gebhart/patrepeval huggingface dataset:
Optimizing techniques to capture and extract environmental DNA for detection and quantification of fish (2015)

Few studies have examined capture and extraction methods for environmental DNA (eDNA) to identify techniques optimal for detection and quantification. In this study, precipitation, centrifugation and filtration eDNA capture methods and six commercially available DNA extraction kits were evaluated for their ability to detect and quantify common carp (Cyprinus carpio) mitochondrial DNA using quantitative PCR in a series of laboratory experiments. Filtration methods yielded the most carp eDNA, and a glass fibre (GF) filter performed better than a similar pore size polycarbonate (PC) filter. Smaller pore sized filters had higher regression slopes of biomass to eDNA, indicating that they were potentially more sensitive to changes in biomass. Comparison of DNA extraction kits showed that the MP Biomedicals FastDNA SPIN Kit yielded the most carp eDNA and was the most sensitive for detection purposes, despite minor inhibition. The MoBio PowerSoil DNA Isolation Kit had the lowest coefficient of variation in extraction efficiency between lake and well water and had no detectable inhibition, making it most suitable for comparisons across aquatic environments. Of the methods tested, we recommend using a 1.5 μm GF filter, followed by extraction with the MP Biomedicals FastDNA SPIN Kit for detection. For quantification of eDNA, filtration through a 0.2-0.6 μm pore size PC filter, followed by extraction with MoBio PowerSoil DNA Isolation Kit was optimal. These results are broadly applicable for laboratory studies on carps and potentially other cyprinids. The recommendations can also be used to inform choice of methodology for field studies.
A bibliometric analysis on literatures of biological invasion. (2009)

Biological invasion is an important barrier for biodiversity conservation and sustainable development of global agriculture and forestry.To better understand the global trend in biological invasion research and to reflect major nations' scientific advances and influences on the world's scientific community in the field,a bibliometric study on biological invasion literature indexed by the Web of Science based on Web of Knowledge during(1991-2006) was carried out using regular search methods.Results indicated that,among all nations,the United States had the largest number of publications,accounting for 41.8% of all related publications worldwide.The average impact factor of the top 10 journals publishing related articles was 4.03.Three journals,Biological Invasions,Ecology and Cancer Research,were the most important and popular ones in this field.The Chinese Academy of Sciences,Fudan University,and Hong Kong University were the top 3 institutions that had the highest numbers of publications with the highest quality in China.
Efficient Neuronal Gene Transfer with AAV8 Leads to Neurotoxic Levels of Tau or Green Fluorescent Proteins (2005)

Adeno-associated virus (AAV) serotype 8 appears to be the strongest of the natural serotypes reported to date for gene transfer in liver and muscle. In this study, we evaluated AAV8 in the brain by several methods, including biophotonic imaging of green fluorescent protein (GFP). In the adult rat hippocampus, levels of GFP expressed were clearly greater with AAV8 than with AAV2 or AAV5 by Western blot and biophotonic imaging and slightly but significantly greater than AAV1 by Western blot. In the substantia nigra, the GFP expression conferred by AAV8 was toxic to dopamine neurons, although toxicity could be avoided with dose titration. At the low dose at which there was no GFP toxicity from the GFP vector, another AAV8 vector for a disease-related (P301L) form of the microtubule-associated protein tau caused a 78% loss of dopamine neurons and significant amphetamine-stimulated rotational behavior. The AAV8 tau vector-induced cell loss was greater than that from AAV2 or AAV5 tau vectors, demonstrating that the increased gene transfer was functional. While the toxicity observed with GFP expression warrants great caution, the efficient AAV8 is promising for animal models of neurodegenerative diseases and potentially as well for gene therapy of brain diseases.
Pulse characterization for the long path laser at LLL (1973)

change as a function of time within the cavity. With these new phenomena introduced into the kinetic model, a best reasonable fit to the experimental data is found by adjusting the reaction rate coefficients within the range of known uncertainty by numerical methods giving a new bound within this range of uncertainty. The experimental parameters modeled are the lasing time, laser pulse energy, and time to laser threshold.
Matching User's Semantics with Data Semantics in Location-Based Services (2005)

