bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of 11 Breast Cancer Susceptibility Loci in African-American Women
Authors: Zheng Wei , Cai Qiuyin , Signorello Lisa B. , Long Jirong , Hargreaves Margaret K. , Deming Sandra L. , Li Guoliang , Li Chun , Cui Yong , Blot William J. 
Published: October 2009

Abstract
Recent genome-wide association studies (GWAS) have identified multiple common genetic risk variants for breast cancer among women of Asian and European ancestry. Investigating these genetic susceptibility loci in other populations would be helpful to evaluate the generalizability of the findings and identify the causal variants for breast cancer. We evaluated 11 GWAS-identified genetic susceptibility loci for breast cancer in a study including 2,594 African-American women (810 cases and 1,784 controls). Two single-nucleotide polymorphisms, rs13387042 (2q35) and rs1219648 (FGFR2 gene), were found to be associated with breast cancer risk. Risk increased nearly linearly with the number of affected risk alleles, with a 2-fold elevated risk for women homozygous for the risk alleles in both single-nucleotide polymorphisms. No additional significant associations, however, were identified for the other nine loci evaluated in the study. The results from this study extend some of the recent GWAS findings to African-Americans and may guide future efforts to identify the causal variants for breast cancer. (Cancer Epidemiol Biomarkers Prev 2009;18(10):2761–4)
No Risk of Maternal EBV Infection for Childhood Leukemia
Authors: Tedeschi Rosamaria , Luostarinen Tapio , Marus Alessia , Bzhalava Davit , Ögmundsdottir Helga M. , Dillner Joakim , De Paoli Paolo , Surcel Heljä-Marja , Pukkala Eero , Lehtinen Matti , Lehtinen Tuula 
Published: October 2009

Abstract
We performed a large nested case-control study within the Finnish and Icelandic maternity cohorts to verify/falsify the association of maternal EBV infection with an increased risk of acute lymphoblastic leukemia (ALL) in the offspring found in previous studies. All hematologic malignancies diagnosed among children born during 1983 to 2006 in Finland and 1997 to 2005 in Iceland were identified through national cancer registries. For each index mother of a leukemia case, three matched control mothers with cancer-free offspring were identified. First trimester sera from 561 ALL and 144 non-ALL index mothers and from 2,105 control mothers were analyzed for antibodies to EBV viral capsid antigen (IgG and IgM), early antigen (IgG) and ZEBRA protein (IgG). Conditional logistic regression-based estimates of odds ratios and 95% confidence intervals adjusted for birth order and sib-ship size were calculated. Overall, there was no evidence of increased risk of ALL associated to EBV viral capsid antigen IgM (odds ratio, 0.9; 95% confidence interval, 0.5-1.8). The early antigen and ZEBRA antibodies (EBV reactivation markers) were also not associated with risk. The data argue against a role of EBV in ALL. (Cancer Epidemiol Biomarkers Prev 2009;18(10):2790–2)
Male salamanders remember individuals based on chemical or visual cues
Authors: Kohn Nancy , Jaeger Robert 
Published: October 2009

AbstractThe use of multiple cues can enhance the detection, recognition, discrimination, and memorability of individuals by receivers. We conducted two experiments, using only males, to test whether territorial red-backed salamanders, Plethodon cinereus, could use only chemical or only visual cues to remember familiar conspecifics. In both experiments, focal males spent significantly more time threatening unfamiliar than familiar male intruders. They also chemoinvestigated the filter paper containing chemical cues of unfamiliar intruders more often than that of familiar intruders. These results suggest that red-backed salamanders can use both chemical and visual cues to recognize familiar individuals, allowing them to distinguish between less threatening neighbours and more threatening intruders in the heterogeneous forest floor habitat, where visual cues alone would not always be available.
The reproductive status of both sexes affects the frequency of mating and the reproductive success of males in the ball roller beetle Canthon cyanellus cyanellus (Coleoptera: Scarabaeidae)
Authors: Favila Mario , Chamorro-Florescano Ivette 
Published: October 2009

