bluuebunny/crossref_metadata_2025 huggingface dataset:
Combined effects of acidification and competition on the feeding preference of a freshwater macroinvertebrate, Asellus aquaticus (Crustacea:Isopoda): a laboratory experiment
Authors: Costantini M. L. , Mancinelli G. , Mandrone S. , Rossi L.
Published: November 2005

To determine the combined effects of stream acidification and competition on the feeding preferences of benthic detritivores we compared, before and after sublethal acid exposure, lab-cultured populations of Asellus aquaticus reared either singly or with the closely related species Proasellus coxalis sensu lato in artificial channels. Both abiotic and biotic stressors reduced A. aquaticus density and affected its food intake. Whereas the presence of P. coxalis sensu lato increased the mass-specific ingestion rate and niche breadth of A. aquaticus according to optimal foraging theory, ingestion rate was reduced following acid exposure. Despite the increased variability in the consumption rate, variability of diet composition among individuals of A. aquaticus declined after acidification above all in the presence of the other species. Resource preferences changed, as a possible result of physiological accommodation to stress and/or selection of individuals that preferentially consumed the most processed plant detritus. The symmetry of niche overlap between the two species increased, strengthening the risk of competitive exclusion of A. aquaticus. The presence of the detritivores increased the buffering capacity of the artificial channels, reducing the rate at which the temporary hardness declined.
Linking male and female morphology to reproductive success in captive southern calamary (Sepioteuthis australis)
Authors: van Camp L. M. , Fairweather P. G. , Steer M. A. , Donnellan S. C. , Havenhand J. N.
Published: November 2005

Sexual selection theory predicts that mating success influences the evolution of traits. Previous behavioural observations of male Sepioteuthis australis have revealed two main mating strategies in the field: (1) large dominant males pair and mate with females, which they defend from (2) smaller males attempting to mate using ‘sneaker’ tactics. The current study examined whether fertilisation of squid eggs laid by polyandrous females within a mesocosm reflected this field-observed size-based mating system. Polymorphic microsatellite loci were used to identify mothers and fathers of embryos, which in turn allowed us to determine the effect of body size, age, and nine other morphological traits on reproductive success. Parentage of 112 embryos was assigned among 14 possible females and 20 candidate males of varying sizes. The mating behaviour observed in captivity was consistent with the size-based strategies seen in the field yet large males did not sire proportionally more offspring; instead nearly all males, regardless of size, sired some offspring. Regression analyses indicated that females did not select sperm based on male size, shape or age. Surprisingly, female contributions were skewed, with younger females contributing more eggs than older females. The possibility of male mate-choice was explored.
Biofilm formation and phenotypic variation enhance predation-driven persistence of
Vibrio cholerae
Authors: Matz Carsten , McDougald Diane , Moreno Ana Maria , Yung Pui Yi , Yildiz Fitnat H. , Kjelleberg Staffan
Published: November 2005

Persistence of the opportunistic bacterial pathogen
Vibrio cholerae
in aquatic environments is the principal cause for seasonal occurrence of cholera epidemics. This causality has been explained by postulating that
V. cholerae
forms biofilms in association with animate and inanimate surfaces. Alternatively, it has been proposed that bacterial pathogens are an integral part of the natural microbial food web and thus their survival is constrained by protozoan predation. Here, we report that both explanations are interrelated. Our data show that biofilms are the protective agent enabling
V. cholerae
to survive protozoan grazing while their planktonic counterparts are eliminated. Grazing on planktonic
V. cholerae
was found to select for the biofilm-enhancing rugose phase variant, which is adapted to the surface-associated niche by the production of exopolymers. Interestingly, grazing resistance in
V. cholerae
biofilms was not attained by exopolymer production alone but was accomplished by the secretion of an antiprotozoal factor that inhibits protozoan feeding activity. We identified that the cell density-dependent regulator
hapR
controls the production of this factor in biofilms. The inhibitory effect of
V. cholerae
biofilms was found to be widespread among toxigenic and nontoxigenic isolates. Our results provide a mechanistic explanation for the adaptive advantage of surface-associated growth in the environmental persistence of
V. cholerae
and suggest an important contribution of protozoan predation in the selective enrichment of biofilm-forming strains in the out-of-host environment.
Computational docking and solution x-ray scattering predict a membrane-interacting role for the histone domain of the Ras activator son of sevenless
Authors: Sondermann Holger , Nagar Bhushan , Bar-Sagi Dafna , Kuriyan John
Published: November 2005

The Ras-specific nucleotide exchange factor son of sevenless (SOS) is a large, multidomain protein with complex regulation, including a Ras-dependent allosteric mechanism. The N-terminal segment of SOS, the histone domain, contains two histone folds, which is highly unusual for a cytoplasmic protein. Using a combination of computational docking, small-angle x-ray scattering, mutagenesis, and calorimetry, we show that the histone domain folds into the rest of SOS and docks onto a helical linker that connects the pleckstrin-homology (PH) and Dbl-homology (DH) domains of SOS to the catalytic domain. In this model, a positively charged surface region on the histone domain is positioned so as to provide a fourth potential anchorage site on the membrane for SOS in addition to the PH domain, the allosteric Ras molecule, and the C-terminal adapter-binding site. The histone domain in SOS interacts with the helical linker, using a region of the surface that in nucleosomes is involved in histone tetramerization. Adjacent surface elements on the histone domain that correspond to the DNA-binding surface of nucleosomes form the predicted interaction site with the membrane. The orientation and position of the histone domain in the SOS model implicates it as a potential mediator of membrane-dependent activation signals.
Conjugated linoleic acid increased C-reactive protein in human subjects
Authors: Smedman Annika , Basu Samar , Jovinge Stefan , Fredrikson Gunilla Nordin , Vessby Bengt
Published: November 2005

