bluuebunny/crossref_metadata_2025_split huggingface dataset:
You can't get there from here: Foundationalism and development
Authors: Allen Jedediah W. P. , Bickhard Mark H. 
Published: May 2011

AbstractThe thesis of our commentary is that the framework used to address what are taken by Carey to be the open issues is highly problematic. The presumed necessity of an innate stock of representational primitives fails to account for the emergence of representation out of a nonrepresentational base. This failure manifests itself in problematic ways throughout Carey's book.
Presuming placeholders are relevant enables conceptual change
Authors: Heintz Christophe 
Published: May 2011

AbstractPlaceholders enable conceptual change only if presumed to be relevant (e.g., lead to the formation of true beliefs) even though their meaning is not yet fully understood and their cognitive function not yet specified. Humans are predisposed to make such presumptions in a communicative context. Specifying the role of the presumption of relevance in conceptual change would provide a more comprehensive account of Quinian bootstrapping.
Cognitive ethology, over-attribution of agency and focusing abilities as they relate to the origin of concepts
Authors: Ristau Carolyn A. 
Published: May 2011

AbstractCarey's superb discussion of the origin of concepts is extended into the field of cognitive ethology. I also suggest that agency may be a default mechanism, often leading to over-attribution. The problem therefore becomes one of specifying the conditions in which agency is not attributed. The significance of attentional/focusing abilities on conceptual development is also emphasized.
Language and mechanisms of concept learning
Authors: Weiskopf Daniel A. 
Published: May 2011

AbstractCarey focuses her attention on a mechanism of concept learning called “Quinian bootstrapping.” I argue that this form of bootstrapping is not dependent upon language or other public representations, and outline a place for language in concept learning generally. Language, perception, and causal reasoning are all sources of evidence that can guide learners toward discovering new and potentially useful categories.
A unified account of abstract structure and conceptual change: Probabilistic models and early learning mechanisms
Authors: Gopnik Alison 
Published: May 2011

AbstractWe need not propose, as Carey does, a radical discontinuity between core cognition, which is responsible for abstract structure, and language and “Quinian bootstrapping,” which are responsible for learning and conceptual change. From a probabilistic models view, conceptual structure and learning reflect the same principles, and they are both in place from the beginning.
How to build a baby: A new toolkit?
Authors: Poulin-Dubois Diane 
Published: May 2011

AbstractCarey proposes a theory of conceptual development that specifies innate conceptual representations that get learning started. Those representations are the output of innate domain-specific input analyzers. I contend that innate core cognition about agency is itself a gradual construction and that the role of Quinian bootstrapping needs elaboration to account for the development of intuitive theories of psychology.
Variable verb placement in second-language German and French: Evidence from production and elicited imitation of finite and nonfinite negated sentences
Authors: SCHIMKE SARAH 
Published: May 2011

ABSTRACTThis study examines the placement of finite and nonfinite lexical verbs and finite light verbs (LVs) in semispontaneous production and elicited imitation of adult beginning learners of German and French. Theories assuming nonnativelike syntactic representations at early stages of development predict variable placement of lexical verbs and consistent placement of LVs, whereas theories assuming nativelike syntax predict variability for nonfinite verbs and consistent placement of all finite verbs. The results show that beginning learners of German have consistent preferences only for LVs. More advanced learners of German and learners of French produce and imitate finite verbs in more variable positions than nonfinite verbs. This is argued to support a structure-building view of second-language development.
Individual and contextual determinants of the duration of diarrhoeal episodes in preschool children: a longitudinal study in an urban setting
Authors: SANTOS C. A. S. T. , STRINA A. , AMORIM L. D. , GENSER B. , ASSIS A. M. O. , PRADO M. S. , BARRETO M. L. 
Published: May 2011

