bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fertility Declines in Less-developed Countries: Components and Implications
Authors: Eberstadt Nicholas N. 
Published: August 2009

Human fertility in the less-developed countries has declined substantially in aggregate over the past fifteen years. Although the declines have not occurred evenly—many countries, according to the best statistical information that is currently available, have yet to be affected—they have been felt in the major population centres of the poor world. Delays in the recognition of fertility decline are often more than a decade in less-developed countries, owing to the state of the art of collecting social statistics; analyses of the present condition, therefore, are necessarily tentative.In the 1960s, the ‘taxonomy’ of fertility decline in the less-developed countries was simple: those nations ‘suffering’ fertility decline were either undergoing rapid development, were geographically distinct as islands, or were ethnically distinct as largely Chinese populations. Such a simple categorization no longer holds up; in fact, it is hard to make any ‘big picture’ generalizations about the nations that are now experiencing a decrease in family size. Future research workers should take this as a cue to look more closely at the ‘micro’ aspects of fertility—those incentives which affect couples directly in their decisions about children—for in the final analysis it is couples and not nations which decide to become parents.Research workers might also with advantage pay closer attention to the connection between economic development and fertility, for the vast array of societies and economies that are now found to have declining fertility rates, would seem to call into question many of the assumptions about the so-called ‘demographic transition’, with which we have lived so comfortably for more than a generation.
Optimal Management of Karst Sites with Cave Fauna Protection
Authors: Tercafs Raymond 
Published: August 2009

An optimal management of large Karst sites, with emphasis on the conservation of cave fauna while allowing recreational use, is proposed. A detailed study of the relative biological value of each section in a reference cave, the east Belgian ‘Grottes de Han’ Cave, was made in comparison with 40 others in Belgium.Computer analysis provided a selection of optimal routes through the Cave. Each different route reflects the synthetic coefficients derived to weight biological and aesthetic values. This method of optimal cave resource control, developed to prevent deterioration in underground environments, can also be applied to other natural sites visited by humans.
The Ecology of Rawa Aopa, a Peat-swamp in Sulawesi, Indonesia
Authors: Zwahlen Robert 
Published: August 2009

Rawa Aopa is a large swamp in South-East Sulawesi, Indonesia — the only major peat-swamp in this mainly mountainous island. Its vegetation and fauna are still quite poorly known. The existing information is summarized here. With the creation of new villages as part of Indonesia's transmigration programme, the human population in this area has increased very rapidly. Pressure on natural resources — especially soils and forests — is increasing, and primary forests are dwindling rapidly. This in turn increases the threats to Rawa Aopa, as erosion in its catchment area inevitably leads to a rapid silting up of the swamp. The swamp has a potential as a source of food (fish and sago) and income (rattan and other products), and it might to some degree become a tourist attraction.From a scientific point of view, the gaps in the knowledge about water-regime, vegetation, and fauna, ought to be remedied. In order to attain sustainable utilization of this area, a thorough plan ought to be made for the whole catchment of Rawa Aopa. The most important measure to take is the protection of the forests covering the hills and the surroundings of the swamp. Also important very widely is the protection of soils. Furthermore, it is recommended to include the northern part of the swamp in the already-existing Rawa Aopa—Watumohai National Park.
Documenting Precision and Accuracy in the Open Data Policy Era
Authors: Moldwin Mark B. , Rose Sara 
Published: August 2009

How often do research papers discuss measurement uncertainty or present error bars in observational or statistical analysis figures?In an attempt to address this issue using space physics as an example, we conducted a survey of 102 observational Journal of Geophysical Research‐Space Physics articles that were published over a time span of 7 months. Unfortunately, the majority (56) did not discuss measurement uncertainty or present error bars in observational or statistical analysis figures.
AGU Announces Open Review Experiment
Authors: Albarède Francis 
Published: August 2009

