bluuebunny/crossref_metadata_2025 huggingface dataset:
Integrating Tobacco Cessation Treatment into Mental Health Care for Patients with Posttraumatic Stress Disorder
Authors: McFall Miles , Atkins David C. , Yoshimoto Dan , Thompson Charles E. , Kanter Evan , Malte Carol A. , Saxon Andrew J.
Published: September 2006

The integration of tobacco cessation treatment into mental health care for posttraumatic stress disorder (PTSD), known as Integrated Care (IC), was evaluated in an uncontrolled feasibility and effectiveness study. Veterans (N = 107) in PTSD treatment at two outpatient clinics received IC delivered by mental health practitioners. Outcomes were seven‐day point prevalence abstinence measured at two, four, six, and nine months post‐enrollment and repeated seven‐day point prevalence abstinence (RPPA) obtained across three consecutive assessment intervals (four, six, and nine months). Abstinence rates at the four assessment intervals were 28%, 23%, 25%, and 18%, respectively, and RPPA was 15%. The number of IC sessions and a previous quit history greater than six months predicted RPPA. Stopping smoking was not associated with worsening PTSD or depression.
Substance Abuse Treatment and Criminal Justice Involvement for SSI Recipients: Results from Washington State
Authors: Luchansky Bill , Nordlund Dan , Estee Sharon , Lund Peter , Krupski Antoinette , Stark Kenneth
Published: September 2006

This study examined the association between receiving substance abuse treatment and subsequent criminal justice involvement. The sample consisted of Supplemental Security Income (SSI) recipients in the state of Washington that were determined to be in need of treatment. Fifty‐two percent of those clients entered substance abuse treatment during the study period, while 48% did not. Arrests, felony convictions and convictions for less serious crimes were tracked for 8343 adults for one year following the end of an index treatment episode. Results showed that entering treatment was associated with reduced risks for each outcome. In addition, further analyses were conducted just on those entering treatment. Among that subset of the study population, the completion of treatment and having an episode of treatment lasting at least 90 days were both associated with reduced criminal justice risks. These results suggest that efforts to provide substance abuse treatment for SSI recipients have the potential to provide substantial public benefits.
The Relationship Between Perceived Exposure to Promotional Smoking Messages and Smoking Status among High School Students
Authors: Peters Ronald J. , Kelder Steven H. , Prokhorov Alexander , Springer Andrew E. , Yacoubian George S. , Agurcia Carolyn A. , Amos Charles
Published: September 2006

Data on self‐reported perceived exposure to pro‐smoking messages were collected from 1,608 high school students surveyed through the ASPIRE (A Smoking Prevention Interactive Experience) Program in Houston, Texas, in 2003. Results indicated that high school smoking quitters had approximately twice the odds of perceived exposure to pro‐smoking messages as nonsmokers through billboard advertisements (Adjusted Odds Ratio [AOR]−2.04, 95% CI: 1.09, 3.81), newspapers &magazines (AOR: 1.97, 95% CI: 1.09,3.56), and movies (AOR: 1.94,95% CI: 1.03,3.65). Smoking experimenters marginally perceived more exposure to pro‐smoking radio messages (AOR−1.31, 95% CI: 1.04, 1.67) and billboard advertisements (AOR−1.28, 95% CI: 1.02, 1.61) compared to nonsmokers. Lastly, current smokers were 1.82 times as likely to report exposure to pro‐smoking poster advertisements as nonsmokers (95% CI: 1.19, 2.79, p <.05). These findings suggest that experimenters and quitters may pay more attention to smoking advertisements than nonsmokers and current smokers.
Readiness to Quit Cigarette Smoking, Intimate Partner Violence, and Substance Abuse among Arrested Violent Women
Authors: Stuart Gregory L. , Meehan Jeffrey , Temple Jeff R. , Moore Todd M. , Hellmuth Julianne , Follansbee Katherine , Morean Meghan
Published: September 2006

Cigarette smoking is a leading cause of preventable mortality in the United States. Not much data are available regarding the prevalence and correlates of cigarette smoking in female perpetrators of intimate partner violence (IPV). Ninety‐eight arrested violent women were recruited from court‐referred batterer intervention programs. The prevalence of smoking in the sample was 62%. Smokers reported higher levels of substance abuse, psychopathology, general violence, and IPV perpetration and victimization than nonsmokers. Most smokers (65%) indicated a desire to quit within the next year. The results highlight the importance of screening for cigarette smoking in violence intervention programs and offering assistance to those who choose to quit.
Phosphorus geochemistry of recent sediments in the South Basin of Lake Winnipeg
Authors: Mayer T. , Simpson S. L. , Thorleifson L. H. , Lockhart W. L. , Wilkinson P.
Published: September 2006

