gebhart/patrepeval huggingface dataset:
Characterization of Pro-Inflammatory Flagellin Proteins Produced by Lactobacillus ruminis and Related Motile Lactobacilli (2012)

Lactobacillus ruminis is one of at least twelve motile but poorly characterized species found in the genus Lactobacillus. Of these, only L. ruminis has been isolated from mammals, and this species may be considered as an autochthonous member of the gastrointestinal microbiota of humans, pigs and cows. Nine L. ruminis strains were investigated here to elucidate the biochemistry and genetics of Lactobacillus motility. Six strains isolated from humans were non-motile while three bovine isolates were motile. A complete set of flagellum biogenesis genes was annotated in the sequenced genomes of two strains, ATCC25644 (human isolate) and ATCC27782 (bovine isolate), but only the latter strain produced flagella. Comparison of the L. ruminis and L. mali DSM20444(T) motility loci showed that their genetic content and gene-order were broadly similar, although the L. mali motility locus was interrupted by an 11.8 Kb region encoding rhamnose utilization genes that is absent from the L. ruminis motility locus. Phylogenetic analysis of 39 motile bacteria indicated that Lactobacillus motility genes were most closely related to those of motile carnobacteria and enterococci. Transcriptome analysis revealed that motility genes were transcribed at a significantly higher level in motile L. ruminis ATCC27782 than in non-motile ATCC25644. Flagellin proteins were isolated from L. ruminis ATCC27782 and from three other Lactobacillus species, while recombinant flagellin of aflagellate L. ruminis ATCC25644 was expressed and purified from E. coli. These native and recombinant Lactobacillus flagellins, and also flagellate L. ruminis cells, triggered interleukin-8 production in cultured human intestinal epithelial cells in a manner suppressed by short interfering RNA directed against Toll-Like Receptor 5. This study provides genetic, transcriptomic, phylogenetic and immunological insights into the trait of flagellum-mediated motility in the lactobacilli.
Zinc Mesoporphyrin Represses Induced Hepatic 5–Aminolevulinic Acid Synthase and Reduces Heme Oxygenase Activity in A Mouse Model of Acute Hepatic Porphyria (2001)

Zinc mesoporphyrin (ZnMP) is a potent inhibitor of heme oxygenase (HO) and represses 5-aminolevulinic acid synthase (ALAS). These properties make it a potential candidate for treatment of inducible acute hepatic porphyrias, diseases characterized by neurovisceral symptoms, and massive ALAS induction. Effects of intraperitoneal ZnMP (2.5-10 micromol/kg/d) and heme arginate (3-6 mg/kg/d) on plasma levels of 5-aminolevulinic acid (ALA), on messenger RNA (mRNA), and activity of hepatic ALAS and HO were studied in porphobilinogen deaminase-deficient mice treated with phenobarbital (100 mg/kg/d) to induce ALAS. ZnMP (5 micromol/kg/d) led to a significant reduction of plasma ALA levels to 31% of controls (P < .01) by lowering the activity of hepatic mitochondrial and cytosolic ALAS to 29% and 25% of controls, respectively (P < .03). ZnMP decreased the mRNA levels of hepatic ALAS to 53% (P < .03) of controls and this repression was more pronounced than that achieved with heme arginate. In contrast to heme arginate, ZnMP led to a significant reduction of HO activity. We conclude that the combined effect of ZnMP on highly induced ALAS and on HO may be of potential benefit for human acute hepatic porphyrias and therefore merits further in vivo investigations addressing questions raised by this study.
α-Complementation-Enabled T7 Expression Vectors and Their Use for the Expression of Recombinant Polypeptides for Protein Transduction Experiments (2004)

Over the past few years protein transduction has emerged as a powerful means for the delivery of proteins into cultured cells and into whole mice. This method is based on the ability of proteins containing protein transduction domains (PTDs), short stretches of 9-16 predominantly basic amino acids, to traverse the cytoplasmic membrane and accumulate inside cells in a time- and dose-dependent fashion. The number of PTDs, both natural and synthetic, is constantly expanding, as is the need to test newly discovered PTDs for their ability to mediate the internalization of the corresponding fusion proteins. Here we describe a strategy and methodology that can be used for the construction of vectors for the T7 RNA polymerase-driven expression of PTD fusions. The cloning in these vectors is facilitated by alpha-complementation. Also, these vectors are small in size (less than 3 kbp) and express influenza virus hemagglutinin tag as well as His tag as part of the fusion for immunological identification and purification respectively of expressed proteins.
Genome Diversity of Pseudomonas aeruginosa PAO1 Laboratory Strains (2009)

