bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular Pathology in Epidemiologic Studies: A Primer on Key Considerations
Authors: Sherman Mark E. , Howatt Will , Blows Fiona M. , Pharoah Paul , Hewitt Stephen M. , Garcia-Closas Montserrat 
Published: April 2010

AbstractThe development of molecular pathologic components in epidemiologic studies offers opportunities to relate etiologic factors to specific tumor types, which in turn may allow the development of better overall risk prediction and provide clues about mechanisms that mediate risk factors. In addition, this research may help identify or validate tissue biomarkers related to prognosis and prediction of treatment responses. In this mini review, we highlight specific considerations related to the incorporation of pathology in epidemiologic studies, using breast cancer research as a model. Issues related to ensuring the representativeness of cases for which research tissue is available and understanding limitations resulting from variable procedures for tissue collection, fixation, and processing are discussed. The growing importance of molecular pathology in clinical medicine has led to increased emphasis on optimized tissue preparation, which should enhance this type of research. In addition, the availability of new technologies including tissue microarrays, image scanning, and automated analysis to achieve high-throughput standardized assessment of immunohistochemical markers, and potentially other assays, is enabling consistent scoring of a growing list of markers in large studies. Concurrently, methodologic research to extend the range of assays that can be done on fixed tissues is expanding possibilities for molecular pathologic studies in epidemiologic research. Cancer Epidemiol Biomarkers Prev; 19(4); 966–72. ©2010 AACR.
International Efforts to Develop Biospecimen Best Practices
Authors: Vaught Jimmie B. , Caboux Elodie , Hainaut Pierre 
Published: April 2010

Abstract
Variables introduced during the processes involved in biospecimen collection, processing, storage, and analysis are among the potential sources of bias in biomarker research. International efforts are under way to develop best practices to standardize biospecimen handling protocols. In general, documents on best practices address three major recurring themes: technical best practices on infrastructure and specimen handling, recommendations on informatics and data management, and recommendations on ethical, legal, and social issues. There are many areas of agreement among various international efforts, but no single set of practices has emerged as a unifying document. The ethical, legal, and social issues are particularly difficult to harmonize due to the many country-specific issues that are governed by a variety of local and federal rules and regulations. Given the increasingly international nature of research involving biomarkers and biospecimens, it will be necessary to continue to cooperate in the development of harmonized evidence-based best practices. Several international organizations including the International Cancer Genome Consortium are engaged in such efforts. Cancer Epidemiol Biomarkers Prev; 19(4); 912–5. ©2010 AACR.
The Organization of European Cancer Institute Pathobiology Working Group and its Support of European Biobanking Infrastructures for Translational Cancer Research
Authors: Riegman Peter H.J. , de Jong Bas W.D. , Llombart-Bosch Antonio 
Published: April 2010

Abstract
Background: Today's translational cancer research increasingly depends on international multi-center studies. Biobanking infrastructure or comprehensive sample exchange platforms to enable networking of clinical cancer biobanks are instrumental to facilitate communication, uniform sample quality, and rules for exchange.
Methods: The Organization of European Cancer Institutes (OECI) Pathobiology Working Group supports European biobanking infrastructure by maintaining the OECI-TuBaFrost exchange platform and organizing regular meetings. This platform originated from a European Commission project and is updated with knowledge from ongoing and new biobanking projects. This overview describes how European biobanking projects that have a large impact on clinical biobanking, including EuroBoNeT, SPIDIA, and BBMRI, contribute to the update of the OECI-TuBaFrost exchange platform.
Results: Combining the results of these European projects enabled the creation of an open (upon valid registration only) catalogue view of cancer biobanks and their available samples to initiate research projects. In addition, closed environments supporting active projects could be developed together with the latest views on quality, access rules, ethics, and law.
Conclusions: With these contributions, the OECI Pathobiology Working Group contributes to and stimulates a professional attitude within biobanks at the European comprehensive cancer centers.
Impact: Improving the fundamentals of cancer sample exchange in Europe stimulates the performance of large multi-center studies, resulting in experiments with the desired statistical significance outcome. With this approach, future innovation in cancer patient care can be realized faster and more reliably. Cancer Epidemiol Biomarkers Prev; 19(4); 923–6. ©2010 AACR.
Establishment and Operation of a Biorepository for Molecular Epidemiologic Studies in Costa Rica
Authors: Cortés Bernal , Schiffman Mark , Herrero Rolando , Hildesheim Allan , Jiménez Silvia , Shea Katheryn , González Paula , Porras Carolina , Fallas Greivin , Rodríguez Ana Cecilia 
Published: April 2010

