bluuebunny/crossref_metadata_2025_split huggingface dataset:
Centile charts of cervical length between 18 and 32 weeks of gestation
Authors: Theron Gerhard , Schabort Christene , Norman Karin , Thompson Mary , Geerts Lut 
Published: September 2008

AbstractObjectiveTo establish a centile chart of cervical length between 18 and 32 weeks of gestation in a low‐risk population of women.MethodsA prospective longitudinal cohort study of women with a low risk, singleton pregnancy using public healthcare facilities in Cape Town, South Africa. Transvaginal measurement of cervical length was performed between 16 and 32 weeks of gestation and used to construct centile charts. The distribution of cervical length was determined for gestational ages and was used to establish estimates of longitudinal percentiles. Centile charts were constructed for nulliparous and multiparous women together and separately.ResultsCentile estimation was based on data from 344 women. Percentiles showed progressive cervical shortening with increasing gestational age. Averaged over the entire follow‐up period, mean cervical length was 1.5 mm shorter in nulliparous women compared with multiparous women (95% CI, 0.4–2.6).ConclusionsEstablishment of longitudinal reference values of cervical length in a low‐risk population will contribute toward a better understanding of cervical length in women at risk for preterm labor.
Bottlenose dolphins using coastal regions adjacent to a Special Area of Conservation in north-east Scotland
Authors: Culloch Ross M. , Robinson Kevin P. 
Published: September 2008

In a four year study of bottlenose dolphins along the southern shore of the outer Moray Firth we show that whilst dolphins were encountered along the majority of the survey area, there was a significant preference to the western section, which is the area directly adjacent to the current Special Area of Conservation (SAC). We also show that 80% of all groups encountered (N = 62) included calves, and that neonates were seen throughout the months of July, August, September and October. The mark–recapture abundance estimates for the southern outer Moray Firth were variable, with a highest annual estimate of 108 (95% CI = 79–129), which is similar to previous estimates for the number of animals using the entire Moray Firth. In contrast, the lowest annual estimate of 61 (95% CI = 48–74) suggests that not all individuals regularly use the entire geographical range of the population and that individual ranging patterns may vary across years. The findings of this study indicate that the southern outer Moray Firth is an important area for this population and that it should not simply be considered as a corridor to other areas of more importance. For this reason, we believe that further consideration of the current management of this population in areas outside the existing SAC is necessary.
Influence of environmental factors on small cetacean distribution in the Spanish Mediterranean
Authors: Gómez de Segura A. , Hammond P.S. , Raga J.A. 
Published: September 2008

Habitat distribution models are one of the most up to date methods to study the habitat usage of wildlife populations. They allow animal distribution to be related to environmental features and also the prediction of the distribution of animals based on this relationship. Seasonal aerial surveys were conducted in central Spanish Mediterranean waters from June 2000 to March 2003 to obtain information on the distribution of cetacean species. Data from the three most common cetacean species (striped dolphin,Stenella coeruleoalba, bottlenose dolphin,Tursiops truncatus, and Risso's dolphin,Grampus griseus) were related, using generalized linear models, to local environmental features: depth, slope, sea surface temperature and chlorophyll concentration. For bottlenose dolphins, no significant relationship was found with any covariate and no dolphins were observed in waters greater than 1000 m. The distribution of both striped and Risso's dolphin was significantly related to depth. The striped dolphin showed a preference for waters between 900 and 1500 m deep and Risso's dolphin for waters more than 1500 m deep. In addition, for the latest two species, maps of distribution were predicted by means of the spatial models. The areas of higher probabilities of occurrence coincide to a large extent with the marine protected areas previously proposed for the conservation of oceanic cetacean species.
Descriptive parameters of pulsed calls for the spinner dolphin,Stenella longirostris, in the Fernando de Noronha Archipelago, Brazil
Authors: Rossi-Santos Marcos R. , da Silva José Martins , Silva Flavio Lima , Monteiro-Filho Emygdio L.A. 
Published: September 2008