Lake Winnipeg supports the largest commercial fishery on Canadian Prairies. It has been influenced by a variety of environmental forces and anthropogenic activities. To gain a better understanding of recent changes in nutrient status of the lake, it is important to reconstruct its previous history from sedimentary records. Lacustrine sediments are known to be an important sink of many dissolved and suspended substances, including phosphorus, hence, they provide a permanent historical record of changes occurring in the lake. These changes may be induced by natural factors or by anthropogenic activities in the watershed. Phosphorus profiles from dated sediment cores collected in 1999 and 1994 from the South Basin of Lake Winnipeg were investigated to determine phosphorus enrichment in recent sediments. To interpret the nutrient status and depositional conditions responsible for the trends in total phosphorus, three operationally defined forms of phosphorus (P) were determined: non-apatite inorganic P, apatite P, and organic P. Significant increases in sediment phosphorus concentrations were observed in the uppermost 20 cm of the cores and several anomalies were observed at depth. A doubling in total phosphorus relative to aluminum over the last fifty years is largely due to increases in the non-apatite inorganic fraction, suggesting that much of sedimentary phosphorus increase is attributable to changes in the nutrient status of the water column related to anthropogenic inputs. Organic phosphorus exhibits a subtle increase in the upper 20 cm of the gravity cores, likely due to increases in the primary productivity of the lake. Except for the slight increase in deeper sediments, apatite phosphorus, which is thought to be of detrital origin, remained fairly constant over the length of the cores. Anomalous spikes in phosphorus concentrations deeper in the cores, comprised mainly of the non-apatite inorganic phosphorus fraction, likely resulted from natural variation in local oxidizing conditions, possibly induced by changes in water circulation and/or changes in sediment deposition rates due to climatic variation. The results of this investigation contribute to increased understanding of the depositional history of phosphorus in the lake over the last millennium.
Environmental risk assessment on aquatic-terrestrial gradients in a freshwater tidal area
Authors: Postma Jaap F. , Keijzers Rineke C. M. , Faber Jack H. , Belfroid Angelique C. , Stroomberg Gerard J. , den Besten Pieter J.
Published: September 2006

Environmental risk assessments are generally performed for either terrestrial or aquatic systems, while these systems sometimes exist in close proximity. The objective of this study is to compare environmental risks along gradients from aquatic to terrestrial conditions. The assessment involved chemical analysis (including bioavailable fractions), as well as bioassays and bioaccumulation experiments using aquatic and terrestrial organisms. The results demonstrate that sediments and soils from neighbouring aquatic and terrestrial systems may render different assessments in terms of environmental risks. Metal availability for oligochaetes appeared to be limited in the aquatic environment as compared to the terrestrial environment, while the reverse was observed for organic contaminants. This paper aims to illustrate the use of various assessment techniques within a framework to compare ecological risks in aquatic and terrestrial environments. The obtained results are useful when considering (a prioritisation of) remedial actions.
A coastal vulnerability index and its application in Xiamen, China
Authors: Hong H. , Cui S. , Zhang L.
Published: September 2006

With the increasing problems of global change, ecological security has become a research focus in the world. Coastal areas that are exposed to both human impact and natural changes are vulnerable. The maintenance of coastal ecological security is a great challenge. Assessment of vulnerability is essential for identifying and recognizing the coastal ecological security status. However, there is a lack of criteria and standards for vulnerability assessment.

We proposed a methodological framework of vulnerability analysis and assessment and used Xiamen city as a case study. Surveys were undertaken to assess the states of Xiamen coastal environment and resources, and the issues associated with human activities. Stakeholders were interviewed about their attitudes regarding Xiamen environment and resources. Constraints of development and management were identified. The methodological framework was presented as a tool to help identify relative vulnerability in order to prioritize actions and assess the vulnerability implications of management and policy decisions.
Climate agreements and technology spillovers—a modeling approach
Authors: Golombek Rolf , Hoel Michael
Published: September 2006

A significant reduction in global greenhouse gas emissions will require development of new technologies if such reductions are to be achieved without excessive costs. An important question is whether an agreement of the Kyoto type, which does not include elements related to research and development of new technologies, will give sufficient incentives to develop such new technologies. On the one hand, since greenhouse gas emissions will become costly for countries and private producers, there will then be incentives to undertake the effort and costs to develop new technologies. On the other hand, research and development in one country is not only advantageous for this country, but usually also for other countries. The reason for this is that producers in these countries will learn from the project in many cases; for example, through (informal) networks, journals, and, in some cases, through the import of goods from the country where the new technology is developed.

The purpose of this paper is to discuss properties of an international climate agreement of the Kyoto type, when research and development investments undertaken in one country are also beneficial for other countries. We examine whether a Kyoto type of agreement can provide the correct social amount of aggregate emissions, and research and development investments in new technologies. We argue that the outcome of a Kyoto type agreement will differ from the social optimum. In particular, for a given level of abatement a Kyoto type agreement provides too few investments relative to the social optimum.
Forecasting Phaeocystis globosa blooms in the Dutch coast by an integrated numerical and decision tree model
Authors: Chen Qiuwen , Mynett Arthur E.
Published: September 2006

