bluuebunny/crossref_metadata_2025_split huggingface dataset:
Scheduling forest core area production using mixed integer programming
Authors: Wei Yu , Hoganson Howard M. 
Published: April 2008

Core area, the area of mature forest protected by a buffer area from edge effects of surrounding habitats, is an important spatial measure describing forest ecological conditions. Three alternative mixed integer programming (MIP) formulations are presented for explicitly scheduling core area production in a forest management scheduling model. Formulations utilize detailed data preprocessing that develops a set of influence zones. Each influence zone identifies an area of the forest that can produce core area. Each zone is influenced by a unique combination of management units (stands) of the forest. The assumed width of the buffer surrounding core area affects both the number of zones in the forest and the number of stands associated with each zone. Numerous test cases were applied, varying the MIP formulation used to describe core area production, the assumed buffer for core area (50 or 100 m), and the set of additional forest-wide constraints to control harvest levels and core area production levels over time. Solution times varied substantially between the alternative MIP formulations. Solution times were substantially less for the formulation that used more, but simpler, spatial constraints. Solution times for large test cases suggest that real-world applications are likely feasible.
Variation in cedar leaf blight (Didymascella thujina) resistance of western redcedar (Thuja plicata)
Authors: Russell John H. , Kope Harry H. , Ades Peter , Collinson Heidi 
Published: April 2008

Western redcedar ( Thuja plicata Donn ex D. Don) seedlings from a population study with family structure were planted at four sites across coastal British Columbia. All seedlings at the time of planting were infected with cedar leaf blight (CLB) ( Didymascella thujina (E.J. Durand) Maire). CLB severity and tree heights were measured at various ages from 2 to 12 years. There were significant site differences in CLB severity with the coastal hypermaritime site showing the most and with the submaritime site showing the least. Population differences in disease severity were evident with British Columbia coastal, low-elevation populations exhibiting the most resistance and with British Columbia high-elevation and California sources showing the least. Population resistance was consistent across all four sites (all r > 0.90, p < 0.001). Coefficients of additive genetic variation in CLB severity at all four sites varied from 13.2% to 20.1% with narrow-sense heritabilities from 0.21 to 0.66. Type B genetic correlations in CLB severity across sites averaged 0.59. Type A genetic correlations between 6 year CLB severity and height at the Jordan River site on western Vanvouver Island and at the site on the Queen Charlotte Islands were –0.96 and –0.86 (p < 0.001), respectively. Results are discussed with respect to climatic influences and prior exposure to CLB on among- and within-population variation in western redcedar natural populations and impact on gene resource management.
Water use by eastern hemlock (Tsuga canadensis) and black birch (Betula lenta): implications of effects of the hemlock woolly adelgid
Authors: Daley Michael J. , Phillips Nathan G. , Pettijohn Cory , Hadley Julian L. 
Published: April 2008

Eastern hemlock ( Tsuga canadensis (L.) Carr.) is a coniferous evergreen species found across the northeastern United States that is currently threatened by the exotic pest hemlock woolly adelgid (HWA; Adelges tsugae Annand). As HWA kills eastern hemlock trees, black birch ( Betula lenta L.) has been found to be a dominant replacement species in the region. Seasonal changes in water use by eastern hemlock and black birch were investigated utilizing whole-tree transpiration measurement techniques. Annual evapotranspiration in an eastern hemlock and deciduous stand was also estimated. During the peak growing season, daily rates of transpiration were 1.6 times greater in black birch. Cumulative transpiration in black birch exceeded hemlock transpiration by 77 mm from June until October. During the dormant season, evapotranspiration rates were higher in the hemlock stand; however, estimated annual evapotranspiration was 327 mm in eastern hemlock compared with 417 mm in the deciduous stand. Our results suggest that a transition from a hemlock-dominated to a black birch-dominated stand will alter the annual water balance with the greatest impact occurring during the peak growing season. Late in the growing season, flow may be unsustainable in streams that normally have light or moderate flow because ofincreased water use by black birch.
Relationships between climate and double rings in Quercus ilex from northeast Spain
Authors: Campelo F. , Gutiérrez E. , Ribas M. , Nabais C. , Freitas H. 
Published: April 2008

