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Effects of taxon sampling on molecular dating for within-genus divergence events,when deep fossils are used for calibration

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Journal of Systematics and Evolution 2009年第5期47卷 383-401页

作者： richard i.MiLNE institute of Molecular Plant Sciences The University of Edinburgh

A universal method of molecular dating that can be applied to all families and genera regardless of their fossil records,or lack thereof,is highly desirable.A possible method for eudicots is to use a large phylogeny calibrated using deep fossils including tricolpate pollen as a fixed(124 mya) calibration *** method was used to calculate node ages within three species-poor disjunct basal eudicot genera,Caulophyllum,Podophyllum and Pachysandra,and sensitivity of these ages to effects such as taxon sampling were then *** deleting from one to three accessions related to each genus in 112 different combinations,a confidence range describing variation due only to taxon sampling was *** for Caulophyllum,Podophyllum and Pachysandra were 8.4-10.6,7.6-20.0,and 17.6-25.0 mya,***,the confidence ranges calculated using bootstrapping were much wider,at 3-19,0-32 and 11-32 mya,***,deleting 10 adjacent taxa had a large effect in Pachysandra only,indicating that undersampling effects are significant among *** to sampling density in neighboring clades,or to the position of the fixed fossil calibration point had small to negligible ***-parametric rate smoothing was more sensitive to taxon sampling effects than was penalized *** wide range for Podophyllum,compared to the other two genera,was probably due to a high degree of rate heterogeneity within this *** ranges calculated by this method could be narrowed by sampling more individuals within the genus of interest,and by sequencing multiple DNA regions from all species in the phylogeny.

关键词： basal eudicots fossil calibration molecular dating North America-East Asia disjunction taxon sampling Tertiary relict tricolpate pollen.

Evolution of systemic therapy of advanced hepatocellular carcinoma

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World Journal of Gastroenterology 2008年第42期14卷 6437-6441页

作者： Thomas Yau Pierre Chan richard epstein Ronnie T Poon Department of Medicine Queen Mary Hospital Department of Surgery Queen Mary Hospital

Hepatocellular carcinoma (HCC) commonly occurs in hepatitis B endemic areas, especially in Asian countries. HCC is highly refractory to cytotoxic chemotherapy. This resistance is partly related to its tumor biology, pharmacokinetic properties, and both intrinsic and acquired drug resistance. There is no convincing evidence thus far that systemic chemotherapy improves overall survival in advanced HCC patients. Other systemic approaches, such as hormonal therapy and immunotherapy, have also disappointing results. Recently, encouraging results have been shown in using sorafenib in the treatment of advanced HCC patients. in this review, we concisely summarize the evolution of developments in the systemic therapy of advanced HCC.

关键词： Advanced hepatocellular carcinoma Chemotherapy Doxorubicin Sorafenib

Hybridization and genome evolution ii： Mechanisms of species divergence and their effects on evolution in hybrids

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Current Zoology 2013年第5期59卷 675-685页

作者： richard i. BAiLEY Fabrice EROUKHMANOFF Glenn-PETER SaeTRE Centre for Ecological and Evolutionary Synthesis (CEES) Department of Biology University of Oslo Norway

Recent genomic studies have highlighted the importance of hybridization and gene exchange in evolution. We ask what factors cause variation in the impact of hybridization, through adaptation in hybrids and the likelihood of hybrid speciation. During speciation, traits that diverge due to both divergent and stabilizing selection can contribute to the buildup of reproductive isolation. Divergent directional selection in parent taxa should lead to intermediate phenotypes in hybrids, whereas stabilizing se- lection can also produce extreme, transgressive phenotypes when hybridization occurs. By examining existing theory and em- pirical data, we discuss how these effects, combined with differences between modes of divergence in the chromosomal distribu- tion of incompatibilities, affect adaptation and speciation in hybrid populations. The result is a clear and testable set of predic- tions that can be used to examine hybrid adaptation and speciation. Stabilizing selection in parents increases transgression in hy- brids, increasing the possibility for novel adaptation. Divergent directional selection causes intermediate hybrid phenotypes and increases their ability to evolve along the direction of parental differentiation. Stabilizing selection biases incompatibilities to- wards autosomes, leading to reduced sexual correlations in trait values and reduced pleiotropy in hybrids, and hence increased freedom in the direction of evolution. Directional selection causes a bias towards sex-linked incompatibilities, with the opposite consequences. Divergence by directional selection leads to greater dominance effects than stabilizing selection, with major but variable impacts on hybrid evolution [Current Zoology 59 （5）： 675-685, 2013].

