bluuebunny/crossref_metadata_2025_split huggingface dataset:
Baltic cod recruitment – the impact of climate variability on key processes
Authors: Köster Friedrich W. , Möllmann Christian , Hinrichsen Hans-Harald , Wieland Kai , Tomkiewicz Jonna , Kraus Gerd , Voss Rüdiger , Makarchouk Andrei , MacKenzie Brian R. , St. John Michael A. , Schnack Dietrich , Rohlf Norbert , Linkowski Tomasz , Beyer Jan E. 
Published: August 2005

Abstract
Large-scale climatic conditions prevailing over the central Baltic Sea resulted in declining salinity and oxygen concentrations in spawning areas of the eastern Baltic cod stock. These changes in hydrography reduced the reproductive success and, combined with high fishing pressure, caused a decline of the stock to the lowest level on record in the early 1990s. The present study aims at disentangling the interactions between reproductive effort and hydrographic forcing leading to variable recruitment. Based on identified key processes, stock dynamics is explained using updated environmental and life stage-specific abundance and production time-series. Declining salinities and oxygen concentrations caused high egg mortalities and indirectly increased egg predation by clupeid fish. Low recruitment, despite enhanced hydrographic conditions for egg survival in the mid-1990s, was due to food limitation for larvae, caused by the decline in the abundance of the copepod Pseudocalanus sp. The case of the eastern Baltic cod stock exemplifies the multitude effects climatic variability may have on a fish stock and underscores the importance of knowledge of these processes for understanding stock dynamics.
Should excessive worry be required for a diagnosis of generalized anxiety disorder? Results from the US National Comorbidity Survey Replication
Authors: RUSCIO AYELET MERON , LANE MICHAEL , ROY-BYRNE PETER , STANG PAUL E. , STEIN DAN J. , WITTCHEN HANS-ULRICH , KESSLER RONALD C. 
Published: August 2005

Background. Excessive worry is required by DSM-IV, but not ICD-10, for a diagnosis of generalized anxiety disorder (GAD). No large-scale epidemiological study has ever examined the implications of this requirement for estimates of prevalence, severity, or correlates of GAD.Method. Data were analyzed from the US National Comorbidity Survey Replication, a nationally representative, face-to-face survey of adults in the USA household population that was fielded in 2001–2003. DSM-IV GAD was assessed with Version 3.0 of the WHO Composite International Diagnostic Interview. Non-excessive worriers meeting all other DSM-IV criteria for GAD were compared with respondents who met full GAD criteria as well as with other survey respondents to consider the implications of removing the excessiveness requirement.Results. The estimated lifetime prevalence of GAD increases by ~40% when the excessiveness requirement is removed. Excessive GAD begins earlier in life, has a more chronic course, and is associated with greater symptom severity and psychiatric co-morbidity than non-excessive GAD. However, non-excessive cases nonetheless evidence substantial persistence and impairment of GAD, high rates of treatment-seeking, and significantly elevated co-morbidity compared with respondents without GAD. Non-excessive cases also have sociodemographic characteristics and familial aggregation of GAD comparable to excessive cases.Conclusions. Individuals who meet all criteria for GAD other than excessiveness have a somewhat milder presentation than those with excessive worry, yet resemble excessive worriers in a number of important ways. These findings challenge the validity of the excessiveness requirement and highlight the need for further research into the optimal definition of GAD.
Beyond the ‘3/4‐power law’: variation in the intra‐and interspecific scaling of metabolic rate in animals
Authors: Glazier Douglas S. 
Published: August 2005