The influence of climatic factors on tree-ring width and the formation of double rings was studied in Quercus ilex L. growing in a coppice stand left unmanaged for 22 years. Ten trees were felled and discs were taken every 30 cm from bole and dominant branches. Dendrometer bands were installed on 10 nearby trees and the data recorded were used to confirm the accuracy of our tree-ring identification. They were also used to relate the seasonal radial growth pattern to double-ring formation. Double rings were frequent and occurred consistently along the stem. Two types of double rings could be recognized according to their width: type I, with the extra growth band accounting for approximately 50% of the tree ring; and type II, with a narrow extra growth band. Type I double rings were formed when approximately 1/2 of the growing-season precipitation occurred during the second growth period of the season and after the summer drought. Type II double rings occurred when approximately 1/3 of the precipitation in the growing season occurred after the summer drought. The formation of double rings was triggered by rainfall in summer and the extra growth-band width was related to summer and autumn environmental conditions. Double rings in Q. ilex can potentially be used in dendroclimatological studies, as they are formed in response to climatic conditions within the growing season.
Relating changes in duff moisture to the Canadian Forest Fire Weather Index System in Populus tremuloides stands in Elk Island National Park
Authors: Otway S. G. , Bork E. W. , Anderson K. R. , Alexander M. E. 
Published: April 2008

The manner in which trembling aspen ( Populus tremuloides Michx.) forest duff moisture changes during the growing season was investigated in Elk Island National Park, Alberta, Canada. A calibration–validation procedure incorporating one calibration site with moisture sampling across three topographic positions was used to develop predictive models, which were subsequently compared with 12 validation sites across three vegetation types throughout the Park. Duff moisture was modelled against the Duff Moisture Code and Drought Code components of the Canadian Forest Fire Weather Index System. Spring, summer, and fall rates of duff moisture change differed (P < 0.050) during calibration, with moisture loss greatest in spring. Additionally, while moisture changes on the south-facing and crest topographic positions were similar during spring, moisture losses were greater (P < 0.050) at these locations compared with the north-facing landscape position. Correlation analysis indicated that duff inorganic content and bulk density were both related to duff moisture but were limited in importance compared with weather-based influences. When compared with predicted values obtained from calibrated models, moderate predictability of duff moisture was found (mean absolute error = 20.7%–54.2%). Relative to the national standard equations, unique but very different empirical relationships were developed between the Duff Moisture Code and Drought Code and the moisture content of the duff layer in aspen forest stands found in Elk Island National Park.
The changing relationships between forestry and the local community in rural northwestern IrelandAn earlier version of this paper was presented at the IUFRO 3.08 conference “Small-scale Forestry and Rural Development,” 18–23 June 2006, Galway, Ireland.
Authors: Fléchard Marie-Christine , Carroll Matthew S. , Cohn Patricia J. , Dhubháin Áine Ní 
Published: April 2008

Following centuries of deforestation, Ireland has undergone a substantial afforestation programme in the last 40 years. This paper presents the results of a case study undertaken to examine local response to afforestation. The study is set in Arigna, a region in northwestern Ireland that has traditionally depended on agriculture but has experienced relatively high rates of afforestation in recent decades. Relying on documentary evidence and in-depth qualitative interviews conducted with local stakeholders, the results suggest more local resistance to afforestation than one might expect in a country that has historically experienced such massive deforestation. Among the reasons uncovered for this resistance is the history of land tenure in rural Ireland, the institutional means by which afforestation has been conducted, the tree species used, and the aesthetic appearance of the forest stands once established. Underlying all of this is an apparently widespread local perception that forestry has benefited outsiders more than locals. Yet, the study also documents local perceptions that those responsible for afforestation have responded to concerns and that resistance to afforestation may be declining, as well as the reasons for this decline. The paper concludes with a discussion of the importance of local history and community involvement in developing socially acceptable forestry.
Risk Factors for Aborted Cardiac Arrest and Sudden Cardiac Death in Children With the Congenital Long-QT Syndrome
Authors: Goldenberg Ilan , Moss Arthur J. , Peterson Derick R. , McNitt Scott , Zareba Wojciech , Andrews Mark L. , Robinson Jennifer L. , Locati Emanuela H. , Ackerman Michael J. , Benhorin Jesaia , Kaufman Elizabeth S. , Napolitano Carlo , Priori Silvia G. , Qi Ming , Schwartz Peter J. , Towbin Jeffrey A. , Vincent G. Michael , Zhang Li 
Published: April 2008