Beginning in September, several AGU journals will introduce an option for “open review,” a public discussion forum on submitted manuscripts that takes place simultaneously with the formal review process. This is a 1‐year experiment to measure community interest.In July, AGU journal editors were provided with guidelines and were asked to consider engaging in the experiment. For journals with multiple editors, all editors had to agree to participate. As a result of editor responses, open review will be available for five journals: Geochemistry, Geophysics, Geosystems; Global Biogeochemical Cycles; JGR—Earth Surface; JGR—Planets; and Radio Science.
Evaluating restoration success and applying adapative management in the Middle Rio Grande Bosque
Authors: Hummel Ondrea , Caplan Todd 
Published: August 2009

AbstractThe U.S. Army Corps of Engineers Albuquerque District, in collaboration with various local partners, has been implementing restoration projects in the Albuquerque Reach of the Middle Rio Grande. These projects have included the removal of the metal jetty jacks, debris, and dense thickets of non-native vegetation (salt cedar, Russian olive, and Siberian elm) that occur in the bosque (riparian forest), creation of wet habitats (such as willow swales and high-flow channels), and revegetation schemes focused on increasing the diversity and quality of wildlife habitat. The goal of many of these projects is to develop a framework to restore the bosque into a more functional and sustainable ecosystem. Projects implemented on the ground are being monitored for various restoration success components – such as vegetation response, wildlife use and response, and surface water-ground water interaction. This monitoring has provided important information in regards to planning future restoration efforts that meet all project objectives. Monitoring has also pointed out where improvement is needed and adaptive management can be implemented. This presentation will give an overview of the various projects and monitoring that has taken place and how information gained has been beneficial.
A novel protein, sperm head and tail associated protein (SHTAP), interacts with cysteine‐rich secretory protein 2 (CRISP2) during spermatogenesis in the mouse
Authors: Jamsai Duangporn , Rijal Sewa , Bianco Deborah M. , O'Connor Anne E. , Merriner Donna J. , Smith Stephanie J. , Gibbs Gerard M. , O'Bryan Moira K. 
Published: August 2009

Background information. CRISP2 (cysteine‐rich secretory protein 2) is a sperm acrosome and tail protein with the ability to regulate Ca2+ flow through ryanodine receptors. Based on these properties, CRISP2 has a potential role in fertilization through the regulation of ion signalling in the acrosome reaction and sperm motility. The purpose of the present study was to determine the expression, subcellular localization and the role in spermatogenesis of a novel CRISP2‐binding partner, which we have designated SHTAP (sperm head and tail associated protein).Results. Using yeast two‐hybrid screens of an adult testis expression library, we identified SHTAP as a novel mouse CRISP2‐binding partner. Sequence analysis of all Shtap cDNA clones revealed that the mouse Shtap gene is embedded within a gene encoding the unrelated protein NSUN4 (NOL1/NOP2/Sun domain family member 4). Five orthologues of the Shtap gene have been annotated in public databases. SHTAP and its orthologues showed no significant sequence similarity to any known protein or functional motifs, including NSUN4. Using an SHTAP antiserum, multiple SHTAP isoforms (∼20–87 kDa) were detected in the testis, sperm, and various somatic tissues. Interestingly, only the ∼26 kDa isoform of SHTAP was able to interact with CRISP2. Furthermore, yeast two‐hybrid assays showed that both the CAP (CRISP/antigen 5/pathogenesis related‐1) and CRISP domains of CRISP2 were required for maximal binding to SHTAP. SHTAP protein was localized to the peri‐acrosomal region of round spermatids, and the head and tail of the elongated spermatids and sperm tail where it co‐localized with CRISP2. During sperm capacitation, SHTAP and the SHTAP—CRISP2 complex appeared to be redistributed within the head.Conclusions. The present study is the first report of the identification, annotation and expression analysis of the mouse Shtap gene. The redistribution observed during sperm capacitation raises the possibility that SHTAP and the SHTAP—CRISP2 complex play a role in the attainment of sperm functional competence.
First report of a haemagglutinin-induced apoptotic pathway in breast cancer cells
Authors: Lam Sze Kwan , Ng Tzi Bun 
Published: August 2009