ABSTRACTIn this review I show that the ‘3/4‐power scaling law’ of metabolic rate is not universal, either within or among animal species. Significant variation in the scaling of metabolic rate with body mass is described mainly for animals, but also for unicells and plants. Much of this variation, which can be related to taxonomic, physiological, and/or environmental differences, is not adequately explained by existing theoretical models, which are also reviewed. As a result, synthetic explanatory schemes based on multiple boundary constraints and on the scaling of multiple energy‐using processes are advocated. It is also stressed that a complete understanding of metabolic scaling will require the identification of both proximate (functional)and ultimate (evolutionary)causes. Four major types of intraspecific metabolic scaling with body mass are recognized [based on the power functionR=aMb, whereRis respiration (metabolic) rate,ais a constant,Mis body mass, andbis the scaling exponent]: Type I: linear, negatively allometric (b<1); Type II: linear, isometric (b=1); Type III: nonlinear, ontogenetic shift from isometric (b=1), or nearly isometric, to negatively allometric (b<1); and Type IV: nonlinear, ontogenetic shift from positively allometric (b> 1) to one or two later phases of negative allometry (b<1). Ontogenetic changes in the metabolic intensity of four component processes (i.e.growth, reproduction, locomotion, and heat production) appear to be important in these different patterns of metabolic scaling. These changes may, in turn, be shaped by age (size)‐specific patterns of mortality. In addition, major differences in interspecific metabolic scaling are described, especially with respect to mode of temperature regulation, body‐size range, and activity level. A‘metabolic‐level boundaries hypothesis’ focusing on two major constraints (surface‐area limits on resource/waste exchange processes and mass/volume limits on power production) can explain much, but not all of this variation. My analysis indicates that further empirical and theoretical work is needed to understand fully the physiological and ecological bases for the considerable variation in metabolic scaling that is observed both within and among species.Recommended approaches for doing this are discussed. I conclude that the scaling of metabolism is not the simple result of a physical law, but rather appears to be the more complex result of diverse adaptations evolved in the context of both physico‐chemical and ecological constraints.
Evolutionary ecology of facultative paedomorphosis in newts and salamanders
Authors: Denoël Mathieu , Joly Pierre , Whiteman Howard H. 
Published: August 2005

ABSTRACTFacultative paedomorphosis is an environmentally induced polymorphism that results in the coexistence of mature, gilled, and fully aquatic paedomorphic adults and transformed, terrestrial, metamorphic adults in the same population. This polymorphism has been of interest to scientists for decades because it occurs in a large number of caudate amphibian taxa as well as in a large diversity of habitats. Numerous experimental and observational studies have been conducted to explain the proximate and ultimate factors affecting these heterochronic variants in natural populations. The production of each alternative phenotype is based on a genotype × environment interaction and research suggests that differences in the environment can produce paedomorphs through several ontogenetic pathways. No single advantage accounts for the maintenance of this polymorphism. Rather, the interplay of different costs and benefits explains the success of the polyphenism across variable environments. Facultative paedomorphosis allows individuals to cope with habitat variation, to take advantage of environmental heterogeneity in the presence of open niches, and to increase their fitness. This process is expected to constitute a first step towards speciation events, and is also an example of biodiversity at the intraspecific level. The facultative paedomorphosis system is thus ripe for future studies encompassing ecology, evolution, behaviour, endocrinology, physiology, and conservation biology. Few other systems have been broad enough to provide varied research opportunities on topics as diverse as phenotypic plasticity, speciation, mating behaviour, and hormonal regulation of morphology. Further research on facultative paedomorphosis will provide needed insight into these and other important questions facing biologists.
How to Simulate the Universe in a Computer
Authors: Knebe Alexander 
Published: August 2005

AbstractIn this contribution a broad overview of the methodologies of cosmological N-body simulations and a short introduction explaining the general idea behind such simulations is presented. After explaining how to set up the initial conditions using a set of N particles two (diverse) techniques are presented for evolving these particles forward in time under the influence of their self-gravity. One technique (tree codes) is solely based upon a sophistication of the direct particle–particle summation whereas the other method relies on the continuous (de-)construction of arbitrarily shaped grids and is realized in adaptive mesh refinement codes.
Correcting the Influence of an Asymmetric Line Spread Function in 2-Degree Field Spectrograph Data
Authors: Martin Nicolas F. , Ibata Rodrigo A. , Conn Blair C. , Irwin Mike J. , Lewis Geraint F. 
Published: August 2005

