bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of Mutations at Position E138 in HIV-1 Reverse Transcriptase and Their Interactions with the M184I Mutation on Defining Patterns of Resistance to Nonnucleoside Reverse Transcriptase Inhibitors Rilpivirine and Etravirine
Authors: Xu Hong-Tao , Colby-Germinario Susan P. , Asahchop Eugene L. , Oliveira Maureen , McCallum Matthew , Schader Susan M. , Han Yingshan , Quan Yudong , Sarafianos Stefan G. , Wainberg Mark A. 
Published: April 2013

ABSTRACT
Impacts of mutations at position E138 (A/G/K/Q/R/V) alone or in combination with M184I in HIV-1 reverse transcriptase (RT) were investigated. We also determined why E138K is the most prevalent nonnucleoside reverse transcriptase inhibitor mutation in patients failing rilpivirine (RPV) therapy. Recombinant RT enzymes and viruses containing each of the above-mentioned mutations were generated, and drug susceptibility was assayed. Each of the E138A/G/K/Q/R mutations, alone or in combination with M184I, resulted in decreased susceptibility to RPV and etravirine (ETR). The maximum decrease in susceptibility to RPV was observed for E138/R/Q/G by both recombinant RT assay and cell-based assays. E138Q/R-containing enzymes and viruses also showed the most marked decrease in susceptibility to ETR by both assays. The addition of M184I to the E138 mutations did not significantly change the levels of diminution in drug susceptibility. These findings indicate that E138R caused the highest level of loss of susceptibility to both RPV and ETR, and, accordingly, E138R should be recognized as an ETR resistance-associated mutation. The E138K/Q/R mutations can compensate for M184I in regard to both enzymatic fitness and viral replication capacity. The favored emergence of E138K over other mutations at position E138, together with M184I, is not due to an advantage in either the level of drug resistance or viral replication capacity but may reflect the fact that E138R and E138Q require two distinct mutations to occur, one of which is a disfavorable G-to-C mutation, whereas E138K requires only a single favorable G-to-A hypermutation. Of course, other factors may also affect the concept of barrier to resistance.
Appropriateness of Empirical Treatment and Outcome in Bacteremia Caused by Extended-Spectrum-β-Lactamase-Producing Bacteria
Authors: Frakking Florine N. J. , Rottier Wouter C. , Dorigo-Zetsma J. Wendelien , van Hattem Jarne M. , van Hees Babette C. , Kluytmans Jan A. J. W. , Lutgens Suzanne P. M. , Prins Jan M. , Thijsen Steven F. T. , Verbon Annelies , Vlaminckx Bart J. M. , Cohen Stuart James W. , Leverstein-van Hall Maurine A. , Bonten Marc J. M. 
Published: April 2013

ABSTRACT

We studied clinical characteristics, appropriateness of initial antibiotic treatment, and other factors associated with day 30 mortality in patients with bacteremia caused by extended-spectrum-β-lactamase (ESBL)-producing bacteria in eight Dutch hospitals. Retrospectively, information was collected from 232 consecutive patients with ESBL bacteremia (due to
Escherichia coli
,
Klebsiella pneumoniae
, and
Enterobacter cloacae
) between 2008 and 2010. In this cohort (median age of 65 years; 24 patients were <18 years of age), many had comorbidities, such as malignancy (34%) or recurrent urinary tract infection (UTI) (15%). One hundred forty episodes (60%) were nosocomial, 54 (23%) were otherwise health care associated, and 38 (16%) were community acquired. The most frequent sources of infection were UTI (42%) and intra-abdominal infection (28%). Appropriate therapy within 24 h after bacteremia onset was prescribed to 37% of all patients and to 54% of known ESBL carriers. The day 30 mortality rate was 20%. In a multivariable analysis, a Charlson comorbidity index of ≥3, an age of ≥75 years, intensive care unit (ICU) stay at bacteremia onset, a non-UTI bacteremia source, and presentation with severe sepsis, but not inappropriate therapy within <24 h (adjusted odds ratio [OR], 1.53; 95% confidence interval [CI], 0.68 to 3.45), were associated with day 30 mortality. Further assessment of confounding and a stratified analysis for patients with UTI and non-UTI origins of infection did not reveal a statistically significant effect of inappropriate therapy on day 30 mortality, and these results were insensitive to the possible misclassification of patients who had received β-lactam–β-lactamase inhibitor combinations or ceftazidime as initial treatment. In conclusion, ESBL bacteremia occurs mostly in patients with comorbidities requiring frequent hospitalization, and 84% of episodes were health care associated. Factors other than inappropriate therapy within <24 h determined day 30 mortality.
The Clinical Isolate Pseudomonas aeruginosa MMA83 Carries Two Copies of the
bla
NDM-1
Gene in a Novel Genetic Context
Authors: Jovčić Branko , Lepsanović Zorica , Begović Jelena , Rakonjac Bojan , Perovanović Jelena , Topisirović Ljubiša , Kojić Milan 
Published: April 2013

