bluuebunny/crossref_metadata_2025 huggingface dataset:
A flexible rank-based framework for detecting copy number aberrations from array data
Authors: LaFramboise Thomas , Winckler Wendy , Thomas Roman K.
Published: January 2009

Motivation: DNA copy number aberration—both inherited and sporadic—is a significant contributor to a variety of human diseases. Copy number characterization is therefore an area of intense research. Probe hybridization-based arrays are important tools used to measure copy number in a high-throughput manner.

Results: In this article, we present a simple but powerful nonparametric rank-based approach to detect deletions and gains from raw array copy number measurements. We use three different rank-based statistics to detect three separate molecular phenomena—somatic lesions, germline deletions and germline gains. The approach is robust and rigorously grounded in statistical theory, thereby enabling the meaningful assignment of statistical significance to each putative aberration. We demonstrate the flexibility of our approach by applying it to data from three different array platforms. We show that our method compares favorably with established approaches by applying it to published well-characterized samples. Power simulations demonstrate exquisite sensitivity for array data of reasonable quality.

Conclusions: Our flexible rank-based framework is suitable for multiple platforms including single nucleotide polymorphism arrays and array comparative genomic hybridization, and can reliably detect gains or losses of genomic DNA, whether inherited, de novo, or somatic.

Availability: An R package RankCopy containing the methods described here, and is freely available from the author's web site (http://mendel.gene.cwru.edu/laframboiselab/).

Contact:  Thomas.LaFramboise@case.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Seasonality of Birth Month of Children With Celiac Disease Differs From That in the General Population and Between Sexes and Is Linked to Family History and Environmental Factors
Authors: Lewy Hadas , Meirson Hadas , Laron Zvi
Published: January 2009

Background:

Patients with autoimmune diseases, such as type 1 diabetes mellitus, atopic dermatitis, autoimmune thyroid diseases, and multiple sclerosis have a different seasonality of month of birth (MOB) from the general population. This study was undertaken to determine the seasonality of MOB in children with celiac disease (CD), an autoimmune‐mediated enteropathy.

Patients and Methods:

The medical records of 431 children with CD (239 girls, 192 boys) were included in the study; 138 girls and 81 boys were under the age of 24 months. Data were analyzed by the cosinor method, which, in addition to statistical significance, provides parameters of rhythms. Statistical differences between groups were also analyzed by the χ2 test.

Results:

Patients with CD showed different patterns from that in the general population, which peaks in September. Boys and girls with CD were found to have a different seasonality of MOB (P < 0.02). Girls whose CD was diagnosed before age 24 months (peak July–August) had a different seasonality of MOB from those whose CD was diagnosed after age 24 months (no rhythm; P < 0.005) and showed a different seasonality from boys whose CD was diagnosed above 24 months (peak July; P < 0.02). In addition, we found a different seasonality of MOB in children with a family history of CD compared with those with no family history (P < 0.001).

Conclusions:

Girls with the diagnosis of CD and patients of both sexes with a family history of CD have a different pattern of seasonality of birth from the general population. This is suggestive of a perinatal virus infection as a plausible candidate for the primary trigger.
Clinical Evidence for Immunomodulatory Effects of Probiotic Bacteria
Authors: Ruemmele FM , Bier D , Marteau P , Rechkemmer G , Bourdet‐Sicard R , Walker WA , Goulet O
Published: January 2009

Close, tightly orchestrated interactions between the intestinal epithelium and the mucosa‐associated immune system are critical for normal intestinal absorptive and immunological functions. Recent data indicate that commensal intestinal microbiota represents a major modulator of intestinal homeostasis. This review analyzes the process of intestinal colonization and the interaction of microbiota with the intestinal epithelium and mucosal immune system, with special reference to the first years of extrauterine life. Dysregulation of the symbiotic interaction between intestinal microbiota and the mucosa may result in a pathological condition with potential clinical repercussions. Based on the concept that there is a beneficial and symbiotic relation between the host and endogenous microbiota, strategies aimed at directly modulating intestinal microbiota with regard to disease prevention or treatment have been developed. One strategy involves administering viable probiotic bacteria. Clinical evidence for the beneficial effect of probiotics in the prevention and/or treatment of necrotizing enterocolitis, infectious and antibiotic‐associated diarrhea, allergic diseases, and inflammatory bowel disorders is reviewed herein.
Anti‐Saccharomyces cerevisiae Antibodies Status Is Associated with Oral Involvement and Disease Severity in Crohn Disease
Authors: Russell RK , Ip B , Aldhous MC , MacDougall M , Drummond HE , Arnott IDR , Gillett PM , McGrogan P , Weaver LT , Bisset WM , Mahdi G , Wilson DC , Satsangi J
Published: January 2009

Objectives:

To determine anti‐Saccharomyces cerevisiae antibodies (ASCA) status and its relation to disease phenotype in patients with inflammatory bowel disease (IBD).

Patients and Methods:

A total of 301 Scottish patients with early‐onset IBD—197 Crohn disease (CD), 76 ulcerative colitis (UC), 28 indeterminate colitis (IC)—and 78 healthy control individuals were studied. ASCA status (IgA, IgG) was determined by enzyme‐linked immunosorbent assay. ASCA status was then analyzed in relation to CD phenotype.

