gebhart/patrepeval huggingface dataset:
Evolution of hypervirulence by a MRSA clone through acquisition of a transposable element (2014)

Staphylococcus aureus has evolved as a pathogen that causes a range of diseases in humans. There are two dominant modes of evolution thought to explain most of the virulence differences between strains. First, virulence genes may be acquired from other organisms. Second, mutations may cause changes in the regulation and expression of genes. Here we describe an evolutionary event in which transposition of an IS element has a direct impact on virulence gene regulation resulting in hypervirulence. Whole-genome analysis of a methicillin-resistant S. aureus (MRSA) strain USA500 revealed acquisition of a transposable element (IS256) that is absent from close relatives of this strain. Of the multiple copies of IS256 found in the USA500 genome, one was inserted in the promoter sequence of repressor of toxins (Rot), a master transcriptional regulator responsible for the expression of virulence factors in S. aureus. We show that insertion into the rot promoter by IS256 results in the derepression of cytotoxin expression and increased virulence. Taken together, this work provides new insight into evolutionary strategies by which S. aureus is able to modify its virulence properties and demonstrates a novel mechanism by which horizontal gene transfer directly impacts virulence through altering toxin regulation.
Introducing Secure Provenance in IoT: Requirements and Challenges (2016)

In current cyber-physical systems, IoT represents interconnection of highly heterogeneous networked entities, providing goods and services to a variety of domains including environment monitoring, energy management, health-care system, and industrial automation. However, in-spite of the advantages of global connectivity, the Internet of Things (IoT) encounter various security challenges and resource constraints including identity management, traceability, storing and processing of veracious sensory data. However, the security research in IoT so far have not focused on provenance and its usefulness in IoT. To keep data traces of IoT devices, provenance can play a vital role as it solves many issues related to data trustworthiness, decision-making, data reconciliation and data replication. In this paper, we have discussed the challenges on technical infrastructure of IP-based, WSN-based and RFID-based IoT. We have identified the possible ways to integrate secure provenance into IoT grounded on security issues and other resource constraints in IoT.
Role of LC–MS/MS in Hair Testing for The Determination of Common Drugs of Abuse and Other Psychoactive Drugs (2013)

Hair testing has been used in toxicological investigations for the last two decades, but only recently a remarkable extension of hair analysis to a variety of application fields was observed, besides drug abuse recognition. The dramatic improvements of LC-MS/MS instrumentation make the detection of tiny amounts of almost whatever drug in hair possible, even after single-dose intake. The progresses observed during the last 5 years in the detection of psychoactive substances in hair are reviewed herein. The literature is partitioned according to the target compounds, namely traditional drugs of abuse, new psychoactive substances and pharmaceutical psychoactive substances. The LC-MS/MS methods presented are addressed to determine a single class of drugs, with the primary aim of accurate quantitation, or to perform multiclass analysis, for rapid and effective screening protocols.
Effect of vitamin D deficiency on amino acid excretion in the phosphate-depleted rat. (1989)