In Dutch coastal waters, in particular the Noordwijk transect and the Wadden Sea, spring algal blooms have occurred almost every year which are usually identified as diatoms or Dinophysis, and followed by Phaeocystis globosa (P. globosa). The blooms of P. globosa incurred adverse impacts on shellfish farming because of the resulted anoxic conditions, and on recreation due to odour and foam. Funded by EU FP5 Harmful Algal Blooms Expert System (HABES) project, the objective of this research was to systematically assimilate the various available knowledge and limited data to develop innovative and practical methods to forecast P. globosa blooms. From previous studies in the Dutch coast, water column irradiance was identified to be a triggering factor to the blooms of P. globosa. Phosphate was also confirmed to be an important limiting factor. The available water column irradiance was related to the vertical position of the species. In this paper, a one-dimensional vertical advection-diffusion model was used to investigate the effects of sinking (buoyancy) and turbulence mixing on the vertical profile of P. globosa concentrations. The numerical model was then integrated with decision tree method to predict possible P. globosa blooms by using the available chemical and biological data. The results of the case study at station Noordwijk 70 were shown to be comparable to the field observations. The research demonstrated that for algal blooms forecasting, an integrated approach gave a good perspective and deserves further efforts because (1) the numerical module could provide understanding of the fundamental mechanisms; (2) the limited water quality and biological data, and the empirical knowledge from experts could be incorporated into the rule-based model.
Lipid peroxidation and Acetylcholinesterase activity as biomarkers in the Black Sailfin Goodeid, Girardinichthys viviparous (Bustamante) exposed to water from Lake Xochimilco (Mexico)
Authors: López-López E. , Sedeño-Díaz J. E. , Perozzi Favari
Published: September 2006

Lake Xochimilco has been the receiver of untreated domestic wastewater, agricultural run off and secondary effluent of a treatment facility, thus becoming the receptor of a mixture of pollutants and their metabolites. Major zones in Lake Xochimilco are urban, agricultural and tourist; all of them exert environmental pressure to the Lake, that has been associated with the extinction of two fish species, and the limited presence of another, Girardinichthys viviparous. Early warning biomarkers of G. viviparous were analyzed after its reintroduction to waters of Lake Xochimilco, in order to evaluate the responses of the fish in the case of their repopulation in their ancient habitat. We examine some indicators of the water quality, the level of lipid peroxidation and the acetylcholinesterase activity in brain, gill, liver and muscle of G. viviparous after exposure to waters of each zone of Lake Xochimilco. The results show that the urban area presents an enrichment of ammonium, related to the sewage; the agricultural zone apparently had the highest concentrations of phosphorous, perhaps derived from the use of fertilizers; and the tourist zone reached elevated values in chlorophyll a and turbidity. Differences were detected in lipid peroxidation and the acetylcholinesterase among the sites and tissues tested. The urban and agricultural zones, produced increases in the lipid peroxidation in muscle, brain, liver and gills. Acetylcholinesterase shows an inhibition in the function of the brain, liver and gills of fish exposed to agricultural waters; however, the muscle shows an increase in all the sites. The observed effects might have health implications for the species studied, although further research would be required.
The Rise and Decline of Prospective Memory Performance across the Lifespan
Authors: Zimmermann Thomas D. , Meier Beat
Published: September 2006

In the present study, the trajectory of prospective memory across the lifespan was investigated in a total of 200 participants from five age groups (4- to 6-year-old children, 13- to 14-year-old adolescents, 19- to 26-year-old adults, 55- to 65-year-old adults, and 65- to 75-year-old adults). In an event-based prospective memory task the prospective and the retrospective components were assessed separately. For the prospective component, the results showed better performance for adolescents and young adults than for children and 65- to 75-year-old adults. In addition, participants belonging to the latter group were more likely to forget the retrospective component after having noticed the prospective memory targets. Overall, these results indicate that across the lifespan prospective memory performance follows a similar inverted u-shape function as is well known for retrospective episodic memory.
The Role of Interference Control in Working Memory: A Study with Children at Risk of Adhd
Authors: Palladino Paola
Published: September 2006

The study aimed to test whether the impairment in a working memory task observed in children at risk of ADHD was due to a lack of control of interfering information being processed whilst carrying out the memory task. Two groups of children at risk of ADHD with or without a learning disability (reading impairment) were compared to a control group in a working memory task. Activation of irrelevant items was tested with a lexical decision task presented immediately after the final recall in about half of the trials. Results showed a poor working memory performance in children at risk of ADHD and reading disability associated with a larger activation of irrelevant information than that of control children. Results indicated that the to-be-excluded and interfering items are still highly accessible to working memory in children that fail the working memory task. The examination of working memory and interference control of children at risk of ADHD with a learning disability revealed a counterintuitive picture of children with poor working memory showing better recall/activation of processed information. This picture is consistent with a view of working memory related to an efficient inhibitory control that influences cognitive functioning.
Gaze Cues Influence the Allocation of Attention in Natural Scene Viewing
Authors: Langton Stephen R. H. , O'donnell Christopher , Riby Deborah M. , Ballantyne Carrie J.
Published: September 2006

