gebhart/patrepeval huggingface dataset:
Sialic acid-dependent attachment of mucins from three mouse strains to Entamoeba histolytica (2013)

Mouse strain-specific differences in the carbohydrate composition of intestinal mucins were hypothesized to account for strain-dependent susceptibility to Entamoeba histolytica. To test this hypothesis, intestinal mucins from susceptible and resistant inbred strains of mice were analyzed for their O-glycan content and for their ability to inhibit amoebic adherence to (GalNAc)12-27-HSA neo-glycoproteins. The results showed that the colorectal mucin O-glycan of susceptible CBA mice was lower in sialic acid content than that of resistant C57BL/6 and BALB/c mice. Mucins from CBA mice were more potent inhibitors of E. histolytica adherence to neo-glycoproteins than were mucins from C57BL/6 or BALB/c mice. Consistent with the role of terminal Gal/GalNAc as a receptor for amoebic adherence, sialidase treatment of C57BL/6 and BALB/c colorectal mucins increased their ability to inhibit E. histolytica adherence to the neo-glycoproteins. These results provide evidence of mouse strain-specific differences in the sialic acids content of mucin O-glycans. These dissimilarities likely contribute to the differential susceptibility of the three mouse strains to E. histolytica infection.
A Performance Comparison of NFS and iSCSI for IP-Networked Storage (2004)

IP-networked storage protocols such as NFS and iSCSI have become increasingly common in to-day’s LAN environments. In this paper, we exper-imentally compare NFS and iSCSI performance for environments with no data sharing across ma-chines. Our micro- and macro-benchmarking results on the Linux platform show that iSCSI and NFS are comparable for data-intensive work-loads, while the former outperforms latter by a factor of two or more for meta-data intensive workloads. We identify aggressive meta-data caching and aggregation of meta-data updates in iSCSI to be the primary reasons for this perfor-mance difference and propose enhancements to NFS to overcome these limitations. 1
Assessment of plasmid profile, exoenzyme activity, and virulence in recent human isolates of Yersinia enterocolitica (1985)

We examined a group of 23 recent clinical isolates of Yersinia enterocolitica recovered from symptomatic patients residing in the New York, N.Y. area. These isolates were tested for the presence of plasmids, exoenzyme activity, mouse lethality, and phenotypic properties postulated to correlate with virulence. Of the 23 isolates, 17 harbored a 60- to 65-kilobase (kb) plasmid. Six isolates were lethal for white mice, showed the phenotypic markers of autoagglutination and calcium dependence for growth at 37 degrees C, and contained a 60- to 65-kb plasmid. Restriction endonuclease analysis with several different enzymes revealed the presence of three distinct plasmid profiles in these isolates. Isolates with a single plasmid of 60 to 70 kb, typical for this species, were detected, but these were of three distinct types as judged from restriction enzyme digestion. One strain was unusual among clinical isolates of Y. enterocolitica in that it contained at least four distinct plasmids. In addition, this nontypable strain showed exoenzymatic activity similar to that of serogroup O8 isolates, was not lethal to mice, and did not require calcium for growth at 37 degrees C.
Dependence of Pharmacokinetics and Biodistribution on Polymer Architecture: Effect of Cyclic versus Linear Polymers (2009)

The ability of a polymer to reptate through a nanopore has an influence on its circulatory half-life and biodistribution, since many physiological barriers contain nanopores. A cyclic polymer lacks chain ends, and therefore, cyclic polymers with molecular weights greater than the renal threshold for elimination should circulate longer than their linear-polymer counterparts when injected into animals. As predicted, radiolabeled cyclic polymers with molecular weights greater than the renal threshold have longer blood circulation times in mice than do linear polymers of comparable molecular weight.
Study on the Effect of Contrast Agent on Biofilms and Their Visualization in Porous Substrate Using X-ray μCT (2020)