Vitamin D deficiency is associated with a generalized aminoaciduria which has been shown to be independent of parathyroid hormone (PTH) and urinary cyclic AMP excretion. To further characterize the mechanism underlying the tubulopathy, weanling rats were placed on one of the following diets for 5 weeks: (1) control [0.7% phosphorus (P), 5.5 micrograms % vitamin D]; (2) D-P- (0.1% P, 0 vitamin D); (3) D+P- (0.1% P, 5.5 micrograms % vitamin D); (4) D-P+ (0.3% P, 0 vitamin D); (5) D-P++ (0.7% P, 0 vitamin D). All diets contained 1.2% calcium (Ca). A group of rats raised on D-P++ for 4 weeks were fed D-P- for 7 days after which they received 500 pmol of 1,25-dihydroxyvitamin D3 [1,25(OH)2D3; SUPP] or an equal volume of the vehicle (ETH). The above diets resulted in partial vitamin D depletion in that 1,25(OH)2D levels were 50.25-79 pg/ml in the presence of very low 25(OH)D concentrations. Augmentation in the urinary excretion of 6 out of 8 amino acids measured was observed in P depletion irrespective of vitamin D status. For the most part, acute supplementation with 1,25(OH)2D3 did not ameliorate the tubulopathy. Plasma PTH and Ca concentrations remained normal in all diets, except D+P-, where plasma Ca was 15.88 +/- 0.54 mg/dl. P depletion was associated with hypercalciuria, hypophosphatemia, avid reabsorption of P and growth retardation, irrespective of vitamin D status. Using taurine as a representative of the amino affected, there was a strong correlation between urinary taurine on the one hand and dietary P content (r = 0.613), plasma P (r = 0.399) and 1,25(OH)2D levels (r = -0.576) on the other. The present study suggests that the aminoaciduria of vitamin D deficiency is not related to elevated levels of PTH. A similar defect may be produced by P depletion, suggesting the possibility of a common pathway for the effect.
Contrast‐enhanced magnetic resonance angiography of the lower extremities: Standard‐dose vs. high‐dose gadodiamide injection (2005)

Ce-MRA with gadodiamide is safe and efficacious. Comparison of two different doses with IA-DSA as the standard of reference showed that the 0.3 mmol/kg dose is superior to the standard 0.1 mmol/kg dose with respect to contrast enhancement, vessel delineation, image quality, and detection of collaterals. However, the 0.1 mmol/kg dose was superior to the high dose in the grading of stenosis.
Immobilization of Osmium Catalysts for Asymmetric Dihydroxylation of Olefins (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Voronoi Treemaps (2006)

Treemaps are a well known method for the visualization of attributed hierarchical data. Previously proposed treemap layout algorithms are limited to rectangular shapes, which cause problems with the aspect ratio of the rectangles as well as with identifying the visualized hierarchical structure. The approach of Voronoi treemaps presented in this paper eliminates these problems through enabling subdivisions of and in polygons. Additionally, this allows for creating treemap visualizations within areas of arbitrary shape, such as triangles and circles, thereby enabling a more flexible adaptation of treemaps for a wider range of applications.
Self-activated in vivo therapeutic cascade of erythrocyte membrane-cloaked iron-mineralized enzymes (2020)

Biomineralization of enzymes for <i>in vivo</i> diagnosis and treatment of diseases remain a considerable challenge, due to their severe reaction conditions and complicated physiological environment. Herein, we reported a biomimetic enzyme cascade delivery nanosystem, tumor-targeted erythrocyte membrane (EM)-cloaked iron-mineralized glucose oxidases (GOx-Fe<sup>0</sup>@EM-A) for enhancing anticancer efficacy by self-activated <i>in vivo</i> cascade to generate sufficient high toxic •OH at tumor site. <b>Methods</b>: An ultra-small Fe<sup>0</sup> nanoparticle (Fe<sup>0</sup>NP) was anchored in the inner cavity of glucose oxidase (GOx) to form iron-mineralized glucose oxidase (GOx-Fe<sup>0</sup>) as a potential tumor therapeutic nanocatalyst. Moreover, erythrocyte membrane cloaking delivery of GOx-Fe<sup>0</sup><i>in vivo</i> was designed to effectively accumulate ultra-small GOx-Fe<sup>0</sup> at tumor site. <b>Results</b>: GOx-Fe<sup>0</sup>@EM-A had satisfactory biocompatibility and light-trigged release efficiency. Erythrocyte membrane cloaking of GOx-Fe<sup>0</sup>@EM-A not only prolongs blood circulation but also protects <i>in vivo</i> enzyme activity of GOx-Fe<sup>0</sup>; Tumor targeting of GOx-Fe<sup>0</sup>@EM-A endowed preferential accumulation at tumor site. After NIR light irradiation at tumor site, erythrocyte membrane of GOx-Fe<sup>0</sup>@EM-A was ruptured to achieve light-driven release and tumor deep penetration of ultra-small nanosize GOx-Fe<sup>0</sup> by the photothermal effect of ICG. Then, GOx-Fe<sup>0</sup> occurred self-activated <i>in vivo</i> cascade to effectively eradicate tumor by producing the highly cumulative and deeply penetrating •OH at tumor site. <b>Conclusion</b>: Tumor-targeted erythrocyte membrane-cloaked iron-mineralized glucose oxidase (GOx-Fe0@EM-A) exhibits a promising strategy for striking antitumor efficacy by light-driven tumor deep penetration and self-activated therapeutic cascade.
Binding and localization of M(r) 72,000 matrix metalloproteinase at cell surface invadopodia. (1993)

