bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mutation at Residue 523 Creates a Second Receptor Binding Site on Human Parainfluenza Virus Type 1 Hemagglutinin-Neuraminidase Protein
Authors: Bousse Tatiana , Takimoto Toru 
Published: August 2006

ABSTRACT
The paramyxovirus hemagglutinin-neuraminidase (HN) is a multifunctional protein mediating hemagglutination (HA), neuraminidase (NA), and fusion promotion activities. It has been a matter of debate whether HN contains combined or separate sites for HA and NA activities. To clear the issue, we determined the presence of the second binding site on human parainfluenza virus (hPIV) type 1, 2, and 3 and Sendai virus (SeV) HN proteins. Results of virus elution from erythrocytes at an elevated temperature and HA inhibition by NA inhibitor BCX-2798 suggest that all hPIVs bind to the receptor only through the NA catalytic site, while SeV HN has an additional receptor binding site. Comparison of SeV and hPIV1 HN sequences revealed two amino acid differences at residues 521 and 523 in the region close to the second binding site identified in Newcastle disease virus HN. We mutated hPIV1 HN at position 523 from Asn to the residue of SeV HN, Asp, and rescued a recombinant SeV that carries the mutated hPIV1 HN by a reverse genetics system. The hPIV1 HN with Asp at position 523 hemagglutinated in the presence of BCX-2798, suggesting that the amino acid difference at position 523 is critical for the formation of a second binding site. Creation of the second binding site on hPIV1 HN, however, did not significantly affect the growth or fusion activity of the recombinant virus. Our study indicates that the presence and requirement of a second binding site vary among paramyxoviruses.
Proteomic and Biochemical Analysis of Purified Human Immunodeficiency Virus Type 1 Produced from Infected Monocyte-Derived Macrophages
Authors: Chertova Elena , Chertov Oleg , Coren Lori V. , Roser James D. , Trubey Charles M. , Bess Julian W. , Sowder Raymond C. , Barsov Eugene , Hood Brian L. , Fisher Robert J. , Nagashima Kunio , Conrads Thomas P. , Veenstra Timothy D. , Lifson Jeffrey D. , Ott David E. 
Published: August 2006

ABSTRACT

Human immunodeficiency virus type 1 (HIV-1) infects CD4
+
T lymphocytes and monocytes/macrophages, incorporating host proteins in the process of assembly and budding. Analysis of the host cell proteins incorporated into virions can provide insights into viral biology. We characterized proteins in highly purified HIV-1 virions produced from human monocyte-derived macrophages (MDM), within which virus buds predominantly into intracytoplasmic vesicles, in contrast to the plasmalemmal budding of HIV-1 typically seen with infected T cells. Liquid chromatography-linked tandem mass spectrometry of highly purified virions identified many cellular proteins, including 33 previously described proteins in HIV-1 preparations from other cell types. Proteins involved in many different cellular structures and functions were present, including those from the cytoskeleton, adhesion, signaling, intracellular trafficking, chaperone, metabolic, ubiquitin/proteasomal, and immune response systems. We also identified annexins, annexin-binding proteins, Rab proteins, and other proteins involved in membrane organization, vesicular trafficking, and late endosomal function, as well as apolipoprotein E, which participates in cholesterol transport, immunoregulation, and modulation of cell growth and differentiation. Several tetraspanins, markers of the late endosomal compartment, were also identified. MDM-derived HIV contained 26 of 37 proteins previously found in exosomes, consistent with the idea that HIV uses the late endosome/multivesicular body pathway during virion budding from macrophages.
Syntactic Features of the Syrohexapla of Ezekiel
Authors: Lund Jerome 
Published: August 2006

AbstractAn analysis of syntactic features found in the Syrohexapla of Ezekiel in comparison to the Peshitta, on the one hand, demonstrates diachronic development within the Syriac language, and in comparison to the Greek, on the other hand, proves that the Syrohexapla translation was made for scholarly purposes, not for congregational use.
The virtual source method: Theory and case study
Authors: Bakulin Andrey , Calvert Rodney 
Published: August 2006