Abstract
Background: The Proyecto Epidemiológico Guanacaste (PEG) has conducted several large studies related to human papillomavirus (HPV) and cervical cancer in Guanacaste, Costa Rica in a long-standing collaboration with the U.S. National Cancer Institute. To improve molecular epidemiology efforts and save costs, we have gradually transferred technology to Costa Rica, culminating in state-of-the-art laboratories and a biorepository to support a phase III clinical trial investigating the efficacy of HPV 16/18 vaccine.
Objective: Here, we describe the rationale and lessons learned in transferring molecular epidemiologic and biorepository technology to a developing country.
Results: At the outset of the PEG in the early 1990s, we shipped all specimens to repositories and laboratories in the United States, which created multiple problems. Since then, by intensive personal interactions between experts from the United States and Costa Rica, we have successfully transferred liquid-based cytology, HPV DNA testing and serology, chlamydia and gonorrhea testing, PCR-safe tissue processing, and viable cryopreservation. To accommodate the vaccine trial, a state-of-the-art repository opened in mid-2004. Approximately 15,000 to 50,000 samples are housed in the repository on any given day, and &gt;500,000 specimens have been shipped, many using a custom-made dry shipper that permits exporting &gt;20,000 specimens at a time. Quality control of shipments received by the NCI biorepository has revealed an error rate of &lt;0.2%. Recently, the PEG repository has incorporated other activities; for example, large-scale aliquotting and long-term, cost-efficient storage of frozen specimens returned from the United States. Using Internet-based specimen tracking software has proven to be efficient even across borders.
Conclusion: For long-standing collaborations, it makes sense to transfer the molecular epidemiology expertise toward the source of specimens. The successes of the PEG molecular epidemiology laboratories and biorepository prove that the physical and informatics infrastructures of a modern biorepository can be transferred to a resource-limited and weather-challenged region. Technology transfer is an important and feasible goal of international collaborations. Cancer Epidemiol Biomarkers Prev; 19(4); 916–22. ©2010 AACR.
Urine Collection and Processing for Protein Biomarker Discovery and Quantification
Authors: Thomas C. Eric , Sexton Wade , Benson Kaaron , Sutphen Rebecca , Koomen John 
Published: April 2010

Abstract
Background: Urine is a useful source of protein for biomarker discovery and assessment because it is readily available, can be obtained by noninvasive collection methods, and enables monitoring of a wide range of physiologic processes and diseases. Urine aliquots provide enough protein for multiple analyses, combining current protocols with new techniques.
Conclusions: Standardized collection and processing protocols are now being established and new methods for protein detection and quantification are emerging to complement traditional immunoassays. The current state of urine collection, specimen processing, and storage is reviewed with regard to discovery and quantification of protein biomarkers for cancer. Cancer Epidemiol Biomarkers Prev; 19(4); 953–9. ©2010 AACR.
A Genome-Wide Association Study of Prognosis in Breast Cancer
Authors: Azzato Elizabeth M. , Pharoah Paul D.P. , Harrington Patricia , Easton Douglas F. , Greenberg David , Caporaso Neil E. , Chanock Stephen J. , Hoover Robert N. , Thomas Gilles , Hunter David J. , Kraft Peter 
Published: April 2010