Results:

Patients with CD had a higher prevalence of ASCA than patients with UC and healthy controls: 82/197 versus 12/76, odds ratio (OR) 3.80 (1.93–7.50) and 82/197 versus 6/78, OR 8.56 (3.55–20.62), respectively. Univariate analysis showed that positive ASCA status was associated with oral CD (17/25 vs 59/153, OR 3.39 [1.38–8.34]), perianal CD (39/77 vs 38/108, OR 1.89 [1.04–3.44]) and the presence of granulomata (63/132 vs 15/52, OR 2.25 [1.13–4.48]) and also with markers of disease severity: raised C‐reactive protein (44/90 vs 12/49, OR 2.95[1.36–6.37]), hypoalbuminemia (44/85 vs 20/74, OR 2.28[1.19–4.37]), and surgery (27/49 vs 54/147, OR 2.11 [1.10–4.06]). From multivariate analysis, the presence of oral disease (adjusted P = 0.001, OR 22.22 [3.41–142.86]) and hypoalbuminemia (adjusted P = 0.01, OR 4.78 [1.40–16.39]) was found to be independently associated with ASCA status. No association was demonstrated between ASCA and IBD candidate genes.

Conclusions:

Patients with CD had a higher prevalence of ASCA than did other patients with IBD. ASCA status described patients with CD who had a specific phenotype, showing an association with markers of disease severity and oral CD involvement.
Multiple whole-genome alignments without a reference organism
Authors: Dubchak Inna , Poliakov Alexander , Kislyuk Andrey , Brudno Michael
Published: January 2009

Multiple sequence alignments have become one of the most commonly used resources in genomics research. Most algorithms for multiple alignment of whole genomes rely either on a reference genome, against which all of the other sequences are laid out, or require a one-to-one mapping between the nucleotides of the genomes, preventing the alignment of recently duplicated regions. Both approaches have drawbacks for whole-genome comparisons. In this paper we present a novel symmetric alignment algorithm. The resulting alignments not only represent all of the genomes equally well, but also include all relevant duplications that occurred since the divergence from the last common ancestor. Our algorithm, implemented as a part of the VISTA Genome Pipeline (VGP), was used to align seven vertebrate and six Drosophila genomes. The resulting whole-genome alignments demonstrate a higher sensitivity and specificity than the pairwise alignments previously available through the VGP and have higher exon alignment accuracy than comparable public whole-genome alignments. Of the multiple alignment methods tested, ours performed the best at aligning genes from multigene families—perhaps the most challenging test for whole-genome alignments. Our whole-genome multiple alignments are available through the VISTA Browser at http://genome.lbl.gov/vista/index.shtml.
The Low-Oxygen-Induced NAC Domain Transcription Factor ANAC102 Affects Viability of Arabidopsis Seeds following Low-Oxygen Treatment
Authors: Christianson Jed A. , Wilson Iain W. , Llewellyn Danny J. , Dennis Elizabeth S.
Published: January 2009

Low-oxygen stress imposed by field waterlogging is a serious impediment to plant germination and growth. Plants respond to waterlogging with a complex set of physiological responses regulated at the transcriptional, cellular, and tissue levels. The Arabidopsis (Arabidopsis thaliana) NAC domain-containing gene ANAC102 was shown to be induced under 0.1% oxygen within 30 min in both roots and shoots as well as in 0.1% oxygen-treated germinating seeds. Overexpression of ANAC102 altered the expression of a number of genes, including many previously identified as being low-oxygen responsive. Decreasing ANAC102 expression had no effect on global gene transcription in plants but did alter expression patterns in low-oxygen-stressed seeds. Increasing or decreasing the expression of ANAC102 did not affect adult plant survival of low-oxygen stress. Decreased ANAC102 expression significantly decreased germination efficiency following a 0.1% oxygen treatment, but increased expression had no effect on germination. This protective role during germination appeared to be specific to low-oxygen stress, implicating ANAC102 as an important regulator of seed germination under flooding.
The Temperature-Sensitive brush Mutant of the Legume Lotus japonicus Reveals a Link between Root Development and Nodule Infection by Rhizobia
Authors: Maekawa-Yoshikawa Makoto , Müller Judith , Takeda Naoya , Maekawa Takaki , Sato Shusei , Tabata Satoshi , Perry Jillian , Wang Trevor L. , Groth Martin , Brachmann Andreas , Parniske Martin
Published: January 2009

The brush mutant of Lotus japonicus exhibits a temperature-dependent impairment in nodule, root, and shoot development. At 26°C, brush formed fewer nodules, most of which were not colonized by rhizobia bacteria. Primary root growth was retarded and the anatomy of the brush root apical meristem revealed distorted cellular organization and reduced cell expansion. Reciprocal grafting of brush with wild-type plants indicated that this genotype only affected the root and that the shoot phenotype was a secondary effect. The root and nodulation phenotype cosegregated as a single Mendelian trait and the BRUSH gene could be mapped to the short arm of chromosome 2. At 18°C, the brush root anatomy was rescued and similar to the wild type, and primary root length, number of infection threads, and nodule formation were partially rescued. Superficially, the brush root phenotype resembled the ethylene-related thick short root syndrome. However, treatment with ethylene inhibitor did not recover the observed phenotypes, although brush primary roots were slightly longer. The defects of brush in root architecture and infection thread development, together with intact nodule architecture and complete absence of symptoms from shoots, suggest that BRUSH affects cellular differentiation in a tissue-dependent way.
The campaign to DNA barcode all fishes, FISH‐BOL
Authors: Ward R. D. , Hanner R. , Hebert P. D. N.
Published: January 2009