Degradation (turnover) of collagenous matrix occurs on the surface of specialized membrane extensions termed "invadopodia," which are sites of cell invasion into the extracellular matrix. Here we show the localization of the M(r) 72,000 type IV collagenase of the matrix metalloproteinase family at invadopodia. When added exogenously, latent M(r) 72,000 collagenase binds to invadopodia of chicken embryo fibroblasts transformed by Rous sarcoma virus, whereupon the bound collagenase loses its propeptide. The collagenase binds to a component contained within the detergent extract of transformed cells, and increased levels of the active M(r) 62,000 form of the collagenase are seen here. Such an association is not detected in the detergent extract derived from normal cells. Using a recently developed cell fractionation procedure to collect cell surfaces enriched in invadopodia, we show that the M(r) 72,000 collagenase associates with the invadopodial fraction and active forms of the enzyme become immobilized on the collagenous surface. Thus, invadopodia direct intense localized degradation of the extracellular matrix by concentrating active membrane-associated collagenases at sites of cellular invasion.
A Novel Light-Sensor-Based Information Transmission System for Indoor Positioning and Navigation (2010)

This paper describes a novel light-sensor-based information transmission system for indoor positioning and navigation with particular benefits for mobile and wearable computers. It can seamlessly extend outdoor GPS tracking to the indoor environment. In a novel manner, fluorescent light is used as the medium to transmit information, which is encoded by using a pulse-frequency modulation technique. The user receives the encoded light information through a photoreceiver. The information is passed into the wearable or mobile computer after the data are decoded. This information allows positioning information to be given to indoor mobile and wearable computers. We design an economical transmitter circuit by adding a few components to a commercial electronic ballast circuit for fluorescent lamps with a price of less than 10 USD. The proposed system can be used in indoor guidance and navigation applications. Exemplary applications are included in the paper, with experimented results detailed.
Biobased Automotive Lubricants (2012)

There is a new impetus for the use of vegetable oils or renewable oils in automotive applications. The environmental factor promises to be a more steady and persistent force in promoting the use of these products than the fluctuating availability of petroleum. However, increased demand for petroleum by emerging economies has led to an increase in the need for petroleum substitutes. Either because of imposed environmental regulations or society's desire for a more environmentally friendly lubricant, the interest and increased use of vegetable-based engine oils and industrial lubricants will continue. Every year in the United States nearly 2.5 billion gallons of lubricants are manufactured; 1.4 % are automotive-related lubricants, and the rest are considered industrial lubricants. Therefore, the automotive engineer should become familiar with greases and oils and their characteristics as they relate to automotive use. Because this chapter deals with automotive lubricants, the emphasis will be placed on the use of vegetable oils within automotive systems. Furthermore, the chapter provides information on the chemistry of vegetable oils, the general performance requirement of lubricants and greases, standard test procedures required for the oil testing, and the issues of biodegradability and toxicity.
Determination of metal-based hydroxyl radical generating capacity of ambient and diesel exhaust particles (2009)

