bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association between Severe Pandemic 2009 Influenza A (H1N1) Virus Infection and Immunoglobulin G2 Subclass Deficiency
Authors: Gordon C.L. , Johnson P.D.R. , Permezel M. , Holmes N.E. , Gutteridge G. , McDonald C.F. , Eisen D.P. , Stewardson A.J. , Edington J. , Charles P.G.P. , Crinis N. , Black M.J. , Torresi J. , Grayson M.L. 
Published: February 2010

Abstract
Severe H1N1 infection appears to be associated with immunoglobulin G2 subclass deficiency in both nonpregnant and pregnant patients. Healthy pregnant women were mildly deficient in immunoglobulin G2, but pregnant women with severe H1N1 infection had lower levels. Immunoglobulin G2 deficiency persisted after recovery in the majority (73%) of cases.
Background . Severe pandemic 2009 influenza A virus (H1N1) infection is associated with risk factors that include pregnancy, obesity, and immunosuppression. After identification of immunoglobulin G2 (IgG2) deficiency in 1 severe case, we assessed IgG subclass levels in a cohort of patients with H1N1 infection.
Methods . Patient features, including levels of serum IgG and IgG subclasses, were assessed in patients with acute severe H1N1 infection (defined as infection requiring respiratory support in an intensive care unit), patients with moderate H1N1 infection (defined as inpatients not hospitalized in an intensive care unit), and a random sample of healthy pregnant women.
Results . Among the 39 patients with H1N1 infection (19 with severe infection, 7 of whom were pregnant; 20 with moderate infection, 2 of whom were pregnant), hypoabuminemia (P&lt;.001), anemia (P&lt;.001), and low levels of total IgG (P=.01), IgG1 (P=.022), and IgG2 (15 of 19 vs 5 of 20; P=.001; mean value ± standard deviation [SD], 1.8±1.7 g/L vs 3.4±1.4 g/L; P=.003) were all statistically significantly associated with severe H1N1 infection, but only hypoalbuminemia (P=.02) and low mean IgG2 levels (P=.043) remained significant after multivariate analysis. Follow-up of 15 (79%) surviving IgG2-deficient patients at a mean (±SD) of 90±23 days (R, 38–126) after the initial acute specimen was obtained found that hypoalbuminemia had resolved in most cases, but 11 (73%) of 15 patients remained IgG2 deficient. Among 17 healthy pregnant control subjects, mildly low IgG1 and/or IgG2 levels were noted in 10, but pregnant patients with H1N1 infection had significantly lower levels of IgG2 (P=.001).
Conclusions . Severe H1N1 infection is associated with IgG2 deficiency, which appears to persist in a majority of patients. Pregnancy-related reductions in IgG2 level may explain the increased severity of H1N1 infection in some but not all pregnant patients. The role of IgG2 deficiency in the pathogenesis of H1N1 infection requires further investigation, because it may have therapeutic implications.
Associations between Breast Milk Viral Load, Mastitis, Exclusive Breast-Feeding, and Postnatal Transmission of HIV
Authors: Lunney Kevin M. , Iliff Peter , Mutasa Kuda , Ntozini Robert , Magder Laurence S. , Moulton Lawrence H. , Humphrey Jean H. 
Published: February 2010

Abstract
Background . Exclusive breast-feeding is protective against postnatal transmission of human immunodeficiency virus (HIV), compared with mixed breast-feeding. Accordingly, exclusive breast-feeding for 6 months is the World Health Organization's recommendation to HIV-infected mothers for whom exclusive replacement feeding is not acceptable, feasible, affordable, safe, or sustainable. The mechanism of exclusive breast-feeding protection is unknown but is hypothesized to be mediated through reduced mastitis.
Methods . We compared breast milk and plasma specimens of exclusive breast-feeding and mixed breast-feeding HIV- positive mothers archived from the ZVITAMBO trial in which mixed breast-feeding was associated with a 2-fold increased risk of postnatal transmission at 18 months. Plasma HIV load, breast milk HIV load and sodium/potassium ratio were measured as a proxy for subclinical mastitis.
Results . Mixed breast-feeding was not associated with mastitis or breast milk HIV load. Mastitis was associated with breast milk HIV load, and this effect increased with increasing maternal plasma HIV load; mastitis was associated with postnatal transmission only when maternal plasma HIV load was high (&gt;3.7 log 10 copies/mL). Initiation of breast-feeding within an hour of delivery was associated with exclusive breast-feeding (adjusted odds ratio, 1.62; 95% confidence interval, 1.02–2.58).
Conclusions . Exclusive breast-feeding is associated with reduced postnatal transmission of HIV from mother to child, but this protection is not mediated by reduced mastitis or breast milk HIV load. The deleterious effect of mastitis increases as the mother's plasma HIV load increases.
Physics and complexity
Authors: Sherrington David 
Published: February 2010