AbstractWe investigate the role of asymmetries in the line spread function of the 2-degree field (2dF) spectrograph and the variations in these asymmetries with the CCD, the plate, the time of observation, and the fibre. A data-reduction pipeline is developed that takes these deformations into account for the calibration and cross-correlation of the spectra. We show that, using the emission lines of calibration lamp observations, we can fit the line spread function with the sum of two Gaussian functions representing the theoretical signal and a perturbation of the system. This model is then used to calibrate the spectra and generate templates by downgrading high-resolution spectra. Thus, we can cross-correlate the observed spectra with templates degraded in the same way. Our reduction pipeline is tested on real observations and provides a significant improvement in the accuracy of the radial velocities obtained. In particular, the systematic errors that were as high as ∼20 km s−1 when applying the AAO reduction package 2DFDR are now reduced to ∼5 km s−1. Even though the 2dF spectrograph is to be decommissioned at the end of 2005, the analysis of archival data and previous studies could be improved by the reduction procedure we propose here.
BVD control in Europe: current status and perspectives
Authors: Moennig Volker , Houe Hans , Lindberg Ann 
Published: August 2005

AbstractFor several decades after the first description of bovine viral diarrhea and its causative agent (BVDV) the economic impact of the infection was underestimated and in addition there were no suitable diagnostics and procedures for a systematic control at hand. Today, there are several estimates on the real economic impact of the infection and during the last 15 years the serological and virological laboratory diagnosis of BVDV infections has improved. Also, successful procedures aimed at eradicating BVDV infections by using a strict test and removal policy for animals persistently infected (PI) with BVDV accompanied by movement restrictions for infected herds have been implemented in the Scandinavian countries. The success of these efforts has encouraged other European countries to follow the same procedures. However, the Scandinavian control strategy might—for a number of reasons—not be acceptable for all European countries. In such cases, the test and removal strategy, with its fundamental elements of biosecurity, removal of PI animals and monitoring of herd status, in combination with systematic vaccination, might be an acceptable compromise. The impact of the BVDV-free status of regions and nations on international trade is not yet clear. In any case, biosecurity measures will be of utmost importance for individual control programs as well as multiple control programs to co-exist in Europe.
Probiotic alternatives to reduce gastrointestinal infections: the poultry experience
Authors: Nava G. M. , Bielke L. R. , Callaway T. R. , Castañeda M. P 
Published: August 2005

AbstractThe intestinal mucosa represents the most active defense barrier against the continuous challenge of food antigens and pathogenic microorganisms present in the intestinal lumen. Protection against harmful agents is conferred by factors such as gastric acid, peristalsis, mucus, intestinal proteolysis, and the intestinal biota. The establishment of beneficial bacterial communities and metabolites from these complex ecosystems has varying consequences for host health. This hypothesis has led to the introduction of novel therapeutic interventions based on the consumption of beneficial bacterial cultures. Mechanisms by which probiotic bacteria affect the microecology of the gastrointestinal tract are not well understood, but at least three mechanisms of action have been proposed: production/presence of antibacterial substances (e.g., bacteriocins or colicins), modulation of immune responses and specific competition for adhesion receptors to intestinal epithelium. The rapid establishment of bacterial communities has been thought to be essential for the prevention of colonization by pathogenic bacteria. Some animal models suggest that the reduction in bacterial translocation in neonatal animals could be associated with an increase in intestinal bacterial communities and bacteriocin-like inhibitory substances produced by these species. This review emphasizes the role of the intestinal microbiota in the reduction of the gastrointestinal infections and draws heavily on studies in poultry.
Garden production systems and food security in Ghana: Characteristics of traditional knowledge and management systems
Authors: Yiridoe Emmanuel K. , Anchirinah Vincent M. 
Published: August 2005

