gebhart/patrepeval huggingface dataset:
Rapid Identification of Bacteria by Direct Matrix-assisted Laser Desorption/Ionization Mass Spectrometric Analysis of Whole Cells (1996)

Several characteristic ions were observed during the direct analysis of a variety of both gram-negative and gram-positive intact bacterial cells by the matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) technique. The entire process, involving absolutely no sample processing, could be completed in less than ten minutes. A number of specific biomarkers, generated reproducibly for each type of cell from the corresponding mass spectrum, permitted the identification, as well as the distinction, of pathogenic bacteria from their non-pathogenic counterparts. In addition, individual strains of a specific organism could also be differentiated easily. Some of these biomarkers correspond to those observed earlier during the MALDI-MS analysis of protein extracts of the same bacteria. This approach, which can yield valuable data for rapid classification and detection of microorganisms, represents a substantial breakthrough for rapid screening of environmental as well as biological samples.
Cutting Edge: Constitutive B Cell Receptor Signaling Is Critical for Basal Growth of B Lymphoma (2006)

B lymphomas account for the majority of the lymphoma cases. BCR expression appears to be important for B lymphoma because most oncogenes are translocated to nonrearranged Ig loci and because all of the variants that arise in anti-idiotypic Ab-treated lymphoma patients remain BCR positive. Based on this and the fact that BCR is required for mature B cell survival, we tested the requirement for continued expression of BCR for the growth and survival of B lymphoma cells. Using Igalpha or Igbeta-specific small interfering RNA (siRNA) to inhibit BCR expression, we demonstrate for the first time that constitutive signaling by BCR is critical for survival and proliferation of both murine and human B lymphoma cells. The BCR signals in lymphoma appear to be mediated by Syk, as it is constitutively active in a variety of B lymphoma cells. Blocking Syk activity by selective inhibitors suppresses growth of several murine and human B lymphomas.
Activation of canonical Wnt signalling is required for TGF-β-mediated fibrosis (2012)

The transforming growth factor-β (TGF-β) signalling pathway is a key mediator of fibroblast activation that drives the aberrant synthesis of extracellular matrix in fibrotic diseases. Here we demonstrate a novel link between transforming growth factor-β and the canonical Wnt pathway. TGF-β stimulates canonical Wnt signalling in a p38-dependent manner by decreasing the expression of the Wnt antagonist Dickkopf-1. Tissue samples from human fibrotic diseases show enhanced expression of Wnt proteins and decreased expression of Dickkopf-1. Activation of the canonical Wnt pathway stimulates fibroblasts in vitro and induces fibrosis in vivo. Transgenic overexpression of Dickkopf-1 ameliorates skin fibrosis induced by constitutively active TGF-β receptor type I signalling and also prevents fibrosis in other TGF-β-dependent animal models. These findings demonstrate that canonical Wnt signalling is necessary for TGF-β-mediated fibrosis and highlight a key role for the interaction of both pathways in the pathogenesis of fibrotic diseases.
Carbon and nitrogen budgets of two Ascidians and their symbiont, Prochloron , in a tropical seagrass meadow (1993)

Two species of ascidian, Didemnum molle Herdman and Lissoclinum voeltzkowi Michaelsen, were collected from a Fijian seagrass meadow. The primary production of their symbiont (Prochloron), the inorganic nitrogen metabolism and the filtration rate were measured to assess the nutritional coupling between the symbiont and the host animal. The loss of organic carbon due to the respiration of D. molle (1.1 µg at. C (mg dry wt)-1 day-1) was greater than that supplied through photosynthesis of the Prochloron (0.69 µg at. C (mg dry wt)-1 day,-1). The carbon supplied through filter-feeding appeared to supplement the ascidian's carbon budget. In contrast, organic carbon from the Prochloron of L. voeltzkowi appeared to meet the colony's respiration needs. The nitrogen budgets of both ascidian colonies were estimated from their respiration rates, the nitrogen requirement of the Prochloron, and the uptake of inorganic nitrogen and particulate organic nitrogen uptake from the water column. The nitrogen incorporated from the surrounding environment could contribute to the net nitrogen gain of the colony. However, our estimate of the nitrogen needed by the Prochloron was much greater than that which could be supplied externally. The amount of nitrogen released by the ascidians was also greater than that which could be supplied externally. This suggests that nitrogen is efficiently recycled within the symbiotic Prochloron-ascidian relationship.
Updated overall survival (OS) analysis of NAPOLI-1: Phase 3 study of nanoliposomal irinotecan (nal-IRI, MM-398), with or without 5-fluorouracil and leucovorin (5-FU/LV), vs 5-FU/LV in metastatic pancreatic cancer (mPAC) previously treated with gemcitabine (gem)-based therapy. (2016)