FISH‐BOL, the Fish Barcode of Life campaign, is an international research collaboration that is assembling a standardized reference DNA sequence library for all fishes. Analysis is targeting a 648 base pair region of the mitochondrial cytochromecoxidase I (COI) gene. More than 5000 species have already been DNA barcoded, with an average of five specimens per species, typically vouchers with authoritative identifications. The barcode sequence from any fish, fillet, fin, egg or larva can be matched against these reference sequences using BOLD; the Barcode of Life Data System (http://www.barcodinglife.org). The benefits of barcoding fishes include facilitating species identification, highlighting cases of range expansion for known species, flagging previously overlooked species and enabling identifications where traditional methods cannot be applied. Results thus far indicate that barcodes separatec.98 and 93% of already described marine and freshwater fish species, respectively. Several specimens with divergent barcode sequences have been confirmed by integrative taxonomic analysis as new species. Past concerns in relation to the use of fish barcoding for species discrimination are discussed. These include hybridization, recent radiations, regional differentiation in barcode sequences and nuclear copies of the barcode region. However, current results indicate these issues are of little concern for the great majority of specimens.
Rare and asymmetrical hybridization of the endemicBarbus carpathicuswith its widespread congenerBarbus barbus
Authors: Lajbner Z. , ŠLechtová V. , ŠLechta V. , ŠVátora M. , Berrebi P. , Kotlík P.
Published: January 2009

In endemic species that co‐occur with widespread congeners, hybridization can lead to an influx of novel and beneficial genetic variation, but high rates of introgression may cause genetic swamping of the endemic species and have detrimental effects on its survival potential. This study examines hybridization between sympatric populations of the Carpathian barbelBarbus carpathicus, a recently discovered cryptic species with a restricted range, and the widespread common barbelBarbus barbus. Based on six diagnostic allozyme loci, a microsatellite locus and mtDNA, hybrids were found to be present at multiple localities within the Vistula River drainage (Baltic Sea) as well as in the Tisza River system of the Danube River drainage (Black Sea). However, the numbers of hybrids were very low; four individuals of 230 fish sampled from the Vistula drainage. Bayesian assessment of their nuclear genotypes suggested that two hybrids in the Vistula drainage and nine in the Tisza system were F1generation, and one in the Vistula drainage and one in the Tisza system were backcrosses (BC) toB. barbus, while no F2or BC toB. carpathicuswere detected. No hybrid carriedB. carpathicusmtDNA and cytonuclear linkage disequilibria showed significant positive associations between hybrid genotypes andB. barbusmtDNA, suggesting unidirectionality in the interspecific mating with a disproportionate contribution ofB. barbusmothers. Despite geographically broad occurrence of hybrids, these data provide evidence of strong constraints on hybridization in the native breeding habitats and the lack of introgression towardsB. carpathicus.
Monitoring of sympathetic tone to assess postoperative pain: skin conductance vs surgical stress index
Authors: Ledowski T. , Ang B. , Schmarbeck T. , Rhodes J.
Published: January 2009

The number of fluctuations in skin conductance per second has been described as a potential tool for monitoring postoperative pain. More recently, the surgical stress index has shown promising correlations with intra‐operative painful stimuli. We compared both methods for their ability to assess postoperative pain, in 100 postoperative patients who were also asked to quantify their level of pain at different time points in the recovery room. The number of fluctuations per second and surgical stress index were significantly different between pain scoring ≤ 5/10 and > 5/10 on a numeric rating scale (mean (SE) number of fluctuations per second 0.12 (0.02) vs 0.21 (0.03), respectively; p = 0.017, and surgical stress index 57 (1.4) vs 64 (1.9) points, respectively; p = 0.001). Both number of fluctuations in skin conductance per second and surgical stress index identified timepoints with moderate to severe pain with only moderate sensitivity and specificity.
Geohistorical and current environmental influences on floristic differentiation in the Ryukyu Archipelago, Japan
Authors: Nakamura Koh , Suwa Rempei , Denda Tetsuo , Yokota Masatsugu
Published: January 2009

Aim  Floristic differentiation in the Ryukyu Archipelago has been explained primarily by geohistory, specifically landbridge formation and vicariance at the Tokara and Kerama Gaps, two deep‐sea channels through the island arc. This ignores current environmental effects, which may also be important. We therefore tested whether the floristic differentiation pattern is explained primarily by the historical effect of the gaps as barriers, or whether a better understanding of floristic differentiation is achieved when both historical and current environmental factors are incorporated.

Location  Ryukyu Archipelago, Japan: an assemblage of continental islands.

Methods  We compiled a presence–absence matrix of 1815 plant species on 26 islands. Floristic dissimilarity distances between islands were calculated using Simpson’s similarity index and analysed using cluster analysis. We also conducted multiple regression on distance matrices (MRM) to examine the significance of the historical factors of the gaps and current environmental factors: geographical distance among islands and differences in island area and maximum elevation.