ABSTRACT

The genetic context of the
bla
NDM-1
gene in the genome of
Pseudomonas aeruginosa
MMA83 was investigated. Sequencing of the cosmid selected for the
bla
NDM-1
gene revealed the presence of two
bla
NDM-1
copies in the genome of
P. aeruginosa
MMA83 in a unique genetic environment. Additionally, mating assays, DNA-DNA hybridization, and an S1 nuclease assay strongly suggest that the
bla
NDM-1
gene in
P. aeruginosa
MMA83 is chromosome borne.
Molecular Characterization of
bla
NDM-1
in a Sequence Type 235 Pseudomonas aeruginosa Isolate from France
Authors: Janvier Frédéric , Jeannot Katy , Tessé Sophie , Robert-Nicoud Marjorie , Delacour Hervé , Rapp Christophe , Mérens Audrey 
Published: April 2013

ABSTRACT

An NDM-1 carbapenemase-producing
Pseudomonas aeruginosa
isolate was recovered from a patient hospitalized in France after a previous hospitalization in Serbia. Genetic studies revealed that the
bla
NDM-1
gene was surrounded by insertion sequence IS
Aba125
and a truncated bleomycin resistance gene. This
bla
NDM-1
region was a part of the variable region of a new complex class 1 integron bearing IS common region 1 (IS
CR1
). The presence of IS
Pa7
upstream of this integron suggests insertion in a chromosomally located Tn
402
-like structure.
Chapter 5.—Origin of the Mississippi Valley Lead and Zinc Deposits—A Critical Summary
Authors: Bastin Edson S. , Behre Chas. H. 
Published: April 2013

INTRODUCTION
To trace fully and in chronological sequence the development of ideas concerning the origin of the lead and zinc ores of the Mississippi Valley region would be of considerable historic interest but a task of discouraging magnitude. It is fortunate, therefore, that the concepts of genesis, though varying much in detail, lend themselves to a grouping in two major categories: (1) The meteoric hypotheses, and (2) the magmatic hypothesis.
In the following summary chronology and the crediting of ideas to their ultimate source will be subordinated to simplicity and brevity of treatment.
As pointed out by Shepard (1898, p. 169–170), the earlier geologists, including Schoolcraft, Featherstonhaugh, Swallow, Owen, and Percival, being familiar mainly with the more steeply inclined vein-like occurrences, were almost unanimous in attributing the mineralization to ascending solutions from deep-seated sources. With the discovery and development of the great blanket deposits which gave little or no evidence of extension to considerable depths, the concept of leaching of the metals from sparse disseminations in the country rocks and concentration in their present location by meteoric waters became the dominant view and was presented in the reports of T. C. Chamberlin, Winslow, Bain, Van Hise, Buckley, Buehler, Grant, Siebenthal, Cox, and others. Shepard and Jenney were notable dissenters from this view. Of recent years, as a consequence of the mounting volume of evidence indicating that the majority of metalliferous deposits were deposited by solutions from magmatic sources and as a consequence of the discovery of numerous though scattered . . .
Chapter 2.—Structural Features of the Mississippi Valley Region and Their Relation to Mineralization
Authors: Giles Albert W. 
Published: April 2013