Abstract
Background: Traditional clinicopathologic features of breast cancer do not account for all the variation in survival. Germline genetic variation may provide additional prognostic information.
Materials and Methods: We conducted a genome-wide association study of survival after a diagnosis of breast cancer by obtaining follow-up data and genotyping information on 528,252 single-nucleotide polymorphisms for 1,145 postmenopausal women with invasive breast cancer (7,711 person-years at risk) from the Nurses' Health Study scanned in the Cancer Genetic Markers of Susceptibility initiative. We genotyped the 10 most statistically significant loci (most significant single-nucleotide polymorphism located in ARHGAP10; P = 2.28 × 10−7) in 4,335 women diagnosed with invasive breast cancer (38,148 years at risk) in the SEARCH (Studies of Epidemiology and Risk factors in Cancer Heredity) breast cancer study.
Results: None of the loci replicated in the SEARCH study (all P &gt; 0.10). Assuming a minimum of 10 associated loci, the power to detect at least one with a minor allele frequency of 0.2 conferring a relative hazard of 2.0 at genome-wide significance (P = 5 × 10−8) was 99%.
Conclusion: We did not identify any common germline variants associated with breast cancer survival overall.
Impact: Our data suggest that it is unlikely that there are common germline variants with large effect sizes for breast cancer survival overall (hazard ratio &gt;2). Instead, it is plausible that common variants associated with survival could be specific to tumor subtypes or treatment approaches. New studies, sufficiently powered, are needed to discover new regions associated with survival overall or by subtype or treatment subgroups. Cancer Epidemiol Biomarkers Prev; 19(4); 1140–3. ©2010 AACR.
Simultaneous Recovery of DNA and RNA from Formalin-Fixed Paraffin-Embedded Tissue and Application in Epidemiologic Studies
Authors: Huang Wen-Yi , Sheehy Timothy M. , Moore Lee E. , Hsing Ann W. , Purdue Mark P. 
Published: April 2010

Abstract
Analysis of DNA, RNA, and protein extracted from tissue specimens in epidemiologic studies is useful for assessing etiologic heterogeneity, mechanisms of carcinogenesis, and biomarkers for prognosis and prediction of treatment responses. Fresh-frozen tissue samples may provide optimal quality nucleic acids, but pose multiple logistical considerations, including rapid access to tissues before histopathologic examination and specialized equipment for freezing, transport, and storage; in addition, morphology is often compromised. In contrast, formalin-fixed paraffin-embedded (FFPE) tissue samples, including enormous archives of existing specimens, represent a valuable source of retrospective biological material for epidemiologic research, although presenting different limitations compared with frozen samples. Recent efforts have made progress toward enhancing the utility of FFPE specimens for molecular analyses, including DNA studies, and increasingly for RNA and other macromolecules. Here, we report the method that we used to simultaneously recover DNA and RNA from FFPE tissue specimens with appreciable quantity and quality and discuss briefly the application of tumor markers in epidemiologic studies. Cancer Epidemiol Biomarkers Prev; 19(4); 973–7. ©2010 AACR.
Spatial and temporal segregation allows coexistence in a hybrid zone among two Mediterranean vipers (Vipera aspis and V. latastei)
Authors: Martínez-Freiría Fernando , Lizana Miguel , Amaral José Pedro do , Brito José C. 
Published: April 2010

Abstract
Mediterranean vipers are ecologically very similar. When in contact, they
constitute an exceptional model to study the effects of competitive
interactions and niche segregation mechanisms. In High Ebro, distinct
methodologies (random visual encounter, road sampling and radio-tracking
surveys, captive maintenance, standardized transects and ad hoc field
observations) were used to compare ecological traits (diet, micro-habitat,
activity, reproductive and demographic) of V. aspis, V. latastei and hybrids
among both species and determine competitive advantages of each form. Diet
preferences were similar but few differences were found in feeding frequency
and annual variation in diet consumption. Males of the three forms compete
for areas with similar characteristics but differences were found mainly
during summer. Significant differences in average movement rates and home
range size were found among males. Fecundity and new-borns fitness were
lower in V. aspis than in V. latastei, whereas hybrids had intermediate
values. Male and female adult hybrids were more abundant than parental
forms, whereas female and juvenile V. latastei and juvenile hybrids had high
road-mortality. The three forms seem to be competing intensely for resources
but the segregation on the spatial and temporal axes of their niches could
be reducing interspecific competition and allowing coexistence. The use of
different resources probably confers reproductive and demographic advantages
for V. latastei and hybrids, respectively. Moreover, reproductive fitness of
hybrids suggests the occurrence of endogenous selection. Comparative thermal
and genetic studies are needed to clarify the limiting factors of vipers and
to establish a model of the hybrid zone.
Ecology of juvenile Northern watersnakes (Nerodia sipedon) inhabiting low-order streams
Authors: Cecala Kristen , Dorcas Michael , Price Steven 
Published: April 2010

