Complex Hypothesis Research Articles

Evaluating scenarios for the evolutionary assembly of the brachiopod body plan

The fossil faunas of the Cambrian provide the only direct insight into the assembly of animal body plans. However, for many animal groups, their early fossil record is linked to disarticulated remains, interpretation of which is problematic since they possess few characters from which their affinity to phyla can be established and, indeed, few characters at all. One such group is the tommotiids, which has been interpreted, on the basis of skeletal anatomy, as a paraphyletic assemblage uniting brachiopods and phoronids, through the acquisition and subsequent modification, or loss, of an imbricated set of dorsal phosphatic sclerites. Here we present a reexamination of the fossil evidence uniting the tommotiids and brachiopods, supplemented with new anatomical data from synchrotron radiation X-ray tomographic microscopy of key tommotiid taxa. The characters used to support the complex hypothesis of character evolution in the brachiopod stem lineage relies on scleritome reconstructions and inferred mode of life which themselves rely on brachiopods being chosen as the interpretative model. We advocate a more conservative interpretation of the affinity of these fossils, based a priori on their intrinsic properties, rather than the modern analogue in whose light they have been interpreted.

Testing multiple biological mediators simultaneously

Modern biomedical and epidemiological studies often measure hundreds or thousands of biomarkers, such as gene expression or metabolite levels. Although there is an extensive statistical literature on adjusting for 'multiple comparisons' when testing whether these biomarkers are directly associated with a disease, testing whether they are biological mediators between a known risk factor and a disease requires a more complex null hypothesis, thus offering additional methodological challenges. We propose a permutation approach that tests multiple putative mediators and controls the family wise error rate. We demonstrate that, unlike when testing direct associations, replacing the Bonferroni correction with a permutation approach that focuses on the maximum of the test statistics can significantly improve the power to detect mediators even when all biomarkers are independent. Through simulations, we show the power of our method is 2-5× larger than the power achieved by Bonferroni correction. Finally, we apply our permutation test to a case-control study of dietary risk factors and colorectal adenoma to show that, of 149 test metabolites, docosahexaenoate is a possible mediator between fish consumption and decreased colorectal adenoma risk. R-package included in online Supplementary Material.

Cytogenetic and DNA barcoding reveals high divergence within the trahira, Hoplias malabaricus (Characiformes: Erythrinidae) from the lower Amazon River

Molecular and cytogenetic data have provided evidence of cryptic speciation in the widespread South American trahira, Hoplias malabaricus. In the present study, karyotypes and DNA barcode sequences of specimens from seven populations inhabiting the lower Amazon River were analyzed in order to characterize the levels of genetic divergence within a single karyomorph. All the specimens presented karyotypes with 2n = 40 chromosomes (20m+20sm) that were consistent with the species' C karyomorph. The DNA barcodes revealed six haplogroups, with clear divergence between populations from Brazil and Argentina. The results support the species complex hypothesis and indicate that a single karyomorph of H. malabaricus may harbor more than one species

The Influence of Presentation Format on the “Bigger is Better” (BIB) Effect

Two experiments tested the "bigger is better" (BIB) effect, whereby bigger objects are perceived more favorably than smaller ones. In Experiment 1, participants directly compared pairs of objects and a strong BIB effect was obtained for both positively and negatively valenced stimuli. In Experiment 2, comparative and absolute evaluations were combined in a single experiment and the BIB effect was mediated for positively and negatively valenced stimuli. Taken in combination, the data support a complex hypothesis that pair-wise presentations induce a comparative process that causes a BIB effect. But when objects are evaluated separately, size and valence interact such that increased size evokes more positive ratings of positive objects and more negative ratings for negative objects.

Nitrate therapy and nitrate tolerance in patients with coronary artery disease

Despite the continuous development of newer drugs, the therapy of coronary artery disease remains challenging. Organic nitrates are among the oldest drugs, but they still remain a widely used adjuvant in the treatment of symptomatic coronary artery disease. While their efficacy in relieving angina pectoris symptoms in acute settings and in preventing angina before physical or emotional stress is undisputed, the chronic use of nitrates has been associated with potentially important side effects such as tolerance and endothelial dysfunction. The identification of the mitochondrial aldehyde dehydrogenase as the enzyme responsible for the bioactivation of nitroglycerin has allowed the formulation of a complex but plausible hypothesis regarding the mechanism of action and the development of the side effects associated with nitrate therapy. Further, the discovery of important differences among nitrates suggests that these drugs should not be considered as a homogeneous class. Finally, the identification of nonhemodynamic properties of nitrates, and newer insight on the mechanism of nitrate tolerance, have led us to question the prognostic impact of these drugs.