We previously showed that conjugated linoleic acid (CLA) increases 15-keto-dihydro-prostaglandin F2α, a marker for cyclooxygenase-mediated lipid peroxidation and thus an indicator of cyclooxygenase-mediated inflammation. The aim of the present study was to investigate the effects of CLA on other indicators of inflammation in human subjects, including C-reactive protein, TNF-α, TNF-α receptors 1 and 2, and vascular cell adhesion molecule-1. In a double-blind, placebo-controlled study, fifty-three human subjects were supplemented with a mixture (4·2g/d) of the isomers cis-9,trans-11 CLA and trans-10,cis-12 CLA or control oil for 3 months. CLA supplementation increased levels of C-reactive protein (P=0·003) compared with the control group. However, no changes in TNF-α, TNF-α receptors 1 and 2, and vascular cell adhesion molecule-1 were detected.
Conjugated linoleic acid enhanced the immune function in broiler chicks
Authors: Zhang Haijun , Guo Yuming , Yuan Jianmin
Published: November 2005

This study was undertaken to investigate the growth performance and immune responses of broiler chicks fed diets supplemented with conjugated linoleic acid (CLA). Two hundred and forty day-old Arbor Acre male broiler chicks were randomly allotted into four dietary treatments with different inclusion levels of CLA (0, 2·5, 5·0 or 10·0g pure CLA/kg) for 6 weeks. Growth performance, lysozyme activity, peripheral blood mononuclear cell (PBMC) proliferation, prostaglandin E2(PGE2) synthesis and antibody production were investigated. There were no significant differences in growth performance among treatments (P>0·05). Chicks fed 10·0g CLA/kg diet produced 40% and 49% more lysozyme activity in serum and spleen than the control group at 21d of age (P<0·05). Dietary CLA enhanced the PBMC proliferation in response to concanavalin A at the age of 21 and 42d (P<0·05). Systemic and peripheral blood lymphocytic synthesis of PGE2in chicks fed 10·0g CLA/kg diet was significantly decreased by 57% and 42% compared to chicks fed control diet (P<0·05). Antibody production to sheep red blood cell and bovine serum albumin were elevated in either 2·5 or 10·0g CLA/kg dietary treatments (P<0·05). The results indicated dietary CLA could enhance the immune response in broiler chicks, but did not alter the growth performance.
Protein recycling in growing rabbits: contribution of microbial lysine to amino acid metabolism
Authors: Belenguer Álvaro , Balcells Joaquim , Guada Jose A. , Decoux Marc , Milne Eric
Published: November 2005

To study the absorption of microbial lysine in growing rabbits, a labelled diet (supplemented with15NH4Cl) was administered to six animals (group ISOT); a control group (CTRL, four rabbits) received a similar, but unlabelled, diet. Diets were administered for 30d. An additional group of six animals were fed the unlabelled diet for 20d and then the labelled diet for 10d while wearing a neck collar to avoid caecotrophy (group COLL), in order to discriminate it from direct intestinal absorption. At day 30 animals were slaughtered and caecal bacteria and liver samples taken. The15N enrichment in amino acids of caecal bacteria and liver were determined by GC–combustion/isotope ratio MS. Lysine showed a higher enrichment in caecal microflora (0·925 atom% excess, APE) than liver (0·215 APE) in group ISOT animals, confirming the double origin of body lysine: microbial and dietary. The COLL group showed a much lower enrichment in tissue lysine (0·007 (se 0·0029) APE for liver). Any enrichment in the latter animals was due to direct absorption of microbial lysine along the digestive tract, since recycling of microbial protein (caecotrophy) was avoided. In such conditions liver enrichment was low, indicating a small direct intestinal absorption. From the ratio of [15N]lysine enrichment between liver and bacteria the contribution of microbes to body lysine was estimated at 23%, with 97% of this arising through caecotrophy. Absorption of microbial lysine through caecotrophy was 119 (se 4·0) mg/d, compared with 406 (se 1·8) mg/d available from the diet. This study confirms the importance of caecotrophy in rabbit nutrition (15% of total protein intake).
Effect of aerobic exercise on lipaemia and its fatty acid profile after a meal of moderate fat content in eumenorrhoeic women
Authors: Kokalas Nikos , Petridou Anatoli , Nikolaidis Michalis G. , Mougios Vassilis
Published: November 2005