AbstractThe juvenile stage for many reptiles is considered “the lost years” because of low capture probabilities, however understanding factors impacting juvenile survivorship and recruitment is critical for conservation of populations. We studied the ecology of juvenile Northern watersnakes, Nerodia sipedon, by intensively sampling a first-order stream and determined the occupancy of juveniles in 30 low-order streams in the Piedmont of North Carolina. Juveniles were relatively abundant within a single stream (n = 62 ± 9), and their capture probabilities were positively related to increasing stream-water temperatures. We also found that juveniles had high survivorship (ϕ = 0.87 ± 0.017). Occupancy of juvenile N. sipedon in low-order, Piedmont streams may be greater at streams that have confluences with high order streams or lakes, which potentially support adult N. sipedon populations. This study provides important information regarding the natural history of juvenile reptiles and indicates the importance of low order streams as habitat for N. sipedon populations.
Anuran life history plasticity: Variable practice in determining the end-point of larval development
Authors: Walsh Patrick Thomas 
Published: April 2010

AbstractPlasticity in the timing of life history events and their impact on individual fitness, particularly the timing of and size at metamorphosis in animals with complex life cycles such as anuran amphibians, has long been of interest to ecologists. For different studies on life history plasticity to be comparable, there must be clearly defined and commonly agreed transition points, but it is unclear how consistently this is being performed in studies using anuran amphibians. In a review of 157 published studies, I found considerable variation in defining the end point of the larval phase. While a slight majority used the emergence of the forelimbs as the conclusion of the larval phase, some used a period within the developmental phase of metamorphic climax and others used the resorption of the tail. Studies included in this review, that assessed the same life history variable at two different developmental stages, reported some differences in results depending on which developmental stage was used. Recent evidence also shows that metamorphic climax is itself a period which can vary with environmental conditions, but, even in studies that included part or all of metamorphic climax in the larval phase, the treatment of individuals during metamorphic climax was not reported. Therefore, I argue that life history studies on anuran amphibians should distinguish the following phases: larval, metamorphic climax, juvenile, adult; that the end of the larval phase is best defined in ecological studies by forelimb emergence and that conditions under which individuals undergo metamorphic climax should be fully described.
Image analysis of the ventral colour pattern discriminates between Spectacled salamanders, Salamandrina perspicillata and S. terdigitata (Amphibia, Salamandridae)
Authors: Angelini Claudio , Utzeri Carlo , Costa Corrado , Menesatti Paolo , Raimondi Stefano 
Published: April 2010

AbstractIn the present study, we applied statistical methods to quantitative image analysis of the persistent and individual ventral colour pattern of Salamandrina salamanders, in order to discriminate between individuals of the two species belonging to this genus. Pictures of 238 individuals from three populations of S. perspicillata and pictures of 95 S. terdigitata from two populations were analysed. Partial least squares discriminant analysis (PLSDA) classified 98.78% of individuals into the correct species. PLSDA reaches lower percentages of correct classification when applied to discriminate individuals from different populations of the same species (74.14% for S. perspicillata, 78.26% for S. terdigitata). An ANOVA analysis of colour abundances in different body sectors reveals significant differences between species. The results show that colour pattern has a specific basis, the most discriminant areas being the head and the pectoral girdle. We discuss these results in the light of the proposed evolutionary scenarios of the species, and suggest that ventral colour patterns were driven by founder effect.
An isolated population of Podarcis vaucheri (Sauria: Lacertidae) in south-eastern Spain: genetic data suggest human-mediated range expansion
Authors: Beddek Menad , Renoult Julien , Geniez Philippe , Crochet Pierre-André 
Published: April 2010

