pinecone/core-2020-05-10-deduplication huggingface dataset:
Models of inflammation: Carrageenan- or complete Freund's Adjuvant (CFA)-induced edema and hypersensitivity in the rat

Animal models of inflammation are used to assess the production of inflammatory mediators at sites of inflammation, the anti-inflammatory properties of agents such as nonsteroidal anti-inflammatory drugs (NSAIDs), and the efficacy of putative analgesic compounds in reversing cutaneous hypersensitivity. This unit details methods to elicit and measure carrageenan- and complete Freund's adjuvant (CFA)-induced cutaneous inflammation. Due to possible differences between the dorsal root sensory system and the trigeminal sensory system, injections of either the footpad or vibrissal pad are described. In this manner, cutaneous inflammation can be assessed in tissue innervated by the lumbar dorsal root ganglion neurons (footpad) and by the trigeminal ganglion neurons (vibrissal pad)
Measuring Motivation and Reward-Related Decision Making in the Rodent Operant Touchscreen System

This is the author accepted manuscript. The final version is available from Wiley via http://dx.doi.org/10.1002/0471142301.ns0834s74This Unit is designed to facilitate implementation of the fixed and progressive ratio paradigms and the effort-related choice task in the rodent touchscreen apparatus to permit direct measurement of motivation and reward-related decision making in this equipment. These protocols have been optimized for use in the mouse and reliably yield stable performance levels that can be enhanced or suppressed by systemic pharmacological manipulation. Instructions are also provided for the adjustment of task parameters to permit use in mouse models of neurodegenerative disease. These tasks expand the utility of the rodent touchscreen apparatus beyond the currently available battery of cognitive assessment paradigms.The protocols presented in this Unit were developed and optimized as part of a research program funded by Wellcome Trust grant 089703/Z/09/Z awarded to TJB and LMS. TJB and LMS also received funding from the Innovative Medicine Initiative Joint Undertaking under grant agreement n° 115008 of which resources are composed of EFPIA in-kind contribution and financial contribution from the European Union’s Seventh Framework Programme (FP7/2007- 2013). TJB and LMS consult for Campden Instruments Ltd
"Drinking in the Dark" (DID): a simple mouse model of binge-like alcohol intake

One of the greatest challenges that scientists face when studying the neurobiology and/or genetics of alcohol (ethanol) consumption is that most preclinical animal models do not voluntarily consume enough ethanol to achieve pharmacologically meaningful blood ethanol concentrations (BECs). Recent rodent models have been developed that promote binge-like levels of ethanol consumption associated with high BECs (i.e., ≥100 mg/dl). This unit describes procedures for an animal model of binge-like ethanol drinking which has come to be called "drinking in the dark" (DID). The "basic" variation of DID involves replacing the water bottle with a bottle containing 20% ethanol for 2 to 4 hr, beginning 3 hr into the dark cycle, on cages of singly-housed C57BL/6J mice. Using this procedure, mice typically consume enough ethanol to achieve BECs >100 mg/dl and to exhibit behavioral evidence of intoxication. An alternative two-bottle (ethanol and water) procedure is also described
Preparation of Single-Cell RNA-Seq Libraries for Next Generation Sequencing

For the past several decades, due to technical limitations, the field of transcriptomics has focused on population-level measurements that can mask significant differences between individual cells. With the advent of single-cell RNA-Seq, it is now possible to profile the responses of individual cells at unprecedented depth and thereby uncover, transcriptome-wide, the heterogeneity that exists within these populations. This unit describes a method that merges several important technologies to produce, in high-throughput, single-cell RNA-Seq libraries. Complementary DNA (cDNA) is made from full-length mRNA transcripts using a reverse transcriptase that has terminal transferase activity. This, when combined with a second “template-switch” primer, allows for cDNAs to be constructed that have two universal priming sequences. Following preamplification from these common sequences, Nextera XT is used to prepare a pool of 96 uniquely indexed samples ready for Illumina sequencing.National Institutes of Health (U.S.) (Centers of Excellence in Genomic Science 1P50HG006193-01)National Institutes of Health (U.S.) (Pioneer Award DP1OD003958-01)Broad Institute of MIT and HarvardHoward Hughes Medical InstituteKlarman Cell Observator
Analysis of Protein Turnover by Quantitative SNAP-Based Pulse-Chase Imaging