Pseudomonas aeruginosa PAO1 is the most commonly used strain for research on this ubiquitous and metabolically versatile opportunistic pathogen. Strain PAO1, a derivative of the original Australian PAO isolate, has been distributed worldwide to laboratories and strain collections. Over decades discordant phenotypes of PAO1 sublines have emerged. Taking the existing PAO1-UW genome sequence (named after the University of Washington, which led the sequencing project) as a blueprint, the genome sequences of reference strains MPAO1 and PAO1-DSM (stored at the German Collection for Microorganisms and Cell Cultures [DSMZ]) were resolved by physical mapping and deep short read sequencing-by-synthesis. MPAO1 has been the source of near-saturation libraries of transposon insertion mutants, and PAO1-DSM is identical in its SpeI-DpnI restriction map with the original isolate. The major genomic differences of MPAO1 and PAO1-DSM in comparison to PAO1-UW are the lack of a large inversion, a duplication of a mobile 12-kb prophage region carrying a distinct integrase and protein phosphatases or kinases, deletions of 3 to 1,006 bp in size, and at least 39 single-nucleotide substitutions, 17 of which affect protein sequences. The PAO1 sublines differed in their ability to cope with nutrient limitation and their virulence in an acute murine airway infection model. Subline PAO1-DSM outnumbered the two other sublines in late stationary growth phase. In conclusion, P. aeruginosa PAO1 shows an ongoing microevolution of genotype and phenotype that jeopardizes the reproducibility of research. High-throughput genome resequencing will resolve more cases and could become a proper quality control for strain collections.
FRACTURE MECHANICS APPLICATIONS TO DRILLING AND BLASTING (1997)

Abstract— This paper gives a brief review of research in rock fracture mechanics as conducted at the Fracture and Photo‐Mechanics Laboratory (FPML) at Vienna University of Technology. The mechanisms pertaining to percussion drilling and blasting are investigated, with specific reference to the application of fracture mechanics. In order to gain an improved understanding of the mechanisms controlling rock fragmentation, a multidisciplinary approach is followed which includes laboratory experiments conducted in plexiglass and rock, in‐situ field experiments and analytical/numerical modelling techniques. Field experiments revealed that percussively drilled holes exhibit a very shallow region of damaged rock. An analytical model to simulate damage accumulation and crack initiation due to elastic waves generated by impacting drill bits was developed. This model, based on damage and fracture mechanics, was incorporated into a numerical finite difference code. Fracture and damage mechanics parameters are related to the moment tensor which is determined experimentally by means of acoustic emission. Small scale model blasts were used to investigate the blast‐induced fractures in the near‐borehole zone as well as in the far field. Analytical and numerical investigations give insight into stress wave and gas driven fracturing. The applicability of the dynamic finite difference program SWIFD to the interaction between stress waves and cracks is illustrated.
Somatic antigens of Haemophilus influenzae as vaccine components (1989)

MURPHY, TIMOTHY F. MD; CAMPAGNARI, ANTHONY A. PHD; NELSON, M. BUD PHD; APICELLA, MICHAEL A. MD Author Information
Synthesis and peptide bond orientation in tetrapeptides containing L‐azetidine‐2‐carboxylic acid and L‐proline (1990)