AbstractIn this study, we investigate the identity and origin of a population of Iberian Wall Lizards (Podarcis hispanicus complex) that we recently discovered inside the distribution range of the nominotypical form P. hispanicus. In the field, these animals were clearly identified as different from this species but their identity remained problematic. Using morphological and mitochondrial DNA analyses, we here identify this population as P. vaucheri, which constitutes a significant range extension for this species. Molecular results suggest a North African origin to this population. However, according to morphological results, these individuals are closer to the Spanish morphotype than to the North African morphotypes of P. vaucheri. Taken together, these results suggest a human-mediated introduction as the origin of this population, with local adaptation or phenotypic plasticity responsible of phenotypic convergence.
Advertisement call of Peltophryne florentinoi (Anura: Bufonidae), an endemic toad from Zapata Swamp, Cuba
Authors: Alonso Roberto , Hernández Maike , Rodríguez Ariel 
Published: April 2010

AbstractThe advertisement call of Peltophryne florentinoi, an endemic toad from Zapata Swamp, Matanzas, Cuba, is described in terms of temporal properties and dominant frequency. A comparison with the advertisement calls produced by the other three species of large toads in Cuba (P. peltocephala, P. fustiger and P. taladai) is also provided. Like other large toads from Cuba, P. florentinoi produces advertisement calls with long duration (> 10 s), low dominant frequency (< 1 kHz), and a series of complex pulses that are composed of two to five sub-pulses. All temporal features of the P. florentinoi call are significantly different from P. fustiger calls: number of pulses, pulse duration, and pulse rate separates it from P. peltocephala. P. florentinoi differs from P. taladai in call duration, number of pulses, and pulse rate. The occurrence of different types of complex pulses differed in all species studied. Typically, P. florentinoi pulses contain three sub-pulses, P. taladai four, and P. fustiger and P. peltocephala contain two sub-pulses. The dominant frequency of the advertisement call of P. florentinoi did not differ from the other species' calls. Call duration and pulse rate are the most useful acoustic properties to distinguish P. florentinoi advertisement calls from those of the other three large Cuban toads.
Foraging behaviour and territoriality of the strawberry poison frog (Oophaga pumilio) in dependence of the presence of ants
Authors: Pröhl Heike , Mebs Dietrich , Ospina Santiago Meneses , Staudt Konrad 
Published: April 2010

AbstractThe present study investigates foraging and territorial behaviour of the strawberry poison frog (Oophaga pumilio) in dependence of the presence of formicine and myrmicine ants, which constitute the main food source of the frogs. Species of the formicine ant genera Brachymyrmex and Paratrechina contain highly toxic alkaloids (pumiliotoxins), which the frogs incorporate and accumulate in their skin what may serve for predator deterrence. Twelve male frogs of two populations (primary and secondary forest) in Hitoy Cerere, Costa Rica, were observed each for a full day. Calling time, feeding attempts and time spent inside and outside the core area of their territories were recorded. Furthermore, twelve males of both populations were observed during the main foraging time to determine, whether the frogs search for prey in specific patches of their territories. The ants inside the core areas of twenty four frog territories were collected and classified to genus. Ants of the genera Brachymyrmex and Paratrechina were classified to species or morphospecies, respectively. The presence of formicine and myrmicine ants in territorial areas was compared to non-territorial sites. We found that formicine ants (Brachymyrmex and Paratrechina) were more present inside the territorial core areas than outside. The higher presence of these ants in the core areas was associated with longer foraging times. We verified that toxic alkaloids of the pumiliotoxin group are present in the dendrobatid frogs of Hitoy Cerere. The results of this study suggest that toxic diet may be linked to territoriality in this frog species.