AbstractThere is limited documented scientific information on garden production systems managed in developing countries, partly because both researchers and research administrators have, until recently, ignored them as legitimate areas of study, and because such production systems have been regarded as informal production activities, managed outside conventional market and economic channels. Yet in a developing country such as Ghana, these production systems are potentially able to contribute substantially to the food security and health needs of households. This study was aimed primarily at providing critical scientific information for understanding the complex web of production and management factors associated with garden production systems. A total of 300 survey responses, representing the Sudan savannah, Guinea savannah and moist deciduous forest agro-ecological zones of Ghana, were analyzed (27% of respondents were females and 73% were males). Several hypotheses from the field agriculture literature were tested to determine their relevance in garden production systems. Although, for the country as a whole, a variety of garden crops are cultivated, each agro-ecological zone concentrated on a set of four major crops, with the actual food crops differing across agro-ecological zones. The type of protective fencing used was not statistically associated with land tenure (i.e., own versus rented land) status of the gardener (χ2=3.285, P=0.4501). Gender responsibilities in garden production and management tended to be more equally shared in the forest agro-ecology, where garden crops are cultivated for household consumption and for generating family income. In contrast, in the two savannah zones, adult males undertook a disproportionate share of activities to produce garden crops that were primarily for marketing. Valuable information on production and management exist within the traditional garden production systems studied, and range from socio-economic, agronomic and medicinal considerations in selecting garden crops and fruit trees, to ecological monitoring systems and strategies for garden management.
Calibrating E-values for hidden Markov models using reverse-sequence null models
Authors: Karplus Kevin , Karchin Rachel , Shackelford George , Hughey Richard 
Published: August 2005

Abstract
Motivation: Hidden Markov models (HMMs) calculate the probability that a sequence was generated by a given model. Log-odds scoring provides a context for evaluating this probability, by considering it in relation to a null hypothesis. We have found that using a reverse-sequence null model effectively removes biases owing to sequence length and composition and reduces the number of false positives in a database search.
Any scoring system is an arbitrary measure of the quality of database matches. Significance estimates of scores are essential, because they eliminate model- and method-dependent scaling factors, and because they quantify the importance of each match. Accurate computation of the significance of reverse-sequence null model scores presents a problem, because the scores do not fit the extreme-value (Gumbel) distribution commonly used to estimate HMM scores' significance.
Results: To get a better estimate of the significance of reverse-sequence null model scores, we derive a theoretical distribution based on the assumption of a Gumbel distribution for raw HMM scores and compare estimates based on this and other distribution families. We derive estimation methods for the parameters of the distributions based on maximum likelihood and on moment matching (least-squares fit for Student's t-distribution).
We evaluate the modeled distributions of scores, based on how well they fit the tail of the observed distribution for data not used in the fitting and on the effects of the improved E-values on our HMM-based fold-recognition methods.
The theoretical distribution provides some improvement in fitting the tail and in providing fewer false positives in the fold-recognition test. An ad hoc distribution based on assuming a stretched exponential tail does an even better job. The use of Student's t to model the distribution fits well in the middle of the distribution, but provides too heavy a tail. The moment-matching methods fit the tails better than maximum-likelihood methods.
Availability: Information on obtaining the SAM program suite (free for academic use), as well as a server interface, is available at and the open-source random sequence generator with varying compositional biases is available at
Contact: karplus@soe.ucsc.edu
Proton NMR spectroscopy shows lipids accumulate in skeletal muscle in response to burn trauma‐induced apoptosis
Authors: Astrakas Loukas G. , Goljer Igor , Yasuhara Shingo , Padfield Katie E. , Zhang Qunhao , Gopalan Suresh , Mindrinos Michael N. , Dai George , Yu Yong‐Ming , Martyn J. A. Jeevendra , Tompkins Ronald G. , Rahme Laurence G. , Tzika A. Aria 
Published: August 2005