Molecular taxonomy and evolutionary hypothesis concerning Astyanax fasciatus (Characiformes, Characidae) from Vila Velha State Park and Tibagi and Iguaçu Rivers

A species complex hypothesis involving Astyanax fasciatus from southern Brazil was tested using 12S mtDNA sequences. Phylogenetic inferences were performed with maximum likelihood, maximum parsimony and Bayesian as phylogenetic methods and Hemigrammus bleheri as the outgroup. Besides 11 sequences from A. fasciatus, the data set was comprised of other partial 12S sequences including material from Astyanax altiparanae (two sequences) and Astyanax sp (four sequences), both from the Iguaçu River. The hypothesis of an A. fasciatus species complex was reinforced given the close relationship between A. altiparanae and Astyanax sp observed in the Bayesian tree. Consequently, a taxonomic revision is necessary for these species.

Electrochemical behavior of a discontinuously A6092/SiC/17.5p metal matrix composite in chloride containing solution

Aluminum alloys are used widely in automotive and aerospace industries. The demand for weight savings materials of superior mechanical, thermal and electrical properties has focused attention on aluminum metal matrix composites (AMMCs). AMMCs have been applied in areas that can cost-effectively capitalize on improvements in specific stiffness, specific strength, fatigue resistance, wear resistance, and coefficient of thermal expansion. However, AMMCs typically have lower damage tolerance properties than their unreinforced counterparts, and hence the extent of application in primary structures has been limited. In this paper, the corrosion resistance of ALCOA peak-aged Al6092/SiC/17.5p composite has been evaluated by recording of impedance spectra during immersion over one week in an air-exposed 3.5% NaCl. Results confirmed the occurrence of galvanic, crevice, intergranular corrosion and pitting attack due to the inhomogeneous structure of the composite which is the main reason behind enhancing the corrosion susceptibility. This paper formulates a complex hypothesis concerning the corrosion mechanisms of A6092/SiC/17.5p metal matrix composite in chloride containing solution as a function of time. A four-stage corrosion mechanism has been proposed to explain the sequence and the reasons of occurrence of each corrosion form.

Misinterpreting by localism: transposing European geology and tectonics onto Jamaica and the Antilles

Abstract ‘Localism’ occurs when geologists are most influenced by data with which they are familiar, applying it to new, but not necessarily appropriate, areas of study. Jamaica has been particularly prone to localist interpretations. Henry T. De la Beche (1796–1855) mapped eastern Jamaica in 1823–1824, and made lithostratigraphic comparisons between Jamaica and Europe that were the first attempt at intercontinental correlation. He correlated the Jamaican succession on the basis of lithological similarity to rocks in Europe. Charles A. Matley (1866–1947) is best remembered for his mapping in North Wales. He was geologist to the second geological survey of Jamaica in 1921 and developed the Basal Complex hypothesis which envisaged a geological structure analogous to that of North Wales, where the deformed Mona Complex underlies the Lower Palaeozoic succession. Matley thus provided a ‘factual’ basis for theories that the Antillean islands were the peaks of a foundered continent. Charles T. Trechmann (1885–1964) was the principal opponent of the Basal Complex hypothesis, not recognising evidence for old basement in Jamaica. His ‘answer’ was the Theory of Mountain Uplift, based on gravitational tectonics, but Trechmann's theory was comparable to the earlier fixist theories of tectonics that he learnt as a student.

The beaver meadow complex revisited – the role of beavers in post‐glacial floodplain development