Investigation of biofilms and visualization using non-destructive imaging techniques like X-ray μCT has recently gained interest. Biofilms are congregations of microorganisms that attach to surfaces and comprise of microbial cells embedded in extracellular polymeric substances (EPS). They are ubiquitous entities that are commonly found in any non-sterile setting and have direct implications on human health. Methods to visualize them in-situ are highly needed to understand their behaviour (attachment and detachment) inside a substrate. Contrast-enhanced X-ray μCT is a 3D imaging technique that is capable of visualising objects that have very low attenuation contrast. The use of contrast agents in X-ray μCT has been an evolving process, however, the possible toxic effect of these chemical compounds against biofilms has not been studied in detail. In this study, we focus on the toxic effect of contrast agents and study the diffusion and drainage of contrast agents in biofilms. We propose using water-soluble potassium bromide (KBr) as a suitable contrast agent for enhancement of the attenuation coefficient of a monoculture of Pseudomonas fluorescens biofilms inside a porous substrate. At the given concentration, KBr proved to be less bactericidal compared to other commonly used contrast agents and at 5% w/v concentration we were able to clearly distinguish between the biofilm and the porous substrate.
Electrically Robust Metal Nanowire Network Formation by In-Situ Interconnection with Single-Walled Carbon Nanotubes (2014)

Modulation of the junction resistance between metallic nanowires is a crucial factor for high performance of the network-structured conducting film. Here, we show that under current flow, silver nanowire (AgNW) network films can be stabilised by minimizing the Joule heating at the NW-NW junction assisted by in-situ interconnection with a small amount (less than 3 wt%) of single-walled carbon nanotubes (SWCNTs). This was achieved by direct deposition of AgNW suspension containing SWCNTs functionalised with quadruple hydrogen bonding moieties excluding dispersant molecules. The electrical stabilisation mechanism of AgNW networks involves the modulation of the electrical transportation pathway by the SWCNTs through the SWCNT-AgNW junctions, which results in a relatively lower junction resistance than the NW-NW junction in the network film. In addition, we propose that good contact and Fermi level matching between AgNWs and modified SWCNTs lead to the modulation of the current pathway. The SWCNT-induced stabilisation of the AgNW networks was also demonstrated by irradiating the film with microwaves. The development of the high-throughput fabrication technology provides a robust and scalable strategy for realizing high-performance flexible transparent conductor films.
Investigation of a failed DNA assay leads to identification of an unexpected contaminant in a commonly used chromatography buffer (2022)

For mammalian cell-derived recombinant biotherapeutics, controlling host cell DNA levels below a threshold is a regulatory requirement to ensure patient safety. DNA removal during drug substance manufacture is accomplished by a series of chromatography-based purification steps and a qPCR-based analytical method is most used to measure DNA content in the purified drug substance to enable material disposition. While the qPCR approach is mature and its application to DNA measurement is widespread in the industry, it is susceptible to trace levels of process-related contaminants that are carried forward. In this study, we observed failures in spike recovery studies that are an integral component of the qPCR-based DNA testing, suggesting the presence of an inhibitory compound in the sample matrix. We generated hypotheses around the origin of the inhibitory compound and generated multiple sample matrices and deployed a suite of analytical techniques including Raman and NMR spectroscopy to determine the origin and identity of the inhibitory compound. The caustic wash step and depth filter extractables were ruled out as root causes after extensive experimentation and DNA testing. Subsequently, 2-(N-morpholino)ethanesulfonic acid (MES), a buffer used in the chromatography unit operations, was identified as the source of the contaminant. A 500-fold concentration followed by Raman and NMR spectroscopy analysis revealed the identity of the inhibitory compound as polyvinyl sulfone (PVS), an impurity that originates in the MES manufacturing process. We have implemented PVS concentration controls for incoming MES raw material, and our work highlights the need for rigor in raw material qualification and control.
WormBase 2012: more genomes, more data, new website (2011)

