bluuebunny/crossref_metadata_2025_split huggingface dataset:
BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models
Authors: Li Chen , Donizelli Marco , Rodriguez Nicolas , Dharuri Harish , Endler Lukas , Chelliah Vijayalakshmi , Li Lu , He Enuo , Henry Arnaud , Stefan Melanie I , Snoep Jacky L , Hucka Michael , Le Novère Nicolas , Laibe Camille 
Published: July 2010

Abstract

Background
Quantitative models of biochemical and cellular systems are used to answer a variety of questions in the biological sciences. The number of published quantitative models is growing steadily thanks to increasing interest in the use of models as well as the development of improved software systems and the availability of better, cheaper computer hardware. To maximise the benefits of this growing body of models, the field needs centralised model repositories that will encourage, facilitate and promote model dissemination and reuse. Ideally, the models stored in these repositories should be extensively tested and encoded in community-supported and standardised formats. In addition, the models and their components should be cross-referenced with other resources in order to allow their unambiguous identification.

Description
BioModels Database http://www.ebi.ac.uk/biomodels/ is aimed at addressing exactly these needs. It is a freely-accessible online resource for storing, viewing, retrieving, and analysing published, peer-reviewed quantitative models of biochemical and cellular systems. The structure and behaviour of each simulation model distributed by BioModels Database are thoroughly checked; in addition, model elements are annotated with terms from controlled vocabularies as well as linked to relevant data resources. Models can be examined online or downloaded in various formats. Reaction network diagrams generated from the models are also available in several formats. BioModels Database also provides features such as online simulation and the extraction of components from large scale models into smaller submodels. Finally, the system provides a range of web services that external software systems can use to access up-to-date data from the database.

Conclusions
BioModels Database has become a recognised reference resource for systems biology. It is being used by the community in a variety of ways; for example, it is used to benchmark different simulation systems, and to study the clustering of models based upon their annotations. Model deposition to the database today is advised by several publishers of scientific journals. The models in BioModels Database are freely distributed and reusable; the underlying software infrastructure is also available from SourceForge https://sourceforge.net/projects/biomodels/ under the GNU General Public License.
Phase II Randomized Comparison of Topotecan Plus Cyclophosphamide Versus Topotecan Alone in Children With Recurrent or Refractory Neuroblastoma: A Children's Oncology Group Study
Authors: London Wendy B. , Frantz Christopher N. , Campbell Laura A. , Seeger Robert C. , Brumback Babette A. , Cohn Susan L. , Matthay Katherine K. , Castleberry Robert P. , Diller Lisa 
Published: July 2010

Purpose Single-agent topotecan (TOPO) and combination topotecan and cyclophosphamide (TOPO/CTX) were compared in a phase II randomized trial in relapsed/refractory neuroblastoma. Because responders often underwent further therapies, novel statistical methods were required to compare the long-term outcome of the two treatments. Patients and Methods Children with refractory/recurrent neuroblastoma (only one prior aggressive chemotherapy regimen) were randomly assigned to daily 5-day topotecan (2 mg/m2) or combination topotecan (0.75 mg/m2) and cyclophosphamide (250 mg/m2). A randomized two-stage group sequential design enrolled 119 eligible patients. Toxicity and response were estimated. Long-term outcome of protocol therapy was assessed using novel methods—causal inference—which allowed adjustment for the confounding effect of off-study therapies. Results Seven more responses were observed for TOPO/CTX (complete response [CR] plus partial response [PR], 18 [32%] of 57) than TOPO (CR+PR, 11 [19%] of 59;P = .081); toxicity was similar. At 3 years, progression-free survival (PFS) and overall survival (OS) were 4% ± 2% and 15% ± 4%, respectively. PFS was significantly better for TOPO/CTX (P = .029); there was no difference in OS. Older age at diagnosis and lack of MYCN amplification predicted increased OS (P < .05). Adjusting for randomized treatment effect and subsequent autologous stem-cell transplantation, there was no difference between TOPO and TOPO/CTX in terms of the proportion alive at 2 years. Conclusion TOPO/CTX was superior to TOPO in terms of PFS, but there was no OS difference. After adjustment for subsequent therapies, no difference was detected in the proportion alive at 2 years. Causal inference methods for assessing long-term outcomes of phase II therapies after subsequent treatment can elucidate effects of initial therapies.
Retrogenes Reveal the Direction of Sex-Chromosome Evolution in Mosquitoes
Authors: Toups Melissa A , Hahn Matthew W 
Published: July 2010