The aim of this work is to describe the repertoire of calls utilized by the spinner dolphins (Stenella longirostris) in the southern Atlantic Ocean. We measured four acoustic parameters of the fundamental frequency of each call: (i) duration; (ii) frequency amplitude; (iii) minimum frequency; and (iv) maximum frequency. We also classified calls by their shape contour by visual inspection of the spectrograms. The obtained values for call duration were 0.046 to 2.08 seconds (mean 0.433, standard deviation (SD) 0.433), amplitude of 0.13 to 2.01 kHz (mean of 0.36, SD 0.29), minimum frequency of 0.22 to 1.80 (mean 0.55, SD 0.29), maximum frequency of 0.46 to 7.50 (mean 1.00, SD 0.89). We classified 73 calls by spectral contour, identifying six basic types of discernible calls, showing heterogeneity among the call types, with C1, C2 and C3 calls presenting higher frequencies, 21, 30 and 23%, respectively. We found that the calls ofS. longirostrisin the Fernando de Noronha Archipelago are more diverse and complex than previously recognized for spinner dolphins and further studies worldwide can reinforce the broad use of this sound for the species repertoire.
Cuvier's beaked whale distribution in the Mediterranean Sea: results from small boat surveys 1996–2007
Authors: Gannier Alexandre , Epinat Justine 
Published: September 2008

A total of 17,651 km of sailboat survey effort obtained with very good sighting conditions was pooled over the period 1995 to 2007 to provide an insight into Cuvier's beaked whales' (Ziphius cavirostris) distribution in the western and central Mediterranean Sea. Although only six confirmed sightings were obtained under such conditions, complementary sightings made a total of eleven confirmed records. Their distribution showed that only slope habitat, and its close proximity, was favourable to the species. In contrast to regions pointed out in the recent literature, such as the Alboran, Ligurian and Ionian Seas, it appeared that the Tyrrhenian Sea was likely to be an important area for Cuvier's beaked whales in the Mediterranean. Sighting rates of 0.1–0.25 sighting/100 km and sighting rates for individuals of 0.2–0.5 individual/100 km were obtained in favourable regions. When compared to sighting rates obtained on Risso's dolphinsGrampus griseusduring the same surveys, the Cuvier's beaked whale appeared to be quite a frequent species in its favoured habitats. The present study contributes a better knowledge of this poorly-known species, in the context of increasing and threatening anthropogenic noises.
Temperature-based summer habitat partitioning between white-beaked and common dolphins around the United Kingdom and Republic of Ireland
Authors: MacLeod Colin D. , Weir Caroline R. , Santos M. Begoña , Dunn Timothy E. 
Published: September 2008

The white-beaked dolphin (Lagenorhynchus albirostris) and short-beaked common dolphin (Delphinus delphis) are two of the most abundant delphinid species in shelf waters around the United Kingdom (UK) and Republic of Ireland (ROI) in the summer season (May–October). As these two species have similar habitat preferences and diets, it might be expected that they would partition their otherwise shared niche to reduce the potential for competition at this time of year. This study used 569 sightings of the two species, collected from shelf waters (<200 m water depth) in the summer season between 1983 and 1998, to investigate whether there is evidence of widespread niche partitioning based on water temperature in this area. Below 13°C, white-beaked dolphins were dominant with 96% of sightings comprising this species. In contrast, above 14°C, 86% of sightings comprised common dolphins. A classification tree analysis found that of the four eco-geographical variables analysed (water depth, seabed slope, seabed aspect and sea surface temperature), temperature was the most important variable for separating the occurrence of the two species. These results are consistent with widespread temperature-based niche partitioning between white-beaked and common dolphins in shelf waters around the UK and ROI. As temperature is important in determining the relative distribution of these species, the range of the white-beaked dolphin might be expected to contract in response to increasing sea temperature resulting from global climate change, while that of the common dolphin may expand.
Biological consequences of global warming: does sea surface temperature affect cetacean distribution in the western Ligurian Sea?
Authors: Azzellino A. , Gaspari S.A. , Airoldi S. , Lanfredi C. 
Published: September 2008