Since its release in 2000, WormBase (http://www.wormbase.org) has grown from a small resource focusing on a single species and serving a dedicated research community, to one now spanning 15 species essential to the broader biomedical and agricultural research fields. To enhance the rate of curation, we have automated the identification of key data in the scientific literature and use similar methodology for data extraction. To ease access to the data, we are collaborating with journals to link entities in research publications to their report pages at WormBase. To facilitate discovery, we have added new views of the data, integrated large-scale datasets and expanded descriptions of models for human disease. Finally, we have introduced a dramatic overhaul of the WormBase website for public beta testing. Designed to balance complexity and usability, the new site is species-agnostic, highly customizable, and interactive. Casual users and developers alike will be able to leverage the public RESTful application programming interface (API) to generate custom data mining solutions and extensions to the site. We report on the growth of our database and on our work in keeping pace with the growing demand for data, efforts to anticipate the requirements of users and new collaborations with the larger science community.
Hereditary pancreatic cancer (2011)

Alias: Familial pancreatic cancer Inheritance It has been estimated that as many as 10% of pancreatic cancers have a hereditary basis; five genetic syndromes have been identified that are associated with the familial aggregation of pancreatic cancer; these include: The second breast cancer syndrome (BRCA2), the familial atypical multiple mole melanoma (FAMMM), the Peutz-Jeghers Syndrome, the hereditary pancreatitis and the hereditary non-polyposis colorectal cancer (HNPCC) syndrome. Most kindreds with familial pancreatic cancer, however, do not fall into one of these well-defined syndromes and these are referred to simply as family pancreatic cancer.
ChemInform Abstract: OXIDATION OF SUBSTITUTED AROMATIC COMPOUNDS BY PEROXYDISULFATE. HOMOLYTIC BENZYLATION AND OXIDATIVE COUPLING REACTION (1981)

Abstract Während bei der Behandlung des Methoxytoluols (Ia) mit Peroxydisulfat/Ag(I) in Gegenwart von protoniertem Isochinolin (II) bzw. Chinolin (IV) eine homolytische Benzylierung unter Bildung der Produkte (III) bzw. (Va) + (V b) erfolgt, wird mit dem Dimethoxytoluol (Ib) nur das Kupplungsprodukt (VI) erhalten (Darstellung in 65proz. Ausb. durch Reaktion von (Ib) bei Abwesenheit von (II)).
(Dimesityl)boron Benzodithiophenes: Synthesis, Electrochemical, Photophysical and Theoretical Characterization (2022)

Triarylboranes containing linear or angular benzodithiophene moieties and bearing one or two dimesitylboron units were synthesized. The electrochemical and optical features of these compounds were investigated by cyclic voltammetry, UV/Vis and fluorescence spectroscopy while DFT calculations were run to analyze the energetic landscape of these systems. For both linear and angular benzodithiophenes, symmetrical disubstitution leads to the highest photoluminescence yields. The linear benzodithiophene disubstituted with two dimesitylboron units proved to be the most interesting and promising molecule as an electron-transport material for organic electronics owing to its LUMO energy level of -2.84 eV which is close to those of commonly used electron transport materials like bathocuproine or bathophenantroline.
Stability of commonly nebulized drugs in heated and humid condition (2018)

Placement of nebulizer prior to heated humidifier has been reported to improve efficiency of aerosol delivery during ventilator support. Drugs nebulized in this position must travel through humidifier, rainout in reservoir and may be subjected to extended periods of heat up to 50&#xb0;C. Toxic degradation may develop, posing potential risk to patient. The aim of this study was to evaluate chemical stability of commonly inhaled drugs administered to mechanically ventilated patients subjected to extended period of 50&#xb0;C. Formulations of 8 comonly inhaled drugs were diluted to 50 mL total volume in water and exposed to 50oC for 7 days to simulate effect of heat in humidifier. High Performance Liquid Chromatography (HPLC) was performed before and after heating to determine drug stability and degradation. Drug integrity, color or pH changes were noted. Epinephrine, levalbuterol, tobramycin and colistin demonstrated&gt;10% reduction in concentration but only acetylcysteine had additional peaks in HPLC chromatogram demonstrating potential degradation and possible production of by product. Changes in color were observed with epinephrine and acetylcysteine. All drugs retained their integrity after subjecting them to 50oC for 7 days except acetylcysteine. Acetylcysteine changed color and had new peak in HPLC chromatogram. Color change with epinephrine was not associated with any new peak in HPLC chromatogram. Further studies should determine whether acetylcysteine changes would result in any off gassing of vapor that might harm the patient. [Med-Science 2018; 7(2.000): 269-76]
Applications of PCR in the Diseases of Genetic Isolates (1992)