AbstractSeveral studies have shown that males assess female reproductive status and use different mechanisms to increase their reproductive success. However, a male's reproductive status can also affect its own reproductive success. In Canthon cyanellus cyanellus, a male–female pair makes several brood balls during nesting and both care for the brood balls. However, in females that are transported to the nest by males, the spermatheca is often already filled with viable sperm from other males, such that sperm competition is strong. We analyze the effect of the reproductive status of males and females on the frequency of mating during brood ball construction, as well as the reproductive success of males that nest with previously mated females. Virgin and previously mated males copulated with the same frequency before the construction of each brood ball when they nested with virgin females. However, when both types of males nested with previously mated females, the frequency of mating increased before the construction of the first brood ball. The paternity of previously mated males was significantly higher (82%) than that of virgin males (62%). Therefore, the reproductive status of both sexes of C. c. cyanellus affects the frequency of mating and the reproductive success of males.
Using a behaviour discovery curve to predict optimal observation time
Authors: Lea Stephen , Leaver Lisa , Jule Kristen 
Published: October 2009

AbstractBehavioural observations are vital to furthering our knowledge of species' ecology. Determining a method for formalising the length of behavioural observation time (coined Behaviour Discovery Curve) is practical for both reducing disturbance to the animals observed and limiting costs to the researcher. This paper suggests a method of calculating behaviour discovery curves, which allows researchers to estimate the optimal amount of data to collect when establishing an ethogram. The curve is fitted to a logarithmic model that predicts the rate of new behaviours that will be observed in any given length of observation time. To illustrate the methods, 31 captive red pandas (Ailurus fulgens fulgens) were observed for 30 h each and a behaviour discovery curve was estimated for each animal based on the rate at which new behaviours were observed. We demonstrate how to use the curve in the evaluation of an ethogram, whilst also providing an indication of how many more behaviours would be observed in a specified longer observation period. This is an important consideration in the creation of any ethogram, since there are currently no standard methodologies for establishing ethograms, and no guidelines on how much data is 'sufficient' for determining a species' behavioural repertoire. The curve does not allow an estimate of the total size of the behavioural repertoire, but does allow a systematic analysis of the likely costs and benefits of further observation. We also suggest a method for quantifying the degree of idiosyncrasy of a population.
Innovation in groups: does the proximity of others facilitate or inhibit performance?
Authors: Morand-Ferron Julie , Overington Sarah , Cauchard Laure , Lefebvre Louis 
Published: October 2009

AbstractForaging innovation, in which an individual eats a novel food or uses a novel foraging technique, has been observed in a wide range of species. If other individuals are nearby, they may adopt the innovation, thus spreading it through the population. Much research has focused on this social transmission of behaviour, but the effect of social context on the emergence of novel behaviour is unclear. Here, we examine the effect of social context on innovative feeding behaviour in the Carib grackle (Quiscalus lugubris), an opportunistic, gregarious bird. We test the effect of the proximity of conspecifics, while eliminating the direct effects of interference, scrounging, or aggression. Using a repeated-measures design, we found that birds took significantly longer to contact novel foraging tasks when in the presence of others vs. alone, and during playbacks of alarm calls vs. a control sound. Further, performance of a food-processing behaviour decreased when birds were with others, and individuals adjusted their behaviour depending on their distance from conspecifics. Our results suggest that feeding in groups may slow down or inhibit innovative foraging behaviour in this species. We discuss the implications of a trade-off between feeding in groups and taking advantage of new feeding opportunities.
Behavioural responses to alarm cues by free-ranging rainbow darters (Etheostoma caeruleum)
Authors: Woods  , Mathis  , Crane  
Published: October 2009