ABSTRACT Mobility is having a tremendous impact on the design and use of information technology. Information services, in particular, are heavily challenged by this new framework, which calls for innovative solutions. One of the major issues for flexible information services is how to be able to correctly understand what is being requested by users, and how to find information that is relevant to the request. This paper focuses on such semantic issues, aiming at outlining the general problem as well as the specificity attached to location-based services, one of the major trends in mobile information systems. Categories and Subject Descriptors H.3.5 [ INFORMATION STORAGE AND RETRIEVAL ]: Online Information Services – data sharing. H.2.4 [ DATABASE MANAGEMENT ]: Systems – query processing. H.1.2 [ MODELS AND PRINCIPLES ]: User/Machine Systems – human factors, human information processing. General Terms Management, Design, Human Factors. Keywords Knowledge Management, Ontology, Location-based Services, User Profiles, Query Processing, Databases, Peer-to-Peer
Disruption of Mitochondrial Calcium Homeostasis after Chronic α-Naphthylisothiocyanate Administration: Relevance for Cholestasis (2002)

Background Hepatocyte dysfunction caused by impaired mitochondrial function has been pointed out as a probable leading cause of cholestatic liver injury. The aim of this study was to evaluate liver mitochondrial bioenergetics that followed repeated in vivo administration of α-naphthylisothiocyanate, a known cholestatic agent. Methods Serum markers of liver injury and endogenous adenine nucleotides were measured in α-naphthylisothiocyanate-treated rats (intraperitoneally, 100 mg/Kg/wkx6 wk). Changes in membrane potential, mitochondrial respiration, as well as alterations in mitochondrial calcium homeostasis were monitored. Results In rats injected with α-naphthylisothiocyanate, liver injury with cholestasis developed within 48 hours, as indicated by both serum enzyme activities and total bilirubin concentration. However, 1 week after the last injection, serum enzyme activity returned to control levels. In addition, after chronic α-naphthylisothiocyanate administration, no alterations in mitochondrial respiratory function and membrane potential were observed. Associated with these parameters, mitochondria from treated animals exhibited increased susceptibility to disruption of mitochondrial calcium homeostasis by calcium phosphate and by bile acids, which was probably caused by induction of permeability transition pore. Conclusions Our data suggest that chronic cholestasis in rats leads to impaired mitochondrial function due to the disruption of mitochondrial calcium homeostasis. The initiating event is the induction of a cyclosporine A-sensitive release of calcium. This event may be an important determinant of the progression of cholestatic liver injury and associated liver cirrhosis. In addition, in the present study we observed that impairment of mitochondrial function is potentiated by chenodeoxycholate, a bile acid that is known to be toxic. Ursodeoxycholate (the β- epimer of chenodeoxycholate) is approved for the treatment of chronic cholestatic liver disease. Interestingly, we show that the susceptibility to the cyclosporine A-sensitive release of calcium was increased by the combination of both bile acids. These results indicate that the reported improvement of biochemical parameters in cholestatic patients treated with ursodeoxycholate would not prevent the associated mitochondrial dysfunction. This may explain the progression of the histological stage and the maintenance of symptoms during cholestasis.
Microglia-Based Phenotypic Screening Identifies a Novel Inhibitor of Neuroinflammation Effective in Alzheimer’s Disease Models (2016)

Currently, anti-AD drug discovery using target-based approaches is extremely challenging due to unclear etiology of AD and absence of validated therapeutic protein targets. Neuronal death, regardless of causes, plays a key role in AD progression, and it is directly linked to neuroinflammation. Meanwhile, phenotypic screening is making a resurgence in drug discovery process as an alternative to target-focused approaches. Herein, we employed microglia-based phenotypic screenings to search for small molecules that modulate the release of detrimental proinflammatory cytokines. The identified novel pharmacological inhibitor of neuroinflammation (named GIBH-130) was validated to alter phenotypes of neuroinflammation in AD brains. Notably, this molecule exhibited comparable in vivo efficacy of cognitive impairment relief to donepezil and memantine respectively in both β amyloid-induced and APP/PS1 double transgenic Alzheimer’s murine models at a substantially lower dose (0.25 mg/kg). Therefore, GIBH-130 constitutes a unique chemical probe for pathogenesis research and drug development of AD, and it also suggests microglia-based phenotypic screenings that target neuroinflammation as an effective and feasible strategy to identify novel anti-AD agents.
MATHEMATICAL MODELS IN LINGUISTICS (1973)