Abstract
The mosquito Anopheles gambiae has heteromorphic sex chromosomes, while the mosquito Aedes aegypti has homomorphic sex chromosomes. We use retrotransposed gene duplicates to show an excess of movement off the An. gambiae X chromosome only after the split with Ae. aegypti, suggesting that their ancestor had homomorphic sex chromosomes.
Nature of Auditory Processing Disorder in Children
Authors: Moore David R. , Ferguson Melanie A. , Edmondson-Jones A. Mark , Ratib Sonia , Riley Alison 
Published: July 2010

OBJECTIVE:
We tested the specific hypothesis that the presentation of auditory processing disorder (APD) is related to a sensory processing deficit.

METHODS:
Randomly chosen, 6- to 11-year-old children with normal hearing (N = 1469) were tested in schools in 4 regional centers across the United Kingdom. Caregivers completed questionnaires regarding their participating children's listening and communication skills. Children completed a battery of audiometric, auditory processing (AP), speech-in-noise, cognitive (IQ, memory, language, and literacy), and attention (auditory and visual) tests. AP measures separated the sensory and nonsensory contributions to spectral and temporal perception.

RESULTS:
AP improved with age. Poor-for-age AP was significantly related to poor cognitive, communication, and speech-in-noise performance (P &lt; .001). However, sensory elements of perception were only weakly related to those performance measures (r &lt; 0.1), and correlations between auditory perception and cognitive scores were generally low (r = 0.1–0.3). Multivariate regression analysis showed that response variability in the AP tests, reflecting attention, and cognitive scores were the best predictors of listening, communication, and speech-in-noise skills.

CONCLUSIONS:
Presenting symptoms of APD were largely unrelated to auditory sensory processing. Response variability and cognitive performance were the best predictors of poor communication and listening. We suggest that APD is primarily an attention problem and that clinical diagnosis and management, as well as further research, should be based on that premise.
Weathering Sequence of Clay‐size Minerals in Soils and Sediments
Authors: Jackson M. L. , Hseung Y. , Corey R. B. , Evans E. J. , Heuvel R. C. Vanden 
Published: July 2010

AbstractStudies were made of several clays of soils and other deposits to clarify the nature of weathering of layer silicates. Data obtained by X‐ray diffraction, thermal, R(OH)n sorption, and elemental analyses lead to the proposal of general occurrence of interstratified X‐amorphous zones in 2:1 layer silicates. As weathering of true micas proceeds through illite, intermediates, vermiculite, and montmorin, a given K interlayer is rapidly depleted of K along a preferential weathering plane, leading to some degree of expansion. Concurrent hydroxylation by H+ addition to the octohedral layer together with dealumination accounts for loss of some of the mica layer charge. Increasing proportions of such weathered planes leads to various combinations of X‐amorphous and X‐crystalline zones typical of illite, vermiculite, and montmorin found in soils and other deposits, accounting for their diffraction properties; internal surface; K, H2O, and OH contents; and exchange properties. Functional continuity of mineral weathering in Great Soil Groups of China through layer silicates (including kaolinite), gibbsite, hematite, and anatase is demonstrated.
Root Channels and Roots in Forest Soils
Authors: Gaiser R. N. 
Published: July 2010

AbstractThe frequency, size, and stages in the development of vertical channels formed in the soil through the decay of the roots of hardwood trees are reported for a site located in southeastern Ohio. Data were obtained by exposing the soil profile by trenching. A diagram was prepared showing the location of root channels and living roots. Additional data on channels were obtained by probing the soil with a flexible wand to locate regions of low resistance which indicated the presence of vertical root channels. The vertical channels found exceeded 4,000 per acre. The estimate is low because not all channels could be discovered by the means employed. It is likely that vertical channels are interconnected by lateral channels formed by decayed root systems. Because channels contain materials relatively more permeable to water than the surrounding soil horizons, it is probable than the channels serve as pathways for the rapid movement of a large part of the free water in the soil profile.
Characteristics of Some Podzolic, Brown Forest, and Chernozem Soils of the Northern Portion of the Lake States
Authors: Nygard Iver J. , McMiller P. R. , Hole Francis D. 
Published: July 2010