Background—The congenital long-QT syndrome (LQTS) is an important cause of sudden cardiac death in children without structural heart disease. However, specific risk factors for life-threatening cardiac events in children with this genetic disorder have not been identified.Methods and Results—Cox proportional-hazards regression modeling was used to identify risk factors for aborted cardiac arrest or sudden cardiac death in 3015 LQTS children from the International LQTS Registry who were followed up from 1 through 12 years of age. The cumulative probability of the combined end point was significantly higher in boys (5%) than in girls (1%;P<0.001). Risk factors for cardiac arrest or sudden cardiac death during childhood included corrected QT interval [QTc] duration >500 ms (hazard ratio [HR]; 2.72; 95% confidence interval [CI], 1.50 to 4.92;P=0.001) and prior syncope (recent syncope [<2 years]: HR, 6.16; 95% CI 3.41 to 11.15;P<0.001; remote syncope [≥2 years]: HR, 2.67; 95% CI, 1.22 to 5.85;P=0.01) in boys, whereas prior syncope was the only significant risk factor among girls (recent syncope: HR, 27.82; 95% CI, 9.72 to 79.60;P<0.001; remote syncope: HR, 12.04; 95% CI, 3.79 to 38.26;P<0.001). β-Blocker therapy was associated with a significant 53% reduction in the risk of cardiac arrest or sudden cardiac death (P=0.01).Conclusions—LQTS boys experience a significantly higher rate of fatal or near-fatal cardiac events than girls during childhood. A QTc duration >500 ms and a history of prior syncope identify risk in boys, whereas prior syncope is the only significant risk factor among girls. β-Blocker therapy is associated with a significant reduction in the risk of life-threatening cardiac events during childhood.
Dinámica de estereotipos de género y poder: un estudio transcultural
Authors: López-Zafra Esther , García-Retamero Rocío , Diekman Amanda , Eagly Alice H. 
Published: April 2008

Las características que se atribuyen a hombres y mujeres influyen hasta el punto de determinar qué es correcto o no hacer, y también pueden influir en la participación y en la asunción de distintos roles sociales que impliquen poder. Tradicionalmente, los hombres han ocupado puestos de poder público mientras que las mujeres se han centrado en el ámbito privado. En este estudio transcultural pretendemos comprobar si el que mujeres y hombres ocupen roles que se asociaban con el otro género, influye en la percepción sobre los estereotipos de género y sobre el poder, y si esto se produce de manera diferente en función de las transformaciones sociales del contexto en que se encuentran. Para ello 720 personas de España, Alemania y Estados Unidos de América participan en un experiment. Entre nuestros resultados encontramos que se percibe que las mujeres han ganado, y seguirán haciéndolo en lo sucesivo, más poder público, y que también tienen más características masculinas. Este resultado es mayor en España que en Alemania y EEUU, por lo que encontramos un efecto importante del context.
Mediación penal adulta y reincidencia. El grado de satisfacción de los infractores y las víctimas
Authors: Soria Miguel-Ángel , Armadans Inmaculada , Viñas Ma Rosa , Manzano Juan 
Published: April 2008