Exercise prior to eating has repeatedly been shown to reduce postprandial lipaemia. The aim of the present study was to investigate whether this effect was manifest in the presence of two factors that independently mitigate postprandial lipaemia: eumenorrhoea and moderate fat intake. Eight healthy eumenorrhoeic rowers consumed a meal of moderate fat content (35% total energy, 0·66g/kg body mass) 14h after having either rowed at 55% of maximal aerobic power (81% of maximal heart rate) for 80min or rested. Both trials were performed during the luteal phase. Blood samples were drawn before the meal and for 8h postprandially for the measurement of individual fatty acids in the triacylglycerol and NEFA fractions, as well as of glucose, insulin and oestradiol. Plasma oestradiol concentrations were not significantly different in the two trials. The postprandial lipaemic response, expressed as either plasma triacylglycerol concentration or area under the triacylglycerol–time curve, was 35% lower (P<0·05) after exercise. The postprandial glycaemic and insulinaemic responses were also lower, indicating increased insulin sensitivity, whereas the NEFA response was higher, suggesting a lower entrapment of dietary fatty acids in adipose tissue after exercise. Finally, exercise increased the proportion of unsaturated:saturated NEFA during the postprandial period. In conclusion, aerobic exercise performed 14h before a moderate-fat meal reduced postprandial lipaemia in women in the luteal phase. This effect shows the potential of exercise to mitigate even moderate lipaemic responses in eumenorrhoeic women.
Glycaemic index and glycaemic load in the diet of healthy schoolchildren: trends from 1990 to 2002, contribution of different carbohydrate sources and relationships to dietary quality
Authors: Buyken Anette E. , Dettmann Wiebke , Kersting Mathilde , Kroke Anja
Published: November 2005

Despite intense discussion of the glycaemic index (GI) and glycaemic load (GL) concepts, data on the GI or GL levels in the diet of children are scarce. The present analysis determined trends in the levels of GI or GL of healthy children from 1990 to 2002 and examined the contribution of carbohydrate (CHO) sources to the overall GL, and the relationships of the GI and GL to the overall dietary quality. The analysis includes three cohorts of participants from the Dortmund Nutritional and Anthropometrical Longitudinally Designed study, aged 7–8 years in 1990 (n 53), 1996 (n 46) and 2002 (n 56). A GI value was assigned to all CHO foods recorded over three consecutive days. In comparison with 1990, 7–8-year-old children in 2002 had slightly higher GI (56·5 v. 55·1%; P=0·03) and GL (17·5 v. 16·7g/MJ; P=0·04) levels. In all three time periods the combined contribution of the ‘tolerated food groups’ (i.e. sweets, soft drinks, cakes and cookies, and salty snacks) to the overall GL exceeded that of bread and rolls (1990, 31 v. 24%; 1996, 29 v. 31%; 2002, 28 v. 25%). Conversely, rice and fried or mashed potatoes had only a minor impact. Children in the lowest GI tertile, but not those in the lowest GL tertile, had a better nutrient profile and a more favourable food choice. In conclusion, partial replacement of high-GI ‘tolerated food groups’ for low-GI foods would help to reverse the slight recent increases in GI and GL, and to improve the overall dietary quality of 7–8-year-old children.
A provisional database for the silicon content of foods in the United Kingdom
Authors: Powell J. J. , McNaughton S. A. , Jugdaohsingh R. , Anderson S. H. C. , Dear J. , Khot F. , Mowatt L. , Gleason K. L. , Sykes M. , Thompson R. P. H. , Bolton-Smith C. , Hodson M. J.
Published: November 2005

Si may play an important role in bone formation and connective tissue metabolism. Although biological interest in this element has recently increased, limited literature exists on the Si content of foods. To further our knowledge and understanding of the relationship between dietary Si and human health, a reliable food composition database, relevant for the UK population, is required. A total of 207 foods and beverages, commonly consumed in the UK, were analysed for Si content. Composite samples were analysed using inductively coupled plasma–optical emission spectrometry following microwave-assisted digestion with nitric acid and H2O2. The highest concentrations of Si were found in cereals and cereal products, especially less refined cereals and oat-based products. Fruit and vegetables were highly variable sources of Si with substantial amounts present in Kenyan beans, French beans, runner beans, spinach, dried fruit, bananas and red lentils, but undetectable amounts in tomatoes, oranges and onions. Of the beverages, beer, a macerated whole-grain cereal product, contained the greatest level of Si, whilst drinking water was a variable source with some mineral waters relatively high in Si. The present study provides a provisional database for the Si content of UK foods, which will allow the estimation of dietary intakes of Si in the UK population and investigation into the role of dietary Si in human health.
Effect of acetic acid feeding on the circadian changes in glycogen and metabolites of glucose and lipid in liver and skeletal muscle of rats
Authors: Fushimi Takashi , Sato Yuzo
Published: November 2005

