bluuebunny/crossref_metadata_2025 huggingface dataset:
Genetic and Genomic Interactions of Animals with Different Ploidy Levels
Authors: Bogart J.P. , Bi K.
Published: June 2013

Polyploid animals have independently evolved from diploids in diverse taxa across the tree of life. We review a few polyploid animal species or biotypes where recently developed molecular and cytogenetic methods have significantly improved our understanding of their genetics, reproduction and evolution. Mitochondrial sequences that target the maternal ancestor of a polyploid show that polyploids may have single (e.g. unisexual salamanders in the genus Ambystoma) or multiple (e.g. parthenogenetic polyploid lizards in the genus Aspidoscelis) origins. Microsatellites are nuclear markers that can be used to analyze genetic recombinations, reproductive modes (e.g. Ambystoma) and recombination events (e.g. polyploid frogs such as Pelophylax esculentus). Hom(e)ologous chromosomes and rare intergenomic exchanges in allopolyploids have been distinguished by applying genome-specific fluorescent probes to chromosome spreads. Polyploids arise, and are maintained, through perturbations of the ‘normal' meiotic program that would include pre-meiotic chromosome replication and genomic integrity of homologs. When possible, asexual, unisexual and bisexual polyploid species or biotypes interact with diploid relatives, and genes are passed from diploid to polyploid gene pools, which increase genetic diversity and ultimately evolutionary flexibility in the polyploid. When diploid relatives do not exist, polyploids can interact with another polyploid (e.g. species of African Clawed Frogs in the genus Xenopus). Some polyploid fish (e.g. salmonids) and frogs (Xenopus) represent independent lineages whose ancestors experienced whole genome duplication events. Some tetraploid frogs (P. esculentus) and fish (Squaliusalburnoides) may be in the process of becoming independent species, but diploid and triploid forms of these ‘species' continue to genetically interact with the comparatively few tetraploid populations. Genetic and genomic interaction between polyploids and diploids is a complex and dynamic process that likely plays a crucial role for the evolution and persistence of polyploid animals. See also other articles in this themed issue.
UK Renal Registry 15th Annual Report: Chapter 1 UK RRT Incidence in 2011: National and Centre-Speciﬁc Analyses
Authors: Gilg Julie , Rao Anirudh , Fogarty Damian
Published: June 2013

Introduction: This chapter describes the characteristics of adult patients starting renal replacement therapy (RRT) in the UK in 2011 and the incidence rates for RRT in Primary Care Trusts and Health Boards (PCT/HBs) in the UK. Methods: Basic demographic and clinical characteristics are reported on patients starting RRT at all UK renal centres. Presentation time, deﬁned as time between ﬁrst being seen by a nephrologist and start of RRT, was also studied. Age and gender standardised ratios for incidence rates in PCT/HBs were also calculated. Results: In 2011, the incidence rate in the UK was similar to 2010 at 108 per million population (pmp). There were wide variations between PCT/HBs in standardised incidence ratios. For the 2006-2011 incident cohort analysis the range was 0.42 to 2.52 (IQR 0.85, 1.20). The median age of all incident patients was 64.9 years (IQR 50.9, 75.1). For transplant centres this was 63.8 years (IQR 49.5, 74.3) and for non-transplanting centres 66.2 years (IQR 52.4, 76.0). The median age for non-Whites was 58.4 years. Diabetic renal disease remained the single most common cause of renal failure (25%). By 90 days, 67.1% of patients were on haemodialysis, 19.2% on perito- neal dialysis, 7.8% had had a transplant and 5.8% had died or stopped treatment. This is the second year in a row that the percentage on peritoneal dialysis has increased and, in 2011, this was most notable in the 65-74 age group. There was a lot of variability in use of PD with some centres having over twice the average percentage on PD. The mean eGFR at the start of RRT was 8.7 ml/min/1.73 m2 similar to the previous four years. Late presentation (<90 days) fell from 23.9% in 2006 to 19.6% in 2011. There was no relationship between social deprivation and presentation pattern. Conclusions: Incidence rates have plateaued in England over the last six years. There has been an increase in the percentage of new patients still on RRT at 90 days after starting who were on PD at 90 days (19.2 to 20.4%).
UK Renal Registry 15th Annual Report: Chapter 2 UK RRT Prevalence in 2011: National and Centre-Speciﬁc Analyses
Authors: Shaw Catriona , Pruthi Rishi , Pitcher David , Fogarty Damian
Published: June 2013

