bluuebunny/crossref_metadata_2025_split huggingface dataset:
Parallel Adaptation: One or Many Waves of Advance of an Advantageous Allele?
Authors: Ralph Peter , Coop Graham 
Published: July 2010

AbstractModels for detecting the effect of adaptation on population genomic diversity are often predicated on a single newly arisen mutation sweeping rapidly to fixation. However, a population can also adapt to a new environment by multiple mutations of similar phenotypic effect that arise in parallel, at the same locus or different loci. These mutations can each quickly reach intermediate frequency, preventing any single one from rapidly sweeping to fixation globally, leading to a “soft” sweep in the population. Here we study various models of parallel mutation in a continuous, geographically spread population adapting to a global selection pressure. The slow geographic spread of a selected allele due to limited dispersal can allow other selected alleles to arise and start to spread elsewhere in the species range. When these different selected alleles meet, their spread can slow dramatically and so initially form a geographic patchwork, a random tessellation, which could be mistaken for a signal of local adaptation. This spatial tessellation will dissipate over time due to mixing by migration, leaving a set of partial sweeps within the global population. We show that the spatial tessellation initially formed by mutational types is closely connected to Poisson process models of crystallization, which we extend. We find that the probability of parallel mutation and the spatial scale on which parallel mutation occurs are captured by a single compound parameter, a characteristic length, which reflects the expected distance a spreading allele travels before it encounters a different spreading allele. This characteristic length depends on the mutation rate, the dispersal parameter, the effective local density of individuals, and to a much lesser extent the strength of selection. While our knowledge of these parameters is poor, we argue that even in widely dispersing species, such parallel geographic sweeps may be surprisingly common. Thus, we predict that as more data become available, many more examples of intraspecies parallel adaptation will be uncovered.
Detection of Heterozygous Mutations in the Genome of Mismatch Repair Defective Diploid Yeast Using a Bayesian Approach
Authors: Zanders Sarah , Ma Xin , RoyChoudhury Arindam , Hernandez Ryan D , Demogines Ann , Barker Brandon , Gu Zhenglong , Bustamante Carlos D , Alani Eric 
Published: July 2010

Abstract
DNA replication errors that escape polymerase proofreading and mismatch repair (MMR) can lead to base substitution and frameshift mutations. Such mutations can disrupt gene function, reduce fitness, and promote diseases such as cancer and are also the raw material of molecular evolution. To analyze with limited bias genomic features associated with DNA polymerase errors, we performed a genome-wide analysis of mutations that accumulate in MMR-deficient diploid lines of Saccharomyces cerevisiae. These lines were derived from a common ancestor and were grown for 160 generations, with bottlenecks reducing the population to one cell every 20 generations. We sequenced to between 8- and 20-fold coverage one wild-type and three mutator lines using Illumina Solexa 36-bp reads. Using an experimentally aware Bayesian genotype caller developed to pool experimental data across sequencing runs for all strains, we detected 28 heterozygous single-nucleotide polymorphisms (SNPs) and 48 single-nt insertion/deletions (indels) from the data set. This method was evaluated on simulated data sets and found to have a very low false-positive rate (∼6 × 10−5) and a false-negative rate of 0.08 within the unique mapping regions of the genome that contained at least sevenfold coverage. The heterozygous mutations identified by the Bayesian genotype caller were confirmed by Sanger sequencing. All of the mutations were unique to a given line, except for a single-nt deletion mutation which occurred independently in two lines. All 48 indels, composed of 46 deletions and two insertions, occurred in homopolymer (HP) tracts [i.e., 47 poly(A) or (T) tracts, 1 poly(G) or (C) tract] between 5 and 13 bp long. Our findings are of interest because HP tracts are present at high levels in the yeast genome (&gt;77,400 for 5- to 20-nt HP tracts), and frameshift mutations in these regions are likely to disrupt gene function. In addition, they demonstrate that the mutation pattern seen previously in mismatch repair defective strains using a limited number of reporters holds true for the entire genome.
Epidemiology of Postconcussion Syndrome in Pediatric Mild Traumatic Brain Injury
Authors: Barlow Karen Maria , Crawford Susan , Stevenson Andrea , Sandhu Sandeep Sona , Belanger François , Dewey Deborah 
Published: July 2010