The aim of the present study is to investigate the effect of acetic acid feeding on the circadian changes in glycogen concentration in liver and skeletal muscle. Rats were provided meal once daily (09.00–13.00 hours) for 10d. On the 11th day, they were either killed immediately or given 9g diet containing either 0 (control) or 0·7g/kg-diet acetic acid beginning at 09.00 hours for 4h, as in the previous regimen. Rats in the fed group were killed at 4, 8 or 24h after the start of feeding. At 4h after the start of feeding, the acetic acid group had significantly greater liver and gastrocnemius muscle glycogen concentrations (P<0·05). Also, at this same point, liver xylulose-5-phosphate, a key stimulator of glycolysis, the ratio of fructose-1,6-bisphosphate to fructose-6-phosphate in skeletal muscle, which reflects phosphofructokinase-1 activity, and liver malonyl-CoA, an allosteric inhibitor of carnitine palmitoyl-transferase, were significantly lower in the acetic acid group than in the control group (P<0·05). In addition, the acetic acid group had a significantly lower serum lactate concentration and lower ratio of insulin to glucagon than the control group at the same point (P<0·05). We conclude that a diet containing acetic acid may enhance glycogen repletion but not induce supercompensation, a large increase in the glycogen level that is beneficial in improving performance, in liver and skeletal muscle by transitory inhibition of glycolysis. Further, we indicate the possibility of a transient enhancement of fatty acid oxidation in liver by acetic acid feeding.
Humoral defence improvement and haematopoiesis stimulation in sows and offspring by oral supply of shark-liver oil to mothers during gestation and lactation
Authors: Mitre Romain , Etienne Michel , Martinais Sophie , Salmon Henri , Allaume Patrick , Legrand Philippe , Legrand Alain B.
Published: November 2005

Shark-liver oil (SLO) contains two bioactive lipids: alkylglycerols andn-3 PUFA. Alkylglycerols have immunostimulating and haematopoietic properties, whilen-3 PUFA are essential for optimal neonatal development. We investigated the beneficial effects of dietary supplementation with 32g SLO/d to twelve pregnant and then lactating sows (from day 80 of pregnancy to weaning) on the growth and immune status of their offspring, compared with a control group. Sows were vaccinated against Aujeszky's disease 21d before term. Blood samples were collected from sows before treatment, on delivery and 14d later, and from five piglets per litter on days 2, 21 and 36 after birth; colostrum and milk samples were collected 12h, 14 and 28d postpartum. Compared with controls, supplemented sows had higher levels of both erythrocytes and Hb in their blood, and higher concentrations of IgG, alkylglycerols andn-3 PUFA in their mammary secretions. In piglets from supplemented sows, leucocytes and IgG were higher. Supplementation with SLO resulted in an increase in Aujeszky antibodies in both blood and colostrum of sows after vaccination, together with an increase in Aujeszky antibodies in piglet blood. Our findings demonstrate that improvement of both passive and active immune status in piglets is related to the consumption of alkylglycerols associated withn-3 PUFA in the sow diet. The overall improvement in offspring health status by SLO supplementation to the mother could be of interest for optimisation of the lipid diet during and after pregnancy.
Online submission and peer‐review systems
Authors: Ware Mark
Published: November 2005

We report on a research study commissioned by ALPSP into the current status of online submission and peer‐review systems, the perceptions of these by authors, referees and editors, and the impact of their introduction on journals.
The Big Deal — ten years on
Authors: Nicholas David , Huntington Paul , Russell Bill , Watkinson Anthony , Jamali Hamid R. , Tenopir Carol
Published: November 2005

This paper describes the highlights of an exploratory deep log analysis of journal usage on OhioLINK, conducted as part of the MaxData project. OhioLINK, the original ‘Big Deal’, provides a single digital platform of nearly 6,000 full‐text journals for more than 600,000 people in Ohio and the investigation aimed to assess it after approximately 10 years. The data was generated from an SPSS analysis of the raw (unprocessed) server logs for June 2004 to December 2004. Approximately 1,215,000 items were viewed on campus in October 2004 and 1,894,000 items viewed off campus between June and December 2004. There are a number of usage analyses including: demand and activity; number and name of journal; date of publication; subject/discipline of journal and method of searching/navigating.
Review
Authors: Parker Robert
Published: November 2005

The Attitudes of Chinese Academics to Foreign Scholarly Journals; Part 1 – Report, Part 2 – Appendices. Global Publishing Information (Publishers Association and the British Council) March 2005. Free to ALPSP and PA members; £249 to others.
Challenges and opportunities: China's university presses in transition
Authors: Liping Wang
Published: November 2005

An account is given of the history of university presses in China since their inception in the early 1980s. Some have become very large publishing houses. Their position now, in the face of further economic reforms and proposals for commercialization, coupled with the removal of fiscal and other protections, is also considered.
Scholarly journal publishing in New Zealand
Authors: Rowland Fytton
Published: November 2005

Learned societies and other non‐profit organizations in New Zealand publish scholarly journals in a number of disciplines, many of them subjects in which New Zealand has a particular economic interest. Although most of the journals are small, a surprising number of them have paid, rather than voluntary academic, editors. Some have launched electronic versions, but only one has experimented with open access (OA). In a number of cases this lack of interest in OA is because the society cannot see a business model that would render the society as a whole economically viable. Some of the smallest journals, published only annually, may have the most assured future because their operation is entirely voluntary.
Characterization of anERADGene asVPS30/ATG6Reveals Two Alternative and Functionally Distinct Protein Quality Control Pathways: One for Soluble Z Variant of Human α-1 Proteinase Inhibitor (A1PiZ) and Another for Aggregates of A1PiZ
Authors: Kruse Kristina B. , Brodsky Jeffrey L. , McCracken Ardythe A.
Published: November 2005