In two experiments we examined whether the allocation of attention in natural scene viewing is influenced by the gaze cues (head and eye direction) of an individual appearing in the scene. Each experiment employed a variant of the flicker paradigm in which alternating versions of a scene and a modified version of that scene were separated by a brief blank field. In Experiment 1, participants were able to detect the change made to the scene sooner when an individual appearing in the scene was gazing at the changing object than when the individual was absent, gazing straight ahead, or gazing at a nonchanging object. In addition, participants’ ability to detect change deteriorated linearly as the changing object was located progressively further from the line of regard of the gazer. Experiment 2 replicated this change detection advantage of gaze-cued objects in a modified procedure using more critical scenes, a forced-choice change/no-change decision, and accuracy as the dependent variable. These findings establish that in the perception of static natural scenes and in a change detection task, attention is preferentially allocated to objects that are the target of another's social attention.
Essential roles of DC-derived IL-15 as a mediator of inflammatory responses in vivo
Authors: Ohteki Toshiaki , Tada Hiroyuki , Ishida Kazuto , Sato Taku , Maki Chikako , Yamada Taketo , Hamuro Junji , Koyasu Shigeo
Published: September 2006

Interleukin (IL)-15 is expressed in a variety of inflammatory diseases. However, the contribution of dendritic cell (DC)–derived IL-15 to the development of diseases is uncertain. Using established models of Propionibacterium acnes (P. acnes)– and zymosan-induced liver inflammation, we observed granuloma formation in the livers of wild-type (WT) and RAG-2−/− mice but not in those of IL-15−/− mice. We demonstrate that this is likely caused by an impaired sequential induction of IL-12, IFN-γ, and chemokines necessary for monocyte migration. Likewise, lethal endotoxin shock was not induced in P. acnes– and zymosan-primed IL-15−/− mice or in WT mice treated with a new IL-15–neutralizing antibody. In both systems, proinflammatory cytokine production was impaired. Surprisingly, neither granuloma formation, lethal endotoxin shock, nor IL-15 production was induced in mice deficient for DCs, and adoptive transfer of WT but not IL-15−/− DCs restored the disease development in IL-15−/− mice. Collectively, these data indicate the importance of DC-derived IL-15 as a mediator of inflammatory responses in vivo.
State-dependent Block of BK Channels by Synthesized Shaker Ball Peptides
Authors: Li Weiyan , Aldrich Richard W.
Published: September 2006

Crystal structures of potassium channels have strongly corroborated an earlier hypothetical picture based on functional studies, in which the channel gate was located on the cytoplasmic side of the pore. However, accessibility studies on several types of ligand-sensitive K+ channels have suggested that their activation gates may be located near or within the selectivity filter instead. It remains to be determined to what extent the physical location of the gate is conserved across the large K+ channel family. Direct evidence about the location of the gate in large conductance calcium-activated K+ (BK) channels, which are gated by both voltage and ligand (calcium), has been scarce. Our earlier kinetic measurements of the block of BK channels by internal quaternary ammonium ions have raised the possibility that they may lack a cytoplasmic gate. We show in this study that a synthesized Shaker ball peptide (ShBP) homologue acts as a state-dependent blocker for BK channels when applied internally, suggesting a widening at the intracellular end of the channel pore upon gating. This is consistent with a gating-related conformational change at the cytoplasmic end of the pore-lining helices, as suggested by previous functional and structural studies on other K+ channels. Furthermore, our results from two BK channel mutations demonstrate that similar types of interactions between ball peptides and channels are shared by BK and other K+ channel types.
Acute Oxygen Sensing in Heme Oxygenase-2 Null Mice
Authors: Ortega-Sáenz Patricia , Pascual Alberto , Gómez-Díaz Raquel , López-Barneo José
Published: September 2006

Hemeoxygenase-2 (HO-2) is an antioxidant enzyme that can modulate recombinant maxi-K+ channels and has been proposed to be the acute O2 sensor in the carotid body (CB). We have tested the physiological contribution of this enzyme to O2 sensing using HO-2 null mice. HO-2 deficiency leads to a CB phenotype characterized by organ growth and alteration in the expression of stress-dependent genes, including the maxi-K+ channel α-subunit. However, sensitivity to hypoxia of CB is remarkably similar in HO-2 null animals and their control littermates. Moreover, the response to hypoxia in mouse and rat CB cells was maintained after blockade of maxi-K+ channels with iberiotoxin. Hypoxia responsiveness of the adrenal medulla (AM) (another acutely responding O2-sensitive organ) was also unaltered by HO-2 deficiency. Our data suggest that redox disregulation resulting from HO-2 deficiency affects maxi-K+ channel gene expression but it does not alter the intrinsic O2 sensitivity of CB or AM cells. Therefore, HO-2 is not a universally used acute O2 sensor.
The Two ATP Binding Sites of Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) Play Distinct Roles in Gating Kinetics and Energetics
Authors: Zhou Zhen , Wang Xiaohui , Liu Hao-Yang , Zou Xiaoqin , Li Min , Hwang Tzyh-Chang
Published: September 2006