BACKGROUND:
Much disagreement exists as to whether postconcussion syndrome (PCS) is attributable to brain injury or to other factors such as trauma alone, preexisting psychosocial problems, or medicolegal issues. We investigated the epidemiology and natural history of PCS symptoms in a large cohort of children with a mild traumatic brain injury (mTBI) and compared them with children with an extracranial injury (ECI).

METHODS:
This investigation was a prospective, consecutive controlled-cohort study of 670 children who presented to a tertiary referral emergency department with mTBI and 197 children who presented with ECI. For all participants, data were collected by use of a telephone interview of a parent 7 to 10 days after injury. If a change from preinjury symptoms was reported by a parent, follow-up continued monthly until symptom resolution. Outcomes were measured by using the Post Concussion Symptom Inventory, Rivermead Postconcussion Symptom Questionnaire, Brief Symptom Inventory, and Family Assessment Device.

RESULTS:
There was a significant difference between the mTBI and ECI groups in their survival curves for time to symptom resolution (log rank [Mantel-Cox] 11.15, P &lt; .001). Three months after injury, 11% of the children in the mTBI group were symptomatic (13.7% of children older than 6 years) compared with 0.5% of the children in the ECI group. The prevalence of persistent symptoms at 1 year was 2.3% in the mTBI group and 0.01% in the ECI group. Family functioning and maternal adjustment did not differ between groups.

CONCLUSIONS:
Among school-aged children with mTBI, 13.7% were symptomatic 3 months after injury. This finding could not be explained by trauma, family dysfunction, or maternal psychological adjustment. The results of this study provide clear support for the validity of the diagnosis of PCS in children.
Iron Deficiency Anemia and Cognitive Function in Infancy
Authors: Carter R. Colin , Jacobson Joseph L. , Burden Matthew J. , Armony-Sivan Rinat , Dodge Neil C. , Angelilli Mary Lu , Lozoff Betsy , Jacobson Sandra W. 
Published: July 2010

OBJECTIVES:
This study examined effects of iron deficiency anemia (IDA) on specific domains of infant cognitive function and the role of IDA-related socioemotional deficits in mediating and/or moderating these effects.

METHODS:
Infants were recruited during routine 9-month visits to an inner-city clinic. IDA was defined as hemoglobin level &lt;110 g/L with ≥2 abnormal iron deficiency indicators (mean corpuscular volume, red cell distribution width, zinc protoporphyrin, transferrin saturation, and ferritin). At 9 and 12 months, the Fagan Test of Infant Intelligence (FTII); A-not-B task; Emotionality, Activity, and Sociability Temperament Survey; and Behavior Rating Scale were administered. Analyses were adjusted for potential confounders, including age and sociodemographic variables.

RESULTS:
Twenty-eight infants met criteria for IDA, 28 had nonanemic iron deficiency (NA ID) and 21 had iron sufficiency (IS). There was a linear effect for object permanence at 9 months: infants with IDA were least likely to exhibit object permanence, IS most likely, and NA ID intermediate. Infants with IDA and those with hemoglobin level ≤105 g/L showed poorer recognition memory on the FTII than infants without IDA. The Behavior Rating Scale orientation/engagement measure partially mediated these effects. Stronger effects of IDA on these outcomes were seen in infants who scored more poorly on the socioemotional measures.