The aim of this study was to assess if sea surface temperature does affect cetacean distribution in the western Ligurian Sea. Relationships with temperature were investigated for: striped dolphin (Stenella coeruleoalba), fin whale (Balaenoptera physalus) and sperm whale (Physeter macrocephalus). Remotely sensed sea surface temperature (SST) data were studied. A series of 20 monthly images (i.e. June to September monthly images from 1996 to 2000) was considered. Concurrently, distribution data collected during shipboard summer surveys, and covering an area of about 20,000 km2 in the western Ligurian Sea, were analysed. The relationship between the three species presence and SST was investigated by using a grid of 3 × 3 nautical mile cell units. For every cell the SST mean, standard deviation, coefficient of variance and the deviation from the monthly average were calculated. Finally, binary logistic regression functions allowed to assess significant (P < 0.05) relationships with temperature in these species. These logistic models, were able to predict 60–78% of the species presence(1)/absence(0) cells, and suggest the need for further investigations spanning longer time periods to assess how the global climate change has been changing and will change in the future cetacean distribution in the western Ligurian Sea.
Large-scale seasonal distribution of fin whales (Balaenoptera physalus) in the central Mediterranean Sea
Authors: Aïssi Mehdi , Celona Antonio , Comparetto Giorgia , Mangano Renata , Würtz Maurizio , Moulins Aurélie 
Published: September 2008

Fin whales (Balaenoptera physalus) are the only mysticete regularly found in the Mediterranean Sea. Its exceptional high abundance during the summer period in the north-western Mediterranean is essentially due to productive waters, but outside of this spatio-temporal window its distribution still remains quite unknown. This paper investigates the distribution of the fin whale on large-scales during the 2002–2006 period. Three areas of the central Mediterranean Sea were selected: the Ligurian Sea in the north-western Mediterranean belonging to the Pelagos Sanctuary; the area connecting both Mediterranean basins in the south-western Mediterranean, the Strait of Messina; and the waters surrounding the island of Lampedusa, in the central Mediterranean. Of the 41,270 km covered by the three surveys, a total of 98 sightings was recorded corresponding to 198 fin whales. Results display a year round distribution along synchronic seasonal dispatching, with a feeding behaviour occurrence in the northern part of the Pelagos Sanctuary during late spring and summer. They indicate high abundance in the Lampedusa area from late winter to early spring manifesting feeding activity. In the Strait of Messina, our results point out the importance of this area as a seasonal feeding ground and an important location for regular autumn transfers between both Mediterranean basins. According to the feeding ground in the two Mediterranean basins, whales change foraging strategy, one being single animals or animal pairs searching for prey in the water column while the other strategy is associated with more individuals feeding on the surface. The strategies differ also by their ecological conditions, such as depth affinity and shoreline distance.
STREAM: Static Thermodynamic REgulAtory Model of transcription
Authors: Bauer Denis C. , Bailey Timothy L. 
Published: September 2008

Abstract
Motivation: Understanding the transcriptional regulation of a gene in detail is a crucial step towards uncovering and ultimately utilizing the regulatory grammar of the genome. Modeling transcriptional regulation using thermodynamic equations has become an increasingly important approach towards this goal.
Here, we present stream, the first publicly available framework for modeling, visualizing and predicting the regulation of the transcription rate of a target gene. Given the concentrations of a set of transcription factors (TFs), the TF binding sites (TFBSs) in a regulatory DNA region, and the transcription rate of the target gene, stream will optimize its parameters to generate a model that best fits the input data. This trained model can then be used to (a) validate that the given set of TFs is able to regulate the target gene and (b) to predict the transcription rate under different conditions (e.g. different tissues, knockout/additional TFs or mutated/missing TFBSs).
Availability: The platform independent executable of stream, as well as a tutorial and the full documentation, are available at http://bioinformatics.org.au/stream/. stream requires Java version 5 or higher.
Contact: d.bauer@imb.uq.edu.au; t.bailey@imb.uq.edu.au
DESHARKY: automatic design of metabolic pathways for optimal cell growth
Authors: Rodrigo Guillermo , Carrera Javier , Prather Kristala Jones , Jaramillo Alfonso 
Published: September 2008

