bluuebunny/crossref_metadata_2025_split huggingface dataset:
The study of function in behavioural ecology
Authors: Cuthill Innes 
Published: November 2005

AbstractIn 1963, a landmark paper by Niko Tinbergen laid out the aims and methods of ethology and, in so doing, extended and clarified Julian Huxley's classification of the different ways in which one can investigate biological processes. I discuss the status of one of these "four Why questions", that of function or survival value, and the relationship of Tinbergen's ethology to behavioural ecology, the main field asking functional questions about animal behaviour today. Function itself can be defined in many different ways and behavioural ecologists themselves use it both in the context of current utility and selective history. I review these definitions in the light of analyses by philosophers of science, behavioural ecologists and, of course, Tinbergen's own use of the word. I defend the view, accepted by many philosophers of science, that the definition of 'function' must have a historical component, both to avoid teleology and to retain the everyday sense of questioning 'What is it for?' That said, in reviewing the different methods that can be used to determine function, I defend the view that investigations of current utility, as practised by behavioural ecologists, can provide the most important clues to the selective forces that have shaped behaviours. Finally, I consider the evolution of the discipline of behavioural ecology, its current status and future prospects.
Tinbergen's fourth question, ontogeny: sexual and individual differentiation
Authors: Crews David , Groothuis Ton 
Published: November 2005

Abstract
Based on Tinbergen's view of the study of behavioural development we describe some recent advances and their importance in this field. We argue that the study of behavioural development should combine both proximate and ultimate approaches, and can help to understand how early subtle environmental factors shape consistent individual variation both between and within sexes. This is illustrated by reviewing the profound effects of incubation temperature on the development of brain and social behaviour in the leopard gecko, a species with temperature-dependent sex determination, and the effects of early exposure to steroid hormones on social behaviour in rodents and especially birds. Both are maternal effects: incubation temperature can be partly determined by the nest site where the mother deposited her eggs, while in both oviparous and viviparous vertebrates maternal hormones reach and influence the embryo. In the gecko, incubation temperature affects sexual and aggressive behaviour, growth, the hypothalamus-pituitary-gonadal axis, as well as the size, connectivity and metabolic capacity of certain brain areas. In this way not only is the gonad type determined, but so too is the morphological, physiological, neural, and behavioural phenotype established that explains much of within-sex variation. In rodents, maternal hormones affect similar aspects. In avian species, maternal hormones, deposited in the eggs, vary systematically between and within clutches and have both short- and long-lasting effects on competitive behaviour. Evidence suggests that mothers adaptively adjust hormone allocation to the environmental context. In addition, we discuss some effects of postnatal experience on behavioural development in geckos, mice and bird species. Our results also illustrate how the study of animal models other than rodents can help in understanding important developmental processes.
The Momentum Imbalance Paradox Revisited
Authors: Nof Doron 
Published: November 2005

Abstract
The classical problem of a point source situated along a southern boundary emptying buoyant water into a (β plane) ocean is revisited. Pichevin and Nof (PN) have shown that, in contrast to the view prevailing at the time, such an inviscid outflow does not simply turn to the right. Rather, it bifurcates into two branches: a steady branch that does turn to the right (eastward) and an unsteady branch that periodically sheds eddies to the left (westward). This partition is because a simple turn to the right of the entire outflow leaves the outflow’s long-shore momentum flux unbalanced, creating a paradox. In contrast, the branching allows the westward-drifting eddies (westward branch) to balance the momentum flux of the steady current (eastward branch). Although the analytical PN solution is useful and informative, it is cumbersome and difficult to apply to actual outflows. Here, a considerably simpler nonlinear analytical solution is presented. Using the idea that the eddies grow slowly relative to their rotation rate, it is shown that an intense (i.e., large Rossby number) and large relative vorticity outflow dumps most of its mass flux (Q) into the eddies (66%). (The remaining 33% goes into the eastward long-shore current.) By contrast, a weak outflow (i.e., an outflow with weak anticyclonic vorticity −αf, where α is analogous to the Rossby number and is much smaller than unity and f is the Coriolis parameter) dumps most of its water into the downstream current [(1–2α)Q]. Unexpectedly, this partition of mass turns out to be the same as the one taking place on an f plane. (Note that this is not at all the case for southward outflow nor is it the case for either eastward or westward outflow, where β alters the balance drastically.) Although the above partition of mass is independent of β, the size of the eddies generated by the above process is a function of β. It is given by [768g′Q/βπf 2α(2 − α)(1 + 2α)]1/5, where g′ is the reduced gravity. This gives a reasonable estimate for the Loop Current eddies’ size and generation frequency. Numerical simulations are in agreement with the above nonlinear solution, though the agreement is not necessarily any better than that of PN.
On the Separation of a Barotropic Western Boundary Current from a Cape
Authors: Munday David R. , Marshall David P. 
Published: November 2005