Numerous studies have suggested the association of reactive oxygen species (ROS) with adverse health effects derived from exposure to airborne particulate matter (PM) and diesel exhaust particles (DEP). This redox activity has been attributed to both inorganic and organic species present in these particles, but a clear distinction has not been established between the contribution of each. This article describes an application of an analytical procedure, based on the reaction of salicylic acid with hydroxyl radical to form dihydroxybenzoate (DHBA) isomers, to measure transition metal-based redox activity associated with ambient and diesel exhaust particles. In the procedure, ascorbic acid (AA) is used as electron source for reduction of metal ions and oxygen to generate superoxide, which is further reduced to hydroxyl radical in the presence of transition metal ions. Hydroxyl radical reacts with salicylate to generate DHBA isomers, which are measured by high-performance liquid chromatography (HPLC) with electrochemical detector. Both copper (Cu) and iron (Fe) ions generated DHBA isomers in a concentration-dependent manner but at different rates. The procedure was applied to DEP and ambient particles and the results showed Cu ion to be the major contributor to DHBA formation. The procedure provides a quantitative measure of transition metal-based redox activity associated with ambient samples with different physicochemical properties.
Biological applications of mathematical modelling (2010)

Mathematical modelling has greatly increased our ability to gain an understanding of many complex biological phenomena. A model can be treated as a hypothesis that can be accepted or rejected on the basis of its ability to predict the experimentally observed results. Numerical simulation techniques are most powerful when a mathematical model is based on understood individual elements of the biological systems, but where their aggregate behaviour cannot be depicted by current theory. In the absence of unexpected interactions, the input–output relationship can be quite accurately calculated. Experimentally inaccessible and sometimes unexpected interactions can be recovered and evaluated by simple comparison of computed versus experimental results. Such use has made mathematical simulation an indispensable tool in the biosciences.
FACTORS INFLUENCING THE ACCURACY OF TASK COMPLETION TIME ESTIMATES (2004)

Whilst considerable research has found that people tend to underestimate their task completion times (e.g., Buehler et al., 1994), factors that might influence the accuracy of temporal predictions have received little empirical treatment. The research presented in this thesis identified two distinct factors that mediated time estimation accuracy and bias. One factor was task duration, whereas the other factor was the person’s prior experience of the task. There was evidence that having prior experience of performing all or a substantial part of the same task enabled participants to more accurately estimate its duration. Additionally, predictions were more accurate when participants viewed tasks before making time estimates. Contrary to the theory of the planning fallacy (Kahneman &amp; Tversky, 1979), these findings suggest that people do take account of their previous task performance, and use such distributional information to good effect. However, there was evidence of time prediction bias when unrelated tasks were completed beforehand, suggesting that erroneous information about previous task performance was used when making a subsequent estimate. The directional nature of time estimation bias was also highlighted in the present research. In general, there was some evidence of temporal overestimation on tasks with a duration of up to four or five minutes, whereas participants tended to underestimate their completion times on tasks that took between eight and 16 minutes to complete. These findings indicate that task duration influences the direction in which time estimates are biased (i.e., under or overestimation), with the temporal underestimation indicative of the planning fallacy occurring on tasks of at least eight minutes' duration. The present research has potential implications for task duration estimation in everyday life, and outlines conditions under which prediction bias can be reduced. The present findings are discussed in relation to the theory of the planning fallacy and the potential role of cognitive judgemental heuristics in determining temporal misestimation.
A New Approach to Treatment Vaccines Preparation (2015)

Preparation of very specific individual vaccine would be as follows: After surgery and removal of the tumor, the tumor lysate would be prepared and analyzed by proteomics procedure.Proteomics analysis with comparison to normal tissue lysate would identify protein(s) unique to the tumor.Next step is purification of the tumor specific protein(s).From this point one can use the purified protein as a therapeutic vaccine or sequence it for further characterization and perhaps making recombinant version of it for preparation of monoclonal antibody, which can be used for immunotherapy as well.None.
TEST ON GAS REMOVING ABILITY OF CANISTER FOR ORGANIC GAS WITH METHYL BROMIDE (1966)