AbstractThe morphology of the six great soil groups — Chernozem, Degraded Chernozem, Gray Wooded, Brown Forest, Brown Podzolic, and Podzol — with laboratory data is presented.The general distribution of these soils is shown on a schematic map. Of the five soil forming factors, three — climate, living matter, and parent materials — change notably from west to east. The other factors, topography, and age, are reasonably uniform in the areas selected for the modal soil profiles. Additional maps, illustrations of soil profiles, and related landscapes accompany the acticle. Tables of profile characteristics and laboratory analyses are arranged to show a summarized comparison of the various soil horizons of each soil.
Microclimate and Water Vapor Exchange at the Soil Surface
Authors: Brawand Hans , Kohnke Helmut 
Published: July 2010

Abstract

Estimates were obtained on the annual water vapor exchange through adsorption, condensation, and evaporation at the ground surface under field conditions. The investigation was coordinated with measurements of environmental microclimatic conditions. For a 2‐month period data were obtained also on nocturnal water accretions on corn and soybean leaves.
A small area of land on the Purdue University dairy farm near West Lafayette, Ind., was chosen as site for the field experiments. Five sampling conditions were employed, in which 20 small metal dishes served as containers for various soil and water samples. Each sampling set consisted of four filled dishes, two of the dishes to be placed on the ground surface of bare soil and the other two on meadow, during experimental periods.

The annual moisture gains from adsorption and condensation of atmospheric water vapor are estimated at 1.22 inches for bare soil, and 0.99 inch for soil having grass‐clover vegetation. The water vapor transfer from the subsoil to the soil surface, not including evaporational losses, attained 1.34 inches of water on bare ground and 0.77 inch on meadow. This results in total moisture gains of 2.56 inches and 1.76 inches, respectively. The field tests indicated that 0.59 inch of water per month per acre of ground collected on corn leaves in summer. Similarly, soybeans yielded 1.32 inches in the same period. This accumulated moisture on the plant leaves in clear nights consists of condensational water from the atmosphere and of guttation.

Water vapor transfer from the subsoil toward the top layer normally remains confined to night hours during the period from March to October. Under the same conditions, a two‐directional moisture loss from the ground surface layer takes place in the daytime: a part of the moisture can be driven to greater soil depths, while perhaps a larger part is subject to evaporation. Water vapor transfer from the subsoil to the surface may be a continuous process in winter, unless the soil is water saturated.
The Influence of Applied Boron, Magnesium, and Potassium on the Growth and Chemical Composition of Red Clover Grown under Greenhouse Conditions
Authors: Tucker T. C. , Smith F. W. 
Published: July 2010

AbstractThe objective of this investigation was to determine by means of greenhouse experiment the influence of application of boron, magnesium, and potassium on the yield and chemical composition of red clover grown on Kansas soils.A factoral design of greenhouse experiment in which a single rate of application of boron, magnesium, and potassium was made to each of four soil materials was used for the growth of red clover. Yield data were collected for four clippings of plant material. Chemical analyses were made for phosphorus, potassium, magnesium, and boron.Applications of potassium to the soil always increased the potassium content of the red clover plants and significantly the total yield of red clover for each soil type. Approximately 1% potassium in the plant material was the critical lower limit for this element, insofar as growth response was concerned.Boron applications increased the boron content of the plant material regularly and considerably. A critical lower limit of about 28 to 30 ppm B in red clover plant material was established as being necessary for prevention of boron deficiency. Cherokee subsoil was more deficient in boron than any of the surface soil samples used in this study.Magnesium applications to the soil were generally effective in increasing magnesium concentrations in the plant material only when potassium was not included as a part of the chemical treatment. A critical lower limit of about 0.5% magnesium in red clover plant material was required for optimum growth.A definite positive correlation was established between percent phosphorus and percent magnesium in the plant material. The mean value was 0.535. This correlation was most marked on soils which had low magnesium activity as indicated by relatively low percentage magnesium saturation on the exchange complex.A definite negative correlation between percentage composition of potassium and percentage composition magnesium was established. The mean value was 0.683. Potassium was shown to exert control over magnesium and not vice versa.
Influence of Double‐cut Plow Mulch Tillage on Number and Activity of Microorganisms
Authors: Gamble S. J. R. , Edminster T. W. , Orcutt Fred S. 
Published: July 2010