AbstractThe problem of western boundary current separation is investigated using a barotropic vorticity model. Specifically, a boundary current flowing poleward along a boundary containing a cape is considered. The meridional gradient of the Coriolis parameter (the β effect), the strength of dissipation, and the geometry of the cape are varied. It is found that 1) all instances of flow separation are coincident with the presence of a flow deceleration, 2) an increase in the strength of the β effect is able to suppress flow separation, and 3) increasing coastline curvature can overcome the suppressive β effect and induce separation. These results are supported by integrated vorticity budgets, which attribute the acceleration of the boundary current to the β effect and changes in flow curvature. The transition to unsteady final model states is found to have no effect upon the qualitative nature of these conclusions.
Diagnosing Mesoscale Vertical Motion from Horizontal Velocity and Density Data
Authors: Sanz Enric Pallàs , Viúdez Álvaro 
Published: November 2005

Abstract
The mesoscale vertical velocity is obtained by solving a generalized omega equation (ω equation) using density and horizontal velocity data from three consecutive quasi-synoptic high-resolution surveys in the Alboran Sea. The Atlantic Jet (AJ) and the northern part of the Western Alboran Gyre (WAG) were observed as a large density anticyclonic front extending down to 200–230 m. The horizontal velocity uh in the AJ reached maxima of 1.2 m s−1 for the three surveys, with extreme Rossby numbers of ζ/f ≈ −0.9 in the WAG and +0.9 in the AJ (where ζ is the vertical vorticity and f is the Coriolis parameter). The generalized ω equation includes the ageostrophic horizontal flow. It is found that the most important “forcing” term in this equation is ( fζph + ∇hϱ) · ∇2huh, where ζph is the horizontal (pseudo) vorticity and ϱ is the buoyancy. This term is related to the horizontal advection of vertical vorticity by the vertical shear velocity, uhz · ∇hζ. Extreme values of the diagnosed vertical velocity w were located at 80–100 m with max{w} ⊂ [34, 45] and min{w} ⊂ [−64, −34] m day−1. Comparison with the quasigeostrophic (QG) ω equation shows that, because of the large Rossby numbers, non-QG terms are important. The differences between w and the QG vertical velocity are mainly related to the divergence of the ageostrophic part of the total Q vector (Qh ≡ ∇huh · ∇hϱ) in the ω equation.
The Ventilation of the Deep Gulf of Mexico
Authors: Rivas David , Badan Antoine , Ochoa José 
Published: November 2005