The role of the amino acid proline in influencing the secondary and tertiary structure of proteins and polypeptides has been an area of active study for many years. We have investigated this problem by incorporating the four-membered ring amino acid, azetidine-2-carboxylic acid, into some proline polypeptides. An adjunct to the synthesis of the peptides was the synthesis of azetidine-2-carboxylic acid and its resolution. We developed an improved synthesis of N-benzhydryl-2-carbobenzyloxy azetidine, an essential intermediate required for the synthesis of L-azetidine-2-carboxylic acid. This amino acid was subsequently obtained via the partial hydrogenation of the N-benzhydryl compound, under mild conditions. Our ability to isolate the intermediate N-benzhydryl-2-carboxylic acid demonstrated that the rate of cleavage of the O-benzyl ester group in this molecule is faster than the cleavage of the N-benzhydryl group. The tetrapeptides, Boc-(L-Pro)3-L-Aze-Opcp, and Boc-(L-Aze-L-Pro)2-Opcp (Boc: t-butoxycarbonyl; Pro: proline; Aze: azetidine-2-carboxyl acid; Opcp: pentachlorophenyl), were prepared using traditional solution peptide synthesis. They were characterized by direct chemical ionization-mass spectrometry, CD spectra, and 13C- and 1H-nmr spectroscopy. The assessment of the secondary structure of the two peptides using the methods noted above has led us to conclude that the compound Boc-(L-Aze-L-Pro)2-Opcp, in trifluoroethanol, has an all-cis peptide bond conformation with phi and psi torsion angles compatible with a left-handed helix. The secondary structure assessment of the peptide Boc-(L-Pro)3-L-Aze-Opcp, in chloroform or trifluoroethanol, leads to an assignment of both cis and trans peptide bonds as being present in the peptide. We have interpreted this latter finding as indicating that the introduction of the azetidine group into a peptide containing three consecutive proline residues in a linear sequence perturbs the normal proline peptide secondary structure in this tetrapeptide.
An Integrated μLED Optrode for Optogenetic Stimulation and Electrical Recording (2012)

In this letter, we developed an integrated neural probe prototype for optogenetic stimulation by microscale light-emitting diode (μLED) and simultaneous recording of neural activities with microelectrodes on a single-polyimide platform. Optogenetics stimulates in vivo neural circuits with high-cellular specificity achieved by genetic targeting and precise temporal resolution by interaction of light-gated ion channels with optical beam. In our newly developed optrode probe, during optogenetic stimulation of neurons, continuous sensing of neuronal activities in vicinity of the activation site can provide feedback to stimulation or examine local responses in signal pathways. In the device, focusing the light from the μLED was achieved with an integrated photo-polymerized lens. The efficacy of the optrode for cortical stimulation and recording was tested on mice visual cortex neurons expressing channelrhodopsin-2. Stimulation intensity and frequency-dependent spiking activities of visual cortex were recorded. Our device has shown advantages over fiber-coupled laser-based optrode in terms of closed-loop integration, single-implant compactness and lower electrical power requirements, which would be clinically applicable for future prosthetic applications in personalized medicine.
Triplex formation inhibits HER-2/neu transcription in vitro. (1993)

Triplex-forming oligonucleotides (TFOs) have been shown to bind to target DNA sequences in several human gene promoters such as the c-myc oncogene, the epidermal growth factor receptor, and the dihydrofolate reductase genes. TFOs have been shown to inhibit transcription in vitro and gene expression in cell culture of the c-myc and other genes. The HER-2/neu oncogene, which is overexpressed in breast cancer and other human malignancies, contains a purine-rich sequence in its promoter, which is favorable for purine:purine:pyrimidine (R:R:Y) triplex formation. Although its function in the HER-2/neu promoter is unknown, this purine-rich site is homologous to a protein-binding sequence in the promoter of the epidermal growth factor receptor that is necessary for efficient transcription of this gene. We have shown that this sequence is a site for nuclear protein binding by incubation with a crude nuclear extract. We describe the formation of an interstrand triplex using a purine-rich oligonucleotide antiparallel to this purine-rich target sequence of the HER-2/neu promoter. Triplex formation by the oligonucleotide prevents protein binding to the target site in the HER-2/neu promoter in vitro. We have shown that this oligonucleotide is a potent and specific inhibitor of HER-2/neu transcription in an in vitro assay. The triplex target site contains a single pyrimidine base that does not conform to the R:R:Y triplex motif. In an attempt to abrogate the potentially destabilizing effects of this pyrimidine base on triplex formation, we have substituted an abasic linker for the pyrimidine residue in the triplex forming oligonucleotide. Triplex formation with the modified oligonucleotide appears to occur with approximately equivalent binding affinity. Triplex formation in the HER-2/neu oncogene promoter prevents transcription in vitro and may represent a future modality for specific inhibition of this gene in vivo.
The Immunosuppressive Properties of the HIV Vpr Protein Are Linked to a Single Highly Conserved Residue, R90 (2009)