Introduction: This chapter describes the characteristics of adult patients on renal replacement therapy (RRT) in the UK in 2011. The prevalence rates per million population (pmp) were calculated for Primary Care Trusts in England, Health and Social Care areas in Northern Ireland, Local Health Boards in Wales and Health Boards (HB) in Scotland (PCT/HB areas). Methods: Data were electronically collected from all 71 renal centres within the UK. A series of cross-sectional and longitudinal analyses were performed to describe the demographics of prevalent RRT patients in 2011 at centre and national level. Age and gender standardised ratios for prevalence rates in PCT/ HBs were calculated. Results: There were 53,207 adult patients receiving RRT in the UK on 31st December 2011. The UK adult prevalence of RRT was 842 pmp. This represented an annual increase in prevalent numbers of approximately 4%, although there was variation between centres and PCT/HB areas. The growth rate from 2010 to 2011 for prevalent patients by treatment modality in the UK was an increase of 1.7% for haemodialysis (HD), a fall of 2.2% for peritoneal dialysis (PD) and an increase of 4.7% with a functioning transplant. There has been a slow but steady decline in the proportion of dialysis patients receiving PD since 2000. In contrast, the number of patients receiving home HD has increased 16% since 2010. Median RRT vintage for patients on HD was 3.3 years, PD 1.8 years and for those patients with a transplant, 10.3 years. The median age of prevalent patients was 58.2 years (HD 66.5 years, PD 62.7 years, transplant 51.7 years) compared to 55 years in 2000. For all ages the prevalence rate in men exceeded that in women, peaking in age group 75-79 years at 2,918 pmp in males. For females the peak was in age group 65-69 years at 1,460 pmp. The most common recorded renal diagnosis was glomerulonephritis (biopsy proven/not biopsy proven) (19%), followed by uncertain (18%). Transplantation was the most common treatment modality (48.6%), HD in 43.9% and PD 7.6%. However, HD was increasingly common with increasing age and transplantation less common. Conclusions: The HD and transplant population continued to expand whilst the PD population contracted. There were national, regional and dialysis centre level variations in prevalence rates. Prevalent patients were on average three years older than 10 years ago. This has implications for service planning and ensuring equity of care for RRT patients.
UK Renal Registry 15th Annual Report: Chapter 4 Demography of the UK Paediatric Renal Replacement Therapy Population in 2011
Authors: Pruthi Rishi , O'Brien Catherine , Casula Anna , Braddon Fiona , Lewis Malcolm , Maxwell Heather , Tse Yincent , Inward Carol , Sinha Manish D
Published: June 2013

Aims: To describe the demographics of the paediatric RRT population under the age of 16 years in the UK and to analyse changes in demography with time. Methods: Data were collected from all 13 paediatric renal centres within the UK. A series of cross-sectional and longitudinal analyses were performed to describe the demographics of paediatric RRT patients. Results: A total of 856 children and young people under 18 with ERF were receiving treatment at paediatric nephrology centres in 2011. At the census date, 80.1% had a functioning transplant, 10.5% were receiving peritoneal dialysis (PD) and 9.4% were receiving haemodialysis (HD). In patients aged <16 years the prevalence of ERF was 56.8 pmarp and the incidence 8.3 pmarp. Analysis of trends over the last 15 years shows that both incidence and prevalence are increasing. A third of the prevalent patients had one or more reported comorbidities. At transfer to adult services, 86% of patients had a functioning renal transplant. Pre-emptive transplantation was seen to occur in 31% of children starting RRT under 16 years, with lower rates seen in girls and ethnic minorities. Survival in childhood amongst children starting RRT was the lowest in those aged less than 2 years. Conclusions: The data provided in this report show increasing trends over 15 years in the incidence and prevalence of established renal failure. This is important for the planning of the provision of care for children needing renal replacement therapy. Further research is required to understand the gender and ethnic differences in pre-emptive transplantation rates and the reduced survival amongst children aged less than 2 years.
UK Renal Registry 15th Annual Report: Chapter 5 Survival and Causes of Death of UK Adult Patients on Renal Replacement Therapy in 2011: National and Centre-Specific Analyses
Authors: Steenkamp Retha , Shaw Catriona , Feest Terry
Published: June 2013