The Z variant of human α-1 proteinase inhibitor (A1PiZ) is a substrate for endoplasmic reticulum-associated protein degradation (ERAD). To identify genes required for the degradation of this protein, A1PiZ degradation-deficient (add) yeast mutants were isolated. The defect in one of these mutants, add3, was complemented by VPS30/ATG6, a gene that encodes a component of two phosphatidylinositol 3-kinase (PtdIns 3-kinase) complexes: complex I is required for autophagy, whereas complex II is required for the carboxypeptidase Y (CPY)-to-vacuole pathway. We found that upon overexpression of A1PiZ, both PtdIns 3-kinase complexes were required for delivery of the excess A1PiZ to the vacuole. When the CPY-to-vacuole pathway was compromised, A1PiZ was secreted; however, disruption of autophagy led to an increase in aggregated A1PiZ rather than secretion. These results suggest that excess soluble A1PiZ transits the secretion pathway to the trans-Golgi network and is selectively targeted to the vacuole via the CPY-to-vacuole sorting pathway, but excess A1PiZ that forms aggregates in the endoplasmic reticulum is targeted to the vacuole via autophagy. These findings illustrate the complex nature of protein quality control in the secretion pathway and reveal multiple sites that recognize and sort both soluble and aggregated forms of aberrant or misfolded proteins.
CAR-1, a Protein That Localizes with the mRNA Decapping Component DCAP-1, Is Required for Cytokinesis and ER Organization inCaenorhabditis elegansEmbryos
Authors: Squirrell Jayne M. , Eggers Zachary T. , Luedke Nancy , Saari Bonnie , Grimson Andrew , Lyons Gary E. , Anderson Philip , White John G.
Published: November 2005

The division of one cell into two requires the coordination of multiple components. We describe a gene, car-1, whose product may provide a link between disparate cellular processes. Inhibition of car-1 expression in Caenorhabditis elegans embryos causes late cytokinesis failures: cleavage furrows ingress but subsequently regress and the spindle midzone fails to form, even though midzone components are present. The localized accumulation of membrane that normally develops at the apex of the cleavage furrow during the final phase of cytokinesis does not occur and organization of the endoplasmic reticulum is aberrant, indicative of a disruption in membrane trafficking. The car-1 gene has homologues in a number of species, including proteins that associate with RNA binding proteins. CAR-1 localizes to P-granules (germ-line specific ribonucleoprotein particles) and discrete, developmentally regulated cytoplasmic foci. These foci also contain DCAP-1, a protein involved in decapping mRNAs. Thus, CAR-1, a protein likely to be associated with RNA metabolism, plays an essential role in the late stage of cytokinesis, suggesting a novel link between RNA, membrane trafficking and cytokinesis in the C. elegans embryo.
Sequence-based heuristics for faster annotation of non-coding RNA families
Authors: Weinberg Zasha , Ruzzo Walter L.
Published: November 2005

Motivation: Non-coding RNAs (ncRNAs) are functional RNA molecules that do not code for proteins. Covariance Models (CMs) are a useful statistical tool to find new members of an ncRNA gene family in a large genome database, using both sequence and, importantly, RNA secondary structure information. Unfortunately, CM searches are extremely slow. Previously, we created rigorous filters, which provably sacrifice none of a CM's accuracy, while making searches significantly faster for virtually all ncRNA families. However, these rigorous filters make searches slower than heuristics could be.

Results: In this paper we introduce profile HMM-based heuristic filters. We show that their accuracy is usually superior to heuristics based on BLAST. Moreover, we compared our heuristics with those used in tRNAscan-SE, whose heuristics incorporate a significant amount of work specific to tRNAs, where our heuristics are generic to any ncRNA. Performance was roughly comparable, so we expect that our heuristics provide a high-quality solution that—unlike family-specific solutions—can scale to hundreds of ncRNA families.

Availability: The source code is available under GNU Public License at the supplementary web site.

Contact:  zasha@cs.washington.edu

Supplementary information:   (Technical details, results, C++ code)
mILD: a tool for constructing and analyzing matrices of pairwise phylogenetic character incongruence tests
Authors: Planet Paul J. , Sarkar Indra Neil
Published: November 2005

Summary: Pairwise comparisons of disagreement in phylogenetic datasets offer a powerful tool for isolating historical incongruence for closer analysis. Statistically significant phylogenetic character incongruence may reflect important differences in evolutionary history, such as horizontal gene transfer. Such testing can also be used to specify possible combinations of datasets for further phylogenetic analysis. The process of comparing multiple datasets can be very time consuming, and it is sometimes unclear how to combine data partitions given the observed patterns of incongruence. Here we present an application that automates the process of making pairwise comparisons between large numbers of phylogenetic datasets using the Incongruence Length Difference (ILD) test. The application also implements strategies for data combination based on the patterns of incongruence observed in pairwise comparisons.

Availability: The application is freely available as a Perl script that interacts with the command-line version of PAUP*.