4126 Background: NAPOLI-1 is a global, randomized Phase 3 study evaluating nal-IRI—a nanoliposomal irinotecan—with or without 5-FU/LV vs 5-FU/LV in 417 mPAC patients previously treated with gem-based therapy. Primary survival analysis was based on 313 events. nal-IRI+5-FU/LV significantly improved OS (primary endpoint), 6.1 months (mo) vs 4.2 mo; with 5-FU/LV (unstratified hazard ratio [HR] = 0.67; P = 0.012). The primary endpoint was supported by improved progression-free survival, time to treatment failure, objective response and CA19-9 response rates, and manageable toxicities. An updated analysis of OS, 6- and 12-month-survival estimates, and safety is presented. Methods: The updated descriptive analysis of OS, based on 378 events (25 May 2015), includes data from all randomized patients across the 3 arms. The final OS analysis will also be presented. Results: After 378 OS events, nal-IRI+5-FU/LV (n = 117) retained an OS advantage relative to 5-FU/LV (n = 119): 6.2 mo (95% confidence interval [CI], 4.8–8.4) vs 4.2 mo (95% CI, 3.3–5.3) with an unstratified HR of 0.75 (P = 0.0417). In contrast, there was no OS advantage with nal-IRI monotherapy (n = 151) vs 5-FU/LV (n = 149): 4.9 mo [95% CI, 4.2–5.6] vs 4.2 mo [95% CI, 3.6–4.9], HR = 1.08; P = 0.5. Six-month survival estimates were 53% (95% CI, 44–62%) for nal-IRI+5-FU/LV vs 38% (95% CI, 29–47%) for 5-FU/LV; 12-month survival estimates were 26% (95% CI, 18–35%) for nal-IRI+5-FU/LV vs 16% (95% CI, 10–24%) for 5-FU/LV. With events in nearly all patients, the OS curves converge at ~20 mo with 19 patients (16.2%) surviving beyond 20 mo. This is a reason for attenuation of the HR estimate and unstratified log rank p-value. The most common ≥ grade 3 adverse events occurring at a ≥ 2% incidence in nal-IRI-containing arms were neutropenia, diarrhea, vomiting, and fatigue. Conclusions: In an updated analysis, the median OS benefit for nal-IRI+5-FU/LV over 5-FU/LV was maintained with a similar safety profile. nal-IRI+5-FU/LV may be a new standard of care for mPAC patients previously treated with gem-based therapy. Clinical trial information: NCT01494506.
From classroom to courtroom: Can academics be effective expert witnesses? (2012)

In addition to fundamental research, materials science is also big business, with new innovations constantly entering the marketplace. And where there are new innovations, there are also patents and frequently, disputes. When the law intervenes, academic experts are required. Dr. Glenn Prestwich, Professor at the University of Utah and an experienced expert witness, looks at what is expected of academics in the courtroom, and what they can expect in return.
Formation of Deep Electron Traps by Yb3+ Codoping Leads to Super-Long Persistent Luminescence in Ce3+-Doped Yttrium Aluminum Gallium Garnet Phosphors (2018)

The Y<sub>3</sub>Al<sub>2</sub>Ga<sub>3</sub>O<sub>12</sub>:Ce<sup>3+</sup>-Cr<sup>3+</sup> compound is one of the brightest persistent phosphors, but its persistent luminescence duration is not so long because of the relatively shallow Cr<sup>3+</sup> electron trap. To compare the vacuum referred binding energy of the electron trapping state by Cr<sup>3+</sup> and lanthanide ions, we selected Yb<sup>3+</sup> as a deeper electron trapping center. The Y<sub>3</sub>Al<sub>2</sub>Ga<sub>3</sub>O<sub>12</sub>:Ce<sup>3+</sup>-Yb<sup>3+</sup> phosphors show Ce<sup>3+</sup>:5d → 4f green persistent luminescence after blue light excitation. The formation of Yb<sup>2+</sup> was confirmed by the increased intensity of absorption due to Yb<sup>2+</sup>:4f-5d at 585 nm during the charging process. This result indicates that the Yb<sup>3+</sup> ions act as electron traps by capturing an electron. From the thermoluminescence glow curves, it was found that the Yb<sup>3+</sup> trap makes a much deeper electron trap with a 1.01 eV depth than the Cr<sup>3+</sup> electron trap with a 0.81 eV depth. This deeper Yb<sup>3+</sup> trap provides a much slower detrapping rate of filled electron traps than the Cr<sup>3+</sup>-codoped persistent phosphor. In addition, by preparing transparent ceramics and optimizing Ce<sup>3+</sup> and Yb<sup>3+</sup> concentrations, the Y<sub>3</sub>Al<sub>2</sub>Ga<sub>3</sub>O<sub>12</sub>:Ce<sup>3+</sup>(0.2%)-Yb<sup>3+</sup>(0.1%) as-made transparent ceramic phosphor showed super-long persistent luminescence for over 138.8 h after blue light charging.
Efficacy of a live oral cholera vaccine in human volunteers. (1976)