AbstractA decreased availability of plant food throughout the growing season has been observed for some stubble mulch practices. To determine if the microflora were involved as a possible factor in this plant food availability difference, comparative data were obtained from double‐cut and turnplow soil samples. Under the conditions of this investigation the following microbiological factors may be related to the plant food tie‐up problems: (a) The environmental conditions of better oxygen supply and more organic matter in the 0–6 inch horizon seem to favor the stimulation of the soil fungi in the mulch plots. This group of soil microorganisms might cause a temporary loss of nitrate‐nitrogen as a result of protein synthesis by the mold cells. (b) Biochemical nitrification as determined with the perfusion apparatus of Lees and Quastel showed slightly lower amounts of nitrate‐nitrogen formed from the mulch than from the turnplow samples. In addition, the soil pH should be considered as an environmental factor which may have considerable influence on the activity of the soil population. It is believed that these factors might be temporarily involved in the plant food tieup problems found to be associated with stubble mulch tillage practices at Virginia Polytechnic Institute.
Effect of Different Sources and Rates of Application of Fertilizer Materials on the pH and N, P, K, and Mg Content of the Soil to Which They Were Applied
Authors: Vittum M. T. , Lathwell D. J. , Stanford G. 
Published: July 2010

AbstractA fertilizer experiment comparing the effects of different sources of N, P, and K, and different rates of application of complete fertilizer on the yield of beets, cabbage, peas, sweet corn, and tomatoes was conducted on a soil which, for the preceding 20 years, had been fertilized according to good commercial practice with a “complete” fertilizer high in phosphorus. After 5 years of consecutive application of the differential treatments, soil analyses showed the following results: (1) No significant difference in soil pH, ammonium N, nitrate N, P, K, or Mg from inorganic sources of N versus 40% of organic N; ordinary superphosphate versus “double” superphosphate; or muriate of potash versus 50% of the potash in the form of sulfate of potashmagnesia; (2) Significant decrease in pH and Mg and significant increase in nitrate N, P, and K with increasing rates of application of complete fertilizer; (3) No interaction between sources of fertilizer nutrients and rates of application; and (4) After 5 years of intensive vegetable cropping without addition of any fertilizer, available P, K, and Mg in the soil were 28, 86, and 557 pounds per acre, respectively. According to present New York standards, these values are classified as “very high,” “medium,” and “very high,” respectively.
The Effect of the Addition of Organic Materials on the Decomposition of an Organic Soil
Authors: Bingeman C. W. , Varner J. E. , Martin W. P. 
Published: July 2010

AbstractGlucose, alfalfa insolubles, and complete alfalfa uniformly labeled with carbon‐14 were added to an organic soil to determine under controlled conditions, if the loss of the soil due to biological decomposition could be counteracted. Carbon‐14 labeled material was used so that it could be determined whether or not there was an increase in the decomposition of the native organic matter as a result of the added material, and, if this was true, whether the soluble fraction of the added materials, or the insoluble fraction, was chiefly responsible.The materials were added, the soil incubated, and CO2 collected at intervals. The insoluble fraction of alfalfa caused a larger breakdown of native organic matter than solubles alone or complete alfalfa. It was impossible to build up the organic content of the soil, under these conditions, but the net loss of carbon was diminished by the addition of the organic materials.
Influence of Alfalfa Green Manure on the Availability of Phosphorus to Corn
Authors: Nielsen K. F. , Pratt P. F. , Martin W. P. 
Published: July 2010