关键词： Evolvability Constraints Dimensionality Hybrid Adaptation

Hybridization and genome evolution i： The role of contingency during hybrid speciation

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Current Zoology 2013年第5期59卷 667-674页

作者： Fabrice EROUKHMANOFF richard i. BAiLEY Glenn-PETER SaeTRE Centre for Ecological and Evolutionary Synthesis (CEES) Department of Biology University of Oslo Norway

Homoploid hybrid speciation （HHS） involves the recombination of two differentiated genomes into a novel, func- tional one without a change in chromosome number. Theoretically, there are numerous ways for two parental genomes to recom- bine. Hence, chance may play a large role in the formation of a hybrid species. if these genome combinations can evolve rapidly following hybridization and sympatric situations are numerous, recurrent homoploid hybrid speciation is a possibility. We argue that three different, but not mutually exclusive, types of contingencies could influence this process. First, many of these ＂hopeful monsters＂ of recombinant parent genotypes would likely have low fitness. Only specific combinations of parental genomic con- tributions may produce viable, intra-fertile hybrid species able to accommodate potential constraints arising from intragenomic conflict. Second, ecological conditions （competition, geography of the contact zones or the initial frequency of both parent spe- cies） might favor different outcomes ranging from sympatric coexistence to the formation of hybrid swarms and ultimately hybrid speciation. Finally, history may also play an important role in promoting or constraining recurrent HHS if multiple hybridization events occur sequentially and parental divergence or isolation differs along this continuum. We discuss under which conditions HHS may occur multiple times in parallel and to what extent recombination and selection may fuse the parent genomes in the same or different ways. We conclude by examining different approaches that might help to solve this intriguing evolutionary puz- zle [Current Zoology 59 （5）： 667-674, 2013].

关键词： Dimensionality Genetic Mosaicism Hybridization Speciation

The conjunction of factors that lead to formation of giant gold provinces and deposits in non-arc settings

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Geoscience Frontiers 2016年第3期7卷 303-314页

作者： David i.Groves richard J.Goldfarb M.Santosh Centre for Exploration Targeting UWA State Key Laboratory of Geological Processes and Mineral Resources China University of Geosciences U.S.Geological Survey Denver Federal Center Centre for Tectonics Resources and Exploration Dept. of Earth SciencesUniversity of Adelaide Division of interdisciplinary Science Faculty of ScienceKochi University

it is quite evident that it is not anomalous metal transport,nor unique depositional conditions,nor any single factor at the deposit scale,that dictates whether a mineral deposit becomes a giant or not.A hierarchical approach thus is required to progressively examine controlling parameters at successively decreasing scales in the total mineral system to understand the location of giant gold deposits in non-arc *** giant orogenic,intrusion-related gold systems（iRGS） and Carlin-type gold deposits and iron oxide-copper-gold（iOCG） deposits,there are common factors among all of these at the lithospheric to crustal *** are sited in giant gold provinces controlled by complex fundamental fault or shear zones that follow craton margins or,in the case of most Phanerozoic orogenic giants,define the primary suture zones between tectonic *** provinces of iRGS,iOCG,and Carlin-type deposits require melting of metasomatized lithosphere beneath craton margins with ascent of hybrid lamprophyric to granitic magmas and associated heat flux to generate the giant *** iRGS and iOCG deposits require direct exsolution of volatile-rich magmatic-hydrothermal fluids,whereas the association of such melts with Carlin-type ores is more indirect and *** orogenic gold provinces show no direct relationship to such *** from metamorphic fluids,but show an indirect relationship to lamprophyres that reflect the mantle connectivity of controlling first-order *** contrast to their province scale similarities,the different giant gold deposit styles show contrasting critical controls at the district to deposit *** orogenic gold deposits,the giants appear to have formed by conjunction of a greater number of parameters to those that control smaller deposits,with resultant geometrical and lithostratigraphic complexity as a guide to their *** are few giant iRGS due to their inferior fluid-flux systems relative to orogeni