Contact:  sarkar@amnh.org

Supplementary information:
Improved spliced alignment from an information theoretic approach
Authors: Zhang Miao , Gish Warren
Published: November 2005

Motivation: mRNA sequences and expressed sequence tags represent some of the most abundant experimental data for identifying genes and alternatively spliced products in metazoans. These transcript sequences are frequently studied by aligning them to a genomic sequence template. For existing programs, error-prone, polymorphic and cross-species data, as well as non-canonical splice sites, still present significant barriers to producing accurate, complete alignments.

Results: We took a novel approach to spliced alignment that meaningfully combined information from sequence similarity with that obtained from PSSM splice site models. Scoring systems were chosen to maximize their power of discrimination, and dynamic programming (DP) was employed to guarantee optimal solutions would be found. The resultant program, EXALIN, performed better than other popular tools tested under a wide range of conditions that included detection of micro-exons and human–mouse cross-species comparisons. For improved speed with only a marginal decrease in splice site prediction accuracy, EXALIN could perform limited DP guided by a result from BLASTN.

Availability: The source code, binaries, scripts, scoring matrices and splice site models for human, mouse, rice and Caenorhabditis elegans utilized in this study are posted at . The software (scripts, source code and binaries) is copyrighted but free for all to use.

Contact:  gish@blast.wustl.edu

Supplementary information:
BioThesaurus: a web-based thesaurus of protein and gene names
Authors: Liu Hongfang , Hu Zhang-Zhi , Zhang Jian , Wu Cathy
Published: November 2005

BioThesaurus is a web-based system designed to map a comprehensive collection of protein and gene names to protein entries in the UniProt Knowledgebase. Currently covering more than two million proteins, BioThesaurus consists of over 2.8 million names extracted from multiple molecular biological databases according to the database cross-references in iProClass. The BioThesaurus web site allows the retrieval of synonymous names of given protein entries and the identification of protein entries sharing the same names.

Availability: BioThesaurus is accessible for online searching at

Contact: hfliu@umbc.edu

Supplementary information: Supplementary data are accessible at
SSEP-Domain: protein domain prediction by alignment of secondary structure elements and profiles
Authors: Gewehr Jan E. , Zimmer Ralf
Published: November 2005

Motivation: The prediction of protein domains is a crucial task for functional classification, homology-based structure prediction and structural genomics. In this paper, we present the SSEP-Domain protein domain prediction approach, which is based on the application of secondary structure element alignment (SSEA) and profile–profile alignment (PPA) in combination with InterPro pattern searches. SSEA allows rapid screening for potential domain regions while PPA provides us with the necessary specificity for selecting significant hits. The combination with InterPro patterns allows finding domain regions without solved structural templates if sequence family definitions exist.

Results: A preliminary version of SSEP-Domain was ranked among the top-performing domain prediction servers in the CASP 6 and CAFASP 4 experiments. Evaluation of the final version shows further improvement over these results together with a significant speed-up.

Availability: The server is available at

Contact:  jan.gewehr@bio.ifi.lmu.de

Supplementary information: The supplementary data are available at
The Dangers of Extreme Counterfactuals
Authors: King Gary , Zeng Langche
Published: November 2005

We address the problem that occurs when inferences about counterfactuals—predictions, “what-if” questions, and causal effects—are attempted far from the available data. The danger of these extreme counterfactuals is that substantive conclusions drawn from statistical models that fit the data well turn out to be based largely on speculation hidden in convenient modeling assumptions that few would be willing to defend. Yet existing statistical strategies provide few reliable means of identifying extreme counterfactuals. We offer a proof that inferences farther from the data allow more model dependence and then develop easy-to-apply methods to evaluate how model dependent our answers would be to specified counterfactuals. These methods require neither sensitivity testing over specified classes of models nor evaluating any specific modeling assumptions. If an analysis fails the simple tests we offer, then we know that substantive results are sensitive to at least some modeling choices that are not based on empirical evidence. Free software that accompanies this article implements all the methods developed.
First gut contents in a Cretaceous sea turtle
Authors: Kear Benjamin P
Published: November 2005

Modern sea turtles utilize a variety of feeding strategies ranging from herbivory to omnivory. In contrast, the diets of fossil sea turtles are poorly known. This study reports the first direct evidence: inoceramid bivalve shell pieces (encased in phosphatic material) preserved within the body cavities of several small protostegid turtles (cf.Notochelone) from the Lower Cretaceous of Australia. The shell fragments are densely packed and approximately 5–20 mm across. Identical shell accumulations have been found within coprolite masses from the same deposits; these are of a correct size to have originated fromNotochelone, and indicate that benthic molluscs were regular food items. The thin, flexible inoceramid shells (composed of organic material integrated into a prismatic calcite framework) appear to have been bitten into segments and ingested, presumably in conjunction with visceral/mantle tissues and encrusting organisms. Although protostegids have been elsewhere interpreted as potential molluscivores, their primitive limb morphology is thought to have limited them to surface feeding. However, the evidence here that at least some forms were able to utilize benthic invertebrate prey indicates that, like modern sea turtles, protostegids probably exhibited a much broader range of feeding habits.
Predicting the consequences of carry-over effects for migratory populations
Authors: Norris D. Ryan , Taylor Caz M
Published: November 2005