Introduction: These analyses examine a) survival from the start of renal replacement therapy (RRT) based on the total incident UK RRT population reported to the UK Renal Registry, b) survival of prevalent patients. Changes in survival between 1997 and 2011 are also reported. Methods: Survival was calculated for both incident and prevalent patients on RRT and compared between the UK countries after adjustment for age. Survival of incident patients (starting RRT during 2010) was calculated both from the start of RRT and from 90 days after starting RRT, both with and without censoring at transplantation. Prevalent dialysis patients were censored at transplantation; this means that the patient is considered alive up to the point of transplantation, but the patient's status post-transplant is not considered. Both Kaplan-Meier and Cox adjusted models were used to calculate survival. Causes of death were analysed for both groups. The relative risk of death was calculated compared with the general UK population. Results: The unadjusted 1 year after 90 day survival for patients starting RRT in 2010 was 87.3%, representing an increase from the previous year (86.6%). In incident patients aged 18-64 years, the unadjusted 1 year survival had risen from 86.0% in patients starting RRT in 1997 to 92.6% in patients starting RRT in 2010 and for those aged ≥65 it had increased from 63.9% to 77.0% over the same period. The age-adjusted one year survival (adjusted to age 60) of prevalent dialysis patients increased from 88.1% in the 2001 cohort to 89.8% in the 2010 cohort. Prevalent diabetic patient one year survival rose from 82.1% in the 2002 cohort to 84.7% in the 2010 cohort. The age-standardised mortality ratio for prevalent RRT patients compared with the general population was 18 for age group 30-34 and 2.5 at age 85+ years. In the prevalent RRT dialysis population, cardiovascular disease accounted for 22% of deaths, infection and treatment withdrawal 18% each and 25% were recorded as other causes of death. Treatment withdrawal was a more frequent cause of death in those incident patients aged ≥65 than in younger patients. The median life years remaining for a 25-29 year old on RRT was 18 years and approximately three years for a 75+ year old. Conclusions: Survival of patients starting RRT has improved in the 2010 incident cohort. The relative risk of death on RRT compared with the general population has fallen since 2001.
UK Renal Registry 15th Annual Report: Chapter 7 Clinical, Haematological and Biochemical Parameters in Patients Receiving Renal Replacement Therapy in Paediatric Centres in the UK in 2011: National and Centre-Speciﬁc Analyses
Authors: Pruthi Rishi , Maxwell Heather , Casula Anna , Braddon Fiona , Lewis Malcolm , O'Brien Catherine , Tse Yincent , Inward Carol , Sinha Manish D
Published: June 2013

Background: The British Association for Paediatric Nephrology Registry was established to analyse data related to renal replacement therapy (RRT) in children. The registry receives data from the 13 paediatric nephrology centres in the UK. Aims: To provide centre speciﬁc data so that individual centres can reflect on the contribution that their data makes to the national picture and to determine the extent to which their patient parameters meet nationally agreed audit standards for the management of children with established renal failure. Methods: Data returns have been a mixture of electronic and paper returns. Data were analysed to calculate summary statistics and where applicable the percentage achieving an audit standard. The standards used were those set out by the Renal Association and the National Institute for Health and Clinical Excellence. Results: Anthropometric data conﬁrmed that children receiving RRT were short compared to healthy peers. Amongst patients with a height of <2 SD between 2001 and 2011, 31% were receiving growth hormone if they were on dialysis compared to 10% if they had a functioning transplant. Blood pressure control remained challenging with wide inter-centre variation although this was signiﬁcantly better in children with a functioning transplant. Over a third of haemodialysis patients and a quarter of peritoneal dialysis patients were anaemic, compared to only 7% of transplanted patients. ESA use in the dialysis population exceeded 90% amongst anaemic patients. The control of renal bone disease remained challenging. Conclusions: Optimizing growth in children on RRT remained challenging and the control of bone biochemistry in children on dialysis was imperfect. The likelihood of complete electronic reporting in the near future with plans for quarterly reporting in the format of the recently ﬁnalised NEW paediatric dataset will hopefully improve quality of data and their reporting, allowing improvements in patient care.
Lost in a Triangle: U.S.-Soviet Back-Channel Documents on the Japan Factor in Tripartite Diplomacy, 1969–1972
Authors: Zubok Vladislav
Published: June 2013