Abstract
Motivation: The biological solution for synthesis or remediation of organic compounds using living organisms, particularly bacteria and yeast, has been promoted because of the cost reduction with respect to the non-living chemical approach. In that way, computational frameworks can profit from the previous knowledge stored in large databases of compounds, enzymes and reactions. In addition, the cell behavior can be studied by modeling the cellular context.
Results: We have implemented a Monte Carlo algorithm (DESHARKY) that finds a metabolic pathway from a target compound by exploring a database of enzymatic reactions. DESHARKY outputs a biochemical route to the host metabolism together with its impact in the cellular context by using mathematical models of the cell resources and metabolism. Furthermore, we provide the sequence of amino acids for the enzymes involved in the route closest phylogenetically to the considered organism. We provide examples of designed metabolic pathways with their genetic load characterizations. Here, we have used Escherichia coli as host organism. In addition, our bioinformatic tool can be applied for biodegradation or biosynthesis and its performance scales with the database size.
Availability: Software, a tutorial and examples are freely available and open source at http://soft.synth-bio.org/desharky.html
Contact: alfonso.jaramillo@polytechnique.fr
Supplementary information: Supplementary data are available at Bioinformatics online.
Longitudinal study of parental movie restriction on teen smoking and drinking in Germany
Authors: Hanewinkel Reiner , Morgenstern Matthis , Tanski Susanne E. , Sargent James D. 
Published: September 2008

ABSTRACTAims  To determine if adolescents who report that their parents restrict viewing movies based on rating have a lower risk of trying smoking and drinking alcohol in the future.Design  Prospective observational study. A cohort of 2110 German adolescents younger than 15 years who had never smoked or drunk alcohol at baseline were surveyed 12–13 months later to determine smoking and binge drinking initiation. Risk of substance use was assessed as a function of parental restriction on viewing FSK‐16 movies (movies that only those aged 16 years and over would be allowed to see in theaters).Findings  The percentage of students who tried smoking was 16.3%, 10.9% initiated binge drinking and 5.0% used both substances during the follow‐up period. There was a significant effect of parental movie restriction on each substance use outcome measure after controlling for covariates. Compared with adolescents whose parents never allowed them to view FSK‐16 movies, the adjusted relative risk [(RR) (95% confidence interval (CI)] for use of both substances were 1.64 (1.05–2.58) for adolescents allowed to view them once in a while, 2.30 (1.53–3.45) for sometimes and 2.92 (1.83–4.67) for all the time. FSK‐16 restrictions were associated with lower viewership of all classes of movies, but especially FSK‐16/18 movies; in addition, FSK‐16 restrictions were associated with substantially lower exposure to movie depiction of tobacco and alcohol use, suggesting a mediational mechanism for the association.Conclusions  Among young adolescents, parental restriction from viewing movies rated for older adolescents/adults decreases the risk of substance use in the future.
Risk and speed of transitions to first alcohol dependence symptoms in adolescents: a 10‐year longitudinal community study in Germany
Authors: Behrendt Silke , Wittchen Hans‐Ulrich , Höfler Michael , Lieb Roselind , Low Nancy Chooi Ping , Rehm Jürgen , Beesdo Katja 
Published: September 2008