关键词： Giant gold deposits Orogenic gold Carlin deposits iron oxide-copper-gold deposits intrusion-related gold systems Lithosphere

Effects of glycaemic management on diabetic kidney disease

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World Journal of Diabetes 2017年第5期8卷 172-186页

作者： richard J Macisaac George Jerums Elif i Ekinci Department of Endocrinology and Diabetes St Vincent’s Hospital Department of Medicine University of Melbourne Endocrine Centre Austin Health

Hyperglycaemia contributes to the onset and progression of diabetic kidney disease(DKD). Observational studies have not consistently demonstrated a glucose threshold, in terms of HbA1c levels, for the onset of DKD. Tight glucose control has clearly been shown to reduce the incidence of micro-or macroalbuminuria. However, evidence is now also emerging to suggest that intensive glucose control can slow glomerular filtration rate loss and possibly progression to end stage kidney disease. Achieving tight glucose control needs to be balanced against the increasing appreciation that glucose targets for the prevention of diabetes related complications need be individualised for each patient. Recently, empagliflozin which is an oral glucose lowering agent of the sodium glucose cotransporter-2 inhibitor class has been shown to have renal protective effects. However, the magnitude of empagliflozin's reno-protective properties are over and above that expected from its glucose lowering effects and most likely largely result from mechanisms involving alterations in intra-renal haemodynamics. Liraglutide and semaglutide, both injectable glucose lowering agents which are analogues of human glucagon like peptide-1 have also been shown to reduce progression to macroalbuminuria through mechanisms that remain to be fully elucidated. Here we review the evidence from observational and interventional studies that link good glucose control with improved renal outcomes. We also briefly review the potential reno-protective effects ofnewer glucose lowering agents.

关键词： Diabetic nephropathy Albuminuria Glucose control Glomerular filtration rate Diabetes Chronic kidney disease Empagliflozin Liraglutide Semaglutide

Eye contact and sociability data suggests that Australian dingoes were never domesticated

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Current Zoology 2022年第4期68卷 423-431页

作者： J William O Ballard Chloe Gardner Lucille Ellem Sonu Yadav richard i Kemp Department of Ecology Environmentand EvolutionLatrobe UniversityMelbourneVIC 3086Australia Department of BioSciences The University of MelbourneMelbourneVIC 3010Australia School of Life and Environmental Sciences University of SydneyCamperdownNSW 2006Australia Bargo Dingo Sanctuary BargoNSW 2574Australia School of Biotechnology and Biomolecular Sciences UNSW SydneySydneyNSW 2052Australia School of Psychology UNSW SydneySydneyNSW 2052Australia

Dogs were the first animal to become domesticated by humans,and they represent a classic model system for unraveling the processes of *** compare Australian dingo eye contact and socialization with Basenji and German Shepherd dog(GSD)*** dingoes arrived in Australia 5,000–8,000 BP,and there is debate whether they were domesticated before their *** Basenji represents a primitive breed that diverged from the remaining breeds early in the domestication process,while GSDs are a breed dog selected from existing domestic dogs in the late *** conducted a 4-phase study with unfamiliar and familiar investigators either sitting passively or actively calling each *** found 75%of dingoes made eye contact in each *** contrast,86%of Basenjis and 96%of GSDs made eye *** also exhibited shorter eye-gaze duration than breed dogs and did not respond to their name being called ***,quantified as a canid coming within 1m of the experimenter,was lowest for dingoes and highest for *** sociability duration,dingoes spent less time within 1m of the experimenter than either breed *** compared with previous studies,these data show that the dingo is behaviorally intermediate between wild wolves and Basenji dogs and suggest that it was not domesticated before it arrived in ***,it remains possible that the accumulation of mutations since colonization has obscured historical behaviors,and dingoes now exist in a feralized retamed *** morphological and genetic data are required to resolve this conundrum.