By Maurice Gross: pp. xvi, 159. £2.10. (Prentice-Hall, Inc., New Jersey, 1972.)
Helicobacter pylori CagA-Dependent Macrophage Migration Inhibitory Factor Produced by Gastric Epithelial Cells Binds to CD74 and Stimulates Procarcinogenic Events (2006)

Macrophage migration inhibitory factor (MIF) is a proinflammatory cytokine that has recently been implicated in carcinogenesis. Helicobacter pylori, which is closely linked to gastric cancer, induces the gastric epithelium to produce proinflammatory cytokines, including MIF. MIF can bind to CD74, which we have previously shown to be highly expressed on the surface of gastric epithelial cells (GEC) during H. pylori infection. In this study, we sought to investigate the role of the H. pylori-induced MIF on epithelial proliferation and procarcinogenic events. Upon establishing a role for the H. pylori CagA virulence factor in MIF production, MIF binding to CD74 on GEC was confirmed. rMIF and H. pylori were shown to increase GEC proliferation, which was decreased when cagA- strains were used and when CD74 was blocked by mAbs. Apoptosis was also decreased by MIF, but increased by cagA- strains that induced much lower amounts of MIF than the wild-type bacteria. Furthermore, MIF binding to CD74 was also shown to decrease p53 phosphorylation and up-regulate Bcl-2 expression. This data describes a novel system in which an H. pylori virulence factor contributes to the production of a host factor that in turn up-regulates procarcinogenic events by the gastric epithelium.
Applications of optical microspheres to microwaves and millimeter waves (2019)

International audience
Non-tracking web analytics (2012)

Today, websites commonly use third party web analytics services t obtain aggregate information about users that visit their sites. This information includes demographics and visits to other sites as well as user behavior within their own sites. Unfortunately, to obtain this aggregate information, web analytics services track individual user browsing behavior across the web. This violation of user privacy has been strongly criticized, resulting in tools that block such tracking as well as anti-tracking legislation and standards such as Do-Not-Track. These efforts, while improving user privacy, degrade the quality of web analytics. This paper presents the first design of a system that provides web analytics without tracking. The system gives users differential privacy guarantees, can provide better quality analytics than current services, requires no new organizational players, and is practical to deploy. This paper describes and analyzes the design, gives performance benchmarks, and presents our implementation and deployment across several hundred users.
Radiation effects on the respiratory system (2005)

This paper discusses the lung response to irradiation in the context of accidental radiation exposure. The lung is a relatively radiation sensitive organ with a response to irradiation that is complex, involving killing of lung cells, death of endothelial cells, influx of inflammatory cells, and waves of inflammatory cytokines and reactive oxygen species (ROS) production. Two major functional outcomes are observed, radiation pneumonitis and radiation fibrosis. Elevated levels of the cytokine, transforming growth factor-β (TGF-β), appear to play an important role in the development of radiation-induced lung injury, particularly fibrosis. There is limited evidence from animal studies that irradiation of the bone marrow and bone marrow transplantation may affect the lung response, but information regarding irradiation of other organs is lacking. Protection against functional and histopathological damage has been demonstrated for a number of different agents when given before (and after) irradiation (e.g. amifostine, captopril, manganese superoxide dismutase (MnSOD), superoxide dismutase (SOD) mimetic). To what extent protection can be provided by agents given only after irradiation is uncertain and although steroids can relieve the symptoms of pneumonitis, it remains unclear whether they can protect against the development of late fibrosis.
Hemoconcentration of Creatinine Minimally Contributes to Changes in Creatinine during the Treatment of Decompensated Heart Failure (2022)

During ADHF therapy, increases in serum creatinine are driven predominantly by changes in filtration, with minimal contribution from change in VD.
Achilles Tendon Injuries: A Comparison of Surgical Repair Versus No Repair in a Rat Model (1993)