Assessment of protein dynamics in living cells is crucial for understanding their biological properties and functions. The SNAP-tag, a self labeling suicide enzyme, presents a tool with unique features that can be adopted for determining protein dynamics in living cells. Here we present detailed protocols for the use of SNAP in fluorescent pulse-chase and quench-chase-pulse experiments. These time-slicing methods provide powerful tools to assay and quantify the fate and turnover rate of proteins of different ages. We cover advantages and pitfalls of SNAP-tagging in fixed- and live-cell studies and evaluate the recently developed fast-acting SNAPf variant. In addition, to facilitate the analysis of protein turnover datasets, we present an automated algorithm for spot recognition and quantification.FCT doctoral fellowships: (SFRH/BD/74284/2010, SFRH/BD/33567/2008); FCT grants: (BIA-BCM/100557/2008, BIA-PRO/100537/2008); Fundação Calouste Gulbenkian; European Commission FP7 programme; EMBO installation grant
A Quantum Electrodynamical Foundation for Molecular Photonics

In this review the authors describe some of the advances in the quantum electrodynamical formulation of theory for molecular photonics. Earlier work has been extended and reformulated for application to real dispersive media—as reflected in the new treatment of refractive, dissipative, and resonance properties. Applications of the new theory have revealed new quantum optical features in two quite different aspects of the familiar process of second harmonic generation, one operating through local coherence within small particles and the other, a coherence between the quantum amplitudes for fundamental and harmonic excitation. Where the salient experiments have been performed, they exactly match the theoretical predictions
Journey to the Deep Sea Vents

This six-day unit provides an in-depth look at the dynamic forces at work on the sea floor. Throughout the unit, students collect their findings in a portfolio. The comprehensive curriculum materials include teacher tools with individually downloadable readings, detailed daily breakdowns of tasks that include teacher strategies for using the activities, a portfolio grading sheet, a project rubric sheet, and additional readings. The unit has a hands-on experiment, in which students create a mini underwater geyser to understand how hot water behaves within a body of cold water and three activities about how scientists find deep sea vents - Searching the Ocean for Deep Sea Vents (Web-based slide show), Find the Deep Sea Vent (Web investigation), and Find a Plume, Find a Vent (online computer activity). In addition, the unit includes two activities about the thriving ecosystems found in deep sea vents called Is It Alive? and It's Aliiive - Or Is It? Educational levels: High school, Middle school
Ion Beam Methods – Introduction

Ion beam techniques are used with ion energies from eV to many MeV and a very wide range of ion species to characterise materials at length scales from sub-nm to sub-mm and in a wide variety of different ways. Many of these techniques are non destructive. Atomic concentration can be determined from matrix elements (the stoichiometry) to minor and trace elements (at ng/g sensitivity and better), in one dimension (depth profiles), two dimensions (elemental maps), and three dimensions with full tomography being feasible. There is sensitivity to the whole Periodic Table one way or another, with nuclear techniques for isotopic sensitivity, and high resolution mass spectrometry for obtaining isotopic ratios at ultra-high sensitivities of 1014 and better. Other techniques include ultra-high resolution microscopy, characterisation of semiconductor device defects at high spacial resolution, and the investigation of damage processes in the nuclear irradiation of materials. ION BEAM METHODS for thin film materials have major application areas from archaeology to zoology (including materials science, geology, cultural heritage, electronics and many others)
Graphical symbol recognition

International audienceThe chapter focuses on one of the key issues in document image processing i.e., graphical symbol recognition. Graphical symbol recognition is a sub-field of a larger research domain: pattern recognition. The chapter covers several approaches (i.e., statistical, structural and syntactic) and specially designed symbol recognition techniques inspired by real-world industrial problems. It, in general, contains research problems, state-of-the-art methods that convey basic steps as well as prominent concepts or techniques and research standpoints/directions that are associated with graphical symbol recognition
Quantum decoherence and the Glauber dynamics from the Stochastic limit