(1992). Applications of PCR in the Diseases of Genetic Isolates. Annals of Medicine: Vol. 24, No. 3, pp. 191-194.
Expression array annotation using the BioMediator biological data integration system and the BioConductor analytic platform. (2003)

This paper presents the implementation of a model for expression array annotation (EAA) using the BioMediator biological data integration system along with BioConductor, an analytic tools platform. The model presented addresses the need for annotation sources identified during BioConductor inverted exclamation mark s development. Annotation provides us with well-curated genomic background knowledge for expression array analysis and interpretation. Annotation requests are constructed and posted to the query interface of the EAA package (the EAA model implemented as a component of BioConductor). The software enumerates all possible annotation paths for queries. These are then transformed to PQL queries and processed by BioMediator. Annotation entities returned from the EAA package answer the annotation request.
High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping (2006)

Array-CGH is a powerful tool for the detection of chromosomal aberrations. The introduction of high-density SNP genotyping technology to genomic profiling, termed SNP-CGH, represents a further advance, since simultaneous measurement of both signal intensity variations and changes in allelic composition makes it possible to detect both copy number changes and copy-neutral loss-of-heterozygosity (LOH) events. We demonstrate the utility of SNP-CGH with two Infinium whole-genome genotyping BeadChips, assaying 109,000 and 317,000 SNP loci, to detect chromosomal aberrations in samples bearing constitutional aberrations as well tumor samples at sub-100 kb effective resolution. Detected aberrations include homozygous deletions, hemizygous deletions, copy-neutral LOH, duplications, and amplifications. The statistical ability to detect common aberrations was modeled by analysis of an X chromosome titration model system, and sensitivity was modeled by titration of gDNA from a tumor cell with that of its paired normal cell line. Analysis was facilitated by using a genome browser that plots log ratios of normalized intensities and allelic ratios along the chromosomes. We developed two modes of SNP-CGH analysis, a single sample and a paired sample mode. The single sample mode computes log intensity ratios and allelic ratios by referencing to canonical genotype clusters generated from approximately 120 reference samples, whereas the paired sample mode uses a paired normal reference sample from the same individual. Finally, the two analysis modes are compared and contrasted for their utility in analyzing different types of input gDNA: low input amounts, fragmented gDNA, and Phi29 whole-genome pre-amplified DNA.
Synthesis of Biodegradable Hydrogel Nanoparticles for Bioapplications Using Inverse Miniemulsion RAFT Polymerization (2011)

We report the synthesis of biodegradable hydrogel nanoparticles using a RAFT inverse miniemulsion cross-linking polymerization process with 2-(dimethylamino)ethyl methacrylate (DMAEMA) as monomer. The experimental conditions were optimized to yield a colloidally stable miniemulsion polymerization, which required protonation of DMAEMA using aqueous hydrogen chloride to ensure minimal partitioning to the continuous phase (cyclohexane). The nanoparticles were cross-linked using a disulfide cross-linker, thereby enabling subsequent degradation of the polymer network to its constituent primary chains by exposure to a reductive environment. The molecular weight distributions of the constituent primary chains were consistent with satisfactory control/livingness during the polymerization. These biodegradable hydrogel nanoparticles may have potential application as nanocarriers for encapsulation and controlled release of siRNA.
Posttranslational modifications of the β subunit of a cryptomonad phycoerythrin (1989)