This study supports Vpr as an HIV virulence factor during HIV infection and for the first time provides a link between evolutionary conservation of Vpr and its ability to suppress IL-12 secretion by DC. DC activated in the presence of Vpr would be defective in the production of IL-12, thus contributing to the prevailing Th2 cytokine profile associated with progressive HIV disease. These findings should be considered in the design of future immunotherapies that incorporate Vpr as an antigen.
Parkinson's Disease: Activity of L-Dopa Decarboxylase in Discrete Brain Regions (1970)

The activity of L-dopa decarboxylase was greatly reduced in the striatum, less so in the hypothalamus, and unchanged in the cortex of brains of patients with Parkinson's disease. However, it appears that even in the striatum enough activity remained to allow for the formation of dopamine from L-dopa in patients treated with large doses of L-dopa.
Versatile fabrication of arbitrarily shaped multi-membrane hydrogels suitable for biomedical applications (2012)

In this work, arbitrarily shaped multi-membrane hydrogels were successfully fabricated from gel-core templates using the layer-by-layer (LbL) method. Namely, the first gel membrane layer was formed around a gel-core template when the crosslinker loaded gel-core was soaked in a polysaccharide solution, and it was then ripened in a crosslinker solution, in which the crosslinker was loaded for the fabrication of the following layer. The formation and control of the gel membrane layer were studied in detail. The results indicated that a reasonably rapid crosslinking of the polysaccharide was essential for the successful preparation of a multi-membrane hydrogel, irrespective of chemical or physical crosslinking. The formation of a gel membrane layer was found to be controlled by the diffusion of the crosslinker. The chemically and the physically crosslinked multi-membrane hydrogels were characterized, and the chemically crosslinked chitosan multi-membrane hydrogel exhibited a unique sub-layered microstructure. The chitosan multi-membrane hydrogel which was sensitive to pH was fabricated using terephthalaldehyde as the crosslinker, and the hydrogel displayed LbL disintegration in acidic medium. Chondrocytes were cultivated in the presence of the multi-membrane hydrogel, and they could be easily attached to proliferate quickly. Because of the arbitrary shape, solid or hollow structure, pH sensitivity and biocompatibility, the polysaccharide multi-membrane hydrogels are promising materials for biomedical applications.
Glucosinolates, structures and analysis in food (2010)

Glucosinolates (GLS) are sulfur rich, anionic secondary metabolites found principally in the plant order Brassicales. This review focuses on identifying the range of GLS structures identified to date and summarises the current state of taxonomic reclassifications of GLS producing plants. Those Brassica species that are available to growers in the UK are highlighted and progress in the aspects of analytical chemistry relevant to conducting accurate determinations of GLS content of foods is reviewed. The degradation and derivatisation workflows that have been utilized for conducting “glucosinolate analysis” are summarized. A review is made of aspects of extraction, isolation, determination of purity, ultraviolet (UV) and mass spectrometry (MS) parameters, extinction coefficients, UV response factors, quantification procedures, and the availability of stable isotope labeled internal standards, and certified reference materials. An electronic database of structures, formulae and accurate masses of both the 200 known, and a further 180 predicted GLS, is provided for use in mass spectrometry.
Preservation of Basal Inner Ear Structures in Cochlear Implantation (2004)

The aim of this report was to examine basal trauma in implanted human temporal bones and discuss modified approaches to the basal cochlear turn to avoid destruction of basal cochlear structures. Thirty-three human temporal bones were implanted with four different cochlear implant electrode arrays manufactured by MED-EL using either a caudal approach cochleostomy or round window membrane insertions. All specimens were processed with a special histological technique that allows sectioning of undecalcified bone with the electrode in situ. All bones were evaluated histologically in terms of basal cochlear trauma. Two pathomechanisms of basal trauma could be distinguished and were evaluated separately, buckling of the basal end of the array and trauma by drilling. Using the caudal approach cochleostomy, the total percentage of destructive basal trauma was 48% compared to less than 15% when performing round window membrane insertions. Although it is still unclear whether basal cochlear trauma influences apical cochlear function or not, adapted surgical procedures and no forceful insertion maneuvers should be used when performing cochlear implantations with hearing preservation.
A Configurable Pixel Cache for Fast Image Generation (1987)