AbstractGreenhouse work was conducted in which alfalfa and KH2PO4, singly and in combination, were used as phosphate fertilizers. These materials were layered into pots of Wooster silt loam representing three levels of residual phosphorus. The availability to corn of the phosphorus in these carriers of phosphorus and in the soil was measured by the use of radiotracer techniques. A series of Neubauer tests were carried out to determine the time rate of release of phosphorus from alfalfa.Results indicate that the phosphorus in the alfalfa was not as available as in the KH2PO4. However, the alfalfa increased the availability of the residual phosphorus. The Neubauer tests indicated that the phosphorus from the alfalfa was most available during the period between 46 and 64 days after being incorporated into these soils.
Cationic Activities in Systems of Plant Roots
Authors: McLean E. O. , Baker F. E. 
Published: July 2010

AbstractThe activities and mean free bonding energies of Na, K, and Ca on alfalfa, soybean, red top, and Reed canary grass roots were determined by the use of the clay membrane electrode technique. Samples of electrodialyzed roots were saturated with each cation by addition as the hydroxide after the exchange capacity of the roots had been previously determined.Examination of the techniques employed showed that reproducible determinations of the activities could be made after a five minute contact of the clay membrane electrode with the root system. Identical readings from both small and large electrodes indicated that there was no problem in obtaining a representative cross section of the root systems for measurement. There was no appreciable liquid junction potential at the point of contact of KCl bridge with the root system. The cations added were found to be practically all recoverable in a 0.1N HCl extraction without serious contamination from ions within the roots.It was possible to determine a value for the cation exchange capacity of the roots by titrating the electrodialyzed roots with base, stirring, and maintaining the system at pH 7 for ten minutes. Bonding energy determinations on these systems indicate that K is bonded stronger than Na on alfalfa roots, but Na is bonded stronger than K on soybean roots. The legume roots held all of the cations with greater energy than did those of the grasses; however, there was a shift in the relative values obtained for the grass root systems when compared to those of the legumes.
Soil Structural Stability of Brookston Clay as a Factor in Sugar Beet Yields
Authors: Zwerman Paul J. , Page J. B. , Yoder R. E. 
Published: July 2010

AbstractThe purpose of this research was to determine the influence of the structural stability of soil upon the yield of sugar beets.Structural units of soil between one‐eighth inch and one‐fourth inch were used in 20 small plots. The main comparison made was of highly stable structure (12% organic matter) against highly unstable structure (5% organic matter). The top soil (10 inches) of each of 10 of these plots was made up of stable soil structure. The other 10 plots were made up of unstable structure. Five rainfall conditions were studied: frequent half‐inch, no rain, natural rain for 1947, 4 inches per week, and rain similar to 1942. There were 16 harvested beets on each plot or 64 per rainfall condition. Film‐glass cloth houses used to protect the soil from natural rainfall transmitted only one‐half of the sunlight. Apparently this light factor was responsible for the highest beet yield under natural rain and sunlight.There were no differences in yield associated with soil structural differences except in the case of 4 inches rain per week. This difference was significant. Differences in yield as affected by rainfall were significant for all comparisons except “ideal” rain and 1942 rain.
X‐Ray Characteristics of Clay Minerals as Related to Potassium Fixation
Authors: Kunze G. W. , Jeffries C. D. 
Published: July 2010

AbstractEvidence is presented to support on structural grounds the early potassium fixation theories based on entrapment of the potassium ion due to the closure of the interlayer spaces. Field surface samples (0–6 in.) of 15 soils classified as Gray‐Brown Podzolics from which the clay was extracted served as experimental material. The soil‐clays were saturated with potassium and a divalent cation and the effect on the basal spacings noted. X‐ray diffraction results suggested that those soil‐clays which showed a strong 10 angstrom line when potassium saturated as contrasted to a strong 14 angstrom line when saturated with a divalent cation were relatively high fixers of potassium. Those soil‐clays which showed little or no shifting of the larger basal spacings toward 10 angstroms when saturated with potassium were found to be relatively low fixers of potassium.