ABSTRACTWe evaluate the validity of the beaver‐meadow complex hypothesis, used to explain the deposition of extensive fine sediment in broad, low‐gradient valleys. Previous work establishes that beaver damming forms wet meadows with multi‐thread channels and enhanced sediment storage, but the long‐term geomorphic effects of beaver are unclear. We focus on two low‐gradient broad valleys, Beaver Meadows and Moraine Park, in Rocky Mountain National Park (Colorado, USA). Both valleys experienced a dramatic decrease in beaver population in the past century and provide an ideal setting for determining whether contemporary geomorphic conditions and sedimentation are within the historical range of variability of valley bottom processes. We examine the geomorphic significance of beaver‐pond sediment by determining the rates and types of sedimentation since the middle Holocene and the role of beaver in driving floodplain evolution through increased channel complexity and fine sediment deposition. Sediment analyses from cores and cutbanks indicate that 33–50% of the alluvial sediment in Beaver Meadows is ponded and 28–40% was deposited in‐channel; in Moraine Park 32–41% is ponded sediment and 40–52% was deposited in‐channel. Radiocarbon ages spanning 4300 years indicate long‐term aggradation rates of ~0.05 cm yr‐1. The observed highly variable short‐term rates indicate temporal heterogeneity in aggradation, which in turn reflects spatial heterogeneity in processes at any point in time. Channel complexity increases directly downstream of beaver dams. The increased complexity forms a positive feedback for beaver‐induced sedimentation; the multi‐thread channel increases potential channel length for further damming, which increases the potential area occupied by beaver ponds and the volume of fine sediment trapped. Channel complexity decreased significantly as surveyed beaver population decreased. Beaver Meadows and Moraine Park represent settings where beaver substantially influence post‐glacial floodplain aggradation. These findings underscore the importance of understanding the historical range of variability of valley bottom processes, and implications for environmental restoration. Copyright © 2011 John Wiley & Sons, Ltd.

HapMap-based study of human soluble glutathione S-transferase enzymes

Glutathione S-transferase enzymes (GSTs; EC: 2.5.1.18) constitute the principal phase II superfamily, which plays a key role in cellular detoxification. GST genes are organized in chromosomal clusters; most of these genes are polymorphic, mainly due to single nucleotide substitutions. Different studies proved significant interethnic differences in GST allelic frequencies but, at present, the role of natural selection in human genetic variability of GSTs is poorly understood. The aim of this study is to investigate the role of natural selection in shaping single nucleotide polymorphism (SNP) diversity of soluble GST genes. Using the HapMap database, we analyzed the population differences in the soluble GST genes using the phasing data from unrelated individuals shared among 11 populations in the International HapMap project. A Fst-based selection test was applied to HapMap data to detect soluble GST loci under selection. Comparisons between GST gene polymorphisms among HapMap populations highlight that ethnicity is an influencing factor of GST genetic variability. By applying a genome scan based on F-statistics, we identified nine SNPs that present F-coefficients significantly more different than those expected under neutrality (rs2239892, rs3814309, rs7483, rs1571858, rs929166, rs11807, rs4715344, rs4715354, and rs3734431). Our study confirms that GST gene variation reflects human demographic history, but it also demonstrates that natural selection could shape the genetic profile of some GST SNPs. Moreover, the identification of human genome regions and targets of natural selection may have detected candidate genes for complex diseases. In analyzing the literature, we provide complex disease hypothesis (male infertility, embryotoxicity) for the identified GST SNPs.

Managing emergent knowledge through deferred action design principles

PurposeThe aim of this paper is to examine empirically the relevance of the theory of deferred action for knowledge management systems (KMS) design in practice.Design/methodology/approachThe study adopts a case study approach to examine knowledge work and knowledge management in virtual teamwork in a large UK telecommunications company to understand the occurrence of emergent knowledge and how it is managed by virtual team leaders. The section in the company studied is described as a “knowledge intensive organization” dealing with the company's e‐commerce activities.FindingsThe analysis confirms the complex adaptive system hypothesis – a complex system adapts to its environment through self‐organization. The data reveal the behaviour of the virtual team to be self‐organizing and adaptive to its environment. It confirms the knowledge tacitness hypothesis and social embeddedness of knowledge hypothesis as important determinants of knowledge sharing. Specifically, the data reveal the main issues concerning knowledge sharing practices of virtual team workers and the crucial team leader's role in the effectiveness of the teams' capability to develop social links to externalise and share tacit knowledge to accomplish tasks.Research limitations/implicationsIn this paper, the authors contribute “emergent knowledge” as a third category of organizational knowledge in addition to the existing tacit and explicit knowledge that needs to be considered when designing KMS. It also derives socio‐technical systems design principles based on the theory of deferred action, and a tentative development process with metrics is then proposed for KMS design that caters for emergent, tacit, and explicit knowledge.Practical implicationsExisting models such as the SECI model do not acknowledge emergent knowledge or its conversion into explicit knowledge. The theory of deferred action is invoked to derive design principles, termed deferred systems design principles, to depict how explicit knowledge, tacit knowledge, and emergent knowledge can be represented to design knowledge management systems for “emergent organizations”.Originality/valueThe study contributes to the limited research and lack of consideration of emergent knowledge as an integral part of organizational knowledge, especially in an era of emergent organizations.

A bayesian method for evaluating and discovering disease loci associations.

