bluuebunny/crossref_metadata_2025_split huggingface dataset:
Variability of the Kuroshio Extension Jet, Recirculation Gyre, and Mesoscale Eddies on Decadal Time Scales
Authors: Qiu Bo , Chen Shuiming 
Published: December 2005

Abstract
Twelve years of sea surface height (SSH) data from multiple satellite altimeters are used to investigate the low-frequency changes and the interconnections of the Kuroshio Extension (KE) jet, its southern recirculation gyre, and their mesoscale eddy field. The dominant signal is characterized by the steady weakening of the KE jet/recirculation gyre from 1993 to 1996, followed by a gradual strengthening after 1997. During the weakening period of 1993–96, the KE path migrated southward in general, and this path migration reversed in direction during the strengthening period of the KE jet and recirculation gyre after 1997. By hindcasting the SSH signals using linear vorticity dynamics, it was found that weakening (strengthening) in the KE jet and recirculation gyre is consistent with westward propagation of negative (positive) SSH anomalies generating in the eastern North Pacific and strengthening during their westward propagation. When the KE jet and recirculation gyre were in a weak mode during 1996–2001, the regional eddy kinetic energy level was observed to be higher than when the jet and recirculation gyre were in a strong mode. This negative correlation between the mean flow intensity and the level of regional eddy kinetic energy is found in both the SSH data and the linear vorticity model to result from the migration of the KE jet inflow over the Izu–Ogasawara Ridge. When it is forced southward by the impinging negative SSH anomalies, the KE jet inflow rides over the ridge through a shallow segment, leading to large-amplitude downstream meanders. Impinging of positive SSH anomalies, on the other hand, strengthens the recirculation gyre and forces the inflow northward where it passes through a deep channel, minimizing the path perturbations in the downstream region.
The Shallow and Deep Western Boundary Circulation of the South Atlantic at 5°–11°S
Authors: Schott Friedrich A. , Dengler Marcus , Zantopp Rainer , Stramma Lothar , Fischer Jürgen , Brandt Peter 
Published: December 2005

AbstractRepeated shipboard observation sections across the boundary flow off northeastern Brazil as well as acoustic Doppler current profiler (ADCP) and current-meter records from a moored boundary array deployed during 2000–04 near 11°S are analyzed here for both the northward warm water flow by the North Brazil Undercurrent (NBUC) above approximately 1100 m and the southward flow of North Atlantic Deep Water (NADW) underneath. At 5°S, the mean from nine sections yields an NBUC transport of 26.5 ± 3.7 Sv (Sv ≡ 106 m3 s−1) along the boundary; at 11°S the mean NBUC transport from five sections is 25.4 ± 7.4 Sv, confirming that the NBUC is already well developed at 11°S. At both latitudes a persistent offshore southward recirculation between 200- and 1100-m depth reduces the net northward warm water flow through the 5°S section (west of 31.5°W) to 22.1 ± 5.3 Sv and through the 11°S section to 21.7 ± 4.1 Sv (west of 32.0°W). The 4-yr-long NBUC transport time series from 11°S yields a seasonal cycle of 2.5 Sv amplitude with its northward maximum in July. Interannual NBUC transport variations are small, varying only by ±1.2 Sv during the four years, with no detectable trend. The southward flow of NADW within the deep western boundary current at 5°S is 25.5 ± 8.3 Sv with an offshore northward recirculation, yielding a nine-section mean of 20.3 ± 10.1 Sv west of 31.5°W. For Antarctic Bottom Water, a net northward flow of 4.4 ± 3.0 Sv is determined at 5°S. For the 11°S section, the moored array data show a pronounced energy maximum at 60–70-day period in the NADW depth range, which was identified in related work as deep eddies translating southward along the boundary. Based on a kinematic eddy model fit to the first half of the moored time series, the mean NADW transfer by the deep eddies at 11°S was estimated to be about 17 Sv. Given the large interannual variability of the deep near-boundary transport time series, which ranged from 14 to 24 Sv, the 11°S mean was considered to be not distinguishable from the mean at 5°S.
Pathways into the Pacific Equatorial Undercurrent: A Trajectory Analysis*
Authors: Goodman Paul J. , Hazeleger Wilco , de Vries Pedro , Cane Mark 
Published: December 2005