AbstractRecent measurements over the sill in the Yucatan Channel indicate that the deepest flows between the Caribbean Sea and the Gulf of Mexico, those that take place below the sill level at the Florida Straits, have zero mean net mass transport but carry significant amounts of heat and oxygen. The heat flux associated with the mean exchange exports approximately 150 GW from the deep Gulf toward the Caribbean and may be related to the formation of the Yucatan Undercurrent. The eddy heat transfer is also significantly different from zero and exports on average an additional 60 GW. This eddy transfer is attributable mostly to events that last from a few days to about 1.5 months, during which colder water from deeper levels in the Caribbean (beneath 2000 m) flows over the sill within a bottom boundary layer close to 200 m thick. The colder water is also very rich in oxygen, and the deep exchange sustains the near-bottom oxygen maximum in the Gulf of Mexico, whence that cold water must slide down the northern slope of the Yucatan Sill. Estimates of oxygen transport by diffusion from the deep water into the overlying intermediate water (∼50 m3 s−1) and the oxygen consumption reported in the literature (∼100 m3 s−1) are balanced by the rates of mean and eddy transfers over the sill (∼150 m3 s−1). The near-bottom mass transport [∼0.32 Sv (1 Sv ≡ 106 m3 s−1)] measured across the deepest portion of the central Yucatan Channel suggests a residence time for the deep waters of the Gulf of about 250 yr.
Generalized Conditions for Hydraulic Criticality of Oceanic Overflows
Authors: Pratt Larry , Helfrich Karl 
Published: November 2005

Abstract
Two methods for assessing the hydraulic criticality of an observed or modeled overflow are discussed. The methods are valid for single-layer deep flows with arbitrary potential vorticity and cross section. The first method is based on a purely steady view in which the flow at a given section is divided up into a group of “streamtubes.” A hydraulic analysis requires an extension of Gill’s functional formulation to systems with many degrees of freedom. The general form of the critical condition and associated compatibility condition for such a system are derived and applied to the streamtube model. As an aside, it is shown by example that Gill’s original critical condition can fail to capture all possible critical states, but that this problem is fixed when the multivariable approach is used. It is also shown how Gill’s method can be applied to certain dispersive or dissipative systems. The second method of assessing criticality involves direct calculation of linear, long-wave speeds using a time-dependent version of the streamtube model. This approach turns out to be better suited to the analysis of geophysical datasets. The significance of the local Froude number F is discussed. It is argued that F must take on the value unity at some point across a critical section.
Decadal Variability of Pycnocline Flows from the Subtropical to the Equatorial Pacific*
Authors: Wang Qi , Huang Rui Xin 
Published: November 2005

Abstract
A method based on isopycnal trajectory analysis is proposed to quantify the pathways from the subtropics to the Tropics. For a continuous stratified ocean a virtual streamfunction is defined, which can be used to characterize these pathways. This method is applied to the climatological dataset produced from a data-assimilated model. Analysis indicates that in each layer contours of the virtual streamfunction are a good approximation for streamlines, even if there is a cross-isopycnal mass flux. The zonal-integrated meridional transport per unit layer thickness through each pathway varies in proportion to 1/sinθ, where θ is latitude. The vertical-integrated total transport through pathways behaves similarly. Transport through pathways has a prominent decadal variability. Results suggest that in decadal time scales the interior pathway transport (IPT) anomaly may be mainly caused by the wind stress anomaly at low latitude. The western boundary pathway transport (WBPT) anomaly often has a sign opposite to the IPT anomaly, reflecting compensation between the IPT and the WBPT. However, more often than not the wind stress anomaly within tropical latitudes can also be used to explain the WBPT anomaly.
The Effect of Channel Length on the Residual Circulation in Tidally Dominated Channels
Authors: Li Chunyan , O’Donnell James 
Published: November 2005