Migratory animals present a unique challenge for predicting population size because they are influenced by events in multiple stages of the annual cycle that are separated by large geographic distances. Here, we develop a model that incorporates non-fatal carry-over effects to predict changes in population size and show how this can be integrated with predictive models of habitat loss and deterioration. Examples from Barn swallows, Greater snow geese and American redstarts show how carry-over effects can be estimated and integrated into the model. Incorporation of carry-over effects should increase the predictive power of models. However, the challenge for developing accurate predictions rests both on the ability to estimate parameters from multiple stages of the annual cycle and to understand how events between these periods interact to influence individual success.
A multi-objective evolutionary approach to the protein structure prediction problem
Authors: Cutello Vincenzo , Narzisi Giuseppe , Nicosia Giuseppe
Published: November 2005

The protein structure prediction (PSP) problem is concerned with the prediction of the folded, native, tertiary structure of a protein given its sequence of amino acids. It is a challenging and computationally open problem, as proven by the numerous methodological attempts and the research effort applied to it in the last few years. The potential energy functions used in the literature to evaluate the conformation of a protein are based on the calculations of two different interaction energies:
local
(bond atoms) and
non-local
(non-bond atoms). In this paper, we show experimentally that those types of interactions are in conflict, and do so by using the potential energy function Chemistry at HARvard Macromolecular Mechanics. A multi-objective formulation of the PSP problem is introduced and its applicability studied. We use a multi-objective evolutionary algorithm as a search procedure for exploring the conformational space of the PSP problem.
Numerical simulation of corneal transport processes
Authors: Li Long-yuan , Tighe Brian
Published: November 2005

This paper presents a numerical study on the transport of ions and ionic solution in human corneas and the corresponding influences on corneal hydration. The transport equations for each ionic species and ionic solution within the corneal stroma are derived based on the transport processes developed for electrolytic solutions, whereas the transport across epithelial and endothelial membranes is modelled by using phenomenological equations derived from the thermodynamics of irreversible processes. Numerical examples are provided for both human and rabbit corneas, from which some important features are highlighted.
Self-engineering capabilities of bacteria
Authors: Ben-Jacob Eshel , Levine Herbert
Published: November 2005

Under natural growth conditions, bacteria can utilize intricate communication capabilities (e.g. quorum-sensing, chemotactic signalling and plasmid exchange) to cooperatively form (self-organize) complex colonies with elevated adaptability—the colonial pattern is collectively engineered according to the encountered environmental conditions. Bacteria do not genetically store all the information required for creating all possible patterns. Instead, additional information is cooperatively generated as required for the colonial self-organization to proceed.

We describe how complex colonial forms (patterns) emerge through the communication-based singular interplay between individual bacteria and the colony. Each bacterium is, by itself, a biotic autonomous system with its own internal cellular informatics capabilities (storage, processing and assessment of information). These afford the cell plasticity to select its response to biochemical messages it receives, including self-alteration and the broadcasting of messages to initiate alterations in other bacteria.

Hence, new features can collectively emerge during self-organization from the intracellular level to the whole colony. The cells thus assume newly co-generated traits and abilities that are not explicitly stored in the genetic information of the individuals.
An elastically tethered viscous load imposes a regular gait on the motion of myosin-V. Simulation of the effect of transient force relaxation on a stochastic process
Authors: Schilstra Maria J , Martin Stephen R
Published: November 2005

Myosin-V is a processive molecular motor that moves membrane vesicles along actin tracks. In the simple model for motor and cargo motion investigated here, an elastic connection between motor and cargo transiently absorbs the abrupt mechanical transitions of the motor, and allows smooth relaxation of the cargo to a new position. We use a stochastic description to model motor stepping, with kinetics that depends on the instantaneous force exerted on the motor through the elastic connection. Tether relaxation is modelled as a continuous process, in which the rate is determined by the viscous drag of the cargo and the stiffness profile of the connection. Quantitative combined stochastic–continuous simulation of the dynamics of this system shows that bulky loads can impose a highly regular gait on the motor. If the characteristics of the elastic connection are similar to those of the myosin-II coiled-coil domain, the myosin-V motor, tether and cargo form a true escapement, in which the motor only escapes from its current position after one or more force thresholds have been crossed. Multiple thresholds limit the variation in tether length to values below that of the total step size.
Not so ancient: the extant crown group of
Nothofagus
represents a post-Gondwanan radiation
Authors: Cook Lyn G , Crisp Michael D
Published: November 2005

This study uses a molecular-dating approach to test hypotheses about the biogeography of
Nothofagus
. The molecular modelling suggests that the present-day subgenera and species date from a radiation that most likely commenced between 55 and 40 Myr ago. This rules out the possibility of a reconciled all-vicariance hypothesis for the biogeography of extant
Nothofagus
. However, the molecular dates for divergences between Australasian and South American taxa are consistent with the rifting of Australia and South America from Antarctica. The molecular dates further suggest a dispersal of subgenera
Lophozonia
and
Fuscospora
between Australia and New Zealand after the onset of the Antarctic Circumpolar Current and west wind drift. It appears likely that the New Caledonian lineage of subgenus
Brassospora
diverged from the New Guinean lineage elsewhere, prior to colonizing New Caledonia.