Controversy exists regarding the treatment of Achilles tendon ruptures. The aim of this study was to determine whether surgical repair of the rat Achilles tendon offered any biomechanical, functional, or morphological advantage over no repair. Thirty-two male Sprague-Dawley rats were randomly allocated into four groups: (1) sham operated (skin incision only), (2) no repair (complete division of the Achilles tendon and plantaris tendon without repair), (3) internal splint (plantaris left intact), and (4) Achilles repair (with a modified Kessler-type suture). Functional performance was determined from the measurements of hindpaw prints utilizing the Achilles Functional Index. On day 15, the animals were killed, and biochemical and histological evaluations were performed on both the injured and uninjured Achilles tendon constructs. All groups subjected to Achilles tendon division had a significant initial functional impairment that gradually improved so that by day 15 there were no functional or failure load impairments in any group. The injured tendons in all three groups subjected to Achilles tendon division had a 13-fold increase in the cross-sectional area and were less stiff and more deformable than uninjured and sham-operated tendons on day 15 (P < .001). The magnitude of the biomechanical and morphological changes at postoperative day 15 and the initial impairment and rate of functional recovery were similar for no repair, internal splint, and Achilles repair groups. In summary, this study demonstrates that surgical repair of the Achilles tendon in the rat does not offer any advantage over nonoperative management.
Inhibition of Influenza A and B Viruses by 2′-Deoxy-2′-Fluororibosides (1993)

A series of 2′-deoxy-2′-fluororibosides were evaluated for anti-influenza activity in cell culture and in the mouse pneumonia model. Many were found to be potent inhibitors of Influenza A, in chick embryo fibroblast cells (IC 50 's 0.1–2.9 μM), and in reducing mouse lung virus titres (1–3 log 10 units). Purine analogues proved the most effective, but their activity was an order of magnitude higher in MDCK cells. Anti-influenza activity correlated with intracellular triphosphate levels and with substrate specificity of 2′-deoxycytidine kinase. 2′-deoxy-2′-fluoroguanosine selected for further study was active against all influenza A and B strains tested, including one clinical isolate which proved extremely sensitive when assayed in human tracheal cultures. In vivo, 2′-deoxy-2′-fluoroguanosine (2′-fluorodGuo) was significantly more effective than amantadine or ribavirin in reducing mouse lung virus titre when treatment commenced after infection.
Towards Accurate Personalized Autism Diagnosis Using Different Imaging Modalities: sMRI, fMRI, and DTI (2018)

Autism Spectrum Disorder, ASD, is prevalent lifelong mental disorder associated with difficulties i n s ocial interaction, communication skills, and behavioral patterns. Numerous studies were presented suggesting abnormal development of neural networks in the brain in shape and connectivity. Magnetic resonance imaging, MRI, is used to diagnose the structural (i.e., sMRI) the functionality (i.e., fMRI) of gray matter and connectivity of the white matter (WM), using diffusion tensor imaging, DTI. The goal of this paper is to integrate these perspective to allow a comprehensive and personalized computer aided diagnostic (CAD) for ASD patients.
Repair of circuits by laser seeding and constriction induced plating (1992)

A method of repairing circuit opens on printed circuit boards which is particularly suitable for low-melting-point substrates with small linewidth is proposed. The two-step repair process involves depositing a solid film organometallic over the open defect and forming a metallic layer by localized laser pyrolysis. After cleaning, the part is immersed in acid copper electrolyte and an increasing alternating current passed through the defective line. As a consequence of the construction-induced temperature rise, copper deposition occurs at the defect which restores the electrical and mechanical integrity of defective copper circuitry. Factors determining the selection of suitable precursors are discussed, and three potential compounds for laser seeding are evaluated. The process has been demonstrated on low-melting-point dielectrics such as polytetrafluoroethylene, polyimide, and glass-epoxy and has been found suitable for linewidths as small as 25 mu m.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A golden micro-trap for anesthetic depth monitoring using human breath samples (2012)

