Search

Rh-catalyzed C-H insertion reactions to form β-lactones suffer from post-transition state bifurcations, with the same transition states leading to ketones and ketenes via fragmentation in addition to β-lactones. In such a circumstance, traditional transition state theory cannot predict product selectivity, so we employed

Understanding the detailed mechanism by which the proteins of marine diatoms such as silaffins are able to control the morphology of silica oligomers has eluded synthetic chemists and materials scientists for decades. In this study, we use DFT calculations to determine how individual amino acid residues of silaffin catalyze silica dimerization. The reaction network for formation of a silica dimer was explored using several different small molecules, including water, guanidinium ions, and methylammonium ions, the latter two molecules representing analogs of arginine and lysine, both of which are known to play critical roles in enabling the catalytic function of naturally occurring protein and synthetic analogs of silaffin. It was found that the lysine analog selectively lowers the energy of a direct water removal pathway for silicate dimerization. Comparing the energy landscapes and mechanisms for various catalysts for this reaction provides direct evidence for the role of lysine side chains of silaffins in the oligmerization of silica.

Drifting Fish Aggregating Devices (dFADs) are a major fishing mode for tropical tuna purse seine fisheries worldwide. However, the extent of dFAD use remains poorly understood. We present novel approaches for estimating annual dFAD deployments and number of dFADs monitored by individual vessels, using empirical data and robust estimation procedures. We leveraged observer and logbook data, combined with new dFAD tracking data from the Western and Central Pacific Ocean (WCPO) purse seine fishery, the largest tuna fishery in the world, to evaluate trends in dFAD use across the entire WCPO between 2011 and 2019. Average estimates ranged between 20 000 and 40 000 deployments per year, depending on the methodology, with the total number of deployments appearing relatively stable over the last decade. The median number of active buoys monitored per vessel per day ranged from 45 to 75 depending on the year, well below the current management limit of 350. Our results contrast with other oceans, having fewer buoys monitored per vessel, a unique stable trend, but overall number of deployments two times higher than any other ocean. This study provides a basis for improved monitoring and management of dFAD use in the WCPO, with applicability for other regions.

Understanding the ecological mechanisms underpinning distribution patterns is vital in managing populations of mobile marine species. This study is a first step towards an integrated description of the habitats and spatial distributions of marine predators in the Natural Park of the Coral Sea, one of the world’s largest marine-protected areas at about 1.3 million km2, covering the entirety of New Caledonia’s pelagic waters. The study aims to quantify the benefit of including a proxy for prey abundance in predator niche modelling, relative to other marine physical variables. Spatial distributions and relationships with environmental data were analysed using catch per unit of effort data for three fish species (albacore tuna, yellowfin tuna and dolphinfish), sightings collected from aerial surveys for three cetacean guilds (Delphininae, Globicephalinae and Ziphiidae) and foraging locations identified from bio-tracking for three seabird species (wedge-tailed shearwater, Tahiti petrel and red-footed booby). Predator distributions were modelled as a function of a static covariate (bathymetry), oceanographic covariates (sea surface temperature, chlorophyll-a concentration and 20 °C-isotherm depth) and an acoustically derived micronekton preyscape covariate. While distributions were mostly linked to bathymetry for seabirds, and chlorophyll and temperature for fish and cetaceans, acoustically derived prey abundance proxies slightly improved distribution models for all fishes and seabirds except the Tahiti petrel, but not for the cetaceans. Predicted spatial distributions showed that pelagic habitats occupied by predator fishes did not spatially overlap. Finally, predicted habitats and the use of the preyscapes in predator habitat modelling were discussed.