AbstractResponses of fishes to chemical alarm cues have been well-documented in the laboratory, but relatively few taxa have been tested under free-ranging conditions in natural habitats. While snorkeling in a stream, we exposed rainbow darters (Etheostoma caeruleum) to skin extracts from conspecifics (alarm cue), skin extracts from heterospecifics (no alarm cue) and a blank control. Darters showed a significantly longer latency to move ('freezing') in the presence of the alarm cue relative to the other two stimuli. These results indicate that rainbow darters can detect chemical alarm cues under natural conditions and respond with appropriate antipredator behaviour.
An Assessment of the Surface Longwave Direct Radiative Effect of Airborne Saharan Dust during the NAMMA Field Campaign
Authors: Hansell R. A. , Tsay S. C. , Ji Q. , Hsu N. C. , Jeong M. J. , Wang S. H. , Reid J. S. , Liou K. N. , Ou S. C. 
Published: October 2009

Abstract
In September 2006, NASA Goddard’s mobile ground-based laboratories were deployed to Sal Island in Cape Verde (16.73°N, 22.93°W) to support the NASA African Monsoon Multidisciplinary Analysis (NAMMA) field study. The Atmospheric Emitted Radiance Interferometer (AERI), a key instrument for spectrally characterizing the thermal IR, was used to retrieve the dust IR aerosol optical depths (AOTs) in order to examine the diurnal variability of airborne dust with emphasis on three separate dust events. AERI retrievals of dust AOT are compared with those from the coincident/collocated multifilter rotating shadowband radiometer (MFRSR), micropulse lidar (MPL), and NASA Cloud–Aerosol Lidar and Infrared Pathfinder Satellite Observation (CALIPSO) sensors. The retrieved AOTs are then inputted into the Fu–Liou 1D radiative transfer model to evaluate local instantaneous direct longwave radiative effects (DRELW) of dust at the surface in cloud-free atmospheres and its sensitivity to dust microphysical parameters. The top-of-atmosphere DRELW and longwave heating rate profiles are also evaluated. Instantaneous surface DRELW ranges from 2 to 10 W m−2 and exhibits a strong linear dependence with dust AOT yielding a DRELW of 16 W m−2 per unit dust AOT. The DRELW is estimated to be ∼42% of the diurnally averaged direct shortwave radiative effect at the surface but of opposite sign, partly compensating for the shortwave losses. Certainly nonnegligible, the authors conclude that DRELW can significantly impact the atmospheric energetics, representing an important component in the study of regional climate variation.
Regional Aspects of Prolonged Meteorological Droughts over Mexico and Central America
Authors: Méndez Matías , Magaña Víctor 
Published: October 2009

AbstractMajor prolonged droughts in Mexico during the twentieth century are mainly related to anomalous dry summers, such as those observed in the 1930s, the 1950s, or the 1990s. Droughts in northern Mexico frequently coincide with anomalously wet conditions over Mesoamerica (i.e., southern Mexico and Central America), and vice versa, displaying a dominant “seesaw” structure in persistent precipitation anomalies, mostly in relation to tropical sea surface temperature (SST) anomalies. A warmer North Atlantic Ocean, expressed as a positive phase of Atlantic multidecadal oscillation (AMO), is related to the occurrence of major droughts in North America associated with weaker-than-normal moisture flux into northern Mexico. Drought over northern Mexico may also be related to changes in transient activity in the Caribbean Sea. During the negative phase of the Pacific decadal oscillation (PDO), the Caribbean low-level jet (CLLJ) weakens and easterly wave (EW) activity increases, leading to more tropical convection over Mesoamerica and less moisture flux into northern Mexico. On the other hand, when EW activity is weak over the intra-Americas seas (IAS) (i.e., the Gulf of Mexico and the Caribbean Sea) because of a stronger-than-normal CLLJ, precipitation increases over northern Mexico. Therefore, the interaction between easterly waves and the trade winds over the IAS appears to be crucial to explain the spatial patterns of droughts that have affected Mexico. In addition, low-frequency modulators, such as AMO or PDO, may serve to explain the spatial patterns of severe prolonged droughts in Mexico during the nineteenth century.
Influence of the Icelandic Low on the Variability of Surface Air Temperature in the Gulf of Lion: Implications for Intermediate Water Formation
Authors: Jordi Antoni , Hameed Sultan 
Published: October 2009