SUMMARYThis study investigated individual and contextual factors associated with the duration of diarrhoeal episodes in 693 young children living in a large Brazilian city who were followed-up for at least 3 months. The outcome is analysed as a continuous variable, by means of a hierarchical conceptual model organizing the factors in meaningful blocks. A total of 2397 episodes were recorded (median duration 2 days, interquartile range 1–3 days). Low percentage of households connected to the sewerage system in the neighbourhood, low family purchasing power, high agglomeration, mother aged <19 years, low zinc content in child's diet, and episode severity were significantly associated with longer duration (0·26–0·69 days more). Purchasing power effect was largely mediated by environmental conditions, characteristics of the child, and hygienic behaviour. Environmental conditions acted as a possible effect modifier, enhancing the effect on duration of diarrhoea of the child not having being vaccinated against measles or breastfed for >6 months.
Exposure of phototrophs to 548 days in low Earth orbit: microbial selection pressures in outer space and on early earth
Authors: Cockell Charles S , Rettberg Petra , Rabbow Elke , Olsson-Francis Karen 
Published: May 2011

Abstract
An epilithic microbial community was launched into low Earth orbit, and exposed to conditions in outer space for 548 days on the European Space Agency EXPOSE-E facility outside the International Space Station. The natural phototroph biofilm was augmented with akinetes of Anabaena cylindrica and vegetative cells of Nostoc commune and Chroococcidiopsis. In space-exposed dark controls, two algae (Chlorella and Rosenvingiella spp.), a cyanobacterium (Gloeocapsa sp.) and two bacteria associated with the natural community survived. Of the augmented organisms, cells of A. cylindrica and Chroococcidiopsis survived, but no cells of N. commune. Only cells of Chroococcidiopsis were cultured from samples exposed to the unattenuated extraterrestrial ultraviolet (UV) spectrum (&gt;110 nm or 200 nm). Raman spectroscopy and bright-field microscopy showed that under these conditions the surface cells were bleached and their carotenoids were destroyed, although cell morphology was preserved. These experiments demonstrate that outer space can act as a selection pressure on the composition of microbial communities. The results obtained from samples exposed to &gt;200 nm UV (simulating the putative worst-case UV exposure on the early Earth) demonstrate the potential for epilithic colonization of land masses during that time, but that UV radiation on anoxic planets can act as a strong selection pressure on surface-dwelling organisms. Finally, these experiments have yielded new phototrophic organisms of potential use in biomass and oxygen production in space exploration.
Metagenomic mining for microbiologists
Authors: Delmont Tom O , Malandain Cedric , Prestat Emmanuel , Larose Catherine , Monier Jean-Michel , Simonet Pascal , Vogel Timothy M 
Published: May 2011

Abstract
Microbial ecologists can now start digging into the accumulating mountains of metagenomic data to uncover the occurrence of functional genes and their correlations to microbial community members. Limitations and biases in DNA extraction and sequencing technologies impact sequence distributions, and therefore, have to be considered. However, when comparing metagenomes from widely differing environments, these fluctuations have a relatively minor role in microbial community discrimination. As a consequence, any functional gene or species distribution pattern can be compared among metagenomes originating from various environments and projects. In particular, global comparisons would help to define ecosystem specificities, such as involvement and response to climate change (for example, carbon and nitrogen cycle), human health risks (eg, presence of pathogen species, toxin genes and viruses) and biodegradation capacities. Although not all scientists have easy access to high-throughput sequencing technologies, they do have access to the sequences that have been deposited in databases, and therefore, can begin to intensively mine these metagenomic data to generate hypotheses that can be validated experimentally. Information about metabolic functions and microbial species compositions can already be compared among metagenomes from different ecosystems. These comparisons add to our understanding about microbial adaptation and the role of specific microbes in different ecosystems. Concurrent with the rapid growth of sequencing technologies, we have entered a new age of microbial ecology, which will enable researchers to experimentally confirm putative relationships between microbial functions and community structures.
Response of methanotrophic communities to afforestation and reforestation in New Zealand
Authors: Nazaries Loïc , Tate Kevin R , Ross Des J , Singh Jagrati , Dando John , Saggar Surinder , Baggs Elizabeth M , Millard Peter , Murrell J Colin , Singh Brajesh K 
Published: May 2011