A live attenuated oral cholera vaccine has been given to volunteers with complete safety. The vaccine strain appeared to multiply significantly in intestinal contents and to result in appreciable vibriocidal antibody response. Subsequent challenge with virulent Inaba vibrios demonstrated substantial protection from clinical illness and from vibrio shedding. The possibility of reversion to toxin production is discussed.
Physicochemical and Physiological Mechanisms for the Effects of Food on Drug Absorption: The Role of Lipids and pH (1997)

Drugs are absorbed after oral administration as a consequence of a complex array of interactions between the drug, its formulation, and the gastrointestinal (GI) tract. The presence of food within the GI tract impacts significantly on transit profiles, pH, and its solubilization capacity. Consequently, food would be expected to affect the absorption of co-administered drugs when their physicochemical properties are sensitive to these changes. The physicochemical basis by which ingested food/lipids induce changes in the GI tract and influence drug absorption are reviewed. The process of lipid digestion is briefly reviewed and considered in the context of the absorption of poorly water-soluble drugs. The effect of food on GI pH is reviewed in terms of location (stomach, upper and lower small intestine) and the temporal relationship between pH and drug absorption. Case studies are presented in which postprandial changes in bioavailability are rationalized in terms of the sensitivity of the physicochemical properties of the administered drug to the altered GI environment.
B-Type Natriuretic Peptide and its Precursor in Cardiac Venous Blood from Failing Hearts (2004)

The BNP-32 and proBNP concentrations are closely related in venous cardiac blood. The findings suggest an overall constitutive secretion of processed proBNP, i.e. an N-terminal precursor fragment and BNP-32, in chronic heart failure.
Synthesis, oxidation, and reduction of monocyclic 1,2,3-triazines (1980)

A. Ohsawa, H. Arai, H. Ohnishi and H. Igeta, J. Chem. Soc., Chem. Commun., 1980, 1182 DOI: 10.1039/C39800001182
Substituent Effect in Photochemistry of Carbonyl Compounds: α‐Halovalerophenones. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Current methods for assaying angiogenesisin vitroandin vivo (2004)

Summary Angiogenesis, the development of new blood vessels from an existing vasculature, is essential in normal developmental processes and in numerous pathologies, including diabetic retinopathy, psoriasis and tumour growth and metastases. One of the problems faced by angiogenesis researchers has been the difficulty of finding suitable methods for assessing the effects of regulators of the angiogenic response. The ideal assay would be reliable, technically straightforward, easily quantifiable and, most importantly, physiologically relevant. Here, we review the advantages and limitations of the principal assays in use, including those for the proliferation, migration and differentiation of endothelial cells in vitro , vessel outgrowth from organ cultures and in vivo assays such as sponge implantation, corneal, chamber, zebrafish, chick chorioallantoic membrane (CAM) and tumour angiogenesis models.
Time course of transmitter action at the sympathetic neuroeffector junction in rodent vascular and non‐vascular smooth muscle. (1988)