BackgroundA genome-wide association study (GWAS) typically involves examining representative SNPs in individuals from some population. A GWAS data set can concern a million SNPs and may soon concern billions. Researchers investigate the association of each SNP individually with a disease, and it is becoming increasingly commonplace to also analyze multi-SNP associations. Techniques for handling so many hypotheses include the Bonferroni correction and recently developed Bayesian methods. These methods can encounter problems. Most importantly, they are not applicable to a complex multi-locus hypothesis which has several competing hypotheses rather than only a null hypothesis. A method that computes the posterior probability of complex hypotheses is a pressing need.Methodology/FindingsWe introduce the Bayesian network posterior probability (BNPP) method which addresses the difficulties. The method represents the relationship between a disease and SNPs using a directed acyclic graph (DAG) model, and computes the likelihood of such models using a Bayesian network scoring criterion. The posterior probability of a hypothesis is computed based on the likelihoods of all competing hypotheses. The BNPP can not only be used to evaluate a hypothesis that has previously been discovered or suspected, but also to discover new disease loci associations. The results of experiments using simulated and real data sets are presented. Our results concerning simulated data sets indicate that the BNPP exhibits both better evaluation and discovery performance than does a p-value based method. For the real data sets, previous findings in the literature are confirmed and additional findings are found.Conclusions/SignificanceWe conclude that the BNPP resolves a pressing problem by providing a way to compute the posterior probability of complex multi-locus hypotheses. A researcher can use the BNPP to determine the expected utility of investigating a hypothesis further. Furthermore, we conclude that the BNPP is a promising method for discovering disease loci associations.

Molecular systematics and species limits in the Philippine fantails (Aves: Rhipidura)

Islands have long-attracted scientists because of their relatively simple biotas and stark geographic boundaries. However, for many islands and archipelagos, this simplicity may be overstated because of methodological and conceptual limitations when these biotas were described. One archipelago that has received relatively little recent attention is the Philippine islands. Although much of its biota was documented long ago, taxonomic revision and evolutionary study has been surprisingly scarce, and only a few molecular phylogenetic studies are beginning to appear. We present a molecular phylogeny and taxonomic revision for the Philippine fantails (Aves: Rhipidura) using nuclear and mitochondrial DNA sequences. Our results suggest that current taxonomy underestimates diversity in the group. Some morphologically distinct subspecies warrant species status, whereas one was indistinguishable genetically and morphologically and should not be retained. A few taxa require additional sampling for thorough taxonomic assessment. Patterns of diversity within Philippine Rhipidura mostly corroborate predictions of the Pleistocene aggregate island complex (PAIC) hypothesis, in which diversity is expected to be partitioned by deep water channels separating Pleistocene aggregate islands rather than by current islands. Substantial structure within PAIC clades indicates that additional drivers of diversification should be considered.

Spatial patterns of tree species richness in two temperate forests

Summary1. The relative contribution of external vs. internal clustering mechanisms for determining community structure and its manifestations has been the subject of a continuous debate, but few attempts have been made to examine their single and joint effects in a compound process model.2. In this study, we tested four a priori hypotheses on the relative importance of habitat heterogeneity (topography and soil) and internal clustering mechanisms such as dispersal limitation on the species–area relationship (SAR) in two fully mapped 25‐ha plots of temperate forests in the Changbaishan (CBS) Nature Reserve, China, and the Chequamegon‐Nicolet National Forest in Wisconsin, USA.3. We used the distance decay curve to test the generality of the results obtained for the SAR. To find out if the relative importance of internal and external clustering mechanisms changed with life stage, we conducted separate analyses for small, large and all trees.4. Model selection favoured the most complex hypothesis that assumed an influence of both habitat heterogeneity and internal clustering on SAR and the distance decay curve. For the CBS plot, which shows weak topographical structuring, models were consistent with data only if soil factors were included into assessment of habitat heterogeneity. At the Wabikon plot, we could not test soil variables, but inclusion of topographical variables substantially improved the fit of the distance decay curve.5. In general, the results of the SAR agreed with those of the distance decay curve, but the latter was sensitive to positive habitat‐mediated species associations. The SAR, but not distance decay, distinguished among competing hypotheses for the community of large trees at CBS, where species exhibited only weak clustering.6. Contrary to our expectations, we did not find substantial differences in the relative importance of internal and external clustering mechanisms with life stage.7. Synthesis. Our analysis of spatial community structure for two relatively diverse temperate forests revealed that the factors governing spatial community structure may not substantially differ from those in highly diverse tropical forests. This result adds to our understanding of the ecological processes underlying the spatial diversity structure in natural forest communities.