Abstract
A time-dependent trajectory algorithm is used to determine the sources of the Pacific Ocean Equatorial Undercurrent (EUC) in a global climate model with ¼° (eddy permitting) resolution and forced with realistic winds. The primary sources and pathways are identified, and the transformation of properties in temperature/salinity space is explored. An estimate for the quantity of recirculation, a notoriously difficult property to estimate from observational data, is given. Over two-thirds of the water in the Pacific EUC at 140°W originates south of the equator; 70% of the EUC is ventilated outside of the Tropics (poleward of 13°S or 10°N): three-quarters of these extratropical trajectories travel through the western boundary currents between their subduction and incorporation into the EUC, and one-fifth of the extratropical trajectories enter and leave the tropical band at least once before entering the EUC.
PSE: A tool for browsing a large amount of MEDLINE/PubMed abstracts with gene names and common words as the keywords
Authors: Yoneya Takashi 
Published: December 2005

Abstract
Background
MEDLINE/PubMed (hereinafter called PubMed) is one of the most important literature databases for the biological and medical sciences, but it is impossible to read all related records due to the sheer size of the repository. We usually have to repeatedly enter keywords in a trial-and-error manner to extract useful records. Software which can reduce such a laborious task is therefore required.

Results
We developed a web-based software, the PubMed Sentence Extractor (PSE), which parses large number of PubMed abstracts, extracts and displays the co-occurrence sentences of gene names and other keywords, and some information from EntrezGene records. The result links to whole abstracts and other resources such as the Online Mendelian Inheritance in Men and Reference Sequence. While PSE executes at the sentence-level when evaluating the existence of keywords, the popular PubMed operates at the record-level. Therefore, the relationship between the two keywords, a gene name and a common word, is more accurately captured by PSE than PubMed. In addition, PSE shows the list of keywords and considers the synonyms and variations on gene names. Through these functions, PSE would reduce the task of searching through records for gene information.

Conclusion
We developed PSE in order to extract useful records efficiently from PubMed. This system has four advantages over a simple PubMed search; the reduction in the amount of collected literatures, the showing of keyword lists, the consideration for synonyms and variations on gene names, and the links to external databases. We believe PSE is helpful in collecting necessary literatures efficiently in order to find research targets. PSE is freely available under the GPL licence as additional files to this manuscript.
All dressed up but nowhere to go? Delayed hospital discharges and older people
Authors: Glasby Jon , Littlechild Rosemary , Pryce Kathryn 
Published: December 2005

Objective: Delayed hospital discharges are a key concern in a number of industrialized nations and are the subject of a range of government initiatives in the English National Health Service. The aim of this paper was to review the UK literature on delayed hospital discharges and older people in order to identify and explore the rate and causes of delayed hospital discharges, together with policies and practices that may reduce delayed discharges and improve the experiences of older people. Methods: Literature review based on searches of major health/social-care databases. Sources which explore the rate and cause of delayed discharges in the UK were included. Relevant documents were categorized using the research hierarchy set out in the National Service Framework for Older People and analysed according to criteria for appraising the quality of qualitative research proposed by Mays et al. Results: The review identified 21 studies, which suggest very different rates and causes of delayed discharge in different settings. The studies reveal the importance of rehabilitation services to reduce the rate of delayed discharge, the prevalence of delayed discharges caused by internal hospital factors, and the complex and multi-faceted nature of the factors contributing to delayed discharge. Despite this, the studies have a number of methodological flaws and often fail to include a patient perspective or to consider detailed policies and approaches to reduce the number of delayed discharges. There is also a failure to consider the needs of older people with mental health problems or people from minority ethnic communities. Conclusion: The evidence, as it currently stands, raises a number of issues about current hospital discharge policy, supporting some aspects of the current government agenda in England, but questioning other aspects.
In Vitro Modeling of Paraxial and Lateral Mesoderm Differentiation Reveals Early Reversibility
Authors: Sakurai Hidetoshi , Era Takumi , Jakt Lars Martin , Okada Mitsuhiro , Nakai Shigeru , Nishikawa Satomi , Nishikawa Shin-Ichi 
Published: December 2005