Climate-driven redistribution of tuna threatens to disrupt the economies of Pacific Small Island Developing States (SIDS) and sustainable management of the world’s largest tuna fishery. Here we show that by 2050, under a high greenhouse gas emissions scenario (RCP 8.5), the total biomass of three tuna species in the waters of ten Pacific SIDS could decline by an average of 13% (range = −5% to −20%) due to a greater proportion of fish occurring in the high seas. The potential implications for Pacific Island economies in 2050 include an average decline in purse-seine catch of 20% (range = −10% to −30%), an average annual loss in regional tuna-fishing access fees of US$90 million (range = −US$40 million to –US$140 million) and reductions in government revenue of up to 13% (range = −8% to −17%) for individual Pacific SIDS. Redistribution of tuna under a lower-emissions scenario (RCP 4.5) is projected to reduce the purse-seine catch from the waters of Pacific SIDS by an average of only 3% (range = −12% to +9%), indicating that even greater reductions in greenhouse gas emissions, in line with the Paris Agreement, would provide a pathway to sustainability for tuna-dependent Pacific Island economies. An additional pathway involves Pacific SIDS negotiating within the regional fisheries management organization to maintain the present-day benefits they receive from tuna, regardless of the effects of climate change on the distribution of the fish. Climate change will alter the distribution of tuna, impacting the economies of Pacific Small Island Developing States. This study finds that greater greenhouse gas emissions will worsen these impacts.

Let k be a positive integer at least 2. A graph is k-critical if it can be colored in no fewer than k colors and its proper subgraphs can be colored in fewer than k colors. T. Gallai asked whether a k-critical graph on n vertices contains n distinct ( k − 1 ) -critical subgraphs. This paper gives an affirmative answer to Gallai's question restricted to 4-critical graphs by proving they contain at least 8 3 n − 29 3 odd cycles. For 2-connected nonbipartite graphs, it is shown that the cycle space of such a graph is generated by its odd cycles and that its cyclomatic number provides a sharp lower bound for the number of its odd cycles. For 3-connected nonbipartite graphs, it is shown that the cycle space of such a graph is generated by the set of odd cycles containing any fixed vertex. An initially bipartite ear decomposition is described and is used to show that these graphs contain a spanning 2-connected bipartite subgraph, and contain at least as many odd cycles as the number of their vertices.

A series of computational laboratory experiments aimed at teaching students principles of rational drug design are described and evaluated. These experiments range from an introduction to viewing protein–ligand complexes to optimizing geometries of potential drugs with quantum chemistry and automated docking. Student feedback indicates that such a course increased their appreciation for the roles of chemists in the drug discovery–development process.

Principal Component Analysis on a series of molecular geometries (e.g., a reaction coordinate or trajectory) provides maximum structural variance in the fewest dimensions, and so can offer an objective, comprehensible depiction of the transformation., Most chemical transformations (reactions or conformational changes) that are of interest to researchers have many degrees of freedom, usually too many to visualize without reducing the dimensionality of the system to include only the most important atomic motions. In this article, we describe a method of using Principal Component Analysis (PCA) for analyzing a series of molecular geometries (e.g., a reaction pathway or molecular dynamics trajectory) and determining the reduced dimensional space that captures the most structural variance in the fewest dimensions. The software written to carry out this method is called PathReducer, which permits (1) visualizing the geometries in a reduced dimensional space, (2) determining the axes that make up the reduced dimensional space, and (3) projecting the series of geometries into the low-dimensional space for visualization. We investigated two options to represent molecular structures within PathReducer: aligned Cartesian coordinates and matrices of interatomic distances. We found that interatomic distance matrices better captured non-linear motions in a smaller number of dimensions. To demonstrate the utility of PathReducer, we have carried out a number of applications where we have projected molecular dynamics trajectories into a reduced dimensional space defined by an intrinsic reaction coordinate. The visualizations provided by this analysis show that dynamic paths can differ greatly from the minimum energy pathway on a potential energy surface. Viewing intrinsic reaction coordinates and trajectories in this way provides a quick way to gather qualitative information about the pathways trajectories take relative to a minimum energy path. Given that the outputs from PCA are linear combinations of the input molecular structure coordinates (i.e., Cartesian coordinates or interatomic distances), they can be easily transferred to other types of calculations that require the definition of a reduced dimensional space (e.g., biased molecular dynamics simulations).