Abstract
The authors investigate the interannual variability of surface air temperature in the Gulf of Lion (northwestern Mediterranean Sea) during the winter season, which has been proposed as the dominant factor for the Mediterranean Intermediate Water (WIW) formation. Recent studies suggest that the variability of WIW formation in the Gulf of Lion can be partially explained by the North Atlantic Oscillation. To examine this process in more detail, the authors separate the North Atlantic Oscillation into two centers of action, the Azores high and the Icelandic low. This approach reveals that the pressure of the Icelandic low controls the surface air temperature in the Gulf of Lion, and the influence of the Azores high is insignificant. It is found that the winds over Europe are predominately northerly during winters with high pressure values of the Icelandic low. These conditions also correspond to colder air temperatures in the Gulf of Lion, which have been proposed previously to be correlated with ocean convection to intermediate depths.
Diagnosis of Extended Cold-Season Temperature Anomalies in Alaska
Authors: Shulski Martha , Walsh John , Stevens Eric , Thoman Richard 
Published: October 2009

Abstract
During the early winter of 2002 and late winter of 2007, the Alaskan sector of the North Pacific Ocean region experienced record-breaking temperature anomalies. The duration of these episodes was unusually long, with each lasting more than 1 month: 55 days for the warm anomaly of October–December 2002 and 37 days for the cold anomaly of February–March 2007. Temperature departures over each respective period were the largest for the continental climate of interior Alaska (&gt;10°C) and the smallest for the maritime regions of Alaska (&lt;4°C). Mean temperatures over the event periods in 2002 and 2007 easily ranked as the record warmest and coldest, respectively, for many surface observing stations. In addition, heating degree-day anomalies were on the order of 700 units for these periods. Atmospheric circulation patterns at the surface and upper levels for the circum-Arctic proved to be the driver for these persistent events. The 2002 warm anomaly was driven by enhanced southerly advection associated with an unusually strong Aleutian low and a positive Pacific decadal oscillation index, which resulted in a large area of anomalous temperatures in Alaska and northern Canada. The 2007 cold anomaly was driven by a weakening of the circulation pattern in the subpolar Pacific sector and a strengthening of the Siberian high, with the strongest temperature anomalies in Alaska and northwestern Canada.
Urokinase-type plasminogen activator increases hepatocyte growth factor activity required for skeletal muscle regeneration
Authors: Sisson Thomas H. , Nguyen Mai-Huong , Yu Bi , Novak Margaret L. , Simon Richard H. , Koh Timothy J. 
Published: October 2009

AbstractThe plasminogen system plays a crucial role in the repair of a variety of tissues, including skeletal muscle. We hypothesized that urokinase-type plasminogen activator (uPA) promotes muscle regeneration by activating hepatocyte growth factor (HGF), which, in turn, stimulates proliferation of myoblasts required for regeneration. In our studies, levels of active HGF and phosphorylation of the HGF receptor c-met were increased after muscle injury in wild-type mice. Compared with wild-type animals, mice deficient in uPA (uPA−/−) had markedly reduced HGF levels and c-met activation after muscle damage. This reduced HGF activity in uPA−/− animals was associated with decreased cell proliferation, myoblast accumulation, and new muscle fiber formation. On the other hand, HGF activity was enhanced at early time points in PAI-1−/− mice compared with wild-type mice and the PAI-1−/− animals exhibited accelerated muscle fiber regeneration. Furthermore, administration of exogenous uPA rescued HGF levels and muscle regeneration in uPA−/− mice, and an HGF-blocking antibody reduced HGF activity and muscle regeneration in wild-type mice. We also found that uPA promotes myoblast proliferation in vitro through its proteolytic activity, and this process was inhibited by an HGF-blocking antibody. Together, our findings demonstrate that uPA promotes muscle regeneration through HGF activation and subsequent myoblast proliferation.
PathBinder – text empirics and automatic extraction of biomolecular interactions
Authors: Zhang Lifeng , Berleant Daniel , Ding Jing , Cao Tuan , Syrkin Wurtele Eve 
Published: October 2009