Abstract
Endothelial cells (ECs) are thought to be derived mainly from the vascular endothelial growth factor receptor 2 (VEGFR-2)+ lateral mesoderm during early embryogenesis. In this study, we specified several pathways for EC differentiation using a murine embryonic stem (ES) cell differentiation culture system that is a model for cellular processes during early embryogenesis. Based on the results of in vitro fate analysis, we show that, in the main pathway, committed ECs are differentiated through the VEGFR-2+ platelet-derived growth factor receptor α (PDGFR-α)− single-positive (VSP) population that is derived from the VEGFR-2+PDGFR-α+ double-positive (DP) population. This major differentiation course was also confirmed using DNA microarray analysis. In addition to this main pathway, however, ECs also can be generated from the VEGFR-2−PDGFR-α+ single-positive (PSP) population, which represents the paraxial mesodermal lineage and is also derived from the DP population. Our results strongly suggest that, even after differentiation from the common progenitor DP population into the VSP and PSP populations, these two populations continue spontaneous switching of their surface phenotype, which results in switching of their eventual fates. The rate of this interlineage conversion between VSP and PSP is unexpectedly high. Because of this potential to undergo fate switch, we conclude that ECs can be generated via multiple pathways in in vitro ES cell differentiation.
Psychosocial treatments of suicidal behaviors: A practice‐friendly review
Authors: Comtois Katherine Anne , Linehan Marsha M. 
Published: December 2005

AbstractWorldwide, almost a million people die by suicide each year. Intentional, nonfatal, self‐inflicted injury, including both suicide attempts and acts without suicide intent, also has very high prevalence. This article provides a practice‐friendly review of controlled studies of psychosocial treatments aiming to prevent suicide, attempted suicide, and nonsuicidal self‐inflicted injuries. Despite relatively small sample sizes for a low‐base‐rate outcome such as self‐inflicted injury, several psychotherapies have been found effective, including cognitive therapy, dialectical behavior therapy, problem‐solving therapy, and interpersonal psychotherapy, as well as outreach interventions, such as sending caring letters. The clinical implications of the review are discussed with the goal of translating the science to service—particularly the importance of outreach and treatment of non‐compliance, the assessment and management of suicide risk, and competency in effective psychotherapies. These are critical steps for clinical psychology and psychotherapists to take in their role in suicide prevention. © 2005 Wiley Periodicals, Inc. J Clin Psychol: In Session 62: 161–170, 2006.
Do SSRIs cause suicide in children? The evidence is underwhelming
Authors: Bostwick John Michael 
Published: December 2005

AbstractAfter regulatory agencies in the United Kingdom and United States recommended severe restrictions on antidepressant use in children, many lessons were learned, although one was not that these drugs cause suicide. We learned that pharmaceutical companies selectively released data that reflected positively on their products and that combining suppressed and published data suggested that most of these medications had questionable efficacy. We also learned that the studies lacked uniformity both in which age groups constituted children and which behavior was considered suicidal. Several recent, large nonindustry studies indicated that rates of suicide and suicidal behavior were actually reduced in children who used antidepressants, despite piteous anecdotal tales in the popular press purporting that selective serotonin reuptake inhibitors (SSRIs) caused children to kill themselves. Patients in pharmaceutical trials probably do not represent typical patients in routine clinical practice. Emerging implications are that suicidal behavior—if it does occur—is most likely soon after starting antidepressant use and that prescribers must be both vigilant in educating patients and families about warning signs and available to manage worrisome behavior. © 2005 Wiley Periodicals, Inc. J Clin Psychol: In Session 62: 235–241, 2006.
The case against no‐suicide contracts: The commitment to treatment statement as a practice alternative
Authors: Rudd M. David , Mandrusiak Michael , Joiner Jr. Thomas E. 
Published: December 2005