Interlaboratory evaluations of Mucorales qPCR assays were developed to assess the reproducibility and performance of methods currently used. The participants comprised 12 laboratories from French university hospitals (nine of them participating in the Modimucor study) and 11 laboratories participating in the Fungal PCR Initiative. For panel 1, three sera were each spiked with DNA from three different species (Rhizomucor pusillus, Lichtheimia corymbifera, Rhizopus oryzae). For panel 2, six sera with three concentrations of R. pusillus and L. corymbifera (1, 10, and 100 genomes/ml) were prepared. Each panel included a blind negative-control serum. A form was distributed with each panel to collect results and required technical information, including DNA extraction method, sample volume used, DNA elution volume, qPCR method, qPCR template input volume, qPCR total reaction volume, qPCR platform, and qPCR reagents used. For panel 1, assessing 18 different protocols, qualitative results (positive or negative) were correct in 97% of cases (70/72). A very low interlaboratory variability in Cq values (SD = 1.89 cycles) were observed. For panel 2 assessing 26 different protocols, the detection rates were high (77–100%) for 5/6 of spiked serum. There was a significant association between the qPCR platform and performance. However, certain technical steps and optimal combinations of factors may also impact performance. The good reproducibility and performance demonstrated in this study support the use of Mucorales qPCR as part of the diagnostic strategy for mucormycosis.

Although climate change occurs alongside other anthropogenic ecosystem impacts, little is known about how sea-surface temperature variability influences the ecotoxicology of persistent organic pollutants (POPs). We analyzed POP contaminant levels, and stable isotopes δ(15)N and δ(13)C as measures of trophic position in eggs collected from the Gulf of Alaska and Bering Sea between 1999 and 2010 from two similar avian species with different trophic positions: common murres (Uria aalge) and thick-billed murres (Uria lomvia). The ebb and flow of the Pacific Decadal Oscillation (PDO), a long-lived El Niño-like pattern of climate variability in the Pacific Ocean, predicted both trophic position and polychlorinated biphenyl (PCB) levels in thick-billed murres, but not in common murres. There was a similar pattern of association of the PDO with organochlorine pesticide levels in thick-billed murres, but not in common murres. The magnitude of association in thick-billed murres of PDO with the concentration of a specific PCB congener was a function of the number of chlorine groups on the PCB congener. Although this statistical analysis does not account for all factors contributing to climate variation, this contrast between the species suggests that facultative changes in foraging behavior, reflected in trophic position, can determine how POPs flow through and thereby alter ecosystems under climate change.

Simulating drug binding and unbinding is a challenge, as the rugged energy landscapes that separate bound and unbound states require extensive sampling that consumes significant computational resources. Here, we describe the use of interactive molecular dynamics in virtual reality (iMD-VR) as an accurate low-cost strategy for flexible protein-ligand docking. We outline an experimental protocol which enables expert iMD-VR users to guide ligands into and out of the binding pockets of trypsin, neuraminidase, and HIV-1 protease, and recreate their respective crystallographic protein-ligand binding poses within 5 - 10 minutes. Following a brief training phase, our studies shown that iMD-VR novices were able to generate unbinding and rebinding pathways on similar timescales as iMD-VR experts, with the majority able to recover binding poses within 2.15 Angstrom RMSD of the crystallographic binding pose. These results indicate that iMD-VR affords sufficient control for users to carry out the detailed atomic manipulations required to dock flexible ligands into dynamic enzyme active sites and recover crystallographic poses, offering an interesting new approach for simulating drug docking and generating binding hypotheses., PLOS ONE

The Advanced Placement® Human Geography (AP HG) course has shown tremendous growth since 2001, the first year students took the end-of-course exam. Slightly more than 3,000 students took the exam t...

An efficient synthesis of stereodefined tetrasubstituted acyclic all-carbon olefins has been developed via a bis(2,6-xylyl)phosphate formation of stereoenriched tertiary alcohols, followed by in situ syn-elimination of the corresponding phosphates under mild conditions. This chemistry tolerates a wide variety of electronically and sterically diverse substrates and generates the desired tetrasubstituted olefins in high yields and stereoselectivities (>95:5) in most cases. This stereocontrolled olefin synthesis has been applied to the synthesis of anticancer drug tamoxifen in three steps from commercially available 1,2-diphenylbutan-1-one in 97:3 stereoselectivity and 78% overall yield.