Abstract
With an analytic model, this paper describes the subtidal circulation in tidally dominated channels of different lengths, with arbitrary lateral depth variations. The focus is on an important parameter associated with the reversal of the exchange flows. This parameter (δ) is defined as the ratio between the channel length and one-quarter of the tidal wavelength, which is determined by water depth and tidal frequency. In this study, a standard bottom drag coefficient, CD = 0.0025, is used. For a channel with δ smaller than 0.6–0.7 (short channels), the exchange flow at the open end has an inward transport in deep water and an outward transport in shallow water. This situation is just the opposite of channels with a δ value larger than 0.6–0.7 (long channels). For a channel with a δ value of about 0.35–0.5, the exchange flow at the open end reaches the maximum of a short channel. For a channel with a δ value of about 0.85–1.0, the exchange flow at the open end reaches the maximum of a long channel, with the inward flux of water occurring over the shoal area and the outward flow in the deep-water area. However, near the closed end of a long channel, the exchange flow appears as that in a short channel—that is, the exchange flow changes direction along the channel from the head to the open end of the channel. For a channel with a δ value of about 0.6–0.7, the tidally induced subtidal exchange flow at the open end reaches its minimum when there is little flow across the open end and the water residence time reaches its maximum. The mean sea level increases toward the closed end for all δ values. However, the spatial gradient of the mean sea level in a short channel is much smaller than that of a long channel. The differences between short and long channels are caused by a shift in dynamical balance of momentum or, equivalently, a change in tidal wave characteristics from a progressive wave to a standing wave.
Tumor evasion of the immune system: inhibiting p38 MAPK signaling restores the function of dendritic cells in multiple myeloma
Authors: Wang Siqing , Yang Jing , Qian Jianfei , Wezeman Michele , Kwak Larry W. , Yi Qing 
Published: November 2005

AbstractDendritic cells (DCs) from patients with cancer are functionally defective, but the molecular mechanisms underlying these defects are poorly understood. In this study, we used the murine 5TGM1 myeloma model to examine the effects and mechanisms of tumor-derived factors on the differentiation and function of DCs. Myeloma cells or tumor culture conditioning medium (TCCM) were shown to inhibit the differentiation and function of BM-derived DCs (BMDCs), as evidenced by the down-regulated expression of DC-related surface molecules, decreased IL-12, and compromised capacity of the cells to activate allospecific T cells. Moreover, TCCM-treated BMDCs were inferior to normal BMDCs at priming tumor-specific immune responses in vivo. Neutralizing antibodies against IL-6, IL-10, and TGF-β partially abrogated the effects. TCCM treatment activated p38 mitogen-activated protein kinase (MAPK) and Janus kinase (JNK) but inhibited extracellular regulated kinase (ERK). Inhibiting p38 MAPK restored the phenotype, cytokine secretion, and function of TCCM-treated BMDCs. BMDCs from cultures with TCCM and p38 inhibitor was as efficacious as normal BMDCs at inducing tumor-specific antibody, type 1 T cell, and cytotoxic T lymphocyte (CTL) responses and at prolonging mouse survival. Thus, our results suggested that tumor-induced p38 MAPK activation and ERK inhibition in DCs may be a new mechanism for tumor evasion and that regulating these pathways during DC differentiation provides new strategies for generating potent DC vaccines for immunotherapy in patients with cancer. (Blood. 2006;107:2432-2439)
Recent insights into the role of Notch signaling in tumorigenesis
Authors: Leong Kevin G. , Karsan Aly 
Published: November 2005

AbstractMembers of the Notch family of transmembrane receptors play an important role in cell fate determination. Over the past decade, a role for Notch in the pathogenesis of hematologic and solid malignancies has become apparent. Numerous cellular functions and microenvironmental cues associated with tumorigenesis are modulated by Notch signaling, including proliferation, apoptosis, adhesion, epithelial-to-mesenchymal transition, and angiogenesis. It is becoming increasingly evident that Notch signaling can be both oncogenic and tumor suppressive. This review highlights recent findings regarding the molecular and functional aspects of Notch-mediated neoplastic transformation. In addition, cellular mechanisms that potentially explain the complex role of Notch in tumorigenesis are discussed.
Ancestral sequence alignment under optimal conditions
Authors: Hudek Alexander K , Brown Daniel G 
Published: November 2005