1. Transmitter release from sympathetic postganglionic nerve terminals innervating the guinea-pig and mouse vas deferens and the rat tail artery has been studied in vitro by focal extracellular recording with particular emphasis on the time course of transmitter action underlying the intracellular potential changes. 2. In the absence of stimulation, spontaneous excitatory junction currents (SEJCs) were recorded with amplitudes up to 500 microV and durations between 40 and 100 ms. SEJCs were unaffected by the competitive alpha-adrenoceptor antagonist prazosin but blocked by alpha, beta-methylene ATP which desensitizes P2-purinoceptors. 3. During trains of supramaximal stimuli at 0.1-4 Hz stimulus locked excitatory junction currents (EJCs) were evoked intermittently from the population of varicosities located under the suction electrode. 4. SEJCs were similar in amplitude and time course to EJCs evoked by low-frequency stimulation in the same attachment in all three tissues. 5. SEJCs recorded using either a conventional AC amplifier or a patch clamp amplifier had the same time course. 6. These studies show that the time course of the current underlying the excitatory junction potential is brief and essentially the same in three different tissues. The prolonged time course of the excitatory junction potential in different tissues can be accounted for by the passive membrane properties.
Regulation of expressed truncated smooth muscle myosins. Role of the essential light chain and tail length. (1994)

Regulatory light chain (RLC) phosphorylation controls smooth muscle myosin's ability to act as a molecular motor. If thick filament-regulated myosins share a common structural basis for the "on-off" switch, then the interface between the RLC and essential light chain (ELC) should be as important in smooth muscle myosin as it is for calcium-dependent regulation in molluscan myosin (Xie, X., Harrison, D. H., Schlichting, I., Sweet, R. M., Kalabokis, V. N., Szent-Györgyi, A. G., and Cohen, C. (1994) Nature 368, 306-312). To test this hypothesis, a baculovirus expression system was used to obtain a truncated smooth muscle myosin that contained its native RLC and either smooth ELC, skeletal ELC, or no ELC. Movement of actin in a motility assay by heavy meromyosin (HMM) containing either skeletal or smooth ELC occurred at the same rate and in a phosphorylation-dependent manner. In contrast, substitution of skeletal RLC for smooth RLC produced an inactive molecule. HMM without an ELC moved actin at 25% the rate of control HMM, but the movement was phosphorylation-dependent even without an RLC/ELC interface. Poor regulation was observed, however, when the tail was truncated from 72 to 27 nm even though this species was primarily double-headed. These results suggest that the molecular changes induced at the active site by phosphorylation can occur independent of the ELC, but critically depend upon a stable coiled-coil tail that determines how the RLCs interact at the head/rod junction.
Arbitrary structuring of two-dimensional photonic crystals by use of phase-only Fourier gratings (2004)

The computer-generated holography technique is applied to the structuring of two-dimensional (2D) photonic crystals with inherently embedded arbitrary defects. The technique uses phase-only Fourier gratings as a generator of spot arrays in the focal plane, such that a single exposure produces a 2D array of focused spots with desired defects or modifications in the lattice structure. We demonstrate several types of large-area 2D lattice structures with square, hexagonal, or hybrid lattices embedded with point and (or) line defects. Scanning the Fourier plane in the depth direction throughout multiphoton polymerization media allows 3D lattices with stacked defect layers to be formed.
A Novel Antiinflammatory Maintains Glucocorticoid Efficacy with Reduced Side Effects (2003)

Glucocorticoids (GCs) are commonly used to treat inflammatory disease; unfortunately, the long-term use of these steroids leads to a large number of debilitating side effects. The antiinflammatory effects of GCs are a result of GC receptor (GR)-mediated inhibition of expression of proinflammatory genes as well as GR-mediated activation of antiinflammatory genes. Similarly, side effects are most likely due to both activated and repressed GR target genes in affected tissues. An as yet unachieved pharmaceutical goal is the development of a compound capable of separating detrimental side effects from antiinflammatory activity. We describe the discovery and characterization of AL-438, a GR ligand that exhibits an altered gene regulation profile, able to repress and activate only a subset of the genes normally regulated by GCs. When tested in vivo, AL-438 retains full antiinflammatory efficacy and potency comparable to steroids but its negative effects on bone metabolism and glucose control are reduced at equivalently antiinflammatory doses. The mechanism underlying this selective in vitro and in vivo activity may be the result of differential cofactor recruitment in response to ligand. AL-438 reduces the interaction between GR and peroxisomal proliferator-activated receptor gamma coactivator-1, a cofactor critical for steroid-mediated glucose up-regulation, while maintaining normal interactions with GR-interacting protein 1. This compound serves as a prototype for a unique, nonsteroidal alternative to conventional GCs in treating inflammatory disease.
No Evidence for Genotoxic Effects from 24 h Exposure of Human Leukocytes to 1.9 GHz Radiofrequency Fields (2003)