When new concepts, models, or theories are introduced in a course, their presentation should be accurate, even if depth is not the goal. In a recent publication in this Journal, the Woodward–Hoffmann rules were invoked in the context of a new laboratory experiment, but the associated description was inaccurate. Here we aim to clarify the theoretical background relevant to the described laboratory experiment, and we describe a new computational experiment that could be used to further illuminate the relevant theoretical concepts.

Density functional theory calculations were carried out in order to determine the viability of putative mechanistic pathways for formation of the diterpenoid (+)-chatancin. It was found that a cycloaddition involving a pyrylium ion would have a lower energetic barrier than previously proposed cycloadditions involving a 2H-pyran or furan. All three reactions are predicted to be concerted.

The existence of post-transition state bifurcations on potential energy surfaces for organic and biological reaction mechanisms has been known for decades, but recently, new reports of bifurcations have been occurring at a much higher rate. Beyond simply discovering bifurcations, computational chemists are developing techniques to understand what aspects of molecular structure and vibrations control the product selectivity in systems containing bifurcations. For example, the distribution of products seen in simulations has been found to be extremely sensitive to the local environment of the reacting system (i.e. the presence of a catalyst, enzyme, or explicit solvent molecules). The outlook for the future of this field is discussed, with an eye towards the application of the principles discussed here by experimental chemists to design a reaction setup to efficiently generate desired products.

Dynamics calculations are described for carbocation rearrangements involving product-forming pathways with post-transition-state bifurcations. We show that noncovalent interactions with associated benzene rings (a simple model of aromatic amino acid side chains) can switch inherent dynamical tendencies for competing modes of disrotation, establishing that meaningful changes in dynamically controlled product selectivity can be achieved with few weak noncovalent interactions.

In recent years, engineering educators have begun to focus more on new learning methods that allow students to better understand and practice their subject matter. However, these approaches are not ideal for every student, and can be costly or time consuming to educators and institutions. Instead, a more individualized approach to learning is needed. This paper addresses this challenge through a narrative game system. Building on top of a previously created narrative game, the system utilizes metacognitive strategies (Roadmap, What I Know-What I Want to Know-What I Have Solved, and Think-Aloud-Share-Solve) and a random forest machine learning model to model a student's learning process. Based on data collected from the student, including emotional state, time, and errors in solutions, the system can estimate the current stage in the learning process. The student can then be offered prompts or hints to guide learning in a positive and productive direction, dynamically correcting misconceptions and allowing the student to learn at his/her own pace in a stress-free environment.

Although climate change occurs alongside other anthropogenic ecosystem impacts, little is known about how sea-surface temperature variability influences the ecotoxicology of persistent organic pollutants (POPs). We analyzed POP contaminant levels, and stable isotopes δ15N and δ13C as measures of trophic position, in eggs collected from the Gulf of Alaska and Bering Sea between 1999 and 2010 from two similar avian species with different trophic positions: common murres (Uria aalge) and thick-billed murres (Uria lomvia). The ebb and flow of the Pacific Decadal Oscillation (PDO), a long-lived El Nino-like pattern of climate variability in the Pacific Ocean, predicted both trophic position and polychlorinated biphenyl (PCB) levels in thick-billed murres, but not in common murres. There was a similar pattern of association of the PDO with organochlorine pesticide levels in thick-billed murres, but not in common murres. The magnitude of association in thick-billed murres of PDO with the level of a specific PCB congener was a function of the number of chlorine groups on the PCB congener. Although this statistical analysis does not account for all factors contributing to climate variation, this contrast between the species suggests that facultative changes in foraging behavior, reflected in trophic position, can determine how POPs flow through and thereby alter ecosystems under climate change.

AP Human Geography students need to develop an understanding of what it means to examine the world around them from a geographic perspective. Focusing attention on geography's concern with spatial relationships, place characteristics, and geographic context helps student appreciate the nature of the discipline and the insights it offers. These core geographic concerns should be woven into discussions of the various topics covered in AP Human Geography. Drawing on GIS and related geospatial technologies can facilitate that effort—demonstrating the power and potential of geographical modes of thinking and analysis.