This article examines the impact of Japan on U.S.-Soviet relations during Richard Nixon's first term as U.S. president. Drawing heavily on recently declassified documents pertaining to back-channel negotiations between Nixon's national security adviser, Henry Kissinger, and Soviet Ambassador Anatolii Dobrynin, the article explains why no Soviet-Japanese rapprochement proved feasible even during the height of East-West détente. The enduring hostility was in contrast to the realignments of the other major powers during this period.
The Soviet Factor in U.S.-Japanese Defense Cooperation, 1978–1985
Authors: Hasegawa Tsuyoshi
Published: June 2013

In the crucial period from 1978 to 1975, Japan jettisoned its “omnidirectional” foreign policy and embraced a closer and more integrated defense alliance with the United States. Concern about the Soviet threat was the chief motive for this shift. The deployment of Soviet troops in the Northern Territories (Southern Kuriles), the Soviet invasion of Afghanistan, and the deployment of Soviet Backfire bombers and SS-20 nuclear missiles in the Far East all provided impetus toward closer U.S.-Japanese defense cooperation. As Japan closely aligned its defense policy with the United States, Soviet-Japanese relations correspondingly deteriorated. Normal channels of communication were broken off. As the Japanese government elevated the Northern Territories issue to the forefront of Soviet-Japanese relations, Soviet criticism of Japan escalated. By the time Mikhail Gorbachev took power in 1985, Soviet-Japanese relations had sunk to their lowest point.
Calochaete gen. nov. (Cyanobacteria, Nostocales), a new cyanobacterial type from the “páramo” zone in Costa Rica
Authors: HAUER TOMÁŠ , BOHUNICKÁ MARKÉTA , MÜHLSTEINOVÁ RADKA
Published: June 2013

A new tapered and false branched morphotype of filamentous heterocytous cyanobacterium was isolated from soil material collected on a massif of Chirripó Mountain, Costa Rica. The strain was analyzed morphologically and a sequence of its 16S rRNA gene was compared with available 16S rDNA sequences of organisms with similar morphology, especially those with heteropolar tapering filaments. Phylogenetic analyses revealed that the strain was significantly different from Rivulariaceae, but was closely related to several strains designated as Tolypothrix. However, according to the original descriptions in the literature, members of the genus Tolypothrix possess only very slightly tapering filaments. With regard to all these differences, we decided to describe a new genus—Calochaete gen. nov. with type species C. cimrmanii.
Revision of three species of Euonymus (Celastraceae) from China
Authors: DU CHENG , ZUO YUNJUAN , MA JINSHUANG
Published: June 2013

Through field observations, recollections at known sites and researches on specimens and literature, full descriptions of Euonymus wui, Euonymus pseudovagans and Euonymus mengtzeanus are provided for the first time. The systematic position of Euonymus wui is confirmed to be within sect. Euonymus subsect. Euonymus ser. Pseudovyenomi subser. Pentameri and Euonymus mengtzeanus is confirmed to be within sect. Euonymus subsect. Euonymus ser. Pseudovyenomi subser. Pentameri. Lectotypes for Euonymus pseudovagans and Euonymus mengtzeanus are here designated. Additionally, the conservation status of the three species is evaluated according to IUCN standards (version 3.1).
The Calculus of Consensus Democracy
Authors: McGann Anthony J. , Latner Michael
Published: June 2013