Results  We detected clear patterns of floristic differentiation across the gaps. Using the two gaps as explanatory variables, the MRM showed that both had significant effects on floristic dissimilarity distance. However, when geographical distance was added to the explanatory model, the Kerama Gap effect disappeared. When all five explanatory variables were used, the Tokara Gap and geographical distance had positive effects, but area difference had a negative effect. The Kerama Gap and difference in maximum elevation had no effect.

Main conclusions  The geographical pattern of floristic differentiation appears to indicate the influence of both gaps. However, the MRM indicates that the floristic differentiation across the Kerama Gap is no more than could be explained solely by geographical distance. Across the Tokara Gap, however, floristic differentiation is larger than geographical distance alone can explain. This additional differentiation is attributable to the effect of the historical barrier. To verify the significance of historical effects of vicariance on island biota, the confounding effects of geographical distance must be considered. The distance decay of floristic similarity and negative effect of area difference on floristic differentiation demonstrate that floristic differentiation is better understood by incorporating both historical and current environmental factors.
Phylogenetics of Darwiniothamnus (Asteraceae: Astereae) – molecular evidence for multiple origins in the endemic flora of the Galápagos Islands
Authors: Andrus Nicole , Tye Alan , Nesom Guy , Bogler David , Lewis Carl , Noyes Richard , Jaramillo Patricia , Francisco‐Ortega Javier
Published: January 2009

Aim  The aims of this study were (1) to investigate whether the two growth forms of Darwiniothamnus Harling (Asteraceae) originated from the colonization of a single ancestor, (2) to identify the closest relative(s) of Darwiniothamnus, and (3) to review molecular phylogenies from other plant groups to infer the origin of Galápagos endemics.

Location  Darwiniothamnus is endemic to the Galápagos Islands.

Methods  All putative relatives of Darwiniothamnus plus 38 additional species were included. Nucleotide sequences of the internal transcribed spacers of the nuclear ribosomal DNA were used for Bayesian and parsimony analyses.

Results  Darwiniothamnus is polyphyletic. Two species (D. lancifolius (Hook. f.) Harling and D. tenuifolius (Hook. f.) Harling) are woody shrubs that usually grow to 1–2 m in height; they belong to a clade composed of species otherwise restricted to the Caribbean. These two species are sister to Erigeron bellidiastroides Griseb., a herbaceous species endemic to Cuba. The third species (D. alternifolius Lawesson & Adsersen) is a perennial herbaceous plant, woody at the base and reaching only up to 50 cm in height. It is sister to two Chilean (Coquimbo–Valparaiso region) species that also have a perennial herbaceous habit: E. fasciculatus Colla and E. luxurians (Skottsb.) Solbrig. They are placed in an assemblage restricted to South America. The review of previous molecular phylogenetic studies revealed that two of the endemic genera and endemic species of three non‐endemic genera have their closest relatives in South America. Endemic species belonging to three non‐endemic genera have sister species in North America or the West Indies. One endemic genus and endemic species in three non‐endemic genera have sister taxa with a widespread continental distribution, or their molecular phylogenies yielded equivocal results.

Main conclusions  The flora of Galápagos has affinities with both North America (including the Antilles) and South America. Darwiniothamnus exhibits both patterns: two species of this genus are sister to a taxon endemic to Cuba, supporting a connection between the Cocos plate and the West Indies; the third species, D. alternifolius, provides a link with the Coquimbo–Valparaiso region, suggesting a biogeographical connection between the Nazca plate and southern South America.
The effects of a home‐based intervention for young children with intellectual disabilities in Vietnam
Authors: Shin J. Y. , Nhan N. V. , Lee S.‐B. , Crittenden K. S. , Flory M. , Hong H. T. D.
Published: January 2009

Background  This study was conducted to examine the impact of a 1‐year intervention for children with intellectual disabilities (ID) in Vietnam.

Method  Subjects were 30 preschool‐aged children with ID (ages 3 to 6 years). Sixteen were assigned to an intervention group and 14 to a control group. Based on the Portage Curriculum (CESA 5 2003), the intervention trained parents to work with their children through modelling and coaching by teachers during weekly home visits.

Results  Comparison of pre‐, mid‐ and post‐intervention assessments of the children based on the Vineland Adaptive Behavior Scales (Sparrow et al. 1984a) indicated that the intervention was promising: children in the intervention group improved significantly in most domains of adaptive behaviours, and also performed significantly better than the control group in the areas of personal care and motor skills.

Conclusions  The results from the Vietnam programme are discussed in terms of its implications and strategies for developing programmes for children with disabilities in developing countries.
Coeval versus reciprocal mixed carbonate–siliciclastic deposition, Middle Devonian Baltic Basin, Eastern Europe: implications from the regional tectonic development
Authors: TÄNAVSUU‐MILKEVICIENE KATI , PLINK‐BJÖRKLUND PIRET , KIRSIMÄE KALLE , AINSAAR LEHO
Published: January 2009