Abstract
Methanotrophs use methane (CH4) as a carbon source. They are particularly active in temperate forest soils. However, the rate of change of CH4 oxidation in soil with afforestation or reforestation is poorly understood. Here, soil CH4 oxidation was examined in New Zealand volcanic soils under regenerating native forests following burning, and in a mature native forest. Results were compared with data for pasture to pine land-use change at nearby sites. We show that following soil disturbance, as little as 47 years may be needed for development of a stable methanotrophic community similar to that in the undisturbed native forest soil. Corresponding soil CH4-oxidation rates in the regenerating forest soil have the potential to reach those of the mature forest, but climo-edaphic fators appear limiting. The observed changes in CH4-oxidation rate were directly linked to a prior shift in methanotrophic communities, which suggests microbial control of the terrestrial CH4 flux and identifies the need to account for this response to afforestation and reforestation in global prediction of CH4 emission.
Anaerobic ammonia oxidation in a fertilized paddy soil
Authors: Zhu Guibing , Wang Shanyun , Wang Yu , Wang Chaoxu , Risgaard-Petersen Nils , Jetten Mike SM , Yin Chengqing 
Published: May 2011

Abstract
Evidence for anaerobic ammonium oxidation in a paddy field was obtained in Southern China using an isotope-pairing technique, quantitative PCR assays and 16S rRNA gene clone libraries, along with nutrient profiles of soil cores. A paddy field with a high load of slurry manure as fertilizer was selected for this study and was shown to contain a high amount of ammonium (6.2–178.8 mg kg−1). The anaerobic oxidation of ammonium (anammox) rates in this paddy soil ranged between 0.5 and 2.9 nmolN per gram of soil per hour in different depths of the soil core, and the specific cellular anammox activity observed in batch tests ranged from 2.9 to 21 fmol per cell per day. Anammox contributed 4–37% to soil N2 production, the remainder being due to denitrification. The 16S rRNA gene sequences of surface soil were closely related to the anammox bacteria ‘Kuenenia’, ‘Anammoxoglobus’ and ‘Jettenia’. Most of the anammox 16S rRNA genes retrieved from the deeper soil were affiliated to ‘Brocadia’. The retrieval of mainly bacterial amoA sequences in the upper part of the paddy soil indicated that nitrifying bacteria may be the major source of nitrite for anammox bacteria in the cultivated horizon. In the deeper oxygen-limited parts, only archaeal amoA sequences were found, indicating that archaea may produce nitrite in this part of the soil. It is estimated that a total loss of 76 g N m−2 per year is linked to anammox in the paddy field.
Trends in the Prevalence of Abdominal Obesity and Overweight in English Adults (1993–2008)
Authors: Howel Denise 
Published: May 2011

The rising prevalence of generalized obesity is well documented, but less is known about trends in abdominal obesity. Levels of abdominal obesity and overweight are reported for adults in the Health Survey for England (HSE) by survey year and age for 1993–2008. HSE is a nationally representative cross‐sectional population survey using an interviewer‐administered questionnaire and measurement of waist circumference (WC) by nurse, allowing calculation of abdominal overweight and obesity (≥94 cm and ≥102 cm in men, and ≥80 cm and ≥88 cm in women). A total of 40,001 men and 46,397 women aged 18–67 provided data on WC in this period. Between 1993 and 2008 abdominal overweight rose from 44.9% to 62.3% in men, and from 46.6% to 66.8% in women, while abdominal obesity rose from 19.2% to 35.7% in men, and from 23.8% to 43.9% women. However, the rates of increase over time in England appear to be slowing down: curves with a less than linear increase each year were a better fit to the data than a linear trend. There was some variation across the age range in the time trend in abdominal obesity and overweight, in that the absolute increases over time were slightly less for younger adults.
The effect of TiO2 nanotubes on the sintering behavior and properties of PZT ceramics
Authors: Dung Le Quang Tien , Truong Van Chuong , Do Phuong Anh 
Published: May 2011

Abstract
In this study, the effect of as-prepared annatase TiO
2 nanotubes on the sintering behavior and the piezoelectric properties of lead zirconate titanate (PZT) ceramics was investigated. Two types of PZT (with the use of TiO
2 nanotubes and commercial TiO
2) were prepared by a conventional oxide-mixing method. The density of samples using TiO
2 nanotubes tended to increase and the sintering temperature of these ceramics decreased. The electromechanical coupling factor (k

p
) of PZT ceramics was improved significantly by the use of TiO
2 nanotubes.
FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution
Authors: Ge Huanying , Liu Kejun , Juan Todd , Fang Fang , Newman Matthew , Hoeck Wolfgang 
Published: May 2011