Cystic fibrosis transmembrane conductance regulator (CFTR), a member of the ABC (ATP binding cassette) transporter family, is a chloride channel whose activity is controlled by protein kinase–dependent phosphorylation. Opening and closing (gating) of the phosphorylated CFTR is coupled to ATP binding and hydrolysis at CFTR's two nucleotide binding domains (NBD1 and NBD2). Recent studies present evidence that the open channel conformation reflects a head-to-tail dimerization of CFTR's two NBDs as seen in the NBDs of other ABC transporters (Vergani et al., 2005). Whether these two ATP binding sites play an equivalent role in the dynamics of NBD dimerization, and thus in gating CFTR channels, remains unsettled. Based on the crystal structures of NBDs, sequence alignment, and homology modeling, we have identified two critical aromatic amino acids (W401 in NBD1 and Y1219 in NBD2) that coordinate the adenine ring of the bound ATP. Conversion of the W401 residue to glycine (W401G) has little effect on the sensitivity of the opening rate to [ATP], but the same mutation at the Y1219 residue dramatically lowers the apparent affinity for ATP by >50-fold, suggesting distinct roles of these two ATP binding sites in channel opening. The W401G mutation, however, shortens the open time constant. Energetic analysis of our data suggests that the free energy of ATP binding at NBD1, but not at NBD2, contributes significantly to the energetics of the open state. This kinetic and energetic asymmetry of CFTR's two NBDs suggests an asymmetric motion of the NBDs during channel gating. Opening of the channel is initiated by ATP binding at the NBD2 site, whereas separation of the NBD dimer at the NBD1 site constitutes the rate-limiting step in channel closing.
Protein–RNA interactions: exploring binding patterns with a three-dimensional superposition analysis of high resolution structures
Authors: Morozova N. , Allers J. , Myers J. , Shamoo Y.
Published: September 2006

Motivation: The recognition of specific RNA sequences and structures by proteins is critical to our understanding of RNA processing, gene expression and viral replication. The diversity of RNA structures suggests that RNA recognition is substantially different than that of DNA.

Results: The atomic coordinates of 41 protein–RNA complexes have been used to probe composite nucleoside binding pockets that form the structural and chemical underpinnings of base recognition. Composite nucleoside binding pockets were constructed using three-dimensional superpositions of each RNA nucleoside. Unlike protein–DNA interactions which are dominated by accessibility, RNA recognition frequently occurs in non-canonical and single-strand-like structures that allow interactions to occur from a much wider set of geometries and make fuller use of unique base shapes and hydrogen-bonding ability. By constructing composites that include all van der Waals, hydrogen-bonding, stacking and general non-polar interactions made to a particular nucleoside, the strategies employed are made readily visible. Protein–RNA interactions can result in the formation of a glove-like tight binding pocket around RNA bases, but the size, shape and non-polar binding patterns differ between specific RNA bases. We show that adenine can be distinguished from guanine based on the size and shape of the binding pocket and steric exclusion of the guanine N2 exocyclic amino group. The unique shape and hydrogen-bonding pattern for each RNA base allow proteins to make specific interactions through a very small number of contacts, as few as two in some cases.

Availability: The program ENTANGLE is available from

Contact:  shamoo@rice.edu
Support vector machine learning from heterogeneous data: an empirical analysis using protein sequence and structure
Authors: Lewis Darrin P. , Jebara Tony , Noble William Stafford
Published: September 2006

Motivation: Drawing inferences from large, heterogeneous sets of biological data requires a theoretical framework that is capable of representing, e.g. DNA and protein sequences, protein structures, microarray expression data, various types of interaction networks, etc. Recently, a class of algorithms known as kernel methods has emerged as a powerful framework for combining diverse types of data. The support vector machine (SVM) algorithm is the most popular kernel method, due to its theoretical underpinnings and strong empirical performance on a wide variety of classification tasks. Furthermore, several recently described extensions allow the SVM to assign relative weights to various datasets, depending upon their utilities in performing a given classification task.

Results: In this work, we empirically investigate the performance of the SVM on the task of inferring gene functional annotations from a combination of protein sequence and structure data. Our results suggest that the SVM is quite robust to noise in the input datasets. Consequently, in the presence of only two types of data, an SVM trained from an unweighted combination of datasets performs as well or better than a more sophisticated algorithm that assigns weights to individual data types. Indeed, for this simple case, we can demonstrate empirically that no solution is significantly better than the naive, unweighted average of the two datasets. On the other hand, when multiple noisy datasets are included in the experiment, then the naive approach fares worse than the weighted approach. Our results suggest that for many applications, a naive unweighted sum of kernels may be sufficient.

Availability:  

Contact:  noble@gs.washington.edu

Supplementary information: Supplementary Data are available at Bioinformatics online.
SCAssign: a sparky extension for the NMR resonance assignment of aliphatic side-chains of uniformly 13C,15N-labeled large proteins
Authors: Zhang Lei , Yang Daiwen
Published: September 2006

Summary: SCAssign (side-chain assignment) is a Sparky extension written in Python to assist the NMR resonance assignment of aliphatic side-chains of uniformly 13C,15N-labled large proteins. It is based on a general strategy recently developed in our laboratory that makes use of 4D 13C,15N-edited NOESY, 3D MQ-(H)CCmHm-TOCSY, and prior backbone assignments. The program runs on all operating systems for which Sparky is available, and is easy to install, setup and use. Not only can it accelerate the assignment process, it also allows assignments of weak NOEs in 4D NOESY, which used to be very difficult with manual approach.