The current study extends our previous investigations of 2-h radiofrequency (RF)-field exposures on genotoxicity in human blood cell cultures by examining the effect of 24-h continuous-wave (CW) and pulsed-wave (PW) 1.9 GHz RF-field exposures on both primary DNA damage and micronucleus induction in human leukocyte cultures. Mean specific absorption rates (SARs) ranged from 0 to 10 W/kg, and the temperature within the cultures was maintained at 37.0 +/- 1.0 degrees C for the duration of the 24-h exposure period. No significant differences in primary DNA damage were observed between the sham-treated controls and any of the CW or PW 1.9 GHz RF-field-exposed cultures when processed immediately after the exposure period by the alkaline comet assay. Similarly, no significant differences were observed in the incidence of micronuclei, incidence of micronucleated binucleated cells, frequency of binucleated cells, or proliferation index between the sham-treated controls and any of the CW or PW 1.9 GHz RF-field-exposed cultures. In conclusion, the current study found no evidence of 1.9 GHz RF-field-induced genotoxicity in human blood cell cultures after a 24-h exposure period.
Aromatic amino acid biosynthesis in the yeast Saccharomyces cerevisiae: a model system for the regulation of a eukaryotic biosynthetic pathway (1991)

This review focuses on the gene-enzyme relationships and the regulation of different levels of the aromatic amino acid biosynthetic pathway in a simple eukaryotic system, the unicellular yeast Saccharomyces cerevisiae. Most reactions of this branched pathway are common to all organisms which are able to synthesize tryptophan, phenylalanine, and tyrosine. The current knowledge about the two main control mechanisms of the yeast aromatic amino acid biosynthesis is reviewed. (i) At the transcriptional level, most structural genes are regulated by the transcriptional activator GCN4, the regulator of the general amino acid control network, which couples transcriptional derepression to amino acid starvation of numerous structural genes in multiple amino acid biosynthetic pathways. (ii) At the enzyme level, the carbon flow is controlled mainly by modulating the enzyme activities at the first step of the pathway and at the branch points by feedback action of the three aromatic amino acid end products. Implications of these findings for the relationship of S. cerevisiae to prokaryotic as well as to higher eukaryotic organisms and for general regulatory mechanisms occurring in a living cell such as initiation of transcription, enzyme regulation, and the regulation of a metabolic branch point are discussed.
Purification and characterization of interferons from a continuous myeloblastic cell line. (1982)

Several leukocyte interferon species have been purified from a continuous human myeloblast cell line. The purification procedure involving selective precipitations, gel chromatography, and several steps of high performance liquid chromatography results in interferons with specific activities of 1 to 4 X 10(8) units/mg on bovine MDBK cells. The total yield of interferon is 23%, with the yield of the individual fractions ranging from 0.2 to 11.4%. Five fractions are homogeneous as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Molecular weights of the interferons were estimated by mobility on the sodium dodecyl sulfate gels and range from 17,600 to 26,200. The species differ in their relative antiviral activities on two cell lines, bovine MDBK and human AG-1732. In addition, the pure species have similar, but distinct, amino acid compositions and tryptic peptide profiles. These result support the conclusion that leukocyte interferon consists of several homologous proteins.
Hydride vapor phase epitaxial growth of a high quality GaN film using a ZnO buffer layer (1992)

In hydride vapor phase epitaxial (HVPE) growth of GaN, the sputtered ZnO layer has been found to be one of the best buffer layers because of the fact that physical properties of ZnO are nearly analogous with those of GaN. With a ZnO buffer layer, the reproducibility of growing GaN single crystal by HVPE has been greatly improved. The GaN films grown by this method show excellent crystalline, electrical, and optical properties. In particular, the Hall mobility of 1920 cm2 V−1 s−1 at 120 K is the highest value that has ever been reported by HVPE.
Interleukin‐9 as a T helper type 17 cytokine (2010)

The production of interleukin-9 (IL-9) by CD4 T cells has gathered renewed interest as the result of the observation that its expression is broader than originally thought. This includes the production of IL-9 by a recently characterized subset of CD4 helper T (Th) cells that are termed Th9 as well as production by additional T-cell subsets including Th17 cells. There is an incomplete understanding as to which IL-9-producing T-cell subsets develop under physiological conditions. We describe the conditions used to generate IL-9 in Th17 cells in vitro. We also summarize conditions where both IL-9 and IL-17 are found in vivo and propose that Th17 cells producing IL-9 may co-exist and interact with Th9 cells during conditions of autoimmunity, allergy and infection.