gebhart/patrepeval huggingface dataset:
Shiga toxins and stx phages: highly diverse entities (2014)

Shiga toxins are the main virulence factors of a group of Escherichia coli strains [Shiga toxin-producing E. coli (STEC)] that cause severe human diseases, such as haemorrhagic colitis and haemolytic-uraemic syndrome. The Shiga toxin family comprises several toxin subtypes, which have been differentially related to clinical manifestations. In addition, the phages that carry the Shiga toxin genes (stx phages) are also diverse. These phages play an important role not only in the dissemination of Shiga toxin genes and the emergence of new STEC strains, but also in the regulation of Shiga toxin production. Consequently, differences in stx phages may affect the dissemination of stx genes as well as the virulence of STEC strains. In addition to presenting an overview of Shiga toxins and stx phages, in this review we highlight current knowledge about the diversity of stx phages, with emphasis on its impact on STEC virulence. We consider that this diversity should be taken into account when developing STEC infection treatments and diagnostic approaches, and when conducting STEC control in reservoirs.
The Influence of Chronic Wound Extracts on Inflammatory Cytokine and Histatin Stability (2016)

Chronic ulcers represent a major health burden in our society. Despite many available therapies, a large number of ulcers do not heal. Protein based therapies fail in part due to proteolytic activity in the chronic wound bed. The aim of this in vitro study was to determine whether typical inflammatory cytokines and human salivary histatins remain stable when incubated with chronic wound extracts. Furthermore we determined whether a short exposure of histatins or cytokines was sufficient to exert long term effects on fibroblast migration. Stability of human recombinant cytokines IL-6 and CXCL8, and histatin variants (Hst1, Hst2, cyclic Hst1, minimal active domain of Hst1) in the presence of chronic wound extracts isolated from non-healing ulcers, was monitored by capillary zone electrophoresis. Migration-stimulating activity was assessed using a dermal fibroblast wound healing scratch assay. Histatins and cytokines stayed stable in saline for > 24 h at 37°C, making them ideal as an off-the-shelf product. However, incubation with chronic wound extracts resulted in serious breakdown of Hst1 and Hst2 (~50% in 8 h) and to lesser extent cyclic Hst1 and the minimal active domain of Hst1 (~20% in 8 h). The cytokines IL-6 and CXCL8 were more stable in chronic wound extracts (~40% degradation in 96 h). An initial 8-hour pulse of histatins or cytokines during a 96-hour study period was sufficient to stimulate fibroblast migration equally well as a continuous 96-hour exposure, indicating that they may possibly be used as novel bioactive therapeutics, exerting their activity for up to four days after a single exposure.
Immune Interactions with Cells Infected with Herpes Simplex Virus: Antibodies to Radioiodinated Surface Antigens (1977)

Abstract Lactoperoxidase-catalyzed radioiodination was used to study reactions between surface antigens and antibodies on BHK-21 cells infected with HSV-1 and HSV-2. Isolation of iodinated surface antigens was achieved by indirect immune precipitation of Triton X-100-disrupted cells with antisera to HSV and IgG. Analysis of immune precipitates by polyacrylamide gel electrophoresis (PAGE) revealed at least 10 antigens, ranging in m.w. from 35 × 103 to 160 × 103 daltons. Antigens were detectable on cell surfaces as early as 2 hr post-infection. Electrophoretic patterns of surface antigens induced by HSV-1 were similar to those induced by HSV-2. In both cases the major portion of activity was associated with glycoprotein(s) in the range of 115 × 103 to 130 × 103 daltons. A reduced amount of radioactivity was obtained if cells were reacted with anti-HSV sera before disruption with Triton X-100, suggesting that less surface antigen was accessible to HSV antibody applied directly to intact cells.
A Role for Polymodal C-Fiber Afferents in Nonhistaminergic Itch (2008)