This paper is concerned with complex macroscopic behaviour arising in many-body systems through the combinations of competitive interactions and disorder, even with simple ingredients at the microscopic level. It attempts to indicate and illustrate the richness that has arisen, in conceptual understanding, in methodology and in application, across a large range of scientific disciplines, together with a hint of some of the further opportunities that remain to be tapped. In doing so, it takes the perspective of physics and tries to show, albeit rather briefly, how physics has contributed and been stimulated.
The path to fusion power
Authors: Smith Chris Llewellyn , Cowley Steve 
Published: February 2010

The promise, status and challenges of developing fusion power are outlined. The key physics and engineering principles are described and recent progress quantified. As the successful demonstration of 16 MW of fusion in 1997 in the Joint European Torus showed, fusion works. The central issue is therefore to make it work reliably and economically on the scale of a power station. We argue that to meet this challenge in 30 years we must follow the aggressive programme known as the ‘Fast Track to Fusion’. This programme is described in some detail.
Electrons in one dimension
Authors: Berggren K.-F. , Pepper M. 
Published: February 2010

In this article, we present a summary of the current status of the study of the transport of electrons confined to one dimension in very low disorder GaAs–AlGaAs heterostructures. By means of suitably located gates and application of a voltage to ‘electrostatically squeeze’ the electronic wave functions, it is possible to produce a controllable size quantization and a transition from two-dimensional transport. If the length of the electron channel is sufficiently short, then transport is ballistic and the quantized subbands each have a conductance equal to the fundamental quantum value 2
e
2
/
h
, where the factor of 2 arises from the spin degeneracy. This mode of conduction is discussed, and it is shown that a number of many-body effects can be observed. These effects are discussed as in the spin-incoherent regime, which is entered when the separation of the electrons is increased and the exchange energy is less than
kT
. Finally, results are presented in the regime where the confinement potential is decreased and the electron configuration relaxes to minimize the electron–electron repulsion to move towards a two-dimensional array. It is shown that the ground state is no longer a line determined by the size quantization alone, but becomes two distinct rows arising from minimization of the electrostatic energy and is the precursor of a two-dimensional Wigner lattice.
‘… a metal conducts and a non-metal doesn't’
Authors: Edwards P. P. , Lodge M. T. J. , Hensel F. , Redmer R. 
Published: February 2010

In a letter to one of the authors, Sir Nevill Mott, then in his tenth decade, highlighted the fact that the statement ‘… a metal conducts, and a non-metal doesn’t’ can be true only at the absolute zero of temperature,
T
=0 K. But, of course, experimental studies of metals, non-metals and, indeed, the electronic and thermodynamic transition between these canonical states of matter must always occur above
T
=0 K, and, in many important cases, for temperatures far above the absolute zero. Here, we review the issues—theoretical and experimental—attendant on studies of the metal to non-metal transition in doped semiconductors at temperatures close to absolute zero (
T
=0.03 K) and fluid chemical elements at temperatures far above absolute zero (
T
>1000 K).