We present a theory of comparative political institutions based on the concept of consensus democracy and social choice theory. Unlike Lijphart, we argue that “consensus democracy” is not a special form of democracy characterized by mutual vetoes, but rather the simplest form of democracy, which we refer to as PR-majority rule. We construct a typology of political institutions based on differences with this simple model. Contra Tsebelis’s veto players approach, our theory predicts that PR-majority rule should be the most flexible form of democracy. We test this with data on overall patterns of government spending and on welfare state reform.
The wrong bin bag: A turn to ontology in science and technology studies?
Authors: Woolgar Steve , Lezaun Javier
Published: June 2013

There is in science and technology studies a perceptible new interest in matters of ‘ontology’. Until recently, the term ‘ontology’ had been sparingly used in the field. Now it appears to have acquired a new theoretical significance and lies at the centre of many programmes of empirical investigation. The special issue to which this essay is a contribution gathers a series of enquiries into the ontological and reflects, collectively, on the value of the analytical and methodological sensibilities that underpin this new approach to the make-up of the world. To what extent and in what sense can we speak of a ‘turn to ontology’ in science and technology studies? What should we make of, and with, this renewed interest in matters of ontology? This essay offers some preliminary responses to these questions. First, we examine claims of a shift from epistemology to ontology and explore in particular the implications of the notion of ‘enactment’. This leads to a consideration of the normative implications of approaches that bring ‘ontological politics’ to centre stage. We then illustrate and pursue these questions by using an example – the case of the ‘wrong bin bag’. We conclude with a tentative assessment of the prospects for ontologically sensitive science and technology studies.
Coercion, capacity, and coordination: Predictors of political violence
Authors: Bell Sam R , Cingranelli David , Murdie Amanda , Caglayan Alper
Published: June 2013

Using a risk assessment method developed by Gurr and Moore ( American Journal of Political Science 41: 1079–1103, 1997) and applying O’Brien’s ( Journal of Conflict Resolution 46: 791–811, 2002) risk assessment metrics, we present a global, comparative, cross-national model predicting the states where political violence is likely to increase. Our model predicts more political violence when governments violate the physical integrity rights of their citizens—especially when they frequently imprison citizens for political reasons or make them “disappear”. These coercive techniques may create more citizen dissatisfaction than other types of violations of physical integrity rights, because citizens perceive political imprisonment and disappearances as the direct result of the deliberate policy choices of politicians. Our model also forecasts more political violence in weak states and states that allow dissatisfied citizens to coordinate their anti-government activities. Specifically, we demonstrate that political violence tends to be higher if governments respect their citizens’ right to freedom of assembly and association and offer widespread use of mobile phone and internet technology.
Failing to succeed? The cumulative impact of international mediation revisited
Authors: Böhmelt Tobias
Published: June 2013

Previous studies argue that the cumulation of mediations generally decreases uncertainty and ultimately helps to solve a conflict peacefully. Yet the empirical evidence for this is inconclusive, suggesting that existent theoretical accounts might be incomplete. For addressing this shortcoming, the paper develops an argument for a curvilinear relationship between the cumulation of mediations and mediation effectiveness. Based upon this rationale, it is less likely that initial mediation attempts succeed, but—after a turning point has been reached—subsequent mediations are more likely to induce an effective resolution of a dispute. The author also argues that this effect should be stronger if the same actors mediate over the course of a conflict. The empirical implications of this theoretical revision are tested in a quantitative framework employing data for 1816–2001. The results provide strong support for the theory.
Putting our best boots forward: US military deployments and host-country crime
Authors: Allen Michael A , Flynn Michael E
Published: June 2013

The deployment of military forces abroad has been a major component of the US’s grand strategy since the beginning of the Cold War. However, some scholars have argued that the presence of US military personnel abroad creates a series of negative externalities afflicting local communities. We put some of these claims to the test by looking at the effect of US military deployments on crime rates in the host-state. Using cross-national crime statistics from the United Nations and data on US troop deployments, we examine whether US military deployments are associated with higher levels of criminal activity across a large subset of crimes. In aggregate, the mere presence of troops does not increase the criminal activity in a state; however, there is a conditional effect when we account for a difference in culture between the host-state and the US; the presence of foreign deployed troops is associated with higher levels of property-related crimes in a country. Consequently, this paper contributes to a better understanding of the impact that US military deployments, and US foreign policy more broadly, have had on other countries, and also enhances our understanding of the micro-level factors that might affect relationships between alliance partners
A different fire: Vatican II and new evangelization
Authors: Coleridge Mark
Published: June 2013