We investigate the potential of verifying whether individual purse seine sets were made in association with a fish aggregation device (FAD) or on an unassociated (FAD-free) tuna school, on the basis of low intensity catch sampling by onboard observers. The target tuna catch and length compositions and bycatch amounts were analyzed from more than 50,000 purse seine sets sampled by onboard observers who had, in addition to collecting sampling data on species and size composition of target tunas in the catch, and set-level estimates of total bycatch, also identified the sets as either “associated” or “unassociated”. Classification tree (CT) models were developed based on 2007–2011 observer data and tested for misclassification error rates on 2012 data. Two types of model misclassification errors (MCE) are possible: unassociated sets misclassified as associated (termed false positive or Type I) and associated sets misclassified as unassociated sets (false negative or Type II error). A third error measure, overall MCE, is a weighted average of Type I and Type II errors. The classification rules developed on the basis of observer catch sampling tended to be nearly presence/absence, e.g. greater than 99% skipjack composition or presence of 0.5 kg rainbow runner, likely keyed by the modest observer sample sizes. Overall MCE rates were 21.8% for the initial tuna-only CT model and 14.4% for the bycatch-included model. The improvement in overall classification for the bycatch models derived principally from a reduction in Type I errors. The addition of auxiliary non-sampling variables (e.g., longitude, month) and use of more complex resampling extensions to CT modelling led to little to no improvement in MCE rates. We employed our methodology to analyze a particular subset of the purse seine data, i.e., sets from the FAD-closure periods of 2009–12. The intent was to determine if MCE rates of these particular sets were greater than the MCE rates found in the more general analysis. Reassuringly, the MCE rates of sets during the FAD closure period were found to be equal, or even a bit lower than MCE rates in the broader analyses based on our best performing model.

In this paper we introduce the idea of a pentual which is a 5-player extension of the well-known idea of a duel. We find the elimination probabilities of players under the assumption that each player tries to eliminate the strongest survivor at every stage. We focus mainly on the winning probability of the strongest player among the five and show that in many plausible situations this player does not even have a 20% chance of winning the game.

An acid-catalyzed Prins/semipinacol rearrangement cascade reaction of hydroxylated pinene derivatives that leads to tricyclic fenchone-type scaffolds in very high yields and diastereoselectivity has been developed. Quantum chemical analysis of the selectivity-determining step provides support for the existence of an extremely flat potential energy surface around the transition state structure. This transition state structure appears to be ambimodal, i.e., the fenchone-type tricyclic scaffolds are formed in preference to the competing formation of a bornyl (camphor-type) skeleton under dynamic control via a post-transition state bifurcation (PTSB).

Cophotolysis of noradamantyldiazirine with the phenanthride precursor of dichlorocarbene or phenylchlorodiazirine in pentane at room temperature produces noradamantylethylenes in 11% yield with slight diastereoselectivity. Cophotolysis of adamantyldiazirine with phenylchlorodiazirine in pentane at room temperature generates adamantylethylenes in 6% yield with no diastereoselectivity. (1)H NMR showed the reaction of noradamantyldiazirine + phenylchlorodiazirine to be independent of solvent, and the rate of noradamantyldiazirine consumption correlated with the rate of ethylene formation. Laser flash photolysis showed that reaction of phenylchlorocarbene + adamantene was independent of adamantene concentration. The reaction of phenylchlorocarbene + homoadamantene produces the ethylene products with k = 9.6 × 10(5) M(-1) s(-1). Calculations at the UB3LYP/6-31+G(d,p) and UM062X/6-31+G(d,p)//UB3LYP/6-31+G(d,p) levels show the formation of exocyclic ethylenes to proceed (a) on the singlet surface via stepwise addition of phenylchlorocarbene (PhCCl) to bridgehead alkenes adamantene and homoadamantene, respectively, producing an intermediate singlet diradical in each case, or (b) via addition of PhCCl to the diazo analogues of noradamantyl- and adamantyldiazirine. Preliminary direct dynamics calculations on adamantene + PhCCl show a high degree of recrossing (68%), indicative of a flat transition state surface. Overall, 9% of the total trajectories formed noradamantylethylene product, each proceeding via the computed singlet diradical.