We present a way to image through complex overburden. The method uses surface shots with downhole receivers placed below the most complex part of the troublesome overburden. No knowledge of the velocity model between shots and receivers is required. The method uses time-reversal logic to create a new downward-continued data set with virtual sources (VS's) at the geophone locations. Time reversal focuses energy that passes through the overburden into useful primary energy for the VS. In contrast to physical acoustics, our time reversal is done on a computer, utilizing conventional acquisition with surface shots and downhole geophones. With this approach, we can image below extremely complex (realistic) overburden — in fact, the more complex the better. We recast the data to those with sources where we actually know and can control the waveform that has a downward-radiation pattern that may also be controlled, and is reproducible for 4D even if the near-surface changes or the shooting geometry is altered slightly. To illustrate the method, we apply the VS technique to a synthetic, elastic example with extreme heterogeneity, where conventional approaches fail to image the data. A 4D field-data example shows that the VS method (VSM) enables sensitive reservoir monitoring below a complex, time-variant near surface that is not achievable with surface 4D seismic or conventional 4D vertical seismic profiling (VSP).
Covalent Fixation of the Cyclic Tetramer of a Metallo-porphyrin Based on Self-complementary Quadruple Hydrogen Bonding
Authors: Ohkawa Haruki , Takayama Akihiro , Nakajima Satoshi , Nishide Hiroyuki 
Published: August 2006

Abstract
The stability of quadruple hydrogen bonding in the cyclic tetramer of a metallo-porphyrin before and after a covalent fixation was investigated. According to competition and energy-transfer experiments, the exchange reaction between the cyclic tetramers of the metallo-porphyrin was fully suppressed by the covalent fixation. This spontaneous cyclization–covalent fixation strategy based on olefin metathesis can open the way to the use of cyclic assemblies in a solid phase.
Cycloaddition Reactions of Transition Metal-containing Benzopyrylium and Related Zwitterionic Intermediates
Authors: Kusama Hiroyuki , Iwasawa Nobuharu 
Published: August 2006

Abstract
Recent advances in generation and cycloaddition reactions of transition metal-containing benzopyrylium and related zwitterionic intermediates from o-alkynylphenylcarbonyl or imine derivatives are summarized focussing on the difference of the two reaction pathways, that is, [3 + 2] and [4 + 2] cycloaddition reactions.
Electron Microscopy as a Method of Identifying Clays
Authors: Bates Thomas F. 
Published: August 2006

Abstract
Electron microscope studies show that most of the clay minerals have
morphological characteristics which can be effectively used to aid in their
identification. In addition, detailed studies at high magnification have
provided structural information not obtainable by other means.
In the kaolinite group each of the common minerals has a clear-cut and
diagnostic morphology. However, much more work is needed on flint clays and
the kaolins in soils before the same can be said of these varieties.
Continued study of halloysite reveals significant details pertinent to the
form and structure of the tubular crystals.
Illites from different sources show interesting differences in form
which reflect variation in the degree of crystallinity. An illite from the
Ordovician Oswego formation shows an unusual development of narrow to broad
lath-shaped crystals. Except for lower content of iron and magnesium the
material has all the characteristics of other illites. The thinnest laths
are of the same order of thickness as the flakes of more common illites.
Certain mixed-layer minerals are identical in morphology with some varieties
of illite.
The minerals of the moutmorillonite group have been the most difficult
of the clay minerals to characterize on the basis of morphology. The
lath-shaped crystals of certain beidellites, sauconite, nontronite, and
hectorite are diagnostic. The metal shadowing technique shows that many of
the laths approach one unit cell in thickness.
The morphology of many montmorillonites is dependent upon the mode of
sample preparation. The replica method offers a means of studying clay
particles in their natural state but this technique is still in the early
stages of development as it relates to the clay minerals.
Differential Thermal Analysis of Clays and Carbonates
Authors: Rowland Richards A. 
Published: August 2006

Abstract
Differential thermal analysis (DTA) began soon after the development of
the thermocouple. It has progressed through the systematic development of
better equipment and the cataloguing of typical DTA curves for a variety of
materials until good technique now requires control of the composition and
pressure of the furnace atmosphere as well as consideration of the
thermodynamics and kinetics of the reactions involved. Although differential
thermal analyses have been made for many materials, the major applications
have been concerned with clay and carbonate minerals.
In DTA curves for clay minerals the low-temperature endothermic loop
associated with the loss of water, and the high-temperature exothermic loop
accompanying the formation of new compounds, are changed in shape,
temperature, and intensity by the kind of exchange cations. The
midtemperature-range endothermic loop has a temperature dependence on the
partial pressure of water in the furnace atmosphere.
For the anhydrous normal carbonates the dissociation temperature and its
dependence on the partial pressvire of CO2 are in the
decreasing order Ca, Mg, Mn, Fe, and Zn. The lower temperature loop of
dolomite, the reaction for which must be preceded by an internal
rearrangement, is independent of the pressure of CO2
but may be shifted to a lower temperature by prolonged fine grinding which
accomplishes a similar rearrangement.
Role of Physical Properties of Clays in Soil Science
Authors: Page J. B. 
Published: August 2006