Recent psychophysical and electrophysiological studies in humans suggest the existence of two peripheral pathways for itch, one that is responsive to histamine and a second pathway that can be activated by nonhistaminergic pruritogens (e.g., cowhage spicules). To explore the peripheral neuronal pathway for nonhistaminergic itch, behavioral responses and neuronal activity in unmyelinated afferent fibers were assessed in monkey after topical application of cowhage spicules or intradermal injection of histamine and capsaicin. Cowhage and histamine, but not capsaicin, evoked scratching behavior indicating the presence of itch. In single-fiber recordings, cowhage, histamine and/or capsaicin were applied to the cutaneous receptive field of 43 mechano-heat-sensitive C-fiber (CMH) nociceptors. The majority of CMHs exhibited a prolonged response to cowhage (39 of 43) or histamine (29 of 38), but not to capsaicin (3 of 34). Seven CMHs were activated by cowhage but not histamine. The average response to cowhage was more than twice the response to histamine, and responses were not correlated. The response of the CMHs to a stepped heat stimulus (49 degrees C, 3 s) was either quickly adapting (QC) or slowly adapting (SC). In contrast, the cowhage response was characterized by bursts of two or more action potentials (at approximately 1 Hz). The total cowhage response of the QC fibers (97 action potentials/5 min) was twice that of the SC fibers (49 action potentials/5 min). A subset of QC fibers exhibited high-frequency intraburst discharges ( approximately 30 Hz). These results suggest multiple mechanisms by which CMHs may encode itch to cowhage as well as pain to mechanical and heat stimuli.
Compaction Properties of Spheronized Binary Granular Mixtures (1995)

Two spheronized granular formulations containing 20% anhydrous lactose/80% microcrystalline cellulose (MCC) and 80% anhydrous lactose/20% microcrystalline cellulose were blended in various proportions and compressed. Physical-mechanical properties of the resulting compacts were investigated using tableting indices and compared with powder mixtures of the same compositions. The compacts were compressed at a solid fraction of 0.80 for both powder and bead mixtures. An additional set of bead compacts were made at a solid fraction of 0.87. The thickness of the compacts was measured in the post-ejection stage to investigate their expansion behavior. The tensile strength with and without a stress concentrator and the dynamic indentation hardness of the compacts were determined. The brittle fracture index (BFI) and bonding index (BI) values were also calculated. The microstructure of the beads and compacts were investigated using scanning electron microscopy to observe the bonding phenomena. The results showed that the compacts made from beads underwent different compaction/consolidation behaviors than the powders of the same lactose/MCC compositions. For powdered compacts, the tensile strength with or without a stress concentrator increased with increasing MCC content while the compacts made from beads showed the opposite trend. However, this trend was not seen in the indentation hardness test. The resulting BFI values were all low due to the plastic nature of the materials selected. The BI values of the bead and powder compacts also exhibited opposite tendencies and reflected the divergent mechanical properties of the materials presented in granulated and powdered forms. Microstructure studies revealed the bonding states between the beads in the compacts. Discrepancies in mechanical properties were related to the compressibility, compactibility, and porosities of the excipients studied.
Manipulation of tunneling frequencies using magnetic fields for resonant tunneling effects of surface plasmons (2007)

This work investigates the manipulation of terahertz surface plasmons (SPs) on a semiconductor surface by applying an external static magnetic field. The dispersion relations of the coupled surface magnetoplasmon under the Voigt configuration in the semiconductor-insulator-semiconductor structure are derived. For a TM-polarized wave that is normally incident onto a semiconductor film with periodic narrow grooves on both surfaces, the applied external static magnetic field with the Voigt configuration redshifts the frequencies of the SP-induced resonant tunneling. This phenomenon is attributable to the reduction in the effective plasma frequency by the applied magnetic field.
Calculation of the elementary rate constants of polymer‐analogous reactions and sequence analysis of products (1977)

Abstract A method has been developed for the calculation of elementary rate constants of deceleration and acceleration reactions on polymers in which the reactivity of the group is influenced only by the character of the closest adjacent groups. It is suggested that this method may be valid if the calculation yields a rate constant k ′ 3 , which is independent of conversion. In this case, the sequence analysis of products can be performed by using Markovian first‐order statistics, and the rate constants thus obtained can be used for calculating the relative frequencies of variously long sequences of reacted and unreacted groups and their number‐average length. For markedly accelerated reactions, a simplified method of estimation of the average sequence length involving use of two of the three elementary rate constants, i.e., k 1 and k ′ 2 , has been suggested.
Hypotension in patients administered indigo carmine containing impurities -A case report- (2011)