Irreversibility appears at the microscopic level in radiative phenomena, decoherence, CP violation. Radiation interactions of single atoms are discussed by Walther. A scheme providing optical evidence of macroscopic quantum interference and the associated decoherence are discussed by Arecchi and Montina. Accardi and Kozyrev discuss decoherence of systems coupled with a bosonic field in terms of the stochastic limit. A new view of CP violation as symmetry breaking of antieigenvectors is proposed by Gustafson
Coarse-Grained Picture for Controlling Quantum Chaos

We propose a coarse-grained picture to analyze control problems for quantum
chaos systems. Using optimal control theory, we first show that almost perfect
control is achieved for random matrix systems and a quantum kicked rotor.
Second, under the assumption that the controlled dynamics is well described by
a Rabi-type oscillaion between unperturbed states, we derive an analytic
expression for the optimal field. Finally we numerically confirm that the
analytic field can steer an initial state to a target state in random matrix
systems.Comment: REVTeX4 with graphicx package, 11 pages, 10 figures; replaced
  fig.1(a) and 2(a
HPF to OpenMP on the Origin2000: a case study

The geophysics group at CRS4 has long developed echo reconstruction codes in HPF on distributed-memory machines. Now, however, with the arrival of shared-memory machines and their native OpenMP compilers, the transfer to OpenMP would seem to present the logical next step in our code development strategy. Recent experience with porting one of our important HPF codes to OpenMP does not bear this out—at least not on the Origin2000. The OpenMP code suffers from the immaturity of the standard, and the operating system's handling of UNIX threads seems to severely penalize OpenMP performance. On the other hand, the HPF code on the Origin2000 is fast, scalable and not disproportionately sensitive to load on the machine.1147–1154Pubblicat
Thresholds for gully initiation and sedimentation in Mediterranean Europe

In Mediterranean areas the dynamics of gully development act as an important indicator of desertification. However, little is known about the influence of climate and land-use changes, and almost no field data exist to assess the sensitivity of a landscape to gully erosion. Two important components of gully erosion studies are the prediction of where gullies begin and where they end. To address some of these issues, topographical thresholds for gully initiation and sedimentation in six different Mediterranean study areas were established. Field measurements of local soil surface slope (S) and drainage-basin area (A) at the point of initiation of ephemeral gullies in intensively cultivated fields (five datasets) and permanent gullies in rangelands (three datasets) were carried out. A negative power relationship of the form S = aA−b was fitted through all datasets, and defined as the mean topographical threshold for gullying in the respective area. Topographically controlled slopes of sedimentation at the gully bottom were also measured. Compared to theoretical relationships for channel initiation by overland flow, relatively low values for b are obtained, suggesting a dominance of overland flow and an influence of subsurface flow. The influence of landsliding at steeper slopes appeared from the flattening of the overall negative trend in the higher slope range (S > 0·30) of the integrated dataset. Comparing the threshold lines of our datasets to the average trend lines through data found in literature revealed that vegetation type and cover could better explain differences in topographical thresholds level than climatic conditions. In cultivated fields, soil structure and moisture conditions, as determined by the rainfall distribution, are critical factors influencing topographical thresholds rather than daily rainfall amounts of the gully-initiating events. In rangelands, vegetation cover at the time of incision appears to be the most important factor differentiating between topographical thresholds, overruling the effect of average annual rainfall amounts. Soil texture and rock fragment cover contributed little to the explanation of the relative threshold levels. Differences in regression slopes (b) between the S–A relationships found in this study have been attributed to the soil characteristics in the different study areas, determining the relative importance of subsurface flow and Hortonian overland flow. Sedimentation slopes where both ephemeral and permanent gullies end were generally high because of the high rock fragment content of the transported sediment. A positive relationship was found between the rock fragment content at the apex of the sedimentation fan and the slope of the soil surface at this location. Copyright © 2000 John Wiley & Sons, Ltd
三叉神経吻側核前運動ニューロン軸索終末の超微構造に関する定量的解析