We attempt to illustrate Mott’s insights for delving into such complex phenomena and experimental systems, finding intuitively the dominant features of the science, and developing a coherent picture of the different competing electronic processes. A particular emphasis is placed on the idea of a ‘Mott metal to non-metal transition’ in the nominally metallic chemical elements rubidium, caesium and mercury, and the converse metallization transition in the nominally non-metal elements hydrogen and oxygen. We also review major innovations by D. A. Goldhammer (Goldhammer 1913
Dispersion und absorption des lichtes
) and K. F. Herzfeld (Herzfeld 1927
Phys. Rev.
29
, 701–705. (
doi:10.1103/PhysRev.29.701
)) in a pre-quantum theory description of the metal–non-metal transition, which emphasize the pivotal role of atomic properties in dictating the metallic or non-metallic status of the chemical elements of the periodic table under ambient and extreme conditions; a link with Pauling’s ‘metallic orbital’ is also established here.
Visualizing Fetal Mouse Vasculature by India Ink Injection: Figure 1.
Authors: Nagy Andras 
Published: February 2010

INTRODUCTIONThe technique described in this protocol was first applied in chicken embryos to visualize the circulatory system. The following method is an adaptation of this “classic” method to the mouse. The basic procedure is to dissect 12.5-dpc (days post-coitus) or older embryos with an intact yolk sac and placenta while the circulation is still active. India ink is then injected slowly into a branch of the vitelline vein of the yolk sac. The carbon particles in the ink are distributed into the arterial system by the beating heart. After fixation and clearing, the three-dimensional structure of the fetal arterial system becomes visible.
Calcium Phosphate Transfection of 3T3 Fibroblasts
Authors: Smale Stephen T. 
Published: February 2010

INTRODUCTIONMixing DNA with calcium chloride in a phosphate buffer results in the formation of a DNA/calcium phosphate precipitate which, when layered onto cultured cells, is taken up by endocytosis. The method is used widely for transfecting fibroblasts and other adherent cell types and can be performed easily with reagent-grade chemicals. This protocol describes the calcium phosphate transfection of murine 3T3 fibroblasts. Briefly, cells are grown on 60- or 100-mm tissue culture dishes and passaged 1 d prior to transfection, such that they are ~50% confluent at the time of transfection. This allows the cells to be transfected when most are not in direct contact with other cells. It also allows the cells to reach 100% confluence ~48 h post-transfection, when most transiently transfected cells are harvested. A precipitate containing DNA and calcium phosphate is formed by gradually mixing a phosphate-containing buffer with a solution of DNA and calcium chloride. The mixture is then layered onto a plate containing the adherent cultured cells and growth medium. After the cells have been exposed to the precipitate for a defined period of time, the medium containing the precipitate is removed and fresh medium is added to prevent toxicity. The procedure is suitable for performing both transient and stable transfection experiments.
Transfection by Electroporation of RAW 264.7 Macrophages
Authors: Smale Stephen T. 
Published: February 2010

INTRODUCTIONIn electroporation-based transfection methods, the DNA and cells are mixed in an empirically defined buffer, which establishes the resistance during the electric shock. The solution is placed in a cuvette that is compatible with the electroporation device being used. The mixture is then subjected to a brief high-voltage shock, which induces or stabilizes pores in the plasma membrane through which the DNA enters the cell. The cells are allowed to recover by a brief incubation at room temperature and then transferred to a tissue culture plate or T-flask along with growth medium and serum. Electroporation is an attractive method for transfection because it is more rapid and involves fewer manipulations than other methods and can be used for many types of adherent and nonadherent cells. This protocol describes transfection by electroporation of RAW 264.7 macrophages.
Preparation of the Gel and Column for Chromatofocusing: Figure 1.
Authors: Mohammad Jamil 
Published: February 2010

INTRODUCTIONThe appropriate stationary phase for chromatofocusing depends very much on the intended application. In general, in order to form a linear pH gradient (which is critical for good separation), the stationary phase must provide uniform buffering capacity over the pH separation range of interest. Thus, the functional groups on the matrix must be able to provide high buffering capacity over a broad pH range. Examples of such functional groups are polyethyleneimine (PEI) and a mixture of tertiary and quaternary amines. The most commonly used stationary phases for chromatofocusing are polymer-based stationary phases such as Mono P or polybuffer exchanger (PBE). In this protocol, a column is readied and packed with PBE matrix. The matrix is equilibrated with the buffer that will be used at the start of the separation, and the quality of the packing is assessed using cytochrome c.
Preparation of the Sample for Chromatofocusing: Buffer Exchange and Desalting
Authors: Mohammad Jamil 
Published: February 2010