This article, based on an address given to the ‘Fruits and Future of Vatican II’ symposium, explores the relationship between the insights of Vatican II and John Paul II’s call for a ‘new evangelization’ and considers their implications for today. It argues that the church’s mission to the world is strongly related to its commitment to the contemplation of the face of Chris and to encounter ‘a different fire’.
Tackling capitalism: What Vatican II achieved and what still needs to be done
Authors: Duncan Bruce
Published: June 2013

This article provides an account of papal views of capitalism prior to, during and after Vatican II. It argues that these views offer a consistent critique of capitalist economic systems and challenges the Catholic neoconservative and neoliberal reading of post Vatican II papal teaching. The article suggests that this critique needs to be better communicated and makes some suggestions about what might be done to challenge the seductions of an unsustainable consumerist culture.
The diaspora church: Laity & ‘laicity’ in the post-Vatican II era
Authors: Price Peter
Published: June 2013

This article builds on earlier research and argues that Vatican II and subsequent church teaching on the role of the laity lack the force to effect change in the deeply embedded subjectivization of the laity. It proposes that, in a vastly changed, pluralistic world, a new sense of being Catholic is emerging, requiring a new identity and direction for mission to be developed in the context of the current exodus of Catholics away from close involvement with Eucharistic rituals and other things ‘sacred’. This ‘exodus’ may represent a relocation of the People of God deep into the heart of the sacred world for whose transformation we are given to mission as church. In this sense, it may well turn out to be a blessing, and not a problem.
Implementing Differentiation
Authors: Weber Christine L. , Johnson Linda , Tripp Shane
Published: June 2013

The focus of this case study is to provide an overview of a private school’s journey toward implementing differentiation in their classrooms. An introduction to the school along with background information leads to a relevant need to implement teaching strategies that ensure the success of students who are capable of learning above grade level. The journey that the school takes begins with putting differentiation into practice and describing, in a three-pathway approach, the direction taken for the implementation process. What is learned, along with specific and general issues to consider, exemplifies this work in progress. Helpful resources provide guidance to others interested in starting a similar journey.
The Gatton Academy
Authors: Roberts Julia Link
Published: June 2013

This article describes the Carol Martin Gatton Academy of Mathematics and Science in Kentucky, a residential high school for juniors and seniors supported by the state budget. The school opened in 2007 after 10 years of advocacy and planning, including the retrofitting of Schneider Hall to be the home of the Gatton Academy and The Center for Gifted Studies at Western Kentucky University. Students at the Gatton Academy earn a minimum 60 college hours and a high school diploma. This article describes the mission, the curriculum, benefits to the sending school and school district as well as to the student, support for students, and the recognition for students and the Gatton Academy. This special school is 1 of 15 state residential high schools with a focus on mathematics and science that are supported by the state budget.
Guaranteed cost control for switched recurrent neural networks with interval time-varying delay
Authors: Niamsup Piyapong , Rajchakit Manlika , Rajchakit Grienggrai
Published: June 2013

This paper studies the problem of guaranteed cost control for a class of switched recurrent neural networks with interval time-varying delay. The time delay is a continuous function belonging to a given interval, but not necessary differentiable. A cost function is considered as a nonlinear performance measure for the closed-loop system. The stabilizing controllers to be designed must satisfy some exponential stability constraints on the closed-loop poles. By constructing a set of augmented Lyapunov-Krasovskii functionals, a guaranteed cost controller is designed via memoryless state feedback control, a switching rule for the exponential stabilization for the system is designed via linear matrix inequalities and new sufficient conditions for the existence of the guaranteed cost state-feedback for the system are given in terms of linear matrix inequalities (LMIs). A numerical example is given to illustrate the effectiveness of the obtained result.
Live imaging and analysis of postnatal mouse retinal development
Authors: Nickerson Philip EB , Ronellenfitch Kara M , Csuzdi Nicklaus F , Boyd Jamie D , Howard Perry L , Delaney Kerry R , Chow Robert L
Published: June 2013