AbstractThis article reviews the literature on the use of “no‐suicide contracts” in clinical practice, including conceptual discussions, patient and clinician surveys, and a few empirical studies on clinical utility. Our primary conclusion is that no‐suicide contracts suffer from a broad range of conceptual, practical, and empirical problems. Most significantly, they have no empirical support for their effectiveness in the clinical environment. The authors provide and illustrate the commitment to treatment statement as a practice alternative to the no‐suicide contract. © 2005 Wiley Periodicals, Inc. J Clin Psychol: In Session 62: 243–251, 2006.
Genome Analysis and Functional Characterization of the E2 and RING-Type E3 Ligase Ubiquitination Enzymes of Arabidopsis
Authors: Kraft Edward , Stone Sophia L. , Ma Lingeng , Su Ning , Gao Ying , Lau On-Sun , Deng Xing-Wang , Callis Judy 
Published: December 2005

Abstract
Attachment of ubiquitin to substrate proteins is catalyzed by the three enzymes E1, E2 (ubiquitin conjugating [UBC]), and E3 (ubiquitin ligase). Forty-one functional proteins with a UBC domain and active-site cysteine are predicted in the Arabidopsis (Arabidopsis thaliana) genome, which includes four that are predicted or shown to function with ubiquitin-like proteins. Only nine were previously characterized biochemically as ubiquitin E2s. We obtained soluble protein for 22 of the 28 uncharacterized UBCs after expression in Escherichia coli and demonstrated that 16 function as ubiquitin E2s. Twelve, plus three previously characterized ubiquitin E2s, were also tested for the ability to catalyze ubiquitination in vitro in the presence of one of 65 really interesting new gene (RING) E3 ligases. UBC22, UBC19-20, and UBC1-6 had variable levels of E3-independent activity. Six UBCs were inactive with all RINGs tested. Closely related UBC8, 10, 11, and 28 were active with the largest number of RING E3s and with all RING types. Expression analysis was performed to determine whether E2s or E3s were expressed in specific organs or under specific environmental conditions. Closely related E2s show unique patterns of expression and most express ubiquitously. Some RING E3s are also ubiquitously expressed; however, others show organ-specific expression. Of all the organs tested, RING mRNAs are most abundant in floral organs. This study demonstrates that E2 diversity includes examples with broad and narrow specificity toward RINGs, and that most ubiquitin E2s are broadly expressed with each having a unique spatial and developmental pattern of expression.
Heterotrimeric G Proteins Facilitate Arabidopsis Resistance to Necrotrophic Pathogens and Are Involved in Jasmonate Signaling
Authors: Trusov Yuri , Rookes James Edward , Chakravorty David , Armour David , Schenk Peer Martin , Botella José Ramón 
Published: December 2005

Abstract
Heterotrimeric G proteinshave been previously linked to plant defense; however a role for the Gβγ dimer in defense signaling has not been described to date. Using available Arabidopsis (Arabidopsis thaliana) mutants lacking functional Gα or Gβ subunits, we show that defense against the necrotrophic pathogens Alternaria brassicicola and Fusarium oxysporum is impaired in Gβ-deficient mutants while Gα-deficient mutants show slightly increased resistance compared to wild-type Columbia ecotype plants. In contrast, responses to virulent (DC3000) and avirulent (JL1065) strains of Pseudomonas syringae appear to be independent of heterotrimeric G proteins. The induction of a number of defense-related genes in Gβ-deficient mutants were severely reduced in response to A. brassicicola infection. In addition, Gβ-deficient mutants exhibit decreased sensitivity to a number of methyl jasmonate-induced responses such as induction of the plant defensin gene PDF1.2, inhibition of root elongation, seed germination, and growth of plants in sublethal concentrations of methyl jasmonate. In all cases, the behavior of the Gα-deficient mutants is coherent with the classic heterotrimeric mechanism of action, indicating that jasmonic acid signaling is influenced by the Gβγ functional subunit but not by Gα. We hypothesize that Gβγ acts as a direct or indirect enhancer of the jasmonate signaling pathway in plants.
ArabidopsisCONSTANS-LIKE3 Is a Positive Regulator of Red Light Signaling and Root Growth
Authors: Datta Sourav , Hettiarachchi G.H.C.M. , Deng Xing-Wang , Holm Magnus 
Published: December 2005