Indigo carmine has been used for eight decades with few adverse effects. Several of our patients, however, experienced severe hypotensive episodes after indigo carmine administration within a period of one month. Analysis of the raw materials used to formulate the preparation of indigo carmine we used showed that they contained impurities. Following recall of these impure materials, none of our patients experienced further hypotensive episodes.
Temperature mapping of magnetic resonance-guided laser interstitial thermal therapy (LITT) in lymphangiomas of the head and neck (2000)

The results suggest that LITT can be performed safely with tissue preserving of vital structures and can be effective in the treatment of deep tumors, such as lymphangiomas. However, given the nature of the lesion, the potential for recurrence exists no matter what modality is chosen.
Toxicity and plant growth regulator effects of cytochalasin H isolated from <i>Phomopsis</i> sp. (1976)

A biologically active metabolite was found in crude extracts of an unidentified species of Phomopsis isolated from weevil-damaged pecans. Purified metabolite was toxic to day-old cockerels, with an LD50 of 12.5 mg/kg, and was markedly inhibitory to growth the floral development of tobacco plants at concentrations of 10(-2) to 10(-4) M. IR and 1H-nmr spectra indicated an alkylpheny moiety with a single nitrogen atom present as a secondary amide; and acetate ester, OH, CH3, and a trans-double bond function. Elemental and high-resolution mass-spectral analysis indicated a formula of C30H39NO5 and a molecular weight of 493.2886. The metabolite was identified as cytochalasin H.
Enhanced gene expression in insect cells and silkworm larva by modified polyhedrin promoter using repeated burst sequence and very late transcriptional factor‐1 (2010)

The Burst of expression from polyhedrin (polh) promoter during very late phase of baculovirus infection requires a sequence located between TAAG and the translation initiation site, typically referred to as burst sequence (BS). The expression of polh promoter is stimulated by specifically binding of very late transcriptional factor 1 (VLF-1) to BS. In order to enhance the production of recombinant proteins the polh promoter was modified via a multiple BS bacmid system in which the number of BSs was increased. Compared to an expression from a normal polh promoter, β-glucuronidase (GUS) activity in High Five insect cells was three times higher with a modified polh promoter containing two BSs. Using a modified polh promoter that contains nine BSs in silkworm expression system, β1-3-N-acetylglucosaminyltransferase 2 (β3GnT2) activity per larva was 6.8-fold higher than control. Furthermore, the co-expression of modified promoters along with VLF-1-enhanced β3GnT activity. Thus, an increased optimal number of BS and its co-expression with VLF-1 leads to the production of higher level of gene expression in insect cells and silkworm larvae. This new modified promoter engineered in the current study is the strongest promoter for overexpressing foreign proteins in an eukaryotic cell and system, thus leading a progress in baculovirus-insect cell and silkworm biotechnology.
Identification of a Variant of <i>Fusarium proliferatum</i> That Hydrolyzes Fumonisin B<sub>1</sub> (1998)

Fumonisins are mycotoxins produced primarily by Fusarium moniliforme and Fusarium proliferatum in corn. Normally, the fumonisins display considerable chemical stability at temperatures up to 100 °C at neutral pH and are stable in a pH range of 4−10 at ambient temperature. Fumonisin B1 (FB1) can be produced in bioreactors using F. proliferatum (M5991). Recently, some bioreactor-grown cultures of F. proliferatum were found to rapidly hydrolyze FB1. Subcultures from stock frozen from these FB1-degrading variants continued to degrade FB1 when grown under the same bioreactor conditions. The initial hydrolysis was catalyzed by an esterase and resulted in the appearance of the aminopentol backbone (AP1) of FB1. A cell-free extract retaining the FB1 hydrolytic activity could be obtained by extraction of cell paste with 10% Triton X-100. Activity could be destroyed by heating to 60 °C for 5 min or by the addition of acetonitrile. Keywords: Fusarium proliferatum; fumonisin, esterase
Neuropathy as a presenting feature in fragile X‐associated tremor/ataxia syndrome (2007)

Peripheral neuropathy is common among patients with fragile X-associated tremor ataxia syndrome (FXTAS). Four patients with FXTAS are described with neuropathy as the presenting feature, two having received a prior diagnosis of Charcot-Marie-Tooth (CMT) disease. A fifth is described with neuropathy as the only clinical feature. A functional connection between FXTAS and neuropathy has been suggested by the presence of lamin A/C in the intranuclear, neuronal and astrocytic inclusions of FXTAS, since mutations in lamin A/C are known to give rise to an axonal form of CMT.
Movie Review Mining: a Comparison between Supervised and Unsupervised Classification Approaches (2005)