Background

The explanted, developing rodent retina provides an efficient and accessible preparation for use in gene transfer and pharmacological experimentation. Many of the features of normal development are retained in the explanted retina, including retinal progenitor cell proliferation, heterochronic cell production, interkinetic nuclear migration, and connectivity. To date, live imaging in the developing retina has been reported in non-mammalian and mammalian whole-mount samples. An integrated approach to rodent retinal culture/transfection, live imaging, cell tracking, and analysis in structurally intact explants greatly improves our ability to assess the kinetics of cell production.

Results

In this report, we describe the assembly and maintenance of an in vitro, CO2-independent, live mouse retinal preparation that is accessible by both upright and inverted, 2-photon or confocal microscopes. The optics of this preparation permit high-quality and multi-channel imaging of retinal cells expressing fluorescent reporters for up to 48h. Tracking of interkinetic nuclear migration within individual cells, and changes in retinal progenitor cell morphology are described. Follow-up, hierarchical cluster screening revealed that several different dependent variable measures can be used to identify and group movement kinetics in experimental and control samples.

Conclusions

Collectively, these methods provide a robust approach to assay multiple features of rodent retinal development using live imaging.
Serotonin-immunoreactive neurons in the ventral nerve cord of Remipedia (Crustacea): support for a sister group relationship of Remipedia and Hexapoda?
Authors: Stemme Torben , Iliffe Thomas M , von Reumont Björn M , Koenemann Stefan , Harzsch Steffen , Bicker Gerd
Published: June 2013

Background

Remipedia were initially seen as a primitive taxon within Pancrustacea based on characters considered ancestral, such as the homonomously segmented trunk. Meanwhile, several morphological and molecular studies proposed a more derived position of Remipedia within Pancrustacea, including a sister group relationship to Hexapoda. Because of these conflicting hypotheses, fresh data are crucial to contribute new insights into euarthropod phylogeny. The architecture of individually identifiable serotonin-immunoreactive neurons has successfully been used for phylogenetic considerations in Euarthropoda. Here, we identified neurons in three species of Remipedia with an antiserum against serotonin and compared our findings to reconstructed ground patterns in other euarthropod taxa. Additionally, we traced neurite connectivity and neuropil outlines using antisera against acetylated α-tubulin and synapsin.

Results

The ventral nerve cord of Remipedia displays a typical rope-ladder-like arrangement of separate metameric ganglia linked by paired longitudinally projecting connectives. The peripheral projections comprise an intersegmental nerve, consisting of two branches that fuse shortly after exiting the connectives, and the segmental anterior and posterior nerve. The distribution and morphology of serotonin-immunoreactive interneurons in the trunk segments is highly conserved within the remipede species we analyzed, which allows for the reconstruction of a ground pattern: two posterior and one anterior pair of serotonin-immunoreactive neurons that possess a single contralateral projection. Additionally, three pairs of immunoreactive neurons are found in the medial part of each hemiganglion. In one species (Cryptocorynetes haptodiscus), the anterior pair of immunoreactive neurons is missing.

Conclusions

The anatomy of the remipede ventral nerve cord with its separate metameric ganglia mirrors the external morphology of the animal’s trunk. The rope-ladder-like structure and principal architecture of the segmental ganglia in Remipedia corresponds closely to that of other Euarthropoda. A comparison of the serotonin-immunoreactive cell arrangement of Remipedia to reconstructed ground patterns of major euarthropod taxa supports a homology of the anterior and posterior neurons in Pancrustacea. These neurons in Remipedia possess unbranched projections across the midline, pointing towards similarities to the hexapod pattern. Our findings are in line with a growing number of phylogenetic investigations proposing Remipedia to be a rather derived crustacean lineage that perhaps has close affinities to Hexapoda.
Genomic basis of ecological niche divergence among cryptic sister species of non-biting midges
Authors: Schmidt Hanno , Greshake Bastian , Feldmeyer Barbara , Hankeln Thomas , Pfenninger Markus
Published: June 2013

Background

There is a lack of understanding the evolutionary forces driving niche segregation of closely related organisms. In addition, pinpointing the genes driving ecological divergence is a key goal in molecular ecology. Here, larval transcriptome sequences obtained by next-generation-sequencing are used to address these issues in a morphologically cryptic sister species pair of non-biting midges (Chironomus ripariusandC. piger).