A dimeric 64 kDa HA (haemagglutinin) was isolated with a high yield from dried Phaseolus vulgaris cultivar ‘French bean number 35’ seeds. It inhibited the proliferation of hepatoma HepG2 cells and breast cancer MCF-7 cells with an IC50 of 100 and 2 μM respectively. After exposure of MCF-7 cells to the HA for 24 h, a number of changes were detected in the cells. Growth arrest in the G0/G1 and G2/M phases was observed. The number of cells undergoing early apoptosis and late apoptosis increased. Disruption of the mitochondrial transmembrane potential and disorganization of the inner mitochondrial membrane were induced. Western-blot analysis disclosed that the HA induced apoptosis through the death receptor-mediated pathway.
Characterization of functional activity of ABCB1 and ABCC1 proteins in eggs and embryonic cells of the sea urchin Echinometra lucunter
Authors: De Souza Mônica Queiroz Vasconcelos , Barros Taíssa Valéria , Torrezan Elis , Cavalcanti Airlla Laana de Medeiros , Figueiredo Regina Celia Bressan Queiroz , Marques-Santos Luis Fernando 
Published: August 2009

ABC transporter (ATP-binding-cassette transporter) proteins have been strongly associated with the phenomenon of multidrug resistance in cancer cells. Furthermore, their physiological expression has been studied in many organisms, including bacteria, fungi, plants and vertebrate or invertebrate animals. Their widespread expression through the evolution demonstrates their relevance to the survival of living things. In the present study, we characterized the functional activity of ABCB1 and ABCC1 proteins in gametes and embryonic cells of the sea urchin Echinometra lucunter. The ABC transporter proteins' functional activity was up-regulated post-fertilization. Eggs and spermatozoa of E. lucunter accumulated more C-AM (calcein acetoxymethyl ester), a fluorescent substrate of ABCB1 and ABCC1 proteins, than embryonic cells. Verapamil, reversin 205 and indomethacin were able to increase C-AM influx in eggs and embryos. However, verapamil and reversin 205 were more efficient than indomethacin, suggesting a predominance of ABCB1 protein over ABCC1 protein activity. Multidrug resistance modulating agents, at the concentration range that inhibited ABC transporter proteins, did not block the embryonic development until blastula stage. However, inhibition of ABCB1-mediated efflux by reversin 205 circumvented resistance of embryos to the antimitotic vinca alkaloid vinblastine. Embryonic development was more efficiently blocked when colchicine was previously added to eggs than to embryos 5 min after fertilization. This set of results suggests that these proteins act as a fundamental biochemical barrier conferring a protective physiological role against toxic xenobiotics in E. lucunter embryos.
Residue levels of organochlorines and organophosphates in water, fish and sediments from Lake Victoria-Kenyan portion
Authors: Werimo K. , Bergwerff A. A. , Seinen W. 
Published: August 2009

Water, fish and sediments were sampled from May 2000 to December 2006 at 19 different locations in Lake Victoria-Kenyan part. They were analyzed for organochlorines (HCB, Lindane, DDT and Endosulfan) and organophosphate (diazinon). All organochlorines in water, fish and sediments were below detection limit of 0.5 μg l−1, 1.0 μg kg−1 body weight and 1.0 μg kg−1 dry weight, respectively. Comparison of the results of these samples in Lake Victoria with those analyzed during 1993 suggests that the concentrations of these compounds have not increased in the lake.
Therefore it was concluded that there were neither environmental nor human health hazards posed by these compounds to the water or sediments.
The Place2Be: Measuring the effectiveness of a primary school‐based therapeutic intervention in England and Scotland
Authors: Lee Rachael C. , Tiley Clare E. , White Jemma E. 
Published: August 2009