Abstract

Motivation
The increasingly large amount of free, online biological text makes automatic interaction extraction correspondingly attractive. Machine learning is one strategy that works by uncovering and using useful properties that are implicit in the text. However these properties are usually not reported in the literature explicitly. By investigating specific properties of biological text passages in this paper, we aim to facilitate an alternative strategy, the use of text empirics, to support mining of biomedical texts for biomolecular interactions. We report on our application of this approach, and also report some empirical findings about an important class of passages. These may be useful to others who may also wish to use the empirical properties we describe.

Results
We manually analyzed syntactic and semantic properties of sentences likely to describe interactions between biomolecules. The resulting empirical data were used to design an algorithm for the PathBinder system to extract biomolecular interactions from texts. PathBinder searches PubMed for sentences describing interactions between two given biomolecules. PathBinder then uses probabilistic methods to combine evidence from multiple relevant sentences in PubMed to assess the relative likelihood of interaction between two arbitrary biomolecules. A biomolecular interaction network was constructed based on those likelihoods.

Conclusion
The text empirics approach used here supports computationally friendly, performance competitive, automatic extraction of biomolecular interactions from texts.

Availability

http://www.metnetdb.org/pathbinder.
HPD: an online integrated human pathway database enabling systems biology studies
Authors: Chowbina Sudhir R , Wu Xiaogang , Zhang Fan , Li Peter M , Pandey Ragini , Kasamsetty Harini N , Chen Jake Y 
Published: October 2009

Abstract

Background
Pathway-oriented experimental and computational studies have led to a significant accumulation of biological knowledge concerning three major types of biological pathway events: molecular signaling events, gene regulation events, and metabolic reaction events. A pathway consists of a series of molecular pathway events that link molecular entities such as proteins, genes, and metabolites. There are approximately 300 biological pathway resources as of April 2009 according to the Pathguide database; however, these pathway databases generally have poor coverage or poor quality, and are difficult to integrate, due to syntactic-level and semantic-level data incompatibilities.

Results
We developed the Human Pathway Database (HPD) by integrating heterogeneous human pathway data that are either curated at the NCI Pathway Interaction Database (PID), Reactome, BioCarta, KEGG or indexed from the Protein Lounge Web sites. Integration of pathway data at syntactic, semantic, and schematic levels was based on a unified pathway data model and data warehousing-based integration techniques. HPD provides a comprehensive online view that connects human proteins, genes, RNA transcripts, enzymes, signaling events, metabolic reaction events, and gene regulatory events. At the time of this writing HPD includes 999 human pathways and more than 59,341 human molecular entities. The HPD software provides both a user-friendly Web interface for online use and a robust relational database backend for advanced pathway querying. This pathway tool enables users to 1) search for human pathways from different resources by simply entering genes/proteins involved in pathways or words appearing in pathway names, 2) analyze pathway-protein association, 3) study pathway-pathway similarity, and 4) build integrated pathway networks. We demonstrated the usage and characteristics of the new HPD through three breast cancer case studies.

Conclusion
HPD http://bio.informatics.iupui.edu/HPD is a new resource for searching, managing, and studying human biological pathways. Users of HPD can search against large collections of human biological pathways, compare related pathways and their molecular entity compositions, and build high-quality, expanded-scope disease pathway models. The current HPD software can help users address a wide range of pathway-related questions in human disease biology studies.