Abstract
Background
Multiple genome alignment is an important problem in bioinformatics. An important subproblem used by many multiple alignment approaches is that of aligning two multiple alignments. Many popular alignment algorithms for DNA use the sum-of-pairs heuristic, where the score of a multiple alignment is the sum of its induced pairwise alignment scores. However, the biological meaning of the sum-of-pairs of pairs heuristic is not obvious. Additionally, many algorithms based on the sum-of-pairs heuristic are complicated and slow, compared to pairwise alignment algorithms.
An alternative approach to aligning alignments is to first infer ancestral sequences for each alignment, and then align the two ancestral sequences. In addition to being fast, this method has a clear biological basis that takes into account the evolution implied by an underlying phylogenetic tree.
In this study we explore the accuracy of aligning alignments by ancestral sequence alignment. We examine the use of both maximum likelihood and parsimony to infer ancestral sequences. Additionally, we investigate the effect on accuracy of allowing ambiguity in our ancestral sequences.

Results
We use synthetic sequence data that we generate by simulating evolution on a phylogenetic tree. We use two different types of phylogenetic trees: trees with a period of rapid growth followed by a period of slow growth, and trees with a period of slow growth followed by a period of rapid growth.
We examine the alignment accuracy of four ancestral sequence reconstruction and alignment methods: parsimony, maximum likelihood, ambiguous parsimony, and ambiguous maximum likelihood. Additionally, we compare against the alignment accuracy of two sum-of-pairs algorithms: ClustalW and the heuristic of Ma, Zhang, and Wang.

Conclusion
We find that allowing ambiguity in ancestral sequences does not lead to better multiple alignments. Regardless of whether we use parsimony or maximum likelihood, the success of aligning ancestral sequences containing ambiguity is very sensitive to the choice of gap open cost. Surprisingly, we find that using maximum likelihood to infer ancestral sequences results in less accurate alignments than when using parsimony to infer ancestral sequences. Finally, we find that the sum-of-pairs methods produce better alignments than all of the ancestral alignment methods.
Acquired homotypic and heterotypic immunity against oculogenital Chlamydia trachomatis serovars following female genital tract infection in mice
Authors: Lyons Joseph M , Morré Servaas A , Airo-Brown Lucy P , Peña A Salvador , Ito James I 
Published: November 2005

Abstract

Background

Chlamydia trachomatis is the most common sexually transmitted bacterial pathogen causing female genital tract infection throughout the world. Reinfection with the same serovar, as well as multiple infections with different serovars, occurs in humans. Using a murine model of female C. trachomatis genital tract infection, we determined if homotypic and/or heterotypic protection against reinfection was induced following infection with human oculogenital strains of C. trachomatis belonging to two serovars (D and H) that have been shown to vary significantly in the course of infection in the murine model.

Methods
Groups of outbred CF-1 mice were reinfected intravaginally with a strain of either serovar D or H, two months after initial infection with these strains. Cellular immune and serologic status, both quantitative and qualitative, was assessed following initial infection, and the course of infection was monitored by culturing vaginal samples collected every 2–7 days following reinfection.

Results
Serovar D was both more virulent (longer duration of infection) and immunogenic (higher level of circulating and vaginal IgG and higher incidence of IgA in vaginal secretions) in the mouse genital tract. Although both serovars induced cross-reacting antibodies during the course of primary infection, prior infection with serovar H resulted in only a slight reduction in the median duration of infection against homotypic reinfection (p ~ 0.10), while prior infection with serovar D resulted in significant reduction in the median duration of infection against both homotypic (p < 0.01) and heterotypic reinfection (p < 0.01) when compared to primary infection in age and conditions matched controls.

Conclusion
Serovar D infection resulted in significant homotypic and heterotypic protection against reinfection, while primary infection with serovar H resulted in only slight homotypic protection. In addition to being the first demonstration of acquired heterotypic immunity between human oculogenital serovars, the differences in the level and extent of this immunity could in part explain the stable difference in serovar prevalence among human isolates.