for complex NGS analysis in cancer research for tumours with limited sample resources, or those with prominent stromal cell populations.
Seamless Integration of Initial Sketching and Subsequent Detail Editing in Flower Modeling (2006)

Abstract We present an interactive modeling system for flower composition that supports seamless transformation from an initial sketch to a detailed three‐dimensional (3D) model. To begin, the user quickly sketches the overall appearance of the desired model as a collection of two‐dimensional (2D) strokes on hierarchical billboards. Then the user iteratively replaces the coarse sketch with a detailed 3D model referring to the initial sketch as a guide. Since a flower model consists of many repetitive components, the system helps the user to reuse 3D components to facilitate the modeling process. The global view of the entire model is always shown in a separate window to visualize how local modifications affect the global appearance. Our system helps the user make appropriate design decisions to keep the model consistent with the initial design, which is difficult in traditional bottom‐up plant modeling systems in which the global view only emerges after all of the details are specified. Categories and Subject Descriptors (according to ACM CCS): I.3.6 [Computer Graphics]: Methodology and Techniques – Interaction Techniques.
Irritable bladder syndrome in an animal model: A continuous monitoring study (1995)

Irritable bladder syndrome (IBS) was induced in four female African green monkeys (Cercopithecus aethiops) by the use of intravesical instillation of acetone. The animals were housed in a modified metabolic cage for continuous micturition monitoring, and two uroflowmeters connected to a remote PC monitored the frequency, voided volumes, and peak flows. Before and after, urea absorption studies and urodynamics were obtained for each animal. Urea absorption increased significantly after acetone instillation and returned to baseline after 4 weeks (26 to 66 to 32%). Intravesical acetone instillation produced marked effects on bladder physiology in the first week. Bladder compliance dropped from a baseline of 10.47 to 0.58 ml/cm H2O. The voiding pattern changed from a normal pattern with a mean voided volume of 17.58 ml into marked increase in frequency and dribbling pattern with few voids (mean = 5.03 ml). Systematic behavioral observations were carried out for 4 hours per day utilizing an observation program on a laptop computer. Activity patterns, attention, sterotypic behaviors, and self-directed activities were recorded for each monkey. The animals demonstrated decreased frequency of activity and increased frequency in self-directed activities (groom, scratch), behaviors consistent with an animal experiencing pain or discomfort. The findings suggested that IBS induction in monkeys is feasible and produces a clinical picture similar to interstitial cystitis in humans. It offers a suitable animal model to enhance the understanding of voiding dysfunction with its neural pathways and to test the different therapeutic modalities to control IBS.