AbstractAim: There is increasing awareness of the prevalence of mental health disorders in children in the UK, but research on the efficacy of interventions meeting this need is limited. This study assessed whether The Place2Be model of individual and group intervention has a positive influence on children's social and emotional wellbeing. Providing emotional and therapeutic support to school age children in England and Scotland, The Place2Be delivers school‐based therapeutic interventions to around 47,000 children in 143 primary schools, two secondary schools and one independent school. Method: Strengths and Difficulties Questionnaire data was collected from a national sample of primary school children aged 4–11 (N=1,864) both before and after accessing an individual (n =1,645) or group (n =215) intervention. Results: Repeated measures t‐tests revealed that children had significantly lower Total Difficulties scores post‐intervention than pre‐intervention as rated by their class teachers and parents (Teacher‐rated: p<0.001, d = 0.39; Parent‐rated: p<0.001, d = 0.47). Children also had significantly higher Prosocial scores post‐intervention (Teacher‐rated: p<0.001, d = 0.25; Parent‐rated: p<0.001, d = 0.15). Conclusions: Children's social and emotional behaviour, as perceived by their teachers and parents, was improved following therapeutic intervention with The Place2Be. These findings have important implications for service providers looking to commission projects for the benefit of their local community.
Counselling in UK secondary schools: A comprehensive review of audit and evaluation data
Authors: Cooper Mick 
Published: August 2009

AbstractAims: The purpose of this study was to develop a comprehensive picture of the nature and outcomes of counselling in secondary schools in the UK. Method: Audit and evaluation studies of schools counselling were identified using a systematic literature search. Thirty studies were found and analysed using a variety of methods. Typically, counselling services provided purely person‐centred, or person‐centred‐based, forms of therapy. Results: Averaged across all studies, clients had a mean age of 13.86 and attended for 6.35 sessions of counselling. The average percentage of female clients per study was 56.31%. Most frequently, clients presented with family issues, with anger issues particularly prevalent in males. Around 60% of clients began counselling with ‘abnormal’ or borderline levels of psychological distress. Counselling was associated with large improvements in mental health (mean weighted effect size = 0.81), with around 50% of clinically distressed clients demonstrating clinical improvement. On average, just over 80% of respondents rated counselling as moderately or very helpful, with teachers giving it a mean rating of 8.22 on a 10‐point scale of helpfulness. For clients, the most helpful aspect of counselling was the opportunity to talk and be listened to, while pastoral care staff emphasised the counsellor's independence, expertise and confidentiality. There were some indications that counselling may indirectly benefit students’ capacities to study and learn. Discussion: School‐based counselling appears to be of considerable benefit to young people in the UK, but there is a need for this finding to be verified through controlled trials.
How do secondary school counsellors work with other professionals?
Authors: Cromarty Karen , Richards Kaye 
Published: August 2009

AbstractAim: This study explores how secondary school counsellors work with other professionals within and outside schools in the delivery of services. Method: Sixteen school counsellors from across the UK were interviewed, in four different focus groups – two in England (n=8) and two in Scotland (n=8). Results: The findings indicate that the professional relationships counsellors have with other colleagues have a direct influence upon the quality of the service they feel able to offer. Time spent with colleagues when setting up services was viewed as highly beneficial, as was time spent building relationships and connections with colleagues within the school and from external agencies and organisations, as well as having a senior member of staff to liaise with. It is apparent that attending to relationships outside of the counselling room may influence the positive outcomes for the counselling service and its clients generally. Conclusions: Implications of these findings may influence the ways in which counsellors are employed by commissioners, and how counsellors use their time allocation in schools to ensure that effective services are both achieved and maintained.
info-gibbs: a motif discovery algorithm that directly optimizes information content during sampling
Authors: Defrance Matthieu , van Helden Jacques 
Published: August 2009

Abstract
Motivation: Discovering cis-regulatory elements in genome sequence remains a challenging issue. Several methods rely on the optimization of some target scoring function. The information content (IC) or relative entropy of the motif has proven to be a good estimator of transcription factor DNA binding affinity. However, these information-based metrics are usually used as a posteriori statistics rather than during the motif search process itself.
Results: We introduce here info-gibbs, a Gibbs sampling algorithm that efficiently optimizes the IC or the log-likelihood ratio (LLR) of the motif while keeping computation time low. The method compares well with existing methods like MEME, BioProspector, Gibbs or GAME on both synthetic and biological datasets. Our study shows that motif discovery techniques can be enhanced by directly focusing the search on the motif IC or the motif LLR.
Availability: http://rsat.ulb.ac.be/rsat/info-gibbs
Contact: defrance@bigre.ulb.ac.be
Supplementary information: Supplementary data are available at Bioinformatics online.
The effects of probe binding affinity differences on gene expression measurements and how to deal with them
Authors: Dannemann Michael , Lorenc Anna , Hellmann Ines , Khaitovich Philipp , Lachmann Michael 
Published: August 2009