AbstractCONSTITUTIVE PHOTOMORPHOGENIC1 (COP1) is an E3 ubiquitin ligase that represses photomorphogenesis in the dark. Therefore, proteins interacting with COP1 could be important regulators of light-dependent development. Here, we identify CONSTANS-LIKE3 (COL3) as a novel interaction partner of COP1. A green fluorescent protein–COL3 fusion protein colocalizes with COP1 to nuclear speckles when transiently expressed in plant cells. This localization requires the B-box domains in COL3, indicating a novel function of this domain. A loss-of-function col3 mutant has longer hypocotyls in red light and in short days. Unlike constans, the col3 mutant flowers early and shows a reduced number of lateral branches in short days. The mutant also exhibits reduced formation of lateral roots. The col3 mutation partially suppresses the cop1 and deetiolated1 (det1) mutations in the dark, suggesting that COL3 acts downstream of both of these repressors. However, the col3 mutation exerts opposing effects on cop1 and det1 in terms of lateral roots and anthocyanin accumulation, suggesting that COL3 also has activities that are independent of COP1 and DET1. In conclusion, we have identified COL3 as a positive regulator of photomorphogenesis that acts downstream of COP1 but can promote lateral root development independently of COP1 and also function as a daylength-sensitive regulator of shoot branching.
Morality, Ethics, and Globalization: Lessons from Kant, Hegel, Rawls, and Habermas
Authors: Lachapelle Erick 
Published: December 2005

AbstractThis chapter critically examines the separation of political theory from international theory and argues that a return to the former is essential if IR scholars are to help provide answers to the urgent moral and ethical questions facing world politics in an era of globalization. An examination of the political philosophies of Kant and Hegel demonstrates the importance of political theory for the analysis and practice of global politics today, while the tension between the universal and particular, emerging from Kantian morality and Hegelian ethics, is traced in the recent work of John Rawls and Jürgen Habermas.
Sea-Borne Tourism in Antarctica: Avenues for Further Intergovernmental Regulation
Authors: Molenaar Erik Jaap 
Published: December 2005

AbstractDuring the past 3,5 decades, sea-borne (cruise) tourism in Antarctica has steadily intensified and diversified. So far, the States involved in the Antarctic Treaty System (ATS), who have collectively assumed a mandate as well as a responsibility for governing Antarctica, have been relatively passive as a collective and have largely relied on direct and indirect regulation from outside the ATS, most importantly on self-regulation by the tourism industry through the International Association of Antarctica Tour Operators (IAATO). In view of the gradual intensification and diversification of Antarctic tourism, the abovementioned responsibility of the Consultative Parties to the Antarctic Treaty (ATCPs) and the need to safeguard the international legitimacy of the ATS, this article examines avenues for further international regulation by the ATCPs. This is in part done by exploring the meaning of the acronym IUU (illegal, unreported and unregulated) in the sphere of Antarctic sea-borne tourism, to what extent it occurs and how some forms can be addressed.
Skewness of Spatial Gradients of Turbulent Dissipation Rates in the Mixed Layer
Authors: Thorpe S. A. , Osborn T. R. 
Published: December 2005

Abstract
Temperature ramps or microfronts are coherent tilted structures in the oceanic and atmospheric boundary layers at which there are small, but detectable, changes in mean temperature. Their presence contributes to a nonzero skewness, ST(θ), of the spatial derivatives of temperature, dT/dx, at constant depth within the ocean mixed layer. The skewness ST(θ) has a roughly sinusoidal variation with θ, the direction in which the derivatives are measured relative to the wind. The magnitude of the skewness, |ST(0)|, measured in a direction into the wind (θ = 0) is of order unity, and the sign of ST(0) depends on the heat flux from the air to the water through the sea surface, being positive if the heat flux is positive. Recent observations using an AUV, Autosub, have shown that the mean values of ɛ, the rate of dissipation of turbulent kinetic energy per unit mass, change as temperature ramps are crossed. This observation raises the questions: Is the skewness of the gradient of logɛ, Slogɛ(θ), nonzero in the mixed layer even though ɛ is observed to be lognormal? If so, is Slogɛ(θ) related to ST(θ)? The answer to both of the questions appears to be “yes,” although the magnitude of Slogɛ(θ) is small, of order 5 × 10−2, and no clearly detectable variation with θ is found in the available data.