The Middle Devonian Narva succession in the Baltic Basin represents a significant turnaround in the history of the basin. The detailed study of core and outcrop sections and the three‐dimensional correlations across the Baltic Basin reveal a carbonate‐dominated, mixed retrogressive succession, overlain by a siliciclastic‐dominated, progradational succession. The palaeogeographic reconstructions show how the shallow, tide‐influenced basin expanded from south‐west to north‐east and, later during the transgression, also to the north, south and east. The transgressive portion of the basin fill is dominated by carbonate‐rich sabkha and supratidal to intertidal deposits on the basin margins, and subtidal carbonates in the basin centre. Siliciclastic material was derived by tidal currents and storm waves from the south‐west through a tidal inlet and flood‐tidal delta complex. This initial transgressive phase is characterized by the lack of subsidence or even episodic uplifts in the northern/north‐western part of the basin margin, shown by convergence of timelines and the thin (30 m) transgressive succession. In contrast, on the southern margin, the facies associations stack vertically into a 70 to 80 m thick succession, indicating significantly higher subsidence rates. The upper part of the transgressive phase indicates subsidence across the whole basin. The upper, progradational portion of the basin fill is dominated by coarse, siliciclastic, tide‐influenced deltaic deposits that rapidly prograded from north‐west to south‐east. This detailed study on the Narva succession shows that siliciclastic and carbonate deposition was coeval and that mixing occurred at different temporal and spatial scales. The mixing was controlled by grain‐size, volume and location of siliciclastic input rather than relative sea‐level changes as suggested in widely used reciprocal mixing models. It is suggested that the forebulge of the Scandinavian Caledonian fold‐and‐thrust belt migrated to the north‐western margin of the Baltic Basin during the earliest Eifelian, as indicated by the lack of subsidence and probable uplift in the northern/north‐western margin during the early transgressive phase. The forebulge migration ceased although the forebulge had already started to subside during the later stages of the transgressive phase. The deltaic progradation is interpreted to be associated with the orogenic collapse and uplift in the Scandinavian Caledonides that caused the erosion of the foreland basin fill and the coarse sediment transport into the Baltic Basin.
Design of epidemiological studies measuring genital and plasma HIV‐1 outcomes: lessons from a randomised controlled trial
Authors: Larke Natasha L. , Weiss Helen A. , Mayaud Philippe , Van de Perre Philippe , Clayton Tim , Ouedraogo Abdoulaye , Nagot Nicolas
Published: January 2009

Objective  HIV‐1 genital viral loads have not been extensively used as markers of HIV transmissibility. We set out to determine whether the variability of genital HIV‐1 RNA over time necessitates design adjustments in studies measuring genital shedding to account for this variability.

Methods  We used data from a completed trial of HSV suppressive therapy to estimate the correlation of plasma and genital HIV‐1 RNA quantities sampled at different times. These correlation estimates were used to estimate the relative sample sizes needed to detect an impact on HIV‐1 genital and plasma quantities assuming a variable number of pre‐ and post‐randomisation repeated measurements. The treatment effect on quantities of genital and plasma HIV‐1 RNA were analysed using random effects linear regression.

Results  Post‐randomisation plasma HIV‐1 RNA was highly correlated within‐women, while genital HIV‐1 RNA was less strongly correlated. Related to this, the sample size required to detect a treatment effect on genital HIV‐1 RNA decreased with increasing numbers of post‐randomisation measurements up to 6–7 measurements, but varied less for plasma HIV‐1 RNA. In contrast, repeated pre‐randomisation measurements of plasma HIV‐1 RNA increased study power more than genital HIV‐1 RNA because of the high correlation of plasma HIV‐1 RNA measurements between the pre‐ and post‐randomisation samples. Re‐analysis of the trial data illustrated the increased precision of the treatment effect on genital HIV‐1 with increasing post‐randomisation measurements.

Conclusions  Designs allowing for repeated post‐randomisation measures should be used to increase the precision in estimates of genital HIV‐1 RNA. Repeated post‐randomisation measurements of plasma HIV‐1 RNA are of limited benefit.
Early assessment of the implementation of a national programme for the prevention of mother‐to‐child transmission of HIV in Cameroon and the effects of staff training: a survey in 70 rural health care facilities
Authors: Labhardt Niklaus Daniel , Manga Engelbert , Ndam Mama , Balo Jean‐Richard , Bischoff Alexandre , Stoll Beat
Published: January 2009

Objectives  To assess the availability of equipment and the staff’s knowledge to prevent Mother‐To‐Child Transmission (PMTCT) in rural healthcare facilities recently covered by the national PMTCT programme in Cameroon.

Methods  In eight districts inventories of antiviral drugs and HIV test kits were made on site, using a standardised check‐list. Knowledge of HIV and PMTCT was evaluated with a multiple‐choice (MC) questionnaire based on typical clinical PMTCT cases. Staff participated subsequently in a 2‐day training on HIV/AIDS and the Cameroon PMTCT guidelines. Immediately after training and after 7 months, retention of knowledge was tested with the same questions but in different order and layout.

Results  Sixty two peripheral nurse‐led clinics and the eight district hospitals were assessed. Whereas all district hospitals presented complete equipment, only six of the peripheral clinics (10%) were equipped with both complete testing materials and a full set of drugs to provide PMTCT. Thirty six peripheral facilities (58%) possessed full equipment for HIV‐testing and 8 (13%) stocked all PMTCT drugs. Of 137 nurses, 102 (74%) agreed to the two knowledge tests. Fewer than 66% knew that HIV‐diagnosis requires positive results in two different types of rapid tests and only 19% chose the right recommendation on infant‐feeding for HIV‐positive mothers. Correct answers on drug regimens in different PMTCT settings varied from 25% to 56%. All percentages of correct answers improved greatly with training (P < 0.001) and retention remained high 7 months after training (P < 0.001).