CONCLUSIONS:
These data indicate poorer object permanence and short-term memory encoding and/or retrieval in infants with IDA at 9 months. These cognitive effects were attributable, in part, to IDA-related deficits in socioemotional function. Children with poor socioemotional performance seem to be more vulnerable to the effects of IDA on cognitive function.
The Eye Examination in the Evaluation of Child Abuse
Authors: Levin Alex V. , Christian Cindy W. ,   Committee on Child Abuse and Neglect, Section on Ophthalmology
Published: July 2010

This Clinical Report was revised. See https://doi.org/10.1542/peds.2018-1411.
Retinal hemorrhage is an important indicator of possible abusive head trauma, but it is also found in a number of other conditions. Distinguishing the type, number, and pattern of retinal hemorrhages may be helpful in establishing a differential diagnosis. Identification of ocular abnormalities requires a full retinal examination by an ophthalmologist using indirect ophthalmoscopy through a pupil that has been pharmacologically dilated. At autopsy, removal of the eyes and orbital tissues may also reveal abnormalities not discovered before death. In previously well young children who experience unexpected apparent life-threatening events with no obvious cause, children with head trauma that results in significant intracranial hemorrhage and brain injury, victims of abusive head trauma, and children with unexplained death, premortem clinical eye examination and postmortem examination of the eyes and orbits may be helpful in detecting abnormalities that can help establish the underlying etiology.
Radioactive Phosphorus and the Growth and Metabolic Activities of Soil Microorganisms
Authors: Goring C. A. I. , Clark Francis E. 
Published: July 2010

AbstractExperiments were conducted in quartz sand and in a silt loam to determine effect of differing levels of P32 on the growth and metabolic activity of soil microorganisms. Determinations were made of carbon dioxide evolved and of numbers of microorganisms, and in some experiments, of amounts of soluble phosphate, nitrate, and ammonia.In quartz sand treated with phosphorus, dextrose, urea, and mineral salts, and with differing amounts of P32, activity levels of 0.005 and 0.05 mc gave no appreciable differences. At 0.5 mc P32 per mg of P31, the rate of CO2 production was reduced during the first week, and differences in the soil flora were encountered. Recovery in CO2 production then followed, but the soil flora differences persisted throughout 3 weeks of incubation.In Seymour silt loam treated with 0.5 mc of P32 per mg of P31, there was found no influence on microbial numbers or on carbon dioxide evolution, but the amounts of soluble phosphate, ammonia, and nitrate at the end of 3 weeks were lower than for 0.05‐, 0.05‐, or 0‐mc levels of treatment. When the phosphorus treatment was supplemented with dextrose and urea, no differences in the P or N status of the aliquots could be demonstrated. With dextrose and urea added and a 5.0‐mc level of activity, there was only slight reduction in CO2 evolution and only slight differences in microbial numbers.
The Effect of Cultivation on Erodibility of Soils by Wind
Authors: Chepil W. S. , Englehorn C. L. , Zingg A. W. 
Published: July 2010

AbstractPhysical and chemical analyses of the soil samples chosen at random from over 90 fields from western Kansas during 1949 and 1950 were made to determine the rates of soil deterioration that are associated with the type of agriculture employed since the breaking of the virgin sod.In land that has been utilized for grain production for 19 years about 9 inches of topsoil, constituting all of the A horizon, has been removed, mainly by wind erosion. This land is now much less productive and contains substantially less organic matter and less undecomposed crop residues than the newly broken land. Due to lower amounts of crop residue this “old” cultivated land is more exposed to erosion by wind and water. The soil itself, however, is more resistant to erosion now than when it was first brought under cultivation, due to the presence at the surface of the finer textured and more structurally developed soil of the original B horizon. When the protective influence of crop residues was discounted, the old cultivated land was found to be less than half as erodible as land broken out of virgin sod between 1946 and 1948. With crop failures such as occur on all types of land in dry years, the recently broken land would apparently become most vulnerable to erosion by wind.
Flame Photometric Determination of Exchangeable Magnesium in Soils
Authors: Rich C. I. 
Published: July 2010