Web content mining is intended to help people discover valuable information from large amount of unstructured data on the web. Movie review mining classifies movie reviews into two polarities: positive and negative. As a type of sentiment-based classification, movie review mining is different from other topic-based classifications. Few empirical studies have been conducted in this domain. This paper investigates movie review mining using two approaches: machine learning and semantic orientation. The approaches are adapted to movie review domain for comparison. The results show that our results are comparable to or even better than previous findings. We also find that movie review mining is a more challenging application than many other types of review mining. The challenges of movie review mining lie in that factual information is always mixed with real-life review data and ironic words are used in writing movie reviews. Future work for improving existing approaches is also suggested.
Pyroomacoustics: A Python Package for Audio Room Simulation and Array Processing Algorithms (2018)

We present pyroomacoustics, a software package aimed at the rapid development and testing of audio array processing algorithms. The content of the package can be divided into three main components: an intuitive Python object-oriented interface to quickly construct different simulation scenarios involving multiple sound sources and microphones in 2D and 3D rooms; a fast C implementation of the image source model for general polyhedral rooms to efficiently generate room impulse responses and simulate the propagation between sources and receivers; and finally, reference implementations of popular algorithms for beamforming, direction finding, and adaptive filtering. Together, they form a package with the potential to speed up the time to market of new algorithms by significantly reducing the implementation overhead in the performance evaluation step.
Fructose mediated crosslinking of proteins. (1989)

10-20% of the hexose bound to human ocular lens proteins was found to be attached to epsilon-amino groups of lysyl residues via carbon 2. It was concluded that the proteins had undergone nonenzymatic reactions with endogenous fructose. This process may be important in some mammalian tissues, owing to the high crosslinking potential of fructose.
Regulation of the promoters and transcripts of rpoH, the Escherichia coli heat shock regulatory gene. (1987)

In Escherichia coli the product of the rpoH (htpR) gene, sigma 32, directs RNA polymerase to initiate transcription from heat shock promoters at all temperatures. Transcription of the heat shock genes is increased when cells are exposed to high temperatures because of increased transcription initiation by sigma 32-RNA polymerase. As a step toward understanding the regulation of the heat shock response we have examined the transcription of the rpoH gene. Using S1 mapping, promoter cloning, and in vitro transcription, we have identified the promoters and the terminator for the rpoH transcription unit. The rpoH transcripts are monocistronic and originate from at least three promoters. None of the promoters is recognized by sigma 32-RNA polymerase. Two are recognized by sigma 70-RNA polymerase and are active at both low and high growth temperatures. We do not know what form of RNA polymerase recognizes the third promoter. Transcripts from this promoter are abundant only at high temperature and are present after shift to the lethal temperature of 50 degrees C, even at times when there are no detectable transcripts from the other rpoH promoters. The amount of rpoH mRNA increases fivefold by 8 min after shift from 30 to 43.5 degrees C but rpoH mRNA synthesis increases by less than twofold, indicating that there is post-transcriptional control of the level of rpoH mRNA and presumably of sigma 32.
XPS and SEM characterization of hydrated cerium oxide conversion coatings (1995)

Abstract Cerium‐rich conversion coatings have been deposited onto aluminium 2024‐T351 alloy by immersion into a solution containing 10 g L −1 CeCl 3 and 1% H 2 O 2 in a process described as ‘cerating’. Prior to deposition the alloy had been prepared either by using a standard chemical pretreatment used for aerospace alloys before conversion coating or by polishing. X‐ray photoelectron spectroscopy and scanning electron microscopy have been used to characterize these cerium‐containing conversion coatings. It was found that, during deposition, hydrated cerium oxide initially covered the intermetallics present in the alloy surface and then covered the surface generally. Deposition continued over the intermetallics throughout the conversion coating process, resulting in thick, heavily‐cracked regions considerably greater than the average thickness of the film (>0.3 μm). Elsewhere the coating was generally up to 0.2 μm thick, and appeared to comprised of deposited particles around 100 nm in size.
Identification of Amino Acids in the Binding Pocket of the Human KDEL Receptor (1998)