Abstract
Motivation: Next generation sequencing technology generates high-throughput data, which allows us to detect fusion genes at both transcript and genomic levels. To detect fusion genes, the current bioinformatics tools heavily rely on paired-end approaches and overlook the importance of reads that span fusion junctions. Thus there is a need to develop an efficient aligner to detect fusion events by accurate mapping of these junction-spanning single reads, particularly when the read gets longer with the improvement in sequencing technology.
Results: We present a novel method, FusionMap, which aligns fusion reads directly to the genome without prior knowledge of potential fusion regions. FusionMap can detect fusion events in both single- and paired-end datasets from either RNA-Seq or gDNA-Seq studies and characterize fusion junctions at base-pair resolution. We showed that FusionMap achieved high sensitivity and specificity in fusion detection on two simulated RNA-Seq datasets, which contained 75 nt paired-end reads. FusionMap achieved substantially higher sensitivity and specificity than the paired-end approach when the inner distance between read pairs was small. Using FusionMap to characterize fusion genes in K562 chronic myeloid leukemia cell line, we further demonstrated its accuracy in fusion detection in both single-end RNA-Seq and gDNA-Seq datasets. These combined results show that FusionMap provides an accurate and systematic solution to detecting fusion events through junction-spanning reads.
Availability: FusionMap includes reference indexing, read filtering, fusion alignment and reporting in one package. The software is free for noncommercial use at (http://www.omicsoft.com/fusionmap).
Contact: ge@amgen.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Treatment of acute coronary syndrome: Part 1: Non-ST-segment acute coronary syndrome
Authors: Trost Jeffrey C. , Lange Richard A. 
Published: May 2011

Objective:
Acute coronary syndrome is a common cause of morbidity and mortality, both in the United States and worldwide. The goal of this review is to familiarize clinicians with recent information regarding the diagnosis and treatment of acute coronary syndrome.

Data Sources:
PubMed search and review of the relevant medical literature.

Summary:
Acute coronary syndrome encompasses three clinical diagnoses: unstable angina, non-ST-segment elevation myocardial infarction), and ST-segment elevation myocardial infarction. The definition, pathophysiology, clinical presentation, diagnosis, and treatment of unstable angina/non-ST-segment elevation myocardial infarction are reviewed here. Diagnosing unstable angina/non-ST-segment elevation myocardial infarction is a significant challenge in critically ill patients not initially suspected of having acute coronary syndrome (i.e., noncardiac intensive care unit patients), and diagnostic and treatment strategies for these patients have not been clearly established.

Conclusions:
Patients with acute coronary syndrome benefit from intensive medical therapy, including antianginal, antiplatelet, antithrombotic, and statin agents. Depending on their risk for future cardiovascular events as well as their risk of bleeding complications, patients may benefit from either an early invasive treatment strategy, in which routine coronary revascularization is performed, or a conservative strategy, in which revascularization is reserved for patients with recurrent or provocable cardiac ischemia.
Body Composition Changes in Preterm Infants Following Hospital Discharge
Authors: Ramel Sara E. , Gray Heather L. , Ode Katie L. , Younge Noelle , Georgieff Michael K. , Demerath Ellen W. 
Published: May 2011