Post-transition state bifurcations are described that lead to unexpected byproducts in Rh-promoted C–H insertion reactions., Byproducts of chemical reactions are generally thought to result from the competition between two reaction pathways, each with its own rate-determining transition state structure. We show here, however, that pathways with a single transition state structure followed by a post-transition state bifurcation may also be a source of undesired products, especially those whose appearance is unexpected. The viability of this scenario for intramolecular C–H insertion reactions affording β-lactones via Rh-carbenoid intermediates is assessed through quantum chemical calculations on potential energy surfaces and quasi-classical molecular dynamics simulations. It appears that, in these cases, the rhodium catalyst is to blame for the accessibility of a second, unintended, pathway following the transition state structure for β-lactone formation that leads to fragmentation to a ketene and carbonyl compound. If an unexpected product is formed via a post-transition state bifurcation, conventional strategies for suppressing its formation are unlikely to succeed. Guidelines for recognizing the presence of a post-transition state bifurcation are described here, along with hints at means for controlling product distributions.

In this paper we examine the expected probabilities of survival of each of the three participants in sequential truels assuming uniform distributions for their marksmanships. We start by discussing the two most common sequential truels, one in which everyone has to attempt to eliminate someone on each turn, and the other in which the weakest marksman has the option to abstain. We conjecture that the expected winning probabilities in sequential truels cannot be calculated analytically, and so we estimate these probabilities using multiple computational approaches. We also calculate the expected winning probabilities of each of the participants for one fixed marksmanship at a time. At the end we show that as the three marksmanships approach 0, the sequential truel approaches the simultaneous truel and this explains some aspects of the sequential truel for small marksmanships.

The min-edge clique partition problem asks to find a partition of the vertices of a graph into a set of cliques with the fewest edges between cliques. This is a known NP-complete problem and has been studied extensively in the scope of fixed-parameter tractability (FPT) where it is commonly known as the Cluster Deletion problem. Many of the recently-developed FPT algorithms rely on being able to solve Cluster Deletion in polynomial time on restricted graph structures. We prove new structural properties of cographs which characterize how a largest clique interacts with the rest of the graph. These results imply a remarkably simple polynomial time algorithm for Cluster Deletion on cographs. In contrast, we observe that Cluster Deletion remains NP-hard on a hereditary graph class which is slightly larger than cographs.

The diameter of a graph is the maximum distance between any pair of vertices in the graph. The Diameter-tAugmentation problem takes as input a graph G=(V,E) and a positive integer k and asks whether there exists a set E"2 of at most k new edges so that the graph G"2=(V,[email protected]?E"2) has diameter t. This problem is NP-hard (Schoone et al. 1987) [10], even in the t=2 case (Li et al. 1992) [7]. We give a parameterized reduction from Dominating Set to Diameter-tAugmentation to prove that Diameter-tAugmentation is W[2]-hard for every t.

This review describes unexpected dynamical behaviors of rearranging carbocations and the modern computational methods used to elucidate these aspects of reaction mechanisms. Unique potential energy surface topologies associated with these rearrangements have been discovered in recent years that are not only of fundamental interest, but also provide insight into the way Nature manipulates chemical space to accomplish specific chemical transformations. Cautions for analyzing both experimental and theoretical data on carbocation rearrangements are included throughout.

This review describes unexpected dynamical behaviors of rearranging carbocations and the modern computational methods used to elucidate these aspects of reaction mechanisms. Unique potential energy surface topologies associated with these rearrangements have been discovered in recent years that are not only of fundamental interest, but also provide insight into the way Nature manipulates chemical space to accomplish specific chemical transformations. Cautions for analyzing both experimental and theoretical data on carbocation rearrangements are included throughout.