Abstract
Motivation: When comparing gene expression levels between species or strains using microarrays, sequence differences between the groups can cause false identification of expression differences. Our simulated dataset shows that a sequence divergence of only 1% between species can lead to falsely reported expression differences for &gt;50% of the transcripts—similar levels of effect have been reported previously in comparisons of human and chimpanzee expression. We propose a method for identifying probes that cause such false readings, using only the microarray data, so that problematic probes can be excluded from analysis. We then test the power of the method to detect sequence differences and to correct for falsely reported expression differences. Our method can detect 70% of the probes with sequence differences using human and chimpanzee data, while removing only 18% of probes with no sequence differences. Although only 70% of the probes with sequence differences are detected, the effect of removing probes on falsely reported expression differences is more dramatic: the method can remove 98% of the falsely reported expression differences from a simulated dataset. We argue that the method should be used even when sequence data are available.
Contact: lachmann@eva.mpg.de
Supplementary information: Supplementary data are available at Bioinformatics online.
CoCoa: a software tool for estimating the coefficient of coancestry from multilocus genotype data
Authors: Maenhout Steven , De Baets Bernard , Haesaert Geert 
Published: August 2009

Abstract
Motivation: Phenotypic data collected in breeding programs and marker-trait association studies are often analyzed by means of linear mixed models. In these models, the covariance between the genetic background effects of all genotypes under study is modeled by means of pairwise coefficients of coancestry. Several marker-based coancestry estimation procedures allow to estimate this covariance matrix, but generally introduce a certain amount of bias when the examined genotypes are part of a breeding program. CoCoa implements the most commonly used marker-based coancestry estimation procedures and as such, allows to select the best fitting covariance structure for the phenotypic data at hand. This better model fit translates into an increased power and improved type I error control in association studies and an improved accuracy in phenotypic prediction studies. The presented software package also provides an implementation of the new Weighted Alikeness in State (WAIS) estimator for use in hybrid breeding programs. Besides several matrix manipulation tools, CoCoa implements two different bending heuristics, in case the inverse of an ill-conditioned coancestry matrix estimate is needed.
Availability and Implementation: The software package CoCoa is freely available at http://webs.hogent.be/cocoa. Source code, manual, binaries for 32 and 64-bit Linux systems and an installer for Microsoft Windows are provided. The core components of CoCoa are written in C++, while the graphical user interface is written in Java.
Contact: steven.maenhout@hogent.be
Statistical methods for gene set co-expression analysis
Authors: Choi YounJeong , Kendziorski Christina 
Published: August 2009

Abstract
Motivation: The power of a microarray experiment derives from the identification of genes differentially regulated across biological conditions. To date, differential regulation is most often taken to mean differential expression, and a number of useful methods for identifying differentially expressed (DE) genes or gene sets are available. However, such methods are not able to identify many relevant classes of differentially regulated genes. One important example concerns differentially co-expressed (DC) genes.
Results: We propose an approach, gene set co-expression analysis (GSCA), to identify DC gene sets. The GSCA approach provides a false discovery rate controlled list of interesting gene sets, does not require that genes be highly correlated in at least one biological condition and is readily applied to data from individual or multiple experiments, as we demonstrate using data from studies of lung cancer and diabetes.
Availability: The GSCA approach is implemented in R and available at www.biostat.wisc.edu/∼kendzior/GSCA/.
Contact: kendzior@biostat.wisc.edu
Supplementary information: Supplementary data are available at Bioinformatics online.