Abstract
The physical properties of clay are of extreme importance in soil
science. Plant growth, and hence crop production, within any environmental
condition is largely controlled by soil structure which results from
reactions involving clay. The active clay material in soil, particularly in
combination with small amounts of organic matter, exerts a tremendous effect
on soil properties. This effect may be on structure (the arrangement of soil
particles), or on consistence (the response of the soil to mechanical
manipulation). Where structure is favorable soil grains are clumped together
into effectively larger aggregates so that soils have a more open
arrangement and water and air can move freely and roots function normally.
Where structure is unfavorable, soils tend to be heavy and impervious, and
both the physical and chemical properties of the soil become unfavorable for
plant growth. Soils which are low in clay, such as sands and silts, exhibit
a rather narrow range over which physical properties can change and may be
unfavorable for plants, being droughty and lacking in fertility. Structure
of soil may change through action of natural forces, management practices,
or cropping systems, and it is of great importance that we understand how
structure affects plants, and how it is formed and stabilized by reactions
involving clay.
Combination of clay with relatively small amounts of certain organic
compounds greatly changes the physical properties of the system and the
nature of the combination and the mechanics of the soil structure-forming
process are but little understood. Such changes greatly affect soil
consistence and soil-water relationships as well as soil structure. The
problem is made difficult since the results of any particular combination or
change in clay characteristics must be interpreted not in terms of the clay
system alone but in light of the resultant effect on the complex and dynamic
system which constitutes a soil. Solution of such problems, however, may be
of great importance to our future ability to produce food and fiber
abundantly and efficiently from our limited soil resource.
Importance of Clay in Applied Soil Mechanics
Authors: Hveem Francis N. 
Published: August 2006

Abstract
Interparticle friction is the principal property which permits soils and
granular materials to resist load without formation. Dry soils of virtually
all types are highly stable. The suitability of soils for engineering
purposes depends largely upon their ability to remain in place and support
whatever loads may be placed upon them, either by a permanent engineering
structure or by transient vehicle loads. A study of the properties which
distinguish the more satisfactory from the less satisfactory soils indicates
that in the majority of eases clays are detrimental to stability. It is
apparent that wet clay has the effect of a lubricant in diminishing the
natural resistance due to friction that would otherwise exist. It is
necessary that the civil engineer responsible for construction of any form
of earth work should be informed not only concerning the Quantity of clay
minerals that are present but also about their nature and their potential
influence on the engineering properties of the soil.
Genesis of Clay Minerals in Some Pennsylvanian Shales of Indiana and Illinois
Authors: Murray Haydn H. 
Published: August 2006

AbstractShales of marine, brackish-water, and nonmarine origin, collected from cyclothems of Pennsylvanian age, were analyzed chemically and mineralogically. Clay mineral identifications were accomplished using x-ray diffraction and differential thermal analysis techniques. Summations of the structure amplitudes of the individual clay minerals formed a basis for semi-quantitative ratios between illite and kaolinite-chlorite. Illite was found to be enriched in the marine shales. The origin of the authigenic clay minerals in the shales is discussed from two aspects. The first and probably the more correct uses the thesis that the ultimate clay mineral is built up from a skeletal aluminum-silicate structure; the second discusses the origin of the clay minerals from a purely colloidal point of view. Trace element determinations, pH values, and pipette analyses are also included as a part of this study.
Clay Diagenesis in the Chesapeake Bay Area
Authors: Powers Maurice C. 
Published: August 2006

AbstractThe rivers of the Chesapeake Bay area carry in suspension predominantly a well formed to degraded illite with minor amounts of kaolin and accessory degraded chlorite. Montmorillonite is rare.Electron microscope photographs of suspended and bottom sediment clays in the James estuary indicate a decrease in floccular size and an increase in crystal size with increasing salinity.A chlorite-like clay is forming in the Chesapeake Bay estuaries. Its thermal stability increases with increase in the salinity of the environment and with depth in the sediments. This material seems to arise from the diagenesis of degraded illite in the Chesapeake Bay area, but it has also been observed to result from diagenesis of a montmorillonoid in the Atchafalaya region of the Gulf Coast.The geochemical relations of chloride, sodium, calcium, potassium, and magnesium in the clays of the James estuary support the hypothesis that chlorite is forming in the estuarine and marine environment.
The Decomposition Products of Anorthite Attacked by Pure Water at Elevated Temperatures and Pressure
Authors: Frederickson A. F. , Cox J. E. 
Published: August 2006