Availability: The program, in the form of source code, is provided as free download at . The website also contains installation guide, user manual and demonstrations recorded in Flash.

Contact: Bug reports, questions or comments should be sent to dbsydw@nus.edu.sg.
The prebiotic molecules observed in the interstellar gas
Authors: Thaddeus P
Published: September 2006

Over 130 molecules have been identified in the interstellar gas and circumstellar shells, the largest among them is a carbon chain with 13 atoms and molecular weight of 147 (twice that of the simplest amino acid glycine). The high reliability of astronomical identifications, as well as the fairly accurate quantitative analysis which can often be achieved, is emphasized. Glycine itself has been claimed, but a recent analysis indicates that few, if any, of the astronomical radio lines attributed to glycine are actually from that molecule. Polycyclic aromatic hydrocarbons (PAHs) have long been proposed as the source of the unidentified infrared bands between 3 and 16 μm, but no single PAH has been identified in space, partly because PAHs generally have weak or non-existent radio spectra. A remarkable exception is the non-planar corannulene molecule (C
20
H
10
) that has a strong radio spectrum; in the rich molecular cloud TMC-1, it is found that less than 10
−5
of the carbon is contained in this molecule, suggesting that PAHs are not the dominant large molecules in the interstellar gas, as has been claimed. Owing to inherent spectroscopic limitations, determining the structures of the large molecules in space may require capture of the dust grains, which are continually entering the outer Solar System.
Atmospheric composition and climate on the early Earth
Authors: Kasting James F , Howard M. Tazewell
Published: September 2006

Oxygen isotope data from ancient sedimentary rocks appear to suggest that the early Earth was significantly warmer than today, with estimates of surface temperatures between 45 and 85°C. We argue, following others, that this interpretation is incorrect—the same data can be explained via a change in isotopic composition of seawater with time. These changes in the isotopic composition could result from an increase in mean depth of the mid-ocean ridges caused by a decrease in geothermal heat flow with time. All this implies that the early Earth was warm, not hot.

A more temperate early Earth is also easier to reconcile with the long-term glacial record. However, what triggered these early glaciations is still under debate. The Paleoproterozoic glaciations at approximately 2.4 Ga were probably caused by the rise of atmospheric O
2
and a concomitant decrease in greenhouse warming by CH
4
. Glaciation might have occurred in the Mid-Archaean as well, at approximately 2.9 Ga, perhaps as a consequence of anti-greenhouse cooling by hydrocarbon haze. Both glaciations are linked to decreases in the magnitude of mass-independent sulphur isotope fractionation in ancient rocks. Studying both the oxygen and sulphur isotopic records has thus proved useful in probing the composition of the early atmosphere.
Montmorillonite-catalysed formation of RNA oligomers: the possible role of catalysis in the origins of life
Authors: Ferris James P
Published: September 2006

Large deposits of montmorillonite are present on the Earth today and it is believed to have been present at the time of the origin of life and has recently been detected on Mars. It is formed by aqueous weathering of volcanic ash. It catalyses the formation of oligomers of RNA that contain monomer units from 2 to 30–50. Oligomers of this length are formed because this catalyst controls the structure of the oligomers formed and does not generate all possible isomers. Evidence of sequence-, regio- and homochiral selectivity in these oligomers has been obtained. Postulates on the role of selective versus specific catalysts on the origins of life are discussed. An introduction to the origin of life is given with an emphasis on reaction conditions based on the recent data obtained from zircons 4.0–4.5 Ga.
Early anaerobic metabolisms
Authors: Canfield Don E , Rosing Minik T , Bjerrum Christian
Published: September 2006

Before the advent of oxygenic photosynthesis, the biosphere was driven by anaerobic metabolisms. We catalogue and quantify the source strengths of the most probable electron donors and electron acceptors that would have been available to fuel early-Earth ecosystems. The most active ecosystems were probably driven by the cycling of H2and Fe2+through primary production conducted by anoxygenic phototrophs. Interesting and dynamic ecosystems would have also been driven by the microbial cycling of sulphur and nitrogen species, but their activity levels were probably not so great. Despite the diversity of potential early ecosystems, rates of primary production in the early-Earth anaerobic biosphere were probably well below those rates observed in the marine environment. We shift our attention to the Earth environment at 3.8 Gyr ago, where the earliest marine sediments are preserved. We calculate, consistent with the carbon isotope record and other considerations of the carbon cycle, that marine rates of primary production at this time were probably an order of magnitude (or more) less than today. We conclude that the flux of reduced species to the Earth surface at this time may have been sufficient to drive anaerobic ecosystems of sufficient activity to be consistent with the carbon isotope record. Conversely, an ecosystem based on oxygenic photosynthesis was also possible with complete removal of the oxygen by reaction with reduced species from the mantle.
The origin and emergence of life under impact bombardment
Authors: Cockell Charles S
Published: September 2006