Determination of the partial amino acid sequence of the beta subunit of cryptomonad strain CBD phycoerythrin 566 established the nature, locations, and modes of attachment of the three bilin prosthetic groups and revealed a site of posttranslational methylation. Isolation of peptides cross-linked by a phycobiliviolin led to an unambiguous assignment of two thioether linkages, from residues beta-Cys-50 and beta-Cys-61 to this bilin. Two bilins were attached through single thioether linkages, a phycobiliviolin at beta-Cys-158 and a phycoerythrobilin at beta-Cys-82 (the residue numbering is that for B-phycoerythrin; Sidler, W., Kumpf, B., Suter, F., Morisset, W., Wehrmeyer, W., and Zuber, H. (1985) Biol. Chem. Hoppe-Seyler 366, 233-244). The partial sequences (99 residues) established for phycoerythrin 566 beta subunit showed a 79% identity with that of the red algal Porphyridium cruentum B-phycoerythrin beta subunit. A particularly remarkable finding is that the unique methylasparagine residue at position beta-72, highly conserved in cyanobacterial and red algal phycobiliproteins (Klotz, A. V., and Glazer, A. N. (1987) J. Biol. Chem. 262, 17350-17355), is also present at beta-72 in the cryptomonad phycoerythrin. Comparison of the locations of donor and acceptor bilins in cryptomonad phycoerythrin with those found for cyanobacterial and red algal phycobiliproteins showed different favored pathways of energy migration in the cryptomonad protein.
Evaluation on Relaxation Behaviors of Compressive Residual Stress of Peened Ni-Base Superalloy Alloy 706 Test Specimens after Thermal Aging Treatment (2016)

The operating lifetime of the components made of a large-scale forged material, such as the power generating components in a thermal power plant, is influenced by the initiation of defects such as cracks. Peening is known to be effective for the improvement of fatigue strength and the prevention of the stress corrosion cracking initiation. Shot peening that generates compressive residual stress on the material surface is applied to the stress concentration region of the high-strength large-scale forged material in order to relax the tensile stress, prevents crack initiation and extends operation lifetime. To confirm the durability of the compressive residual stress generated by peening, the influence of thermal aging treatment on the compressive residual stress is evaluated. As a result, it is reported that compression is maintained though compressive residual stress relaxes. The purpose of this study is to develop evaluation method of the relaxation behavior of residual stress generated by shot peening and laser peening during actual plant operations. Shot peening and laser peening were performed on the specimens of Ni-base superalloy Alloy 706, which is used as the material of the discs of gas turbines, and the thermal aging treatment test was performed. It shows that the compressive residual stress decreases to an elastic limit after heating and then relaxes due to creep strain generation. It is found that residual stress was almost determined by the residual stress just after heating.
Photoreprogrammable dual-function grating based on photochromism and selective metal deposition (2011)

We introduce photoreprogrammable dual-function gratings, which show different diffraction in transmission and reflection. Parallel metal lines on the photochromic diarylethene (DAE) surface were prepared by selective metal deposition, enabling one-dimensional diffraction in transmission and reflection. Then, another isomerization pattern was programmed on the DAE layer by light irradiation. This grating generated unique diffraction: one-dimensional diffraction in the reflection but two-dimensional diffraction in the transmission, and a dual-function grating was achieved. This programmed state on the DAE layer could be erased by UV irradiation and could be reprogrammed to generate different diffraction by visible laser scanning. This result shows the great potential of the photoreprogrammable dual-function grating as a key element in various future optical devices and systems.
Comparison of conventional acoustic and MIR radar/acoustic processing of speech signals (1997)

Applications of the micropower impulse radar (MIR) to speech research at the Lawrence Livermore National Laboratory has produced potentially new methods of speech processing. They include the accurate calculation of vocal tract transfer functions, formant, and pitch analysis, and basic phoneme synthesis. These speech parameters have traditionally been in the realm of all-pole LPC calculations. Related research using the MIR radar has supplied an increasingly accurate voiced excitation function, which makes possible transfer function calculations using both poles and zeros, yielding more accurate formant information and more natural sounding synthesis. This paper compares the newly obtained results with traditional LPC and cepstral approaches and demonstrates the improvements based on experimental data from several male and female subjects. The radar data also allow extremely accurate pitch tracking, which is simpler and more robust than that calculated by traditional means. This information can significantly enhance acoustic-based speech processing by allowing pitch adaptive processing.