El objetivo de la investigación es determinar los efectos de la mediación penal sobre la reincidencia y la satisfacción de víctimas y agresores. El estudio se desarrolló en cuatro fases. En una primera se vaciaron 888 expedientes judiciales relativos a los casos de mediación penal atendidos en Cataluña. A continuación se analizó la reincidencia en la informática judicial de los imputados mediante consulta de los expedientes judiciales posteriores a la fecha de finalización de la mediación. Tercero, se construyó una escala de valoración de la satisfacción (CSM-P) y, finalmente, se aplicó la misma por vía telefónica a una muestra de 213 personas, víctimas y agresores. Los resultados obtenidos en el estudio son concordantes con los obtenidos en otros países en la mayoría de variables analizadas. La mediación tuvo un efecto reductor sobre la reincidencia y provocó la aparición de unos niveles de satisfacción elevados entre las partes participantes en el proceso. Pese a los resultados obtenidos, no pudo establecerse una relación directa de la reincidencia con la satisfacción.
Prevention of nosocomial infections in acute respiratory failure patients
Authors: Girou E. 
Published: April 2008

Patients with acute respiratory failure are predisposed to acquire nosocomial infection primarily because they may need ventilatory support, usually invasive mechanical ventilation. The presence of an endotracheal tube impairs natural defences of the respiratory tract and favours airways colonisation and lung infection. Cross transmission of microorganisms may also occurviacontaminated hands of healthcare workers that manipulate invasive devices. Thus, avoiding the endotracheal tube and increasing hand hygiene compliance are major measures to prevent ventilator­associated pneumonia. The use of noninvasive ventilation has been shown to reduce the incidence of nosocomial infections and should be used whenever possible.Using hand rubbing with waterless alcohol­based products evidenced higher efficacy to reduce hand contamination as compared to conventional hand washing with soap. Due to its rapid activity and ease of access, hand rubbing constitutes a promising avenue for improving hand hygiene compliance and thus reducing cross infection.
RNACompress: Grammar-based compression and informational complexity measurement of RNA secondary structure
Authors: Liu Qi , Yang Yu , Chen Chun , Bu Jiajun , Zhang Yin , Ye Xiuzi 
Published: April 2008

Abstract

Background
With the rapid emergence of RNA databases and newly identified non-coding RNAs, an efficient compression algorithm for RNA sequence and structural information is needed for the storage and analysis of such data. Although several algorithms for compressing DNA sequences have been proposed, none of them are suitable for the compression of RNA sequences with their secondary structures simultaneously. This kind of compression not only facilitates the maintenance of RNA data, but also supplies a novel way to measure the informational complexity of RNA structural data, raising the possibility of studying the relationship between the functional activities of RNA structures and their complexities, as well as various structural properties of RNA based on compression.

Results

RNACompress employs an efficient grammar-based model to compress RNA sequences and their secondary structures. The main goals of this algorithm are two fold: (1) present a robust and effective way for RNA structural data compression; (2) design a suitable model to represent RNA secondary structure as well as derive the informational complexity of the structural data based on compression. Our extensive tests have shown that RNACompress achieves a universally better compression ratio compared with other sequence-specific or common text-specific compression algorithms, such as Gencompress, winrar and gzip. Moreover, a test of the activities of distinct GTP-binding RNAs (aptamers) compared with their structural complexity shows that our defined informational complexity can be used to describe how complexity varies with activity. These results lead to an objective means of comparing the functional properties of heteropolymers from the information perspective.

Conclusion
A universal algorithm for the compression of RNA secondary structure as well as the evaluation of its informational complexity is discussed in this paper. We have developed RNACompress, as a useful tool for academic users. Extensive tests have shown that RNACompress is a universally efficient algorithm for the compression of RNA sequences with their secondary structures. RNACompress also serves as a good measurement of the informational complexity of RNA secondary structure, which can be used to study the functional activities of RNA molecules.
Data capture in bioinformatics: requirements and experiences with Pedro
Authors: Jameson Daniel , Garwood Kevin , Garwood Chris , Booth Tim , Alper Pinar , Oliver Stephen G , Paton Norman W 
Published: April 2008

Abstract

Background
The systematic capture of appropriately annotated experimental data is a prerequisite for most bioinformatics analyses. Data capture is required not only for submission of data to public repositories, but also to underpin integrated analysis, archiving, and sharing – both within laboratories and in collaborative projects. The widespread requirement to capture data means that data capture and annotation are taking place at many sites, but the small scale of the literature on tools, techniques and experiences suggests that there is work to be done to identify good practice and reduce duplication of effort.