Conclusions  Prevent Mother‐To‐Child Transmission programmes in settings such as rural Cameroon need to be adapted to the special needs of peripheral nurse‐led clinics. Appropriate short training may considerably improve nurses’ competence in PMTCT. Other important components are regular supervision and measures to guarantee supply of equipment in rural areas.
In‐vivo efficacy of amodiaquine‐artesunate in children with uncomplicated Plasmodium falciparum malaria in western Kenya
Authors: Thwing J. I. , Odero C. O. , Odhiambo F. O. , Otieno K. O. , Kariuki S. , Ord R. , Roper C. , McMorrow M. , Vulule J. , Slutsker L. , Newman R. D. , Hamel M. J. , Desai M.
Published: January 2009

Objectives  To assess the efficacy of amodiaquine‐artesunate in an area with high chloroquine resistance in western Kenya.

Methods  Twenty‐eight day in‐vivo efficacy trial of amodiaquine‐artesunate in 103 children aged 6–59 months in western Kenya with smear‐confirmed uncomplicated Plasmodium falciparum malaria.

Results  The 28‐day uncorrected adequate clinical and parasitological response (ACPR) was 69.0%, with 15.5% Late Clinical Failure and 15.5% Late Parasitologic Failure rates. The PCR‐corrected 28‐day ACPR was 90.2%. Clinical risk factors for recurrent infection (recrudescences and reinfections) were lower axillary temperature at enrolment and low weight‐for‐age Z‐score. The presence of single nucleotide polymorphisms pfcrt 76T and pfmdr1 86Y at baseline was associated with increased risk of recurrent infections, both reinfections and recrudescences.

Conclusion  Although artemether‐lumefantrine (Coartem®) is the first line ACT in Kenya, amodiaquine‐artesunate is registered as an option for treatment of uncomplicated P. falciparum and remains an effective alternative to Coartem® in western Kenya. Continued amodiaquine monotherapy in the private sector may jeopardise the future use of amodiaquine‐artesunate as an alternative artemisinin‐based combination therapy.
Cluster‐sample surveys and lot quality assurance sampling to evaluate yellow fever immunisation coverage following a national campaign, Bolivia, 2007
Authors: Pezzoli Lorenzo , Pineda Silvia , Halkyer Percy , Crespo Gladys , Andrews Nick , Ronveaux Olivier
Published: January 2009

Objective  To estimate the yellow fever (YF) vaccine coverage for the endemic and non‐endemic areas of Bolivia and to determine whether selected districts had acceptable levels of coverage (>70%).

Methods  We conducted two surveys of 600 individuals (25 × 12 clusters) to estimate coverage in the endemic and non‐endemic areas. We assessed 11 districts using lot quality assurance sampling (LQAS). The lot (district) sample was 35 individuals with six as decision value (alpha error 6% if true coverage 70%; beta error 6% if true coverage 90%). To increase feasibility, we divided the lots into five clusters of seven individuals; to investigate the effect of clustering, we calculated alpha and beta by conducting simulations where each cluster’s true coverage was sampled from a normal distribution with a mean of 70% or 90% and standard deviations of 5% or 10%.

Results  Estimated coverage was 84.3% (95% CI: 78.9–89.7) in endemic areas, 86.8% (82.5–91.0) in non‐endemic and 86.0% (82.8–89.1) nationally. LQAS showed that four lots had unacceptable coverage levels. In six lots, results were inconsistent with the estimated administrative coverage. The simulations suggested that the effect of clustering the lots is unlikely to have significantly increased the risk of making incorrect accept/reject decisions.

Conclusions  Estimated YF coverage was high. Discrepancies between administrative coverage and LQAS results may be due to incorrect population data. Even allowing for clustering in LQAS, the statistical errors would remain low. Catch‐up campaigns are recommended in districts with unacceptable coverage.
Population genetic analysis of microsatellite variation of guppies (Poecilia reticulata) in Trinidad and Tobago: evidence for a dynamic source–sink metapopulation structure, founder events and population bottlenecks
Authors: BARSON N. J. , CABLE J. , VAN OOSTERHOUT C.
Published: January 2009

Riverine fish populations are traditionally considered to be highly structured and subject to strong genetic drift. Here, we use microsatellites to analyse the population structure of the guppy (Poecilia reticulata), focussing on the headwater floodplain area of the Caroni drainage in Trinidad. We also analyse the population genetics of guppies in the Northern Drainage in Trinidad, a habitat characterized by rivers flowing directly into the sea, and a small isolated population in Tobago. Upland Caroni populations are highly differentiated and display low levels of genetic diversity. However, we found no evidence to suggest that these upland populations experienced recent population crashes and the populations appear to approach mutation–drift equilibrium. Dominant downstream migration over both short‐ and long‐time frames has a strong impact on the population genetics of lowland Caroni populations. This drainage system could be considered a source–sink metapopulation, with the tributary furthest downstream representing a ‘super sink’, receiving immigrants from rivers upstream in the drainage. Moreover, the effective population size in the lowlands is surprisingly low in comparison with the apparently large census population sizes.
Capturing the superorganism: a formal theory of group adaptation
Authors: GARDNER A. , GRAFEN A.
Published: January 2009