关键词： Basenji dingo domestication German Shepherd dog eye gaze sociability

Structural geometry of orogenic gold deposits： implications for exploration of world-class and giant deposits

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Geoscience Frontiers 2018年第4期9卷 1163-1177页

作者： David i.Groves M.Santosh richard J.Goldfarb Liang Zhang Orebusters Pty Ltd Gwelup 6018 Western Australia Australia State Key Laboratory of Geological Processes and Mineral Resources China University of Geosciences Beijing 100083 China Centre for Tectonics Resources and Exploration Dept. of Earth Sciences University of Adelaide SA 5005 Australia Division of interdisciplinary Science Faculty of Science Kochi University Kochi 780-8520 Japan

With very few exceptions, orogenic gold deposits formed in subduction-related tectonic settings in accretionary to collisional orogenic belts from Archean to Tertiary times. Their genesis, including metal and fluid source, fluid pathways, depositional mechanisms, and timing relative to regional structural and metamorphic events, continues to be controversial. However, there is now general agreement that these deposits formed from metamorphic fluids, either from metamorphism of intra-basinal rock sequences or de-volatilization of a subducted sediment wedge, during a change from a compressional to transpressional, less commonly transtensional, stress regime, prior to orogenic collapse. in the case of Archean and Paleoproterozoic deposits, the formation of orogenic gold deposits was one of the last events prior to cratonization. The late timing of orogenic gold deposits within the structural evolution of the host orogen implies that any earlier structures may be mineralized and that the current structural geometry of the gold deposits is equivalent to that at the time of their formation provided that there has been no significant post-gold orogenic overprint. Within the host volcano-sedimentary sequences at the province scale, world-class orogenic gold deposits are most commonly located in second-order structures adjacent to crustal scale faults and shear zones, representing the first-order ore-forming fluid pathways, and whose deep lithospheric connection is marked by lamprophyre intrusions which, however, have no direct genetic association with gold deposition. More specifically, the gold deposits are located adjacent to ～10°-25° district-scale jogs in these crustal-scale faults. These jogs are commonly the site of arrays of ～70° cross faults that accommodate the bending of the more rigid components, for example volcanic rocks and intrusive sills, of the host belts. Rotation of blocks between these accommodation faults causes failure of more competent units and/or re

关键词： Structural geometry Tectonic history Fluid pathways Orogenic gold deposits Exploration criteria

Assessment of energy utilization and leakages in buildings with building information model energy

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Frontiers of Architectural Research 2017年第1期6卷 29-41页

作者： Egwunatum i. Samuel Esther Joseph-Akwara Akaigwe richard Department of Quantity Surveying Delta State Polytechnic Ozoro 334111 Nigeria Department of Civil Engineering Delta State Polytechnic Ozoro 334111 Nigeria Department of Building Pic Lagos State Nigeria

Given the ability of building information models （BiM） to serve as a multidisciplinary data repository, this study attempts to explore and exploit the sustainability value of BiM in delivering buildings that require less energy for operations, emit tess carbon dioxide, and provide conducive living environments for occupants. This objective was attained by a critical and extensive literature review that covers the following：（1） building energy consumption, （2） building energy performance and analysis, and （3） BiM and energy assessment. Literature cited in this paper shows that linking an energy analysis toot with a BiM model has helped project design teams to predict and create optimized energy consumption by conducting building energy performance analysis utilizing key performance indicators on average thermal transmitters, resulting heat demand, lighting power, solar heat gains, and ventilation heat losses. An in-depth analysis was conducted on a completed BiM integrated construction project utilizing the Arboleda Project in the Dominican Republic to validate the aforementioned findings. Results show that the BiM-based energy analysis helped the design team attain the world＇s first positive energy building. This study concludes that linking an energy analysis tool with a BiM model helps to expedite the energy analysis process, provide more detailed and accurate results, and deliver energy-efficient buildings. This study further recommends that the adoption of level 2 BiM and BiM integration in energy optimization analysis must be demanded by building regulatory agencies for all projects regardless of procurement method （i.e., government funded or otherwise） or size.

关键词： Building informationmodeling Building energy per-formance analysis Sustainability Energy efficiency