AbstractThe Beckman flame spectrophotometer was studied to determine its application to the determination of magnesium in soil extracts. A high flame temperature and a narrow slit width increased the intensity of Mg (2852 Å) relative to the flame background. Centrifuging satisfactorily cleared extracts and prevented most clogging of the atomizer. Fe, Ca, and Na caused significant interference at the Mg band head of 3708 Å particularly with Mg concentrations below 2.00 ME/100 ml. At the 2852 Å line, Ca in concentrations greater than 8 ME Mg/100 ml depressed the Mg intensity; Al or PO4 in concentrations greater than 100 ppm Al or P slightly depressed the Mg intensity, whereas Na in concentrations greater than 10 ME/100 ml increased the intensity. Other elements tested (K, Mn, Fe, S, and Si) at 2852 Å had no apparent effect within concentration ranges usually found in ammonium acetate (1N) and 0.05N HCl soil extracts. Twenty‐four different soils of Virginia were analyzed for exchangeable magnesium by the photometric method, and results did not differ significantly (5% level) from the chemical method. The average recovery of Mg added to 0.05N HCl extracts was 103% and the standard deviation was 5.3%. The most favorable instrumental conditions found were: wave length, 2852 Å; slit width, 0.15 mm; propane pressure, 2.0 cm toluene; oxygen pressure, 75 inches H2O; air pressure, 18 pounds per square inch; sensitivity control, about one turn from the counterclockwise limit. The intensity scale was set on 100 when a solution containing 2.0 ME Mg per 100 ml was atomized and the milliammeter needle brought to zero with the sensitivity control.
The Effect of Humus on Cationic Interactions in a Beidellite Clay
Authors: McLean E. O. 
Published: July 2010

AbstractPrevious studies of cationic interactions have been made for the most part using relatively pure clay minerals. This has been a logical place to start, but to be of maximum practical benefit in solving agronomic problems sooner or later the resulting principles must be projected back to the natural soils. Too little is known about the relationship between ionic activities in plant media and nutrient uptake. But certainly one would not expect close correlation between these activities in pure clay and nutrient uptake from a soil high in this particular clay mineral unless there were no other substances present which possess exchange properties capable of interfering with activities and interactions caused by the clay mineral. In this connection it is obvious that the effect of humus on the cationic activities and their inter‐relationships is of utmost importance.As a follow‐up to a similar study made previously with relatively pure beidellite clay, the present study has dealt with mixtures of 10 parts of the same clay to 1 part of crude humic acid. The activities of K, Na, and Ca in homoionic and in biionic systems were determined using the clay membrane electrode technique.The results obtained are summarized as follows:

The exchange capacity of the clay‐humic acid systems was only 73% of that of the sum of the component parts.

Since the base saturations of the biionic systems were made up on the basis of the sum of the exchange capacities, the actual exchange capacities were exceeded somewhat.

This relatively higher base saturation in the clay‐humus systems resulted in higher activities of the cations in all cases than in the clay alone.

In spite of the higher activities in the clay‐humic acid systems the interactions of the cations were very similar to those in the clay alone.

If the clay‐humic acid systems studied can be considered as somewhat analogous to the situation in the field, this relatively small interference by the humic acid may possibly indicate that information gotten from similar studies with pure clay could be projected with some degree of assurance to a whole soil which contains a predominance of that particular clay mineral.

Evidence is presented in support of the contention that the loss in cation exchange capacity as a result of interaction of the component materials was due to a loss of exchange capacity by the humic acid rather than the obstruction of exchange spots on the clay.
Some Theoretical Aspects of the Flow of Water in Unsaturated Soils
Authors: Klute A. 
Published: July 2010

AbstractThe validity of Darcy's law in unsaturated media and the assumptions made in its use are discussed. The relationship of the permeability coefficient in Darcy's law to various soil parameters is briefly considered, the total soil moisture potential is defined, and its components discussed. By use of the equation of continuity and Darcy's law, an equation of flow is derived, and the general problem of obtaining solutions of this equation is outlined. The special mathematical difficulties encountered when the permeability is considered as a function of the moisture content or the capillary potential are also indicated. A numerical solution of the flow equation for a semi‐infinite system is given, using a functional relationship between the permeability and the moisture content, and the phenomenon of a wetting front is shown to be indicated.
The Prevalence of Strains of Rhizobium phaseoli in Some Midwestern Soils
Authors: Burton J. C. , Allen O. N. , Berger K. C. 
Published: July 2010