From practical requirement for gas removing ability of canister for organic gas with methyl bromide, life of the canister was tested and the breakdown times obtained were 32.3 min and 34.5 min at 5 ppm and 20 ppm of effluent gas concentrations, respectively. Sixteen canisters were tested and the mean deviations were 2.1 min and 1.8 min for each breakdown time, respectively. Concentration of influent methyl bromide gas for present test was 0.5% by volume in air stream of 30 1/min at 20°C. Logarithm of effluent gas concentration was approximately linear to contact time of canister with test air stream and the linear relationship coincided with equation derived by Danby et al. Canister used for present test was certified by the pr, oducing company that its breakdown time was 150 min or more when concentration of effluent gas exceeded 5 ppm using carbon tetrachloride as test gas, concentration of which was 0.5% by volume in influent air stream. The ratio of lives of the canisters for those two gases thus was about 1 : 5. Some consideration was done on adsorptibity of adsorbent from properties of intermolecular interaction of gas in adsorption state.
Adjunctive selective estrogen receptor modulator increases neural activity in the hippocampus and inferior frontal gyrus during emotional face recognition in schizophrenia (2016)

Estrogen has been implicated in the development and course of schizophrenia with most evidence suggesting a neuroprotective effect. Treatment with raloxifene, a selective estrogen receptor modulator, can reduce symptom severity, improve cognition and normalize brain activity during learning in schizophrenia. People with schizophrenia are especially impaired in the identification of negative facial emotions. The present study was designed to determine the extent to which adjunctive raloxifene treatment would alter abnormal neural activity during angry facial emotion recognition in schizophrenia. Twenty people with schizophrenia (12 men, 8 women) participated in a 13-week, randomized, double-blind, placebo-controlled, crossover trial of adjunctive raloxifene treatment (120 mg per day orally) and performed a facial emotion recognition task during functional magnetic resonance imaging after each treatment phase. Two-sample t-tests in regions of interest selected a priori were performed to assess activation differences between raloxifene and placebo conditions during the recognition of angry faces. Adjunctive raloxifene significantly increased activation in the right hippocampus and left inferior frontal gyrus compared with the placebo condition (family-wise error, P<0.05). There was no significant difference in performance accuracy or reaction time between active and placebo conditions. To the best of our knowledge, this study provides the first evidence suggesting that adjunctive raloxifene treatment changes neural activity in brain regions associated with facial emotion recognition in schizophrenia. These findings support the hypothesis that estrogen plays a modifying role in schizophrenia and shows that adjunctive raloxifene treatment may reverse abnormal neural activity during facial emotion recognition, which is relevant to impaired social functioning in men and women with schizophrenia.
Identifying specific profiles in patients with different degrees of painful knee osteoarthritis based on serological biochemical and mechanistic pain biomarkers (2015)

Biochemical and pain biomarkers can be applied to patients with painful osteoarthritis profiles and may provide more details compared with conventional clinical tools. The aim of this study was to identify an optimal combination of biochemical and pain biomarkers for classification of patients with different degrees of knee pain and joint damage. Such profiling may provide new diagnostic and therapeutic options. A total of 216 patients with different degrees of knee pain (maximal pain during the last 24 hours rated on a visual analog scale [VAS]) (VAS 0-100) and 64 controls (VAS 0-9) were recruited. Patients were separated into 3 groups: VAS 10 to 39 (N = 81), VAS 40 to 69 (N = 70), and VAS 70 to 100 (N = 65). Pressure pain thresholds, temporal summation to pressure stimuli, and conditioning pain modulation were measured from the peripatellar and extrasegmental sites. Biochemical markers indicative for autoinflammation and immunity (VICM, CRP, and CRPM), synovial inflammation (CIIIM), cartilage loss (CIIM), and bone degradation (CIM) were analyzed. WOMAC, Lequesne, and pain catastrophizing scores were collected. Principal component analysis was applied to select the optimal variable subset, and cluster analysis was applied to this subset to create distinctly different knee pain profiles. Four distinct knee pain profiles were identified: profile A (N = 27), profile B (N = 59), profile C (N = 85), and profile D (N = 41). Each knee pain profile had a unique combination of biochemical markers, pain biomarkers, physical impairments, and psychological factors that may provide the basis for mechanism-based diagnosis, individualized treatment, and selection of patients for clinical trials evaluating analgesic compounds. These results introduce a new profiling for knee OA and should be regarded as preliminary.