This article describes an approach to fast image generation that uses a high-speed serial scan converter, a somewhat slower frame buffer, and a pixel cache to match the bandwidth between the two. Cache hit rates are improved by configuring the cache to buffer either 4 × 4 or 16 × 1 tiles of frame memory, depending on the type of operation being performed. For line drawing, the implenmention discribed can process 300,000 30-pixel vectors per second. For shaded polygons, the system can fill 16,000 900-pixel polygons per second. In addition to buffering pixel intensity data, the pixel cache also buffer z (depth) values, improving the performance of the z-buffer hidden-surface algorithm. By utilizing z-value caching, the system can process 5800 900-pixel shaded polygons per second with hidden-surface removed.
Software transactional memory (1995)

As we learn from the literature, flexibility in choosing syn-chroni~ation operations greatly simplifies the task of designing highly concurrent programs.Unfortunately,
Efficient excitation transfer from polymer to nanocrystals (2004)

We quantify experimentally the efficiency of excitation transfer from a semiconducting polymer matrix to quantum dot nanocrystals. We study 5±0.5 nm PbS nanocrystals embedded in MEH-PPV (poly[2-methoxy-5-(2′-ethylhexyloxy-p-phenylenevinylene)]) polymer. We determine the excitation transfer efficiency from normalized photoluminescence excitation measurements. When the composites are made using as-synthesized PbS nanocrystals capped by oleate ligands, the excitation transfer efficiency is about 20%. Replacing these ligands with shorter chains results in a factor-of-3 enhancement in the excitation transfer efficiency. Our findings provide guidance to the realization of efficient electroluminescent devices.
Prehospital management of severe traumatic brain injury (2009)

#### Summary points

#### Sources and selection criteria

We searched Medline 1980-2008, Pubmed and the Cochrane library for clinical trials and reviews. The medical subject headings “head injury”, “brain injury”, “trauma”, “prehospital”, and combinations thereof were used. Individual therapeutic options (such as “mannitol”) were also searched for. Search results were individually reviewed and manually cross referenced. Reference lists were searched for additional works. Priority was given to review articles, meta analyses, and well designed large trials. The websites www.braintraumafoundation.org, www.trauma.org, and www.east.org were also searched for additional information.

Traumatic brain injury is a substantial cause of morbidity and mortality in the UK. An estimated 11 000 people per year sustain a severe traumatic brain injury, mostly between ages 15 and 29 years.1 Patients with severe traumatic brain injury have a high mortality rate (30-50%) and many survivors will have persistent severe neurological disability.2 Prompt identification and appropriate early management of traumatic brain injury is essential to optimise outcome, however, few guidelines are available for clinicians on management in the challenging prehospital environment. The 2007 report by the national enquiry into patient outcome and death on the provision of trauma services in the UK3 highlighted concerns about prehospital management of airways and …
Jitter in synchronous residual time stamp (1996)

This paper presents jitter characteristics of synchronous residual time stamp (SRTS) used in ATM adaptation layer (AAL) type 1. It is pointed out that low frequency jitter appears at the receiver output of SRTS, similar to pulse stuffing synchronization. The jitter waveform in the SRTS is presented together with its Fourier series representation, and the low frequency jitter amplitude is determined. There is a parameter called the residue that plays the same role as the stuffing ratio in pulse stuffing synchronization, where the low frequency jitter amplitude exhibits a peak when the residue is a rational number. It is shown that the jitter waveform and the low frequency jitter amplitude are somewhat different from those obtained by the analog with pulse stuffing synchronization. The dependencies of the low frequency jitter amplitude to some parameters are also considered. It appears that the higher the reference frequency, the smaller the resulting low frequency jitter amplitude. Some numerical examples are given to demonstrate the validity of the analysis.