Results
This paper reports on experience gained in the deployment of the Pedro data capture tool in a range of representative bioinformatics applications. The paper makes explicit the requirements that have recurred when capturing data in different contexts, indicates how these requirements are addressed in Pedro, and describes case studies that illustrate where the requirements have arisen in practice.

Conclusion
Data capture is a fundamental activity for bioinformatics; all biological data resources build on some form of data capture activity, and many require a blend of import, analysis and annotation. Recurring requirements in data capture suggest that model-driven architectures can be used to construct data capture infrastructures that can be rapidly configured to meet the needs of individual use cases. We have described how one such model-driven infrastructure, namely Pedro, has been deployed in representative case studies, and discussed the extent to which the model-driven approach has been effective in practice.
Roots of angiosperm formins: The evolutionary history of plant FH2 domain-containing proteins
Authors: Grunt Michal , Žárský Viktor , Cvrčková Fatima 
Published: April 2008

Abstract

Background
Shuffling of modular protein domains is an important source of evolutionary innovation. Formins are a family of actin-organizing proteins that share a conserved FH2 domain but their overall domain architecture differs dramatically between opisthokonts (metazoans and fungi) and plants. We performed a phylogenomic analysis of formins in most eukaryotic kingdoms, aiming to reconstruct an evolutionary scenario that may have produced the current diversity of domain combinations with focus on the origin of the angiosperm formin architectures.

Results
The Rho GTPase-binding domain (GBD/FH3) reported from opisthokont and Dictyostelium formins was found in all lineages except plants, suggesting its ancestral character. Instead, mosses and vascular plants possess the two formin classes known from angiosperms: membrane-anchored Class I formins and Class II formins carrying a PTEN-like domain. PTEN-related domains were found also in stramenopile formins, where they have been probably acquired independently rather than by horizontal transfer, following a burst of domain rearrangements in the chromalveolate lineage. A novel RhoGAP-related domain was identified in some algal, moss and lycophyte (but not angiosperm) formins that define a specific branch (Class III) of the formin family.

Conclusion
We propose a scenario where formins underwent multiple domain rearrangements in several eukaryotic lineages, especially plants and chromalveolates. In plants this replaced GBD/FH3 by a probably inactive RhoGAP-like domain, preserving a formin-mediated association between (membrane-anchored) Rho GTPases and the actin cytoskeleton. Subsequent amplification of formin genes, possibly coincident with the expansion of plants to dry land, was followed by acquisition of alternative membrane attachment mechanisms present in extant Class I and Class II formins, allowing later loss of the RhoGAP-like domain-containing formins in angiosperms.
A systematic survey in Arabidopsis thaliana of transcription factors that modulate circadian parameters
Authors: Hanano Shigeru , Stracke Ralf , Jakoby Marc , Merkle Thomas , Domagalska Malgorzata A , Weisshaar Bernd , Davis Seth J 
Published: April 2008

Abstract

Background
Plant circadian systems regulate various biological processes in harmony with daily environmental changes. In Arabidopsis thaliana, the underlying clock mechanism is comprised of multiple integrated transcriptional feedbacks, which collectively lead to global patterns of rhythmic gene expression. The transcriptional networks are essential within the clock itself and in its output pathway.

Results
Here, to expand understanding of transcriptional networks within and associated to the clock, we performed both an in silico analysis of transcript rhythmicity of transcription factor genes, and a pilot assessment of functional phenomics on the MYB, bHLH, and bZIP families. In our in silico analysis, we defined which members of these families express a circadian waveform of transcript abundance. Up to 20% of these families were over-represented as clock-controlled genes. To detect members that contribute to proper oscillator function, we systematically measured rhythmic growth via an imaging system in hundreds of misexpression lines targeting members of the transcription-factor families. Three transcription factors were found that conferred aberrant circadian rhythms when misexpressed: MYB3R2, bHLH69, and bHLH92.

Conclusion
Transcript abundance of many transcription factors in Arabidopsis oscillates in a circadian manner. Further, a developed pipeline assessed phenotypic contribution of a panel of transcriptional regulators in the circadian system.