This is the author's version of a work that was accepted for publication in Journal of Comparative Neurology. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms, may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Journal of Comparative Neurology, 426(1), 2000, DOI:10.1002/1096-9861(20001009)
Characterisation of Rosa Mosqueta seeds : cell wall polysaccharide composition and light microscopy observations

The utilisation of enzymes for the extraction of vegetable oils from seeds has been a topic of growing interest in recent years. Knowledge of the cell wall polysaccharide composition is important to
select the enzyme(s) necessary for the most effective degradation of the cell walls. The purpose of the present work is to characterise the seeds of Rosa Mosqueta (Rosa aff rubiginosa) by light microscopy
(where several differential staining methods were applied to analyse the seed structure) and by the isolation of cell wall polysaccharide extracts. The mature seed of Rosa Mosqueta has a very thick and
structurally complex seed coat comprising heavily lignified tissue. The embryo has two cell layers of remaining endosperm tissue (indicating that this is an exalbuminous seed), two voluminous cotyledons
that contain the oil, and bundles of provascular tissues distributed perpendicularly to the transverse
axis of the embryo. The major non-cellulosic polysaccharides from the non-lignified tissues are glucuronoxylans and pectic polysaccharides; glucans are also present in small amounts. The major
non-cellulosic polysaccharides from the lignified tissues are glucuronoxylans. Concerning the use of
enzymes for oil extraction, microscopy and cell wall polysaccharide analysis showed that the use of
pectic enzymes followed by a xylanase or a cellulase should be explored.União Europeia (UE) - Contract INCO-DC: 96-2205
A study of floods in the Brahmaputra basin in India

During the summer monsoon months June-September, the Brahmaputra River experiences severe floods that occur year after year causing death and destruction in the Assam Valley and neighbouring Bangladesh. During the period 1987-1998, flood data of 21 gauge/discharge sites on the main Brahmaputra River and its 12 major tributaries have been studied with a view to discovering which sites and tributaries experience frequent floods in different monsoon months and how high flood magnitudes are. It is hoped that this study may be useful to planners and water resources engineers for taking the remedial measures against recurring floods in this region
Intra-seasonal, inter-annual and decadal scale variability in summer monsoon rainfall over India

Using daily rainfall data for the 30-year period of 1960-1989 and following an objective criterion, the pre-active, active and post-active phases of the summer monsoon (June-September) rainfall are clearly delineated for all-India and homogeneous regions of India. It is seen that on average, the monsoon is active for 103 days over northeast (NE-India) India, for 75-78 days over central-northeast (CNE-India) India and so on for all the regions. Average daily normal rainfall (ADNRF) is at a maximum of 14.7 mm over NE-India and at a minimum of 4.6 mm over NW-India. To investigate possible periodic oscillations in daily rainfall, the daily normal rainfall (DNRF) of all the regions is subjected to power spectrum analysis. This analysis reveals that DNRF exhibits periodicities of 5, 8-12 and 20 days over NE-India, about 5 and 40 days over WC-India, 8-12 and 40 days over NW-India and 8-10 and 40 days over PEN-India. Inter-annual and decadal scale variability of the summer monsoon rainfall over homogeneous regions is studied using the summer monsoon rainfall for the period of 1871-1990. It is discovered that summer monsoon rainfall of WC-India and NW-India is dominated by a quasi-biennial oscillation (QBO), whereas summer monsoon rainfall of NE-India and PEN-India is dominated by ENSO-type periodicities. Epochs of increasing and decreasing rainfall are also observed in the summer monsoon rainfall over homogeneous regions of India
Interannual variations of outgoing longwave radiation and Indian summer monsoon rainfall