ABSTRACTBackground  Although in many western countries alcohol use (AU) and symptoms of alcohol dependence (AD) are frequent in adolescence, temporal patterns and trajectories remain understudied. It is unclear whether early onset of AU is associated with the speed of transition to first AD symptoms and whether specific first AD symptoms and their timing are associated with AD.Aims  To examine (i) the incidence patterns of self‐reported first AD symptoms; (ii) whether early AU is associated with the risk and speed of transition to first AD symptoms; and (iii) whether first AD symptoms and their timing are associated with AD.Design  A total of 3021 community subjects from Germany aged 14–24 years at baseline followed prospectively over 10 years. AU, AD symptoms and AD were assessed using the Munich–Composite International Diagnostic Interview (DIA‐X/M‐CIDI).Findings  Among first AD symptoms, tolerance (13.1%) and much time spent (5.0%) were most prevalent. Five to 30% of all first AD symptoms occurred during the first year after first AU. Early AU was not related to the risk of first AD symptoms. The speed of transition to first AD symptoms was greater among those with AU onset in later adolescence. Tolerance and loss of control were associated with AD development (risk difference 3.9% and 15.4%), as was early onset of tolerance, much time spent and loss of control.Conclusion  Early AU and early AD symptoms are frequent among adolescents. Early self‐reported tolerance, much time spent and loss of control are particularly predictive for AD and important targets for early preventive interventions.
Reducing youth alcohol drinking through a parent‐targeted intervention: the Örebro Prevention Program
Authors: Koutakis Nikolaus , Stattin Håkan , Kerr Margaret 
Published: September 2008

ABSTRACTAims  To evaluate a 2.5‐year prevention programme working through parents, targeting drinking among 13–16‐year‐olds.Design  Quasi‐experimental using matched controls with a pre–post, intention‐to‐treat design.Setting  Schools located in inner city, public housing and small town areas.Participants  A total of 900 pupils entering junior high school and their parents, followed longitudinally.Intervention  Parents received information by mail and during parent meetings in schools urging them to: (i) maintain strict attitudes against youth alcohol use and (ii) encourage their youth's involvement in adult‐led, organized activities.Measurements  Evaluation of the implementation used measures of parental attitudes against underage drinking and youths' participation in organized activities. Outcomes were youths' drunkenness and delinquency.Findings  The implementation successfully influenced parents' attitudes against underage drinking, but not youth participation in organized activities. At post‐test, youths in the intervention group reported less drunkenness and delinquency. Effect sizes were 0.35 for drunkenness and 0.38 for delinquency. Findings were similar for boys and girls and for early starters. Effects were not moderated by community type.Conclusions  Working via parents proved to be an effective way to reduce underage drinking as well as delinquency.
Bed occupancy and incidence of Methicillin‐resistant Staphylococcus aureus infection in an intensive care unit
Authors: Howie A. J. , Ridley S. A. 
Published: September 2008

SummaryMethicillin‐resistant Staphylococcus aureus (MRSA) incidence and workload as reflected by daily bed occupancy were assessed retrospectively over a 12‐month period in a mixed adult ICU. All MRSA positive results were retrieved from the Microbiology Department; patients with MRSA were divided into those whose admission swabs were positive and those whose specimens subsequently became positive. There were 619 admissions, 48 of which had MRSA on admission (7.8% incidence) and 16 new MRSA infections in ICU (total incidence 10.3%). The frequency of MRSA acquisition was significantly higher on days when more than seven beds were occupied (0.0090 vs 0.0059 new acquisitions per patient per day, respectively, p = 0.015). In this well staffed but physically small unit local routes of infection transmission may be relevant.
Evaluation of pelvic wedge for gynaecological laparoscopy
Authors: Kundra P. , Kanna V. , Bupathi A. , Sudeep K. 
Published: September 2008

SummarySeventy‐eight ASA 1 and 2 women scheduled for elective diagnostic laparoscopy under general anaesthesia were randomly allocated into two groups. Patients were either positioned with a 20° Trendelenberg tilt (group T) or with a wedge placed under the pelvis (group W). A standard general anaesthetic technique was used in all patients. The endoscopic view of pelvic organs was graded on a four‐point scale by the operating surgeon. Heart rate (HR), mean arterial pressure (MAP), SpO2, and peak airway pressure (Paw) were continuously measured. Significantly more patients (77%) in group W had grade 1 view (clear view of pelvic organs without additional manoeuvres) when compared with group T (46%). Mean Paw increased significantly in group T when compared with group W. The use of a pelvic wedge provides a better view of pelvic viscera than 20° Trendelenberg tilt during gynaecological laparoscopy.