This paper reports a golden micro-trap chip for anesthetic depth monitoring (ADM). The chip selectively captures the anesthetic compound propofol (2,6-diisopropylphenol) by filtering out the other species found in human breath. The 12mm×12mm×1mm silicon-glass chip has an array of high aspect ratio parabolic reflectors inside its 7mm×7mm×0.24mm cavity and is coated with an electroplated gold layer. This device shows subject independent results with the propofol peak area variation within 8%. This microfabricated chip has the potential to accurately quantify the amount of propofol present in human breath sample without incorporating the gas chromatography (GC) column into the testing setup, resulting in faster analysis and reduced cost and complexity.
Recent developments in high temperature coatings for gas turbine airfoils (1983)

The importance of coatings for hot section airfoils has increased with the drive for more cost-effective use of fuel in a wide variety of gas turbine engines. Minor additions of silicon have been found to appreciably increase the oxidation resistance of plasma-sprayed NiCoCrAlY coatings on a single crystal nickel-base superalloy. Increasing the chromium content of MCrAlY coatings substantially increases the resistance to acidic (Na2SO4-SO3) hot corrosion at temperatures of about 1300 F (704 C) but gives no significant improvement beyond contemporary coatings in the range of 1600 F (871 C). Surface enrichment of MCrAlY coatings with silicon also gives large increases in resistance to acidic hot corrosion in the 1300 F region. The resistance to the thermal stress-induced spalling of zirconia-based thermal barrier coatings has been improved by lowering coating stresses with segmented structures and by controlling the substrate temperature during coating fabrication.
Synthesis of a Base-Protectedxylo-LNA Adenine Nucleoside (2003)

Synthesis of (1S,3R,4R,7R)-7-hydroxy-1-hydroxymethyl-3-(6-N-benzoyl-adenin-9-yl)-2,5-dioxabicyclo[2.2.1]heptane (2), a base-protected xylo-LNA adenine nucleoside, has been accomplished using a convergent synthetic strategy starting from 1,2-di-O-acetylfuranose 3.
Purification, Characterization, and Immunogenicity of the Refolded Ectodomain of the Plasmodium falciparum Apical Membrane Antigen 1 Expressed in Escherichia coli (2002)

The apical membrane antigen 1 (AMA1) has emerged as a promising vaccine candidate against malaria. Advanced evaluation of its protective efficacy in humans requires the production of highly purified and correctly folded protein. We describe here a process for the expression, fermentation, refolding, and purification of the recombinant ectodomain of AMA1 (amino acids 83(Gly) to 531(Glu)) of Plasmodium falciparum (3D7) produced in Escherichia coli. A synthetic gene containing an E. coli codon bias was cloned into a modified pET32 plasmid, and the recombinant protein was produced by using a redox-modified E. coli strain, Origami (DE3). A purification process was developed that included Sarkosyl extraction followed by affinity purification on a Ni-nitrilotriacetic acid column. The recombinant AMA1 was refolded in the presence of reduced and oxidized glutathione and further purified by using two ion-exchange chromatographic steps. The final product, designated AMA1/E, was homogeneous, monomeric, and >99% pure and had low endotoxin content and low host cell contamination. Analysis of AMA1/E showed that it had the predicted primary sequence, and tertiary structure analysis confirmed its compact disulfide-bonded nature. Rabbit antibodies made to the protein recognized the native parasite AMA1 and inhibited the growth of the P. falciparum homologous 3D7 clone in an in vitro assay. Reduction-sensitive epitopes on AMA1/E were shown to be necessary for the production of inhibitory anti-AMA1 antibodies. AMA1/E was recognized by a conformation-dependent, growth-inhibitory monoclonal antibody, 4G2dc1. The process described here was successfully scaled up to produce AMA1/E protein under GMP conditions, and the product was found to induce highly inhibitory antibodies in rabbits.
Distinctive control of metabolic pathways byChlorella autotrophicain semicontinuous culture (1996)

The marine microalga Chlorella autotrophica was cultured semicontinuously under light-dark synchronizing conditions at two nutrient concentrations (2 and 4 mmol N.L-1) and five rates of daily renewal (from 10 to 50% of culture volume). Under such conditions, the biochemical composition of C. autotrophica was strongly influenced by the renewal rate, but unlike other marine microalgae, the nutrient concentration had no effect on the biochemical composition of the organic fraction of the microalga at a given growth rate. Results suggest that this species exerts a strong control over metabolic pathways, independent of the nutrient concentration in the medium.