Craters formed by asteroids and comets offer a number of possibilities as sites for prebiotic chemistry, and they invite a literal application of Darwin's ‘warm little pond’. Some of these attributes, such as prolonged circulation of heated water, are found in deep-ocean hydrothermal vent systems, previously proposed as sites for prebiotic chemistry. However, impact craters host important characteristics in a single location, which include the formation of diverse metal sulphides, clays and zeolites as secondary hydrothermal minerals (which can act as templates or catalysts for prebiotic syntheses), fracturing of rock during impact (creating a large surface area for reactions), the delivery of iron in the case of the impact of iron-containing meteorites (which might itself act as a substrate for prebiotic reactions), diverse impact energies resulting in different rates of hydrothermal cooling and thus organic syntheses, and the indiscriminate nature of impacts into every available lithology—generating large numbers of ‘experiments’ in the origin of life. Following the evolution of life, craters provide cryptoendolithic and chasmoendolithic habitats, particularly in non-sedimentary lithologies, where limited pore space would otherwise restrict colonization. In impact melt sheets, shattered, mixed rocks ultimately provided diverse geochemical gradients, which in present-day craters support the growth of microbial communities.
Transcription and translation in an RNA world
Authors: Taylor William R
Published: September 2006

The RNA world hypothesis requires a ribozyme that was an RNA-directed RNA polymerase (ribopolymerase). If such a replicase makes a reverse complementary copy of any sequence (including itself), in a simple RNA world, there is no mechanism to prevent self-hybridization. It is proposed that this can be avoided through the synthesis of a parallel complementary copy. The logical consequences of this are pursued and developed in a computer simulation, where the behaviour of the parallel copy is compared to the conventional reverse complementary copy. It is found that the parallel copy is more efficient at higher temperatures (up to 90°C). A model for the ribopolymerase, based on the core of the large subunit (LSU) of the ribosome, is described. The geometry of a potential active site for this ribopolymerase suggests that it contained a cavity (now occupied by the aminoacyl-tRNA) and that an amino acid binding in this might have ‘poisoned’ the ribopolymerase by cross-reacting with the nucleoside-triphosphate before polymerization could occur. Based on a similarity to the active site components of the class-I tRNA synthetase enzymes, it is proposed that the amino acid could become attached to the nascent RNA transcript producing a variety of aminoacylated tRNA-like products. Using base-pairing interactions, some of these molecules might cross-link two ribopolymerases, giving rise to a precursor of the modern ribosome. A hybrid dimer, half polymerase and half proto-ribosome, could account for mRNA translocation before the advent of protein elongation factors.
Prebiotic materials from on and off the early Earth
Authors: Bernstein Max
Published: September 2006

One of the greatest puzzles of all time is how did life arise? It has been universally presumed that life arose in a soup rich in carbon compounds, but from where did these organic molecules come? In this article, I will review proposed terrestrial sources of prebiotic organic molecules, such as Miller–Urey synthesis (including how they would depend on the oxidation state of the atmosphere) and hydrothermal vents and also input from space. While the former is perhaps better known and more commonly taught in school, we now know that comet and asteroid dust deliver tons of organics to the Earth every day, therefore this flux of reduced carbon from space probably also played a role in making the Earth habitable. We will compare and contrast the types and abundances of organics from on and off the Earth given standard assumptions. Perhaps each process provided specific compounds (amino acids, sugars, amphiphiles) that were directly related to the origin or early evolution of life. In any case, whether planetary, nebular or interstellar, we will consider how one might attempt to distinguish between abiotic organic molecules from actual signs of life as part of a robotic search for life in the Solar System.
Hunger, light level and body size affect refuge use by post‐settlement lingcod Ophiodon elongatus
Authors: Petrie M. E. , Ryer C. H.
Published: September 2006

Using experimental methods, body size, nutritional state (hunger) and light level were investigated as possible determinants of the extent to which juvenile lingcod Ophiodon elongatus used structural refuges. In the laboratory, older, larger individuals (134–162 mm total length, LT) exhibited a higher propensity for structure use than did smaller juvenile fish (78–103 mm LT). In fish of both body sizes, increasing hunger levels caused fish to emerge more readily from refuges than satiated individuals, with this effect most prominent for smaller fish. Diel patterns of ambient illumination were simulated in the laboratory, and refuge use by large individuals decreased significantly in response to lower nocturnal light levels, a pattern that was not observed in the smaller size class. These results indicate an ontogenetic shift in refuge use. During the summer, as post‐settlement fish grew larger, they tended to increase affinity for structurally complex habitat, and also showed divergent patterns of behaviour in relation to hunger and light level.
Male size predicts the ability to defend offspring in the biparental convict cichlid Archocentrus nigrofasciatus
Authors: Gagliardi‐Seeley J. L. , Itzkowitz M.
Published: September 2006

The data from this field study provided evidence that biparental convict cichlid Archocentrus nigrofasciatus pairs with large males had fewer intruders near their offspring compared to pairs with small males. This suggested that large males were more capable of defending their young against predators.
Refuge‐use strategies of stream fishes in response to extreme low flows
Authors: Davey A. J. H. , Kelly D. J. , Biggs B. J. F.
Published: September 2006