Adaptation is conventionally regarded as occurring at the level of the individual organism. However, in recent years there has been a revival of interest in the possibility for group adaptations and superorganisms. Here, we provide the first formal theory of group adaptation. In particular: (1) we clarify the distinction between group selection and group adaptation, framing the former in terms of gene frequency change and the latter in terms of optimization; (2) we capture the superorganism in the form of a ‘group as maximizing agent’ analogy that links an optimization program to a model of a group‐structured population; (3) we demonstrate that between‐group selection can lead to group adaptation, but only in rather special circumstances; (4) we provide formal support for the view that between‐group selection is the best definition for ‘group selection’; and (5) we reveal that mechanisms of conflict resolution such as policing cannot be regarded as group adaptations.
The shape of pterosaur evolution: evidence from the fossil record
Authors: DYKE G. J. , MCGOWAN A. J. , NUDDS R. L. , SMITH D.
Published: January 2009

Abstract Although pterosaurs are a well‐known lineage of Mesozoic flying reptiles, their fossil record and evolutionary dynamics have never been adequately quantified. On the basis of a comprehensive data set of fossil occurrences correlated with taxon‐specific limb measurements, we show that the geological ages of pterosaur specimens closely approximate hypothesized patterns of phylogenetic divergence. Although the fossil record has expanded greatly in recent years, collectorship still approximates a sigmoid curve over time as many more specimens (and thus taxa) still remain undiscovered, yet our data suggest that the pterosaur fossil record is unbiased by sites of exceptional preservation (lagerstätte). This is because as new species are discovered the number of known formations and sites yielding pterosaur fossils has also increased – this would not be expected if the bulk of the record came from just a few exceptional faunas. Pterosaur morphological diversification is, however, strongly age biased: rarefaction analysis shows that peaks of diversity occur in the Late Jurassic and Early Cretaceous correlated with periods of increased limb disparity. In this respect, pterosaurs appear unique amongst flying vertebrates in that their disparity seems to have peaked relatively late in clade history. Comparative analyses also show that there is little evidence that the evolutionary diversification of pterosaurs was in any way constrained by the appearance and radiation of birds.
Condition‐dependent mutation rates and sexual selection
Authors: COTTON S.
Published: January 2009

‘Good genes’ models of sexual selection show that females can gain indirect benefits for their offspring if male ornaments are condition‐dependent signals of genetic quality. Recurrent deleterious mutation is viewed as a major contributor to variance in genetic quality, and previous theoretical treatments of ‘good genes’ processes have assumed that the influx of new mutations is constant. I propose that this assumption is too simplistic, and that mutation rates vary in ways that are important for sexual selection. Recent data have shown that individuals in poor condition can have higher mutation rates, and I argue that if both male sexual ornaments and mutation rates are condition‐dependent, then females can use male ornamentation to evaluate their mate’s mutation rate. As most mutations are deleterious, females benefit from choosing well‐ornamented mates, as they are less likely to contribute germline‐derived mutations to offspring. I discuss some of the evolutionary ramifications of condition‐dependent mutation rates and sexual selection.
Die Mittlere Lebensdauer Der Veterinäranatomen an Deutschsprachigen, Tierärztlichen Bildungsstätten
Authors: Vollmerhaus B. , Vollmerhaus R. , Roos H. , Knospe C. , Reese S.
Published: January 2009

The average lifespan of veterinary anatomists was statistically analysed. All teachers who ever taught veterinary anatomy (formerly ‘zootomy’) and histology/embryology separately or in combination with other subjects in Germany, Austria and Switzerland were included in that circle. The observation period was from the foundation of the veterinary schools up to the present. We find that the average lifespan of this specific group is not different from that of the general population. Comparable previous opinions on the lifespan of anatomists, estimated as shorter than that of the general population by Hyrtl, and longer by Voss, are incorrect. This opportunity is also used to mention our time‐honored; especially the early completed and aged colleagues.
The Relationship Between Foraging Ecology and Lizard Chemoreception: Can a Snake Analogue (Burton’s Legless Lizard,Lialis burtonis) Detect Prey Scent?
Authors: Wall Michael , Shine Richard
Published: January 2009

In lizards and snakes, foraging mode (active vs. ambush) is highly correlated with the ability to detect prey chemical cues, and the way in which such cues are utilized. Ambush‐foraging lizards tend not to recognize prey scent, whereas active foragers do. Prey scent often elicits strikes in actively‐foraging snakes, while ambushers use it to select profitable foraging sites. We tested the influence of foraging ecology on the evolution of squamate chemoreception by gauging the response of Burton’s legless lizard (Lialis burtonisGray, Pygopodidae) to prey chemical cues.Lialis burtonisis the ecological equivalent of an ambush‐foraging snake, feeding at infrequent intervals on relatively large prey, which are swallowed whole. CaptiveL. burtonisdid not respond to prey odour in any manner: prey chemical cues did not elicit elevated tongue‐flick rates or feeding strikes, nor were they utilized in the selection of ambush sites. Like other ambushing lizards,L. burtonisappears to be a visually oriented predator. In contrast, an active forager in the same family, the common scaly‐foot (Pygopus lepidopodus), did tongue‐flick in response to odours of its preferred prey. These results extend the correlation between lizard foraging mode and chemosensory abilities to a heretofore‐unstudied family, the Pygopodidae.
Predation Risks and Anti‐Predation Parental Care Behavior: An Experimental Study in a Tropical Skink
Authors: Huang Wen‐san , Wang Hurng‐Yi
Published: January 2009