AN INTEGRATED FRAMEWORK FOR SUSPECT INVESTIGATION

In a complex crime scene with many possible suspects and conflicting evidence, crime investigation requires scientific and logical steps to narrow down the suspects. Since human investigators have difficulty in fully handling all reasoning in this highly complex hypothesis space, we propose a decision support system to aid the investigation process. The system integrates a rule-based reasoner, a Bayesian network for criminal profiling, and an assumption-based truth maintenance system for evidential reasoning to determine the most plausible suspect. The reasoning process reasons about a profiling classification and an alibi credibility measure. It proved effective in a realistic simulation.

Mouse IPK: A Powerful Tool to Partially Characterize Renal Reperfusion and Preservation Injury.

Main ProblemThe molecular basis of renal preservation injury is not well understood. Since mouse kidney transplantation models are not useful in this setting, a mouse Isolated Perfused Kidney (IPK) model was developed to take advantage of mouse genetic design capabilities for testing complex biological hypothesis regarding mechanisms of preservation injury in transplanted kidneys.MethodsMouse kidneys were recovered, preserved, and reperfused in-vitro with an acellular physiological crystalloid buffer containing hypo-physiological oncotic pressure. Outcome variables were measured to predict preservation injury. These included perfusate flow, vascular resistance, VO2, urine output, GFR, proteinuria, LDH release, and edema. The model was tested by subjecting mouse kidneys to cold storage in University of Wisconsin (UW) solution for 24, 48, or 72 hours (time-dependent preservation injury), cold storage in Euro-Collins Solution (solution dependent preservation injury), and exposure to prior warm ischemia (DCD dependent preservation injury).ResultsThe model accurately predicted the qualitative and quantitative changes in the readouts based on known responses to preservation injury in kidney transplants in large animals and humans.ConclusionThe mouse IPK accurately predicts many of the variables associated with renal organ preservation injury in the very early phases of reperfusion and may provide an attractive model for studying the molecular basis of renal preservation injury.

The new politics of Australian higher education: why universities get rumbled in the budget

This paper questions the dominant arguments that currently frame debate over the political ineffectiveness of the higher education lobby in Australia. Public choice theory is used to advance a more complex hypothesis that takes into account dramatic changes to the political environment over recent decades. This is tested against interview data from policy actors and vice‐chancellors.

Modeling statistic distributions for nonparametric goodness-of-fit criteria for testing complex hypotheses with respect to the inverse Gaussian law

We give percentage point tables and statistic distribution models for non-parametric goodness-of-fit criteria for testing complex hypothesis with respect to the inverse Gaussian law in case of using maximal likelihood estimates.

Impact of Political Reservations in West Bengal Local Governments on Anti-Poverty Targeting

Political reservation for disadvantaged groups is believed to be a way of improving targeting of publicly provided goods to those groups. This paper examines the impact of political reservations for women and scheduled castes and tribe (SC/ST) candidates in local governments in West Bengal, India between 1998-2004 on targeting to landless, low caste and female-headed households. It differs from existing literature by differences in geographic coverage, time span, and use of selfreported household benefits across a broad range of programs. Reservation of chief executive (pradhan) positions in local government for women was associated with a significant worsening of within-village targeting to SC/ST households, and no improvement on any other dimension of targeting. Reservation of pradhan posts for SC/ST members was associated with a significant increase in benefits received by the village as a whole, improvement in intra-village targeting to female-headed households, and to the group (SC or ST) of the pradhan. The effects of women’s reservations are not consistent with simple citizen-candidate or elite capture models of electoral politics. They are consistent with a more complex hypothesis of capture-cum-clientelism which is weakened by election of politically inexperienced women to reserved pradhan posts.

Testing a Dynamic Complex Hypothesis in the Analysis of Land Use Impact on Lake Water Quality

In this study, we proposed a dynamic complex hypothesis that the impact of land use on water quality could vary along the expansion of the buffer size, and there should be an effective buffer zone where the strongest linkage occurs between land use and water quality. The hypothesis was tested and supported by a case study carried out in four watersheds in Hanyang District, China. More specific, buffer analysis and regression model were applied for studying the impacts of land use type, area proportion of land use type, and spatial pattern of land use on water quality. We conclude that not only the proportion of land use but also the spatial pattern moderates the impact of land use on water quality. Our study indicates that the identification of the effective buffer zones can provide new information and ideas for planning and management. Moreover, this study could also partially help to explain the conflicting results on the impact of land use on water quality in buffer versus in catchments in the literatures.