The outgoing longwave radiation (OLR) over tropical Asia has been analysed for a relationship with the Indian summer monsoon rainfall (ISMR: June-September) total using 19 years' data. The ISMR is found to be negatively associated with a simultaneous period of OLR variation over west-central India and the south Equatorial Indian Ocean, and positively associated with that of the variation over the east of Madagascar Sea. The OLR of west-central India, particularly, is strongly coupled with the ISMR. The averaged OLR for west-central India (index A) accounts for 92 of the total variance of the ISMR, and hence, index A (with opposite sign) can be considered as a proxy of the ISMR variability. The relationship between index A and the ISMR is found to be stable. The monthly scale variation of these two parameters (i.e. all-India rainfall and OLR averaged for west-central India) also exhibits a significant association during each of the summer monsoon (June-September) months. However, the association appears better in the latter half (August-September), as compared with the first half (June-July), of the season. The ISMR can be estimated with a high degree of accuracy through a linear regression model using index A. Index A, thus, appears useful in updating the ISMR series, which is generally accomplished by averaging the area weighted rainfall of 306 stations distributed over India. Similarly, index A can be computed with a high degree of accuracy through a linear regression model using the ISMR. The relationship can be utilized in filling the OLR data gap for 1978 over west-central India. The study further provides scope for investigating interannual variability of the Indian summer monsoon in relation to climate variability of the global tropics
Urinary cholesterol excretion in men with benign prostatic hyperplasia and carcinoma of the prostate

Urinary excretion of nonesterified (NEC) and total cholesterol (TC) has been investigated in 79 patients with prostatic adenoma (BPH) and 48 patients with carcinoma of the prostate. Normal range of NEC was determined in 62 healthy individuals and was found to be 0.26-2.2 mg/24 hours (2 SD) with a mean value of 0.76 mg/24 hours. TC ranged from 0.3-2.9 mg/24 hours with a mean value of 0.92 mg/24 hours. In benign prostatic hyperplasia normal values for NEC and TC were determined in stages without residual urine. In contrast patients with BPH and residual urine showed elevated NEC in 42.1% and elevated TC in 61.4%. In prostatic carcinoma NEC hyperexcretion was present in 44.8% of stage A and B and in 52.6% of stage C and D. TC was elevated in 52.2% and 63.2%, respectively. Simultaneous determination of NEC and serum acid phosphatase (SAP) gave a pathologic result of at least one parameter in 51.7% of stage A and B and in 84.2% of stage C and D. If TC and serum acid phosphatase were combined, percentage of elevated values increases to 62.1 of stage A and B and was identical with 84.2 of stage C and D. If BPH with residual urine and other known conditions of urinary cholesterol hyperexcretion in males, pluripotential malignant testicular neoplasms and diseases of kidney and urinary tract, can be excluded with reasonable certainty, both parameters may be of value in diagnosis of prostatic cancer in even early clinical stages of the disease, especially in combination with the determination of SAP.
Comparative evaluation of nonesterified and total urinary cholesterol in papilloma and carcinoma of the bladder

Urinary excretion of nonesterified (NEC) and total cholesterol (TC) has been determined in 137 healthy individuals with a range (2 SD) of 0.26-2.2 mg/24 hours NEC and 0.3-3.0 mg/24 hours TC. 264 patients with various internal diseases revealed normal values of NEC and TC; neoplasias, diseases of the kidney and prostatic adenoma with residual urine had been excluded with reasonable certainty. There was no correlation between urinary cholesterol excretion and cholesterol plasma levels. In papilloma of the bladder (n = 16) NEC hyperexcretion was present in 56%; elevated levels of TC were determined in 68%. In carcinoma of the bladder, T1N0M0-T2N0M0 (n = 28), hyperexcretion of NEC occurred in 50% and of TC in 64%. In advanced clinical stages of the disease, T3N0M0-T4N4M1d (n = 21), elevated values of NEC were detected in 76% and of TC in 90%. Since all macroscopically blood contaminated urinary samples had been excluded, a determination of total urinary cholesterol excretion may be valuable in the diagnosis of papilloma or carcinoma of the bladder in the absence of macrohematuria. Occult blood in urine was present in 33 of the 65 patients with papilloma or carcinoma of the bladder, which was associated in 26 cases with elevated urinary total cholesterol. 32 patients revealed a negative test for occult blood in urine. In 22 of these, hyperexcretion of urinary total cholesterol was observed, indicating diagnostic sensitivity of this parameter for papilloma and carcinoma of the bladder even in the absence of microhematuria. However, one has to regard that elevated urinary cholesterol levels could also occur in other carcinomas of the urogenital system, prostatic adenoma with residual urine and kidney diseases.