AbstractThis study was aimed to ascertain (a) the natural occurrence of R. phaseoli in certain soils, (b) whether any relationships existed between types of nodulation and efficiencies of the strains, and (c) homogeneity of reactions among strains isolated from the same nodule.Variations among the strains in cultural and fermentative characteristics were marked, yet, on the whole, the strains isolated from the same nodules showed more uniformity in litmus milk reactions and ability to utilize the same carbohydrates than did those obtained from different nodules.From a practical point of view bean rhizobia were not abundant in any of the soils tested. Rhizobia isolated from different nodules on the same plant varied widely in efficiency. Of the 85 strains isolated from nodules formed on plants grown in soil‐vermiculite mixtures, only 12 were highly effective. Differences in plant growth response to strains isolated from suspensions of the same nodule were insignificant.
Chromatographic Separations of Inositol Phosphorus Compounds
Authors: Smith Donald H. , Clark Francis E. 
Published: July 2010

AbstractA chromatographic technique for the separation of sodium phytate and its enzymatically produced derivatives is described. From a mixture of sodium phytate and derivatives, nine organic phosphorus compounds were separated in sufficient quantities to permit determination of their inositol/phosphorus ratios. Phosphorus was determined colorimetrically following perchloric acid digestion, and inositol was determined by means of a biological assay. The determinations were replicated sufficiently that the number of phosphorus atoms per molecule of inositol was considered to have been determined to within one atom of the true value in all cases. The identity of the nine separated compounds was tentatively established.
Effects of Legumes in Different Cropping Systems on Yield of Corn
Authors: Reynolds E. B. , Norris M. J. 
Published: July 2010

AbstractThere were no significant differences in the yields of corn in 1950 at College Station where corn followed cotton which was preceded immediately by hairy vetch, Willamette vetch, Austrian Winter peas, Dixie Wonder peas, and Singletary peas plowed under for soil improvement. The application of 60 pounds of nitrogen per acre to the corn, however, produced a highly significant increase in the yield of corn.Of the four legumes and six cropping systems included in the work at Denton, only Hubam and Madrid sweetclovers produced significant increases in the yield of corn in 1950. Corn after Hubam sweetclover for green manure produced only 2 bushels per acre more than corn following Hubam sweetclover for seed. Austrian Winter peas and Dixie Wonder peas did not increase the yield of corn, probably because they made very little growth.
Effect of Fumigation on Soil Aggregation
Authors: Martin J. P. , Aldrich D. G. 
Published: July 2010

AbstractA study was made of the effects of several soil fumigants in moderate and high dosages and of steam sterilization on the aggregation of the <50 µ particles of five soils. The fumigants were injected into dry soil in large screw cap bottles, water sufficient to bring the moisture content of the soil to 50% of capacity was immediately added, and the lids tightly secured. After 3 days the soil was air‐dried, placed in 16‐ounce jars in 420‐gram portions, adjusted to 50% moisture capacity, and incubated. Microbial counts and aggregate analyses were made after 0‐, 10‐, 20‐, 50‐, 100‐, and 250‐day incubation periods.The fumigation treatments markedly affected the microbial population of the soils but had little or no effect on aggregation. In high dosages, D‐D, chloropicrin, and ethylene dibromide slightly increased the aggregation of one soil, namely, Yolo loam at the 0‐day incubation period only. Steam sterilization increased the aggregation of Yolo loam, an unnamed mountain soil, and Hanford sandy loam. In the latter two soils, the effect was not significant after the 0‐day incubation period. Increased aggregation was associated with decreased wettability of the soil.The study indicates that aggregation is influenced more by products of microbial activity during the decomposition of organic waste material than by numbers of microorganisms. Fumigation apparently does not provide sufficient energy material in the form of dead microbial cells and adsorbed fumigant to change the aggregation status of a normal soil significantly, or destruction of organic cementing materials by increased microbial activity counteracts any aggregating effect.