The molecular approach strongly supports fossil-based estimates that
Nothofagus
diverged from the rest of Fagales more than 84 Myr ago. However, the mid-Cenozoic estimate for the diversification of the four extant subgenera conflicts with the palynological interpretation because pollen fossils, attributed to all four extant subgenera, were widespread across the Weddellian province of Gondwana about 71 Myr ago. The discrepancy between the pollen and molecular dates exists even when confidence intervals from several sources of error are taken into account. In contrast, the molecular age estimates are consistent with macrofossil dates. The incongruence between pollen fossils and molecular dates could be resolved if the early pollen types represent extinct lineages, with similar types later evolving independently in the extant lineages.
Handling time promotes the coevolution of aggregation in predator–prey systems
Authors: Schreiber Sebastian J , Vejdani Melanie
Published: November 2005

Predators often have type II functional responses and live in environments where their life history traits as well as those of their prey vary from patch to patch. To understand how spatial heterogeneity and predator handling times influence the coevolution of patch preferences and ecological stability, we perform an ecological and evolutionary analysis of a Nicholson–Bailey type model. We prove that coevolutionarily stable prey and searching predators prefer patches that in isolation support higher prey and searching predator densities, respectively. Using this fact, we determine how environmental variation and predator handling times influence the spatial patterns of patch preferences, population abundances and per-capita predation rates. In particular, long predator handling times are shown to result in the coevolution of predator and prey aggregation. An analytic expression characterizing ecological stability of the coevolved populations is derived. This expression implies that contrary to traditional theoretical expectations, predator handling time can stabilize predator–prey interactions through its coevolutionary influence on patch preferences. These results are shown to have important implications for classical biological control.
Women use voice parameters to assess men's characteristics
Authors: Bruckert Laetitia , Liénard Jean-Sylvain , Lacroix André , Kreutzer Michel , Leboucher Gérard
Published: November 2005

The purpose of this study was: (i) to provide additional evidence regarding the existence of human voice parameters, which could be reliable indicators of a speaker's physical characteristics and (ii) to examine the ability of listeners to judge voice pleasantness and a speaker's characteristics from speech samples. We recorded 26 men enunciating five vowels. Voices were played to 102 female judges who were asked to assess vocal attractiveness and speakers' age, height and weight. Statistical analyses were used to determine: (i) which physical component predicted which vocal component and (ii) which vocal component predicted which judgment. We found that men with low-frequency formants and small formant dispersion tended to be older, taller and tended to have a high level of testosterone. Female listeners were consistent in their pleasantness judgment and in their height, weight and age estimates. Pleasantness judgments were based mainly on intonation. Female listeners were able to correctly estimate age by using formant components. They were able to estimate weight but we could not explain which acoustic parameters they used. However, female listeners were not able to estimate height, possibly because they used intonation incorrectly. Our study confirms that in all mammal species examined thus far, including humans, formant components can provide a relatively accurate indication of a vocalizing individual's characteristics. Human listeners have the necessary information at their disposal; however, they do not necessarily use it.
Does the number of sons born affect long-term mortality of parents? A cohort study in rural Bangladesh
Authors: Hurt L.S , Ronsmans C , Quigley M
Published: November 2005

It has been suggested that bearing sons increases long-term mortality in women, because sons may be more physiologically demanding to produce than daughters. In this historical cohort study in rural Bangladesh, no association between the number of sons born and mortality was seen in women in the unadjusted analyses. However, a significant reduction in mortality with the number of surviving sons was seen. In addition, after adjusting for the number of surviving sons, there was evidence of increasing mortality with the number of sons born, in women. In men, mortality also depended strongly on the number of surviving sons, but not on the number born. These data provide support for negative long-term costs of bearing sons in mothers in rural Bangladesh, and suggest that there are context-specific factors that mask the true effects of sons in some populations.
Facial appearance is a cue to oestrogen levels in women
Authors: Law Smith M.J , Perrett D.I , Jones B.C , Cornwell R.E , Moore F.R , Feinberg D.R , Boothroyd L.G , Durrani S.J , Stirrat M.R , Whiten S , Pitman R.M , Hillier S.G
Published: November 2005

Although many accounts of facial attractiveness propose that femininity in women's faces indicates high levels of oestrogen, there is little empirical evidence in support of this assumption. Here, we used assays for urinary metabolites of oestrogen (oestrone-3-glucuronide, E1G) and progesterone (pregnanediol-3-glucuronide, P3G) to investigate the relationship between circulating gonadal hormones and ratings of the femininity, attractiveness and apparent health of women's faces. Positive correlations were observed between late follicular oestrogen and ratings of femininity, attractiveness and health. Positive correlations of luteal progesterone and health and attractiveness ratings were marginally significant. Ratings of facial attributions did not relate to hormone levels for women wearing make-up when photographed. There was no effect of sex of rater on the relationships between oestrogen and ratings of facial appearance. These findings demonstrate that female facial appearance holds detectable cues to reproductive health that are considered attractive by other people.