ABSTRACTBackground and Objectives:Infants experiencing catch‐up growth devote a greater proportion of their energy to fat deposition, potentially at the expense of gains in lean body mass. The objective of the present study was to compare the body composition of preterm and term infants after hospital discharge and to determine the effect of gestational age (GA), birth size, nutrition, and illness on growth in fat‐free mass (FFM) after hospitalization.Patients and Methods:Anthropometric measurements and body composition testing via air displacement plethysmography were performed on 26 appropriate‐for‐gestational‐age (AGA) preterm (mean GA 31.5 ± 2.7 weeks) and 97 AGA term (mean GA 39.8 ± 1.0 weeks) infants at term corrected age (CA) and at 3 to 4 months CA.Results:At term CA, preterm infants had lower FFM (3.0 vs 3.3 kg, P = 0.001), higher percentage of body fat (18.7% vs 15.2%, P < 0.0001), lower weight (P = 0.04), and shorter length (P = 0.001) than term infants. By 3 to 4 months CA, weight, length, percentage of body fat, and FFM were similar in the 2 groups. GA, inpatient nutrition, and illness were associated with FFM at 4 months CA in the preterm infants (P < 0.05).Conclusions:Markedly lower FFM and higher adiposity were observed in preterm infants at term CA, but these differences had lessened and were no longer statistically significant at 3 to 4 months CA. Although early nutrition was associated with growth trajectories in the hospital, the continuing influence of early illness on postdischarge growth suggests that nonnutritional factors (eg, disturbances in the growth hormone axis) also may affect body composition trajectories of preterm infants.
Ethylene and 1-Methylcyclopropene Differentially Regulate Gene Expression during Onion Sprout Suppression
Authors: Cools Katherine , Chope Gemma A. , Hammond John P. , Thompson Andrew J. , Terry Leon A. 
Published: May 2011

Abstract
Onion (Allium cepa) is regarded as a nonclimacteric vegetable. In onions, however, ethylene can suppress sprouting while the ethylene-binding inhibitor 1-methylcyclopropene (1-MCP) can also suppress sprout growth; yet, it is unknown how ethylene and 1-MCP elicit the same response. In this study, onions were treated with 10 μL L−1 ethylene or 1 μL L−1 1-MCP individually or in combination for 24 h at 20°C before or after curing (6 weeks) at 20°C or 28°C and then stored at 1°C. Following curing, a subset of these same onions was stored separately under continuous air or ethylene (10 μL L−1) at 1°C. Onions treated with ethylene and 1-MCP in combination after curing for 24 h had reduced sprout growth as compared with the control 25 weeks after harvest. Sprout growth following storage beyond 25 weeks was only reduced through continuous ethylene treatment. This observation was supported by a higher proportion of down-regulated genes characterized as being involved in photosynthesis, measured using a newly developed onion microarray. Physiological and biochemical data suggested that ethylene was being perceived in the presence of 1-MCP, since sprout growth was reduced in onions treated with 1-MCP and ethylene applied in combination but not when applied individually. A cluster of probes representing transcripts up-regulated by 1-MCP alone but down-regulated by ethylene alone or in the presence of 1-MCP support this suggestion. Ethylene and 1-MCP both down-regulated a probe tentatively annotated as an ethylene receptor as well as ethylene-insensitive 3, suggesting that both treatments down-regulate the perception and signaling events of ethylene.
Immunohistochemical findings of sebaceous carcinoma and sebaceoma: Retrieval of cytokeratin expression by a panel of anti‐cytokeratin monoclonal antibodies
Authors: ANSAI Shin‐ichi , ARASE Seiji , KAWANA Seiji , KIMURA Tetsunori 
Published: May 2011

AbstractThis study examined immunohistochemical findings of sebaceous carcinoma and sebaceoma. An immunohistochemical study using 13 anti‐cytokeratin (CK) antibodies (anti‐CK1, 5–8, 10 and 14–20) and 35 cases of sebaceous carcinoma (16 cases on ocular and 19 cases on extraocular regions) and 10 cases of sebaceoma (no cases arose on the eyelids) was performed. Overall, those in ocular lesions were almost the same as those for extraocular lesions in sebaceous carcinoma other than CK8. The findings in sebaceous carcinoma were almost equal to those of sebaceoma. Over 75% of cases with sebaceous carcinoma were positive with anti‐CK5 and anti‐CK14 antibodies and negative with anti‐CK1, CK10, CK15, CK17, CK18 and CK20 antibodies. Most cases (50–75%) of those were positive with CK7 and negative with CK6, CK16, CK19 and CK8. The sensitivity and specificity of immunohistochemical detection of sebaceous carcinoma using the panel of anti‐cytokeratin antibodies were lower than those of other antibodies. Immunohistochemical detection of cytokeratins in diagnosing sebaceous carcinoma should be considered to be ancillary to conventional microscopic findings and those of other antibodies.