INTRODUCTIONChromatofocusing separates proteins on the basis of differences in their isoelectric point (pI). Successful chromatofocusing depends on careful preparation of the protein sample, as described in this protocol. The protein must be transferred to the same buffer that will be used to equilibrate the chromatofocusing column. The buffer pH should be higher than the pI of the protein to keep the proteins negatively charged, which facilitates their binding to the column. A protein sample containing particulate matter will decrease the resolution of the separation and shorten the column lifetime. Therefore, it is necessary to remove all insoluble and immiscible material from the sample prior to loading it on the column. The sample is first clarified by filtration or centrifugation and is then transferred into the start buffer using a high-capacity, fast-flowing, size-exclusion column packed with Sephadex G-25.
Removal of Elution Buffer from Protein Sample Fractions after Chromatofocusing
Authors: Mohammad Jamil 
Published: February 2010

INTRODUCTIONChromatofocusing is a technique that separates proteins on the basis of differences in their isoelectric point (pI). Proteins are often eluted from a chromatofocusing column in Polybuffer or Pharmalyte. These buffers typically do not interfere with subsequent amino acid analysis or with the Coomassie blue protein assay. If buffer exchange and/or desalting is required, a number of methods are available to the researcher. Centrifugal filter units work well. As is described in this article, proteins can be concentrated and transferred to another buffer using ammonium sulfate precipitation which, in some cases, is performed in conjunction with hydrophobic interaction chromatography.
Cleaning, Regeneration, and Storage of Chromatofocusing Columns
Authors: Mohammad Jamil 
Published: February 2010

INTRODUCTIONChromatofocusing separates proteins on the basis of differences in their isoelectric point (pI). A chromatofocusing column should be cleaned and regenerated after use, as described in this protocol, to remove any strongly bound substances. The following observations indicate that column cleaning may be necessary: increased back pressure in the column, a color change at the top of the column, loss of resolution, or reduced sample recovery. To avoid these problems, clean the column routinely (e.g., after every fifth or tenth run). More frequent and extended cleaning procedures may be necessary if complex samples are applied. The steps in this article are guidelines. Personal experience with possible contamination should be used to evaluate which cleaning method is suitable.
Four-Dimensional Imaging of Plant Cells During the Cell Cycle
Authors: Fang Yuda , Spector David L. 
Published: February 2010

INTRODUCTIONLive cell imaging is an essential approach for studying the structure, dynamics, and functions of cells in a living plant under normal or stressed growth conditions. The tiny flowering plant, Arabidopsis thaliana, provides an ideal system to apply various live microscopy techniques. Its small size allows fluorescent light to penetrate the tissues, and its plantlets contain different cell types with different ploidy levels and differentiation stages. Its 2C nucleus contains only five pairs of chromosomes in which heterochromatin domains are organized as chromocenters, and these domains are easily resolved under the microscope. In addition, the availability of powerful genetic tools facilitates the investigation of the molecular mechanisms underlying various cellular phenomena. In designing live imaging experiments, one must keep in mind that plants sense light, temperature, osmolarity, humidity, gravity, and nutrition. In addition, plants also have strong circadian rhythms of physiological behavior and gene expression. Moreover, plant tissues are normally thick (having multiple cell layers), and can have strong autofluorescence, especially in green leaves. Therefore, optimized culturing and imaging conditions are essential for successful live cell studies in plants. In this protocol, specific chromatin loci (centromeres) in Arabidopsis are tagged with centromere-specific histone 3 variant (HTR12)-fluorescent protein (FP) fusions, and transgenic plants expressing these fusions are generated. Three- and four-dimensional imaging techniques are used to visualize the organization and dynamics of these specific chromatin loci in interphase and through mitosis. The procedure can be modified easily to accommodate other proteins or structures of interest.
Analysis of Gene Expression by In Situ Hybridization on Adult Zebrafish Brain Sections
Authors: Kühn Enrico , Köster Reinhard W. 
Published: February 2010