INTRODUCTION
The Mississippi Valley is a large area of plains and low plateaus between the Appalachian Mountains on the east and the Cordilleras on the west. It is the southern part of the central stable region of North America. The basement rocks are pre-Cambrian crystallines whose surface is irregular and nearly everywhere buried beneath Paleozoic and later sediments. The ancient crystallines appear at the surface in the Sioux quartzite area of southwestern Minnesota, the Black Hills of western South Dakota, the Baraboo region of Wisconsin, the St. Francis Mountains of eastern Missouri, the Arbuckle Mountains of south-central Oklahoma, the Wichita Mountains of southwestern Oklahoma, and the Central Mineral Region of eastern Texas. In general, however, the thickness of the sedimentary cover is several thousand feet. In the eastern and central parts of the Mississippi Valley the surface rocks are of Paleozoic age, except where overlapped by Coastal Plain Cretaceous and Tertiary sediments. In the western part of the Valley, Cretaceous and Tertiary rocks cover large areas and overlie the older Paleozoic sediments. The Paleozoic sediments were derived mainly from five old landmasses—Laurentia on the north, Appalachia on the east, Llanoria on the south, Columbia on the southwest, and Cascadia on the west. Since their deposition the beds have been flexed into broad domes and basins which constitute the major structural elements of the Mississippi Valley. The deformation of most of the region has been so slight that regional dips of more than one degree are rare. Locally broad and . . .
Chapter 3.—Igneous Rocks of the Mississippi Valley Lead-Zinc Districts
Authors: Tolman Carl , Landes Kenneth K. 
Published: April 2013

GENERAL STATEMENT
The igneous rocks of the Mississippi Valley lead-zinc district are widely distributed, but their total area of outcrop is relatively small (Fig. 13). They include exposed parts of the pre-Cambrian basement, almost wholly confined to the St. Francis Mountains adjacent to the southeastern Missouri lead-producing district, and small bodies which have intrusive contacts with sedimentary rocks of various horizons in the Paleozoic and in the Mesozoic as late as mid-Cretaceous. The rocks of the St. Francis Mountains occupy an area of several hundred square miles, but the other occurrences are so small that they must be indicated diagrammatically on all but very large scale maps. Nevertheless they are important components of the geological setting, and their careful consideration is warranted in order to bring out any possible genetic, structural, or other relationship that they may have to the lead-zinc mineralization.
The igneous rocks show a wide range in petrographic character, but it seems true, both among the pre-Cambrian and among the younger rocks, that they are preponderantly either basic or acidic with a meager development of intermediate types. Of exceptional petrographical interest are the alkalic varieties of Arkansas. The age of most of the igneous rocks younger than pre-Cambrian is indefinitely known, and there is difference of opinion as to whether more than one intrusive epoch is represented. An igneous history of some complexity is indicated in the pre-Cambrian rocks so that probably a considerable range of time in the pre-Cambrian is represented. However, since the pre-Cambrian intrusives . . .
Foreword
Authors: Bastin Edson S. 
Published: April 2013

The Mississippi Valley region has long held the dominant position in the domestic production of both lead and zinc and has been an important factor in bringing the United States into a position of world leadership in the production of these metals. The situation of these deposits in a mid-continent region of continually growing industrial importance, their large areal extent, and prolonged productivity have made them the object of repeated study by State and Federal Geological surveys and by geologists and engineers employed by the mining companies, and an amazingly voluminous literature concerning them has accumulated in the course of nearly 50 years of intermittent investigation.
Almost from the beginning of such studies scientific opinion on the origin of the ores has wavered back and forth between the concept that the ore-depositing solutions emanated from deep-lying bodies of igneous magmas and the view that the metals were scattered in minute amounts through the country rocks and had been dissolved from them by meteoric waters and precipitated in concentrated form in the present ore bodies.
Not in the hope of settling this old and vexing problem but of hastening its eventual solution, these ore deposits became the object of special attention by the National Research Council through a subcommittee of its Committee on the Processes of Ore Deposition that was organized in 1932, and a number of papers that were partly stimulated by this committee’s activities have already been published. The committee felt that its official activities could appropriately be concluded . . .
Melting and Transformation Temperatures of Mineral and Allied Substances
Authors: Kracek F. C. 
Published: April 2013