Low flows were simulated in an artificial stream to determine the refuge‐use strategies of two benthic New Zealand fish species, Canterbury galaxias Galaxias vulgaris and upland bullies Gobiomorphus breviceps, and to investigate how refuge availability and the rate of flow recession affect the type and incidence of refuge use. When riffles dewatered, upland bullies tended to move to runs, whereas Canterbury galaxias showed a stronger propensity to burrow into the substratum. Both species showed a strong and consistent tendency to move upstream when emigrating from riffles. Burrowing was more frequent on coarse substrata and during rapid flow recessions. The incidence of surface stranding increased with the rate of flow recession, but only when interstitial refugia were unavailable, and was higher on gravel than on cobble substrata. The effect of rate of flow recession and substratum size on the probability of stranding depended upon the type of refuge‐use strategy adopted by the fishes. Rate of flow recession affected upland bullies more than Canterbury galaxias, whereas substratum size affected Canterbury galaxias more than upland bullies. These results suggest that the impact of disturbance is contingent upon species‐specific refuge‐use strategies, which result from interplay between refuge availability, the nature of the disturbance and species’ behaviours and morphologies. When component species adopt contrasting refuge‐use strategies, disturbance events may not consistently favour one species over another but rather inflict species‐specific mortality that varies both temporally and spatially.
Temperature‐dependent development rates of cod Gadus morhua eggs
Authors: Geffen A. J. , Fox C. J. , Nash R. D. M.
Published: September 2006

Temperature development relationships were determined for batches of Irish Sea cod Gadus morhua eggs incubated in flow‐through incubators. Hatching began 16·4 days after fertilization (DAF) at 6° C, 10·3 DAF at 8° C, 9·4 DAF at 10° C and 7·4 DAF at 12° C. Egg mortality increased at the higher temperatures, but survival was >80%. Results were compared with published data at four comparable stage end points: the end of blastula, the end of gastrula, the point of growth of the embryo completely surrounding the yolk and the point when 50% of the eggs were hatched. All the studies showed a curvilinear relationship between age at stage and temperature. There was a 12 day inter‐study difference in time to 50% hatch at 2° C and 4 day difference at 10° C. There were no consistent trends that differentiated eastern v. western, or northern v. southern populations. A single model for cod egg incubation time from fertilization to 50% hatch was derived based on data from six cod populations, but it is recommended that individual stock relationships should be used where possible.
Anguilla rostrata glass eel ingress into two, U.S. east coast estuaries: patterns, processes and implications for adult abundance
Authors: Sullivan M. C. , Able K. W. , Hare J. A. , Walsh H. J.
Published: September 2006

A time series of American eel Anguilla rostrata glass eel abundance, timing and size from Little Egg Inlet, New Jersey (16 years) and Beaufort Inlet, North Carolina (18 years) was used to provide a better understanding of ingress patterns at two, U.S. east coast estuaries. There was no evidence of synchronous declines in abundance between the two locations; however, at the Little Egg Inlet site, glass eels arrived later in the season and at significantly smaller sizes over the duration of the series. One significant linkage between sites was revealed: abundance was positively correlated with winter precipitation. Precipitation differed between sites annually and was correlated with El Niño at Beaufort Inlet and, to a lesser extent, the North Atlantic Oscillation at Little Egg Inlet. It is hypothesized that glass eels may use freshwater signals to enhance recruitment to local estuaries, thus influencing year‐class strength, yet the relationship between year‐class strength and adult abundance remains unresolved.
Maternal and paternal hybrid triploids of tetras
Authors: David C. J. , Pandian T. J.
Published: September 2006

Hybrid maternal triploids were generated by crossing grey‐body and red or yellow‐tailed Buenos Aires tetra Hemigrammus caudovittatus (BT) males with albino or black Gymnocorymbus ternetzi [widow tetra (WT)] females and retaining the second polar body by heat shock (HS) or cold shock (CS). Paternal triploids were also generated using 2·5% polyethylene glycol (PEG) incubated BT semen to facilitate the entry of two sperm into an egg of WT. Optimum temperature for CS was identified as 6° C and the optimum age for thermal shocking the zygote as 3 min after fertilization. At hatching, survival was 25, 17 and 5% for the HS, CS and paternal triploids, respectively. At maturity, it was further reduced to >2% and the maturity inordinately delayed. With the presence of undifferentiated ‘steriles’ and almost total absence of females, the expected sex ratio was distorted. Triploid males produced spermatocytes, spermatids but not spermatozoa. Triploidy was confirmed by phenotypic markers, karyotyping, erythrocyte measurement and molecular markers. The fusiform body shape of WT was a dominant phenotypic trait over the typical piscine slender body shape of BT. Polymerase chain reaction products of the genomic DNA of the triploids amplified by OPF6 primer were 300, 450 and 1000 bp length, characteristic of BT, and 500 and 800 bp, typical of WT and thereby confirmed the biparental genomic contribution to the triploids. Analyses of genomic DNA of selected progenies using DMRT‐1 marker showed that (1) like the diploid BT males, the hybrid triploid males were also true genetic males, and amplified 237 and 300 bp products but (2) the triploid steriles amplified all the three products of 100, 237 and 300 bp indicating that they were mosaics but the diploid steriles failed to amplify.