Retention of soluble proteins in the endoplasmic reticulum is dependent on their interaction with the KDEL (Lys-Asp-Glu-Leu) receptor in the Golgi apparatus and their subsequent retrieval back to the endoplasmic reticulum. We have studied the three-dimensional organization of the human KDEL receptor using site-directed mutagenesis and sulfhydryl-specific labeling. We have identified four amino acid residues, Arg-5, Asp-50, Tyr-162, and Asn-165, which we suggest participate in the formation of the ligand binding pocket. Arg-5 and Asp-50 are shown to be located on the lumenal side of the membrane and are inaccessible from the cytoplasm. In addition, our results strongly support a topology of the KDEL receptor similar to the family of G-protein-coupled receptors with seven transmembrane domains. Furthermore, Asp-50 plays a crucial role in the binding of His/Lys-Asp-Glu-Leu ligands, but is not required for Asp-Asp-Glu-Leu binding, suggesting that this residue forms an ion pair with the positively charged amino acid residue positioned 4 residues from the carboxyl terminus of the ligand.
Infusion of donor-derived CD8+ memory T cells for relapse following allogeneic hematopoietic cell transplantation (2018)

Murine models showed that CD8<sup>+</sup>CD44<sup>hi</sup> memory T (T<sub>M</sub>) cells could eradicate malignant cells without inducing graft-versus-host disease (GVHD). We evaluated the feasibility and safety of infusing freshly isolated and purified donor-derived phenotypic CD8<sup>+</sup> T<sub>M</sub> cells into adults with disease relapse after allogeneic hematopoietic cell transplantation (HCT). Phenotypic CD8 T<sub>M</sub> cells were isolated after unmobilized donor apheresis using a tandem immunomagnetic selection strategy of CD45RA depletion followed by CD8<sup>+</sup> enrichment. Fifteen patients received CD8<sup>+</sup> T<sub>M</sub> cells at escalating doses (1 × 10<sup>6</sup>, 5 × 10<sup>6</sup>, or 10 × 10<sup>6</sup> cells per kg). Thirteen received cytoreduction before CD8<sup>+</sup> T<sub>M</sub> cell infusion, and 9 had active disease at the time of infusion. Mean yield and purity of the CD8<sup>+</sup> T<sub>M</sub> infusion were 38.1% and 92.8%, respectively; >90% had CD8<sup>+</sup> T effector memory phenotype, cytokine expression, and secretion profile. No adverse infusional events or dose-limiting toxicities occurred; GVHD developed in 1 patient (grade 2 liver). Ten patients (67%) maintained or achieved response (7 complete response, 1 partial response, 2 stable disease) for at least 3 months after infusion; 4 of the responders had active disease at the time of infusion. With a median follow-up from infusion of 328 days (range, 118-1328 days), median event-free survival and overall survival were 4.9 months (95% confidence interval [CI], 1-19.3 months) and 19.6 months (95% CI, 5.6 months to not reached), respectively. Collection and enrichment of phenotypic CD8<sup>+</sup> T<sub>M</sub> cells is feasible, well tolerated, and associated with a low incidence of GVHD when administered as a manipulated infusion of donor lymphocytes in patients who have relapsed after HCT. This trial was registered at www.clinicaltrials.gov as #NCT01523223.
GDNF is expressed in two forms in many tissues outside the CNS (1994)

A recently cloned neurotrophic factor, Glial Cell Line-Derived Neurotrophic Factor (GDNF), has been implicated in the survival and morphological and functional differentiation of midbrain dopaminergic neurones in vitro. GDNF has therefore been proposed as a factor which may have utility in the treatment of Parkinson's disease. In the present study, we have used RT-PCR to analyse the distribution of GDNF mRNA throughout the newborn rat (P0). We show that GDNF transcripts are present in kidney, lung, bone, heart, liver, spleen, sciatic nerve and blood. Two separate GDNF transcripts are present in different ratios in each tissue investigated. Sequence analysis of both these mRNA species revealed that the shorter transcript (sGDNF) contains a deletion of 78 bp in comparison to the published sequence for GDNF. We speculate that this shorter mRNA arose due to alternative splicing.