ContentsPageTable 111. Elements1422. Oxides1433. Hydrous and hydrated oxides1464. Binary aluminates1485. Binary borates1496. Binary oxide systems1507. Three or more oxides (except SiO2)1528. Binary silicates1539. Ternary and higher silicate systems15510. Aluminosilicates15811. Borosilicates16112. Miscellaneous systems containing silicates16113. Hydrothermal alteration of silicates and other minerals16214. Carbonates16315. Sulfates16416. Oxygen salts16617. Haloids16818. Sulfide-type minerals17019. Ternary sulfides173
Scope of the tables.—These tables list the melting (congruent and incongruent) temperatures, boiling temperatures, and transition temperatures for the more important substances of interest to the geologist, the geochemist, and the petrologist. Eutectic and related data are given when the substance under discussion has been studied as a part of a binary or higher system. The aim in compiling the tables has been to describe the known thermal reactions of the compounds and the systems briefly, but in enough detail to be of use to an investigator in the field where extensive reference books are usually not available.
Arrangement.—The entries are arranged alphabetically by chemical symbol (elements) or formula (compounds). Compounds composed of two or more oxides (except carbonates, sulfates, and other oxygen salts) are entered in the increasing alphabetical order of the constituent oxides.
Mineralogical names are given following the nomenclature employed in Dana-Ford : Textbook of mineralogy (John Wiley and Sons Inc., New York).
Effect of Pressure on Temperatures of Melting and of Solid-Solid Equilibrium, in Systems of One Component
Authors: Birch Francis 
Published: April 2013

ContentsPageTable 121. Melting and solid-solid transitions of elements1771.1. Melting temperatures of A, H2, He, N2, Ne, and O21801.2. Formulas for melting curves1822. Melting and transitions of compounds1833. Liquid-vapor critical data185
In systems containing a single component, the change ΔT of the temperature of equilibrium between two phases resulting from a change of hydrostatic pressure ΔP upon the two phases is given by Clapeyron’s equation, ΔT/ΔP = TΔV/ΔH, where T is the absolute temperature, and ΔV and ΔH are the volume change and heat absorption, respectively, for a given mass of material in passing from one phase to the other. One phase may be considered the “high-temperature” phase, the other, the “low-temperature” phase. Heat is always absorbed in passing from the low-temperature phase to the high-temperature phase at constant pressure (the actual quantity may be negligibly small). In the same way, one of the phases will be the “low-pressure” phase, the other the “high-pressure” phase; in passing from the low-pressure phase to the high-pressure phase at constant temperature, the density always increases, or ΔV is negative. There is, however, no a priori way of knowing whether the high-temperature phase will be the high-pressure phase or the low-pressure phase. The liquid phase is “normally” the high-temperature, low-pressure phase with respect to solid phases; thus, in passing from a “normal” solid phase to the liquid phase, ΔV and ΔH are both positive, and ΔT/ΔP is positive (the melting temperature increases with . . .
Heat Capacity; Heat of Fusion
Authors: Goranson Roy W. 
Published: April 2013

ContentsPageTable 161. Heat capacity of minerals2282. Heat capacity of rocks2353. Heats of transformation and of fusion2374. Heat capacity of gases241
Heat capacities of minerals.—In the tables (in this section), the minerals are classified according to the first elements of their chemical formulae; for example, albite (NaAlSi8O8) will be found under sodium, and calcite (CaCO3) under calcium. The heat data are given in terms of absolute joules per gram (one joule = 0.23895 gram calories at 15°C.).
True or instantaneous heat capacities may be obtained by measuring the amount of heat needed to raise the temperature of the sample one degree or fraction thereof. This is the preferable type of data, available for many materials at low temperatures. At high temperatures this method is experimentally difficult because of large radiation losses so that ordinarily a different technique is employed—namely, the method of mixtures. (See W. P. White, The Modern Calorimeter, N. Y., 1928.) This latter method yields data in the form of mean or interval heat capacities. The mean heat capacity is usually given for the temperature interval between 273.1°K. (0°C.) or room temperature and some higher temperature. The quantity measured is, however, the difference in heat content between some elevated temperature and that of the calorimeter. In order to convert these quantities to true heat capacities the mean heat capacity data (at constant pressure) are fitted to the equation 1c¯p|TTo=a+bTo+T2−cToTwhere c̄p is the mean heat capacity at . . .
Radioactivity: The Earth’s Heat and Geological Age Measurements
Authors: Evans Robley D. , Goodman Clark , Keevil Norman B. 
Published: April 2013