AbstractThe behavior of anorthite under the test conditions is similar to that of other feldspars and quartz. The solubility of anorthite in pure water was measured at 300 bars pressure between 200° and 350°C. Under these conditions, anorthite not only partially dissolves, but also disintegrates by shedding small particles of crystalline material which forms, with matter in true solution, a nonhomogeneous suspension. Two zeolites (afwillite and xonotlite) develop at the higher temperatures. Their stability is determined by the CaO:SiO2 ratio of the solution.The anorthite fragments react with the solution. They maintain their identity although their composition and structure gradually change over a wide temperature range. Possibly the zeolites inherit their structure from the altered anorthite. It is almost certain that xonotlite inherits its structure from afwillite.
The Application of Phase Equilibrium Data to Certain Aspects of Clay Mineralogy
Authors: Roy Rustum 
Published: August 2006

AbstractThe recent interest in the determination of the phase diagrams for many systems involving water as one component has been in those systems which are of greatest importance to clay mineralogy.The importance of both published and more recent work on synthesis of the clay is demonstrated in the ability to prepare chemically pure, mineralogically homogeneous kaolinites, montmorillonites, micas, and chlorites. The stability and identification of the clay minerals are discussed in relation to some of the major problems of clay mineralogy. Some of the chief objections to data obtained by the usual hydrothermal techniques are treated at length.
The Variations of Wyoming Bentonite Beds as a Function of the Overburden
Authors: Williams F. J. , Elsley B. C. , Weintritt D. J. 
Published: August 2006

AbstractThe colloidal properties and base-exchange characteristics of five deposits in four different areas were determined. The variations of the clay were, in general, a function of the amount of overburden and have been related to that dimension.From the standpoint of appearance, two types of clay were found in these areas. The highest grade clay has a yellow color whereas the other type, a blue clay, is customarily found to be of lower grade.Differential thermal studies of the yellow and blue clay, when correlated with variations in colloidal properties, strongly suggest that the change from blue to yellow is due to oxidation of iron.The primary cause for variation in properties is due to the Na/Ca ratio in the exchange positions regardless of whether the iron in the clay is in the ferrous or ferric state. Examination of purified clays indicates that the exchangeable base ratio of the field bentonites lies in a zone of instability. This zone occurs when the divalent ions amount to 40 to 60 percent of the base-exchange capacity.
Mineralogy of Soil Profiles: Iredell and Durham Soils from the Piedmont Province of North Carolina
Authors: Rolfe B. N. 
Published: August 2006

AbstractA comparative study of two soil profiles derived from a biotite-granite and from a metagabbro in the Piedmont Province of North Carolina was made. Intensive weathering of the granite has yielded a soil (Durham) with a clay fraction composed of a kaolinite-halloysite intermediate, mica, and quartz. Restricted weathering of the metagabbro has resulted in a soil (Iredell) with a clay fraction composed of a complex assemblage of chlorite, beidellite, vermiculite, interlayered talc-like minerals, and quartz.The data indicate that the Durham soil is derived from the severe alteration of a granite and that it represents an advanced stage in soil formation. The Iredell soil has been derived from the less active weathering of a metagabbro and represents a retarded, youthful stage in soil formation. The clay mineral assemblage of the Durham is that of a comparatively stable end product of weathering; that of the Iredell is indicative of a complex, unstable early stage in weathering.
Studies of the Clay Fraction of Southwestern Iowa Loess
Authors: Davidson D. T. , Handy R. L. 
Published: August 2006

AbstractThis paper presents data on clay-size material in the loess of southwestern Iowa. Most of the loess samples studied are Wisconsin in age. Regional distribution of clay-size material in the loess is discussed, and data are given on the modes of occurrence of clay in the loess. The following test methods were used to study the clay fractions of selected loess samples: Mechanical analysis, differential thermal analysis, cation-exchange determinations, refractive index determinations, and x-ray diffraction techniques. These tests indicate a uniformity in clay-mineral composition, with montmorillonite and illite group minerals predominating. Clay contents from mechanical analysis are correlated with various properties of the loess; in most cases the properties appear to be linear functions of the clay content. The plastic limit is discussed in detail.
The Use of Salted Pastes of Soil Colloids for X-Ray Analysis
Authors: Barshad Isaac 
Published: August 2006

AbstractA new technique for the x-ray analysis of soil colloids is proposed based on the finding that the interlayer swelling of montmorillonite persists in the presence of salt solutions and that the x-ray reflection representing the d(001) spacings becomes intensified in salted gels. The technique consists in flocculating the colloid from a suspension with sodium chloride, removing the “free” Fe2O3, Al2O3, and SiO2 by means of a solution of sodium citrate and sodium hydrosulfite, separating the cleaned colloid from the solution as a salted paste, and as such subjecting it to x-ray analysis. The method is not only more rapid than other recommended methods for x-ray analysis of soil colloids, but also — and which is of the utmost importance — yields a much more accurate picture of the mineralogical composition, particularly with respect to the content of the mica and the montmorillonite-type clays.