ABSTRACTBurn trauma triggers hypermetabolism and muscle wasting via increased cellular protein degradation and apoptosis. Proton nuclear magnetic resonance (1H NMR) spectroscopy can detect mobile lipids in vivo. To examine the local effects of burn in skeletal muscle, we performed in vivo 1H NMR on mice 3 days after burn trauma; and ex vivo, high‐resolution, magic angle spinning 1H NMR on intact excised mouse muscle samples before and 1 and 3 days after burn. These samples were then analyzed for apoptotic nuclei using a terminal deoxynucleotidyl transferase‐mediated dUTP nick end‐labeling (TUNEL) assay. To confirm our NMR and cell biology results, we used transcriptome analysis to demonstrate that burn trauma alters the expression of genes involved in lipid metabolism and apoptosis. Our results demonstrate that burn injury results in a localized intramyocellular lipid accumulation, which in turn is accompanied by burn‐induced apoptosis and mitochondrial dysfunction, as seen by the up‐regulation of apoptotic genes and down‐regulation of genes that encode lipid oxidation and the peroxisomal proliferator activator receptor γ coactivator PGC‐1β. Moreover, the increased levels of bisallylic methylene fatty acyl protons (2.8 ppm) and vinyl protons (5.4 ppm), in conjunction with the TUNEL assay results, further suggest that burn trauma results in apoptosis. Together, our results provide new insight into the local physiological changes that occur in skeletal muscle after severe burn trauma. Astrakas, L. G., Goljer, I., Yasuhara, S., Padfield, K. E., Zhang, Q., Gopalan, S., Mindrinos, M. N., Dai, G., Yu, Y.‐M., Jeevendra Martyn, J. A., Tompkins, R. G., Rahme, L. G., Tzika, A. A. Proton NMR spectroscopy shows lipids accumulate in skeletal muscle in response to burn trauma induced apoptosis. FASEB J. 19, 1431–1440 (2005)
Nitric oxide mediates increased susceptibility to dopaminergic damage in Nurr1 heterozygous mice
Authors: Imam Syed Z. , Jankovic Joseph , Ali Syed F. , Skinner John T. , Xie Wenjie , Conneely Orla M. , Le Wei‐Dong 
Published: August 2005

ABSTRACTKnocking out of Nurr1 gene, a member of nuclear receptor superfamily, causes selective agenesis of dopaminergic neurons in midbrain. Reduced expression of Nurr1 increases the vulnerability of mesencephalic dopamine neurons to dopaminergic toxins. We evaluated the role of nitric oxide as a possible mechanism for this increased susceptibility. Increased expression of neuronal nitric oxide synthase and increased 3‐nitrotyrosine were observed in striatum of Nurr1 heterozygous (Nurr1 +/−) mice as compared with wild‐type. Increased cytochrome C activation and consecutive release of Smac/DIABLO were also observed in Nurr1 +/− mice. An induction of active Caspase‐3 and p53, cleavage of poly‐ADP (RNase) polymerase and reduced expression of bcl‐2 were observed in Nurr1 +/− mice. Methamphetamine significantly increased these markers in Nurr1 +/− mice as compared with wild‐type. The present data therefore suggest that nitric oxide plays a role as a modulating factor for the increased susceptibility, but not the potentiation, of the dopaminergic terminals in Nurr1 +/− mice. We also report that this increased neuronal nitric oxide synthase expression and increased nitration in Nurr1 +/− mice led to the activation of apoptotic cascade via the differential alterations in the DNA binding activity of transcription factors responsible for the propagation of growth arrest as well as apoptosis. Syed Z.Imam, Jankovic,‡Joseph, Syed F.Ali, John T.Skinner, WenjieXie, Orla M.Conneely, Wei‐DongLe Nitric oxide mediates increased susceptibility to dopaminergic damage in Nurr1 heterozygous mice. FASEB J. 19, 1441–1450 (2005)