In genome-scale RNA interference (RNAi) screens, it is critical to control false positives and false negatives statistically. Traditional statistical methods for controlling false discovery and false nondiscovery rates are inappropriate for hit selection in RNAi screens because the major goal in RNAi screens is to control both the proportion of short interfering RNAs (siRNAs) with a small effect among selected hits and the proportion of siRNAs with a large effect among declared nonhits. An effective method based on strictly standardized mean difference (SSMD) has been proposed for statistically controlling false discovery rate (FDR) and false nondiscovery rate (FNDR) appropriate for RNAi screens. In this article, the authors explore the utility of the SSMD-based method for hit selection in RNAi screens. As demonstrated in 2 genome-scale RNAi screens, the SSMD-based method addresses the unmet need of controlling for the proportion of siRNAs with a small effect among selected hits, as well as controlling for the proportion of siRNAs with a large effect among declared nonhits. Furthermore, the SSMD-based method results in reasonably low FDR and FNDR for selecting inhibition or activation hits. This method works effectively and should have a broad utility for hit selection in RNAi screens with replicates. (Journal of Biomolecular Screening 2010:1123-1131)

Behavioural thermoregulation is important for the success of cool-climate lizards, and a basis of the cold-climate hypothesis for the evolution of viviparity in squamate reptiles. The temperature (Tsel) selected by pregnant females in a thermal gradient is considered to be optimal for embryonic development; however, exposure to Tsel throughout pregnancy has been difficult to estimate in small-bodied lizards as temperature-sensitive telemetry is impractical. In addition, the value of maternal thermophily during pregnancy is controversial: some studies have shown elevated Tsel, whereas others have found lowered Tsel or no change during pregnancy. We estimated indirectly the overall exposure to Tsel during the 4–5 months of pregnancy of the cool-climate, sub-alpine species Oligosoma maccanni (McCann's skink, 3–6 g) from southern New Zealand. The thermal environment available to skinks was modelled using temperature loggers inside validated copper models in basking and retreat sites. Pregnant skinks were able to achieve mean Tsel (28.9 °C) in the field very infrequently (4–15% of each month during the final 4 months of pregnancy). In field thermoregulatory studies, pregnant females did not bask more frequently and did not show altered field body temperature compared with non-pregnant adults, suggesting that all skinks (whether pregnant or not) thermoregulate maximally whenever conditions allow. Further research on cool-climate lizards should address the significance for offspring phenotypes of low and variable exposure to Tsel during pregnancy, as well as the significance of temperatures for embryos in maternal bodies (viviparity) versus nest sites (oviparity) arising from differences in maternal body size. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 96, 541–552.

Bovine keratoconjunctivitis (BKC), colloquially referred to as ‘pinkeye’, is a disease affecting cattle worldwide; it costs cattle producers millions of dollars in economic loss annually. While Moraxella spp. are the primary etiologic agent of pinkeye, surveys of flora from the conjunctivae of livestock from around the world have indicated that a variety of bacterial commensals occupy this niche. We used molecular biology-based methods to determine the composition of bacterial flora in the conjunctivae of normal dairy and beef cattle from Maryland (n = 113), and beef cattle with clinical BKC from Louisiana (n = 42). Three regimens were used: 16S rRNA PCR and DGGE analysis of amplicons; 16S rRNA PCR and cloning of amplicons into Escherichia coli followed by screening and sequencing of clones harboring inserts; and culture of bacteria on chromogenic agar followed by 16S rRNA PCR and sequencing. Most taxa were comprised of saprophytes found in the environment, such as Bacillus, Pantoea, E. coli, and Exiguobacterium. Moraxella spp. were infrequently observed. Some species, such as Propionibacterium acnes, represent taxa not previously associated with the conjunctivae. Bacillus pumilus and Bacillus licheniformis isolates from the conjunctivae of Maryland cattle were genetically distinct from isolates previously implicated in septic infections in cattle at the same location. We conclude that employing 16S rRNA-based methods for bacterial identification can be useful in defining the flora present in the conjunctivae of normal cattle, and those with BKC.