ContentsPageTable 181. Heat flow to the earth’s surface2692. Radioactive content and heat generation in rocks2703. Ultimate products of naturally occurring disintegration processes2714. Isotopic constitution of radioactive elements and their end products2725. Variations in the isotopic composition of common lead2736. Lead age ratios of selected radioactive minerals2747. Age results by lead isotope ratios2758. Helium age ratios of various magnetite deposits276
THE EARTH’S HEAT
A. Loss of heat.—Only a limited amount of data is available on the heat flux transferred to the surface from within the earth. These observations are summarized in Table 18–1 and show a mean value of 1.3 ± 0.1 × 10−6 cal./cm.2/sec., when the necessary correction is made for the effect of the recent ice age. Considering the heat conductivity of the outer granitic layer as 0.006 cal./sec./cm.2/°C./cm., the corresponding surface geothermal gradient is about 2.0 × 10−4°C./cm., or 20°C./km.
This heat is partially transferred to the atmosphere by convection and radiation with subsequent reradiation by the atmosphere into space. The remainder of the heat is radiated directly through the blanketing atmosphere. The proportion of heat loss attributable to each of these processes is still a matter of speculation.
B. Sources of heat.—Aside from the residuum of heat associated with the earth at the time of its formation, the primary sources of heat in the earth are radioactivity, solar radiation, and exothermal chemical changes.
1. Radioactivity: Because . . .
Electrical Properties of Rocks and Minerals
Authors: Slichter Louis B. , Telkes M. 
Published: April 2013

ContentsPageTable 211. Electrical resistivity of rocks and soils3042.1. Electrical resistivity of mineralized rocks3072.2. Electrical resistivity of specular hematite in quartz porphyry3073. Electrical resistivity of metallic sulfides3084. Electrical resistivity of some oxides and miscellaneous minerals3115. Electrical resistivity of hydrocarbons3136.1. Electrical resistivity of natural water3146.2. Electrical resistivity of saline waters3146.3. Effect of water and oil on direct current resistance of sandstone3156.4. Electrical resistivity of wet sand3156.5. Resistivity of soils and sea water measured with high-frequency alternating current3167. Dielectric constant of rocks3178. Dielectric constant of minerals3188.1. Dielectric constant of Rochelle salt, as function of temperature318
ELECTRICAL RESISTIVITY
(1) Electrolytic conductors.—The electrical conductivity of rocks and soils in place is generally due almost entirely to the moisture content. With some exceptions, the solid minerals which constitute the rock or soil are good insulators. Thus, the conductivity is not an essential property of the rock or rock type; it depends not only upon the capacity of the rock to absorb water and upon the kind and structure of its pore spaces, but also upon the amount and composition of the water retained. Hence, the conductivity may depend to an important extent upon the accident of the geological and climatic environment in which the material happens to find itself. It follows that resistivities tabulated in the literature should not be used to predict the . . .
Density at High Pressure; Compressibility
Authors: Birch Francis 
Published: April 2013

ContentsPageTable 41. Compressibility of elements crystallizing in the cubic system432. Compressibility of elements crystallizing in the hexagonal and tetragonal systems463. Compression of a few miscellaneous elements474. Compression and thermal expansion of the alkali metals484.1. Effect of pressure on thermal expansion485. Compression of elements to 50,000 kg/cm2496. Compression of compounds to 50,000 kg/cm2507. Compressibility of cubic compounds528. Compressibility of hexagonal, trigonal, and tetragonal compounds549. Compressibility of orthorhombic compounds5610. Compressibility of monoclinic and triclinic compounds5811. Change of compressibility on melting5912. Compressibility of several artificial and natural glasses6013. Compressibility of rocks at low pressures6114. Compressibility of rocks at high pressures62
Density and specific volume are dependent not only upon the temperature but also upon the stress. A stress system consisting of uniform pressure in all directions is known as “ hydrostatic” pressure; the change of specific volume or of density for not too great changes of hydrostatic pressure may be described in terms of a single coefficient, the compressibility β, defined by β=1V0(dVdP)T=1ρ0(dρdP)T, where V0 is the specific volume, ρ0 the density at 1 atmosphere, and P the pressure. Since dV/dP is intrinsically negative, β is a positive number, with the dimensions of the reciprocal of a pressure or stress. In general, β depends upon the pressure and the temperature. Its reciprocal K is known as the bulk modulus.
The compressibility . . .