The process of parental care can be complex, and it is rarely exhibited by reptiles. How predators influence the timing of parental care is still ambiguous in terrestrial vertebrates. In this study, we demonstrate that female skinks of Mabuya longicaudata adjusted to an experimental manipulation of interspecific intruders which were placed into skink nests. When the intrusion frequency of the reptile‐egg eating snake, Oligodon formosanus, increased, the time spent on maternal care by M. longicaudata was significantly extended. In contrast, female M. longicaudata recognized two sympatric lizards (Sphenomorphus incognitus and Japalura swinhonis) which do not prey upon eggs or adults of M. longicaudata and did not attack those species; consequently, the time spent on egg‐guarding did not significantly differ from the control treatment with intrusion by S. incognitus or J. swinhonis. Mabuya longicaudata also recognized the predatory snake, Elaphe carinata, and when that species entered a skink nest, the skink escaped and never returned. These results emphasize that the time spent on parental care is probably influenced by predators, and the duration of this behavior is dependent on the maternal defensive capability. As egg guarding is the most basic and primitive form of parental care, the current study provides evidence possibly leading to insights into the origin of parental care from reptiles to birds and mammals.
Lack of Sex‐Biased Maternal Investment in spite of a Skewed Birth Sex Ratio in White‐Headed Langurs (Trachypithecus leucocephalus)
Authors: Zhao Qing , Jin Tong , Wang Dezhi , Qin Dagong , Yin Lijie , Ran Wenzhong , Pan Wenshi
Published: January 2009

Numerous hypotheses have been developed to explain sex allocation. In male‐dispersing, female cooperatively breeding species, the local resource competition model predicts male‐biased birth sex ratio, the local resource enhancement model predicts female‐biased birth sex ratio, and the population adjustment model predicts that biased birth sex ratio should not be favored if the two sexes are equally costly to rear. The male quality model predicts that, in polygynous species, females in better physical condition will either produce more sons than daughters or invest more heavily in sons than in daughters. White‐headed langurs are a female philopatry and female cooperatively breeding species. During a 11‐yr study, a total of 133 births were recorded, among which birth sex ratio (M:F = 73:49) was significantly male‐biased. This is consistent with the prediction of the local resource competition model. On the other hand, if mothers balanced their investment between the two sexes, according to Fisher’s population adjustment model, males should be the less‐costly‐to‐rear sex. However, we found no sex difference for infant mortality (12.3% in males and 12.2% in females), and sons induced slightly longer interbirth interval (son: 26.4 ± 1.1 mo, daughter: 24.1 ± 0.6 mo) and lactational period (son: 20.9 ± 1.0 mo, daughters: 19.6 ± 0.5 mo) for their mothers. Thus, the population adjustment model was not supported by this study. The local resource enhancement model was not supported because birth sex ratio did not bias to females who provided more reproductive assistance. On the individual level, probit regression showed no relation between birth sex ratio and group size. Because the group size was considered to be negatively related to female physical condition, our study did not support the male‐quality model. We suggested several possibilities to explain these results.
Current practice of antifungal prophylaxis and treatment in immunocompromised children and adults with malignancies: a single centre approach
Authors: Lehrnbecher Thomas , Mousset Sabine , Sörensen Jan , Böhme Angelika
Published: January 2009

Although various guidelines on antifungal prophylaxis and treatment have been published, the practical approach in the individual clinical setting might considerably differ because of special local circumstances. In addition, there are major differences between paediatric and adult patients regarding antifungal strategies and the use of antifungal compounds. We here present the antifungal approach in the Departments of Hematology and Oncology of the University Hospital of Frankfurt, where per year approximately 350 children and adults are diagnosed with cancer and an additional 100 patients undergo haematopoietic stem cell transplantation. The differences in the approach between the paediatric and adult setting are highlighted.
Cross‐reactivity among fungal allergens: a clinically relevant phenomenon?
Authors: Crameri Reto , Zeller Sabine , Glaser Andreas G. , Vilhelmsson Monica , Rhyner Claudio
Published: January 2009

Atopic patients suffering from allergic asthma, allergic rhinitis, or atopic eczema often have detectable levels of serum IgE antibodies to fungi. Although the association between fungal sensitisation and different forms of allergic diseases, including allergic asthma and life‐threatening allergic bronchopulmonary aspergillosis, is well established, the clinical relevance of cross‐reactivity among different fungal species remains largely unknown. Recent progress in molecular cloning of fungal allergens and the availability of more than 40 completely sequenced fungal genomes facilitates characterisation, cloning, and production of highly pure recombinant allergens, identification of homologous and orthologous allergens widespread among the fungal kingdom, in silico prediction, and experimental in vitro and in vivo verification of cross‐reactivity between homologous pan‐allergens. These studies indicate that cross‐reactivity is an important component of fungal sensitisation.