Both acoustic and sediment surveys were carried out in the Broughton Archipelago, British Columbia, in order to map a former aquaculture site and calibrate acoustic surveys with georeferenced sediment properties. The acoustic surveys included EM3000 Multibeam (including backscatter) and QTC VIEW™ (Series IV) technologies, while the geotechnical survey entailed Van Veen grab sampling of surface sediments and associated analyses. The two acoustic technologies were consistent in their ability to identify distinct regions of seafloor characterized by rock outcrops, consolidated substrates, or gel-mud depositional fields. Both multibeam backscatter data and QTC VIEW™ number-coded classifications were extracted across a range of circular areas located at each georeferenced sampling station (radii: 2, 3, 4, 5, 8, 12, 16, 20 m). Statistical correlations were observed between backscatter and certain geotechnical properties, such as sediment porosity, sediment grain size fractions (

Perchlorate has been detected in U.S. milk samples from many different states. Applying data from a recently reported 9-week experiment in which 16 Holstein dairy cows were administered perchlorate allowed us to derive an equation for the dose-response relationship between perchlorate concentrations in feed/drinking water and its appearance in milk. Examination of background concentrations of perchlorate in the total mixed ration (TMR) fed in addition to the variable dose supplied to treated cows as a ruminal infusate revealed that cows receive significant and variable exposure to perchlorate from the TMR. Weekly examination of the TMR disclosed that a change in ingredients midway through the experiment caused a significant (78%) change in TMR perchlorate concentration. Analyses of the ingredients comprising the TMR revealed that 41.9% of the perchlorate came from corn silage, 22.9% came from alfalfa hay and 11.7% was supplied by sudan grass. Finally, USDA Food and Nutrition Survey data on fluid milk consumption were used to predict potential human exposure from milk that contained concentrations of perchlorate observed in our previous dosing study. The study suggests that reducing perchlorate concentration in dairy feed may reduce perchlorate concentrations in milk as well as the potential to reduce human exposure to perchlorate in milk.

Consider a general linear model with p -dimensional parameter vector beta and i.i.d. normal errors. Let K(1), ..., K(k ), and L be linearly independent vectors of constants such that L(T)beta not equal 0. We describe exact simultaneous tests for hypotheses that Ki(T)beta/L(T)beta equal specified constants using one-sided and two-sided alternatives, and describe exact simultaneous confidence intervals for these ratios. In the case where the confidence set is a single bounded contiguous set, we describe what we claim are the best possible conservative simultaneous confidence intervals for these ratios - best in that they form the minimum k -dimensional hypercube enclosing the exact simultaneous confidence set. We show that in the case of k = 2, this "box" is defined by the minimum and maximum values for the two ratios in the simultaneous confidence set and that these values are obtained via one of two sources: either from the solutions to each of four systems of equations or at points along the boundary of the simultaneous confidence set where the correlation between two t variables is zero. We then verify that these intervals are narrower than those previously presented in the literature.

Many challenges exist for high-stakes testing programs offering continuous computerized administration. The automated assembly of test questions to exactly meet content and other requirements, provide uniformity, and control item exposure can be modeled and solved by mixed-integer programming (MIP) methods. A case study of the computerized licensing examination of the American Institute of Certified Public Accountants is offered as one application of MIP techniques for test assembly. The solution illustrates assembly for a computer-adaptive multistage testing design. However, the general form of the constraint-based solution can be modified to generate optimal test designs for paper-based or computerized administrations, regardless of the specific psychometric model. An extension of this methodology allows for long-term planning for the production and use of test content on the basis of an exact psychometric test designs and administration schedules.

Time series based neural network and fuzzy logic models were developed for fish recruitment analysis using fish stock–recruitment data incorporating environmental information. Data from the Pacific halibut stock with the Pacific Decadal Oscillation (PDO) index as the environmental variable was used for the model development. The neural network model was developed based on the multi-layer feed-forward neural network model with back-propagation learning algorithm. The fuzzy logic model was developed based on the fuzzification of the PDO index into two fuzzy sets denoted as “positive” and “negative” regimes. We compared the performance of these models to the traditional Ricker stock–recruitment model and the Ricker model with PDO as covariate. All four models showed significant residual time series structure in the form of first order autocorrelation. To account for this time series structure, an autoregressive component was added to each model. It was demonstrated that the fuzzy logic model outperformed the traditional Ricker stock–recruitment model, the Ricker model with PDO as covariate and the neural network model as measured by several diagnostic criteria. In addition, the simple Ricker stock–recruitment model corrected with the autoregressive time series residuals outperformed the Ricker model with PDO as covariate, neural network model and fuzzy logic model ignoring the time series residuals. The importance of the PDO to halibut recruitment is discussed in terms of developing a harvest policy.