INTRODUCTIONWhole-mount in situ hybridization is a powerful method for the analysis of gene expression in zebrafish. However, the thickness of adult brain tissue often hampers penetration of reagents, making the direct application of protocols normally used for embryonic stages on adult tissues difficult. This protocol presents a detailed procedure for the dissection, preparation, and processing of the adult zebrafish brain for detection of gene expression in situ using digoxigenin (DIG)-labeled RNA probes on vibratome sections: The entire procedure is presented, including synthesis of labeled antisense RNA, sectioning of the adult zebrafish brain, and in situ hybridization. Using this method, all parts of the tissue are easily labeled and expression patterns are reproduced faithfully between trials. Unlike whole-mount preparations, gene expression examined on vibratome sections can easily be compared to a detailed zebrafish brain atlas and assigned to specific tissues.
Purification of Genomic DNA Extracted from Environmental Sources for Use in a Polymerase Chain Reaction: Figure 1.
Authors: Newman Molli M. , Feminella Jack W. , Liles Mark R. 
Published: February 2010

INTRODUCTIONThe ability to amplify genomic DNA in a polymerase chain reaction (PCR) is dependent upon the purity of the DNA template. Environmental genomic DNA often contains contaminants (e.g., polyphenols, humic acids, polysaccharides) that reduce template purity and can be difficult to remove, thereby inhibiting PCR amplification. There is thus a need for a method to purify extracted genomic DNA without reducing DNA concentration. In this protocol, extracted genomic DNA is embedded in agarose plugs and incubated in a formamide and salt (NaCl) solution to remove contaminants. The NaCl works to deproteinize and stabilize the DNA. The formamide serves to denature the DNA (which will subsequently be renatured within the agarose plug) and any contaminants that may be bound to the DNA. The purified DNA is extracted from the agarose plug using a standard commercial agarose extraction method, and the DNA may then be used as a template for PCR. Genomic DNA purified using this method has been shown to serve as an efficient template for PCR, without significant loss of DNA yield. An additional advantage of the method is that it allows the simultaneous processing of large numbers of samples at once.
DNase-seq: A High-Resolution Technique for Mapping Active Gene Regulatory Elements across the Genome from Mammalian Cells
Authors: Song Lingyun , Crawford Gregory E. 
Published: February 2010

INTRODUCTIONIdentification of active gene regulatory elements is a key to understanding transcriptional control governing biological processes such as cell-type specificity, differentiation, development, proliferation, and response to the environment. Mapping DNase I hypersensitive (HS) sites has historically been a valuable tool for identifying all different types of regulatory elements, including promoters, enhancers, silencers, insulators, and locus control regions. This method utilizes DNase I to selectively digest nucleosome-depleted DNA (presumably by transcription factors), whereas DNA regions tightly wrapped in nucleosome and higher-order structures are more resistant. The traditional low-throughput method for identifying DNase I HS sites uses Southern blots. Here, we describe the complete and improved protocol for DNase-seq, a high-throughput method that identifies DNase I HS sites across the whole genome by capturing DNase-digested fragments and sequencing them by high-throughput, next-generation sequencing. In a single experiment, DNase-seq can identify most active regulatory regions from potentially any cell type, from any species with a sequenced genome.
Live Cell Imaging of Plants
Authors: Fang Yuda , Spector David L. 
Published: February 2010

INTRODUCTIONLive cell imaging is an essential approach for studying the structure, dynamics, and functions of cells in a living plant under normal or stressed growth conditions. The tiny flowering plant, Arabidopsis thaliana, provides an ideal system to apply various live microscopy techniques. Its small size allows fluorescent light to penetrate the tissues, and its plantlets contain different cell types with different ploidy levels and differentiation stages. Its 2C nucleus contains only five pairs of chromosomes in which heterochromatin domains are organized as chromocenters, and these domains are easily resolved under the microscope. In addition, the availability of powerful genetic tools facilitates the investigation of the molecular mechanisms underlying various cellular phenomena. In designing live imaging experiments, one must keep in mind that plants sense light, temperature, osmolarity, humidity, gravity, and nutrition. In addition, plants also have strong circadian rhythms of physiological behavior and gene expression. Moreover, plant tissues are normally thick (having multiple cell layers), and can have strong autofluorescence, especially in green leaves. Therefore, optimized culturing and imaging conditions are essential for successful live cell studies in plants. This article discusses the general experimental considerations and design for live plant imaging studies.