Results

More than eight thousand orthologous open reading frames were screened for interspecific divergence and intraspecific polymorphisms. Despite a small mean sequence divergence of 1.53% between the sister species, 25.1% of 18,115 observed amino acid substitutions were inferred by α statistics to be driven by positive selection. Applying McDonald-Kreitman tests to 715 alignments of gene orthologues identified eleven (1.5%) genes driven by positive selection.

Conclusions

Three candidate genes were identified as potentially responsible for the observed niche segregation concerning nitrite concentration, habitat temperature and water conductivity. Additionally, signs of positive selection in the hydrogen sulfide detoxification pathway were detected, providing a new plausible hypothesis for the species’ ecological differentiation. Finally, a divergently selected, nuclear encoded mitochondrial ribosomal protein may contribute to reproductive isolation due to cytonuclear coevolution.
Comparative genomic analysis of catfish linkage group 8 reveals two homologous chromosomes in zebrafish and other teleosts with extensive inter-chromosomal rearrangements
Authors: Zhang Yu , Liu Shikai , Lu Jianguo , Jiang Yanliang , Gao Xiaoyu , Ninwichian Parichart , Li Chao , Waldbieser Geoff , Liu Zhanjiang
Published: June 2013

Background

Comparative genomics is a powerful tool to transfer genomic information from model species to related non-model species. Channel catfish (Ictalurus punctatus) is the primary aquaculture species in the United States. Its existing genome resources such as genomic sequences generated from next generation sequencing, BAC end sequences (BES), physical maps, linkage maps, and integrated linkage and physical maps using BES-associated markers provide a platform for comparative genomic analysis between catfish and other model teleost fish species. This study aimed to gain understanding of genome organizations and similarities among catfish and several sequenced teleost genomes using linkage group 8 (LG8) as a pilot study.

Results

With existing genome resources, 287 unique genes were identified in LG8. Comparative genome analysis indicated that most of these 287 genes on catfish LG8 are located on two homologous chromosomes of zebrafish, medaka, stickleback, and three chromosomes of green-spotted pufferfish. Large numbers of conserved syntenies were identified. Detailed analysis of the conserved syntenies in relation to chromosome level similarities revealed extensive inter-chromosomal and intra-chromosomal rearrangements during evolution. Of the 287 genes, 35 genes were found to be duplicated in the catfish genome, with the vast majority of the duplications being interchromosomal.

Conclusions

Comparative genome analysis is a powerful tool even in the absence of a well-assembled whole genome sequence. In spite of sequence stacking due to low resolution of the linkage and physical maps, conserved syntenies can be identified although the exact gene order and orientation are unknown at present. Through chromosome-level comparative analysis, homologous chromosomes among teleosts can be identified. Syntenic analysis should facilitate annotation of the catfish genome, which in turn, should facilitate functional inference of genes based on their orthology.
Skin transcriptome profiles associated with coat color in sheep
Authors: Fan Ruiwen , Xie Jianshan , Bai Junming , Wang Haidong , Tian Xue , Bai Rui , Jia Xiaoyun , Yang Lei , Song Yunfei , Herrid Muren , Gao Wenjun , He Xiaoyan , Yao Jianbo , Smith George W , Dong Changsheng
Published: June 2013

Background

Previous molecular genetic studies of physiology and pigmentation of sheep skin have focused primarily on a limited number of genes and proteins. To identify additional genes that may play important roles in coat color regulation, Illumina sequencing technology was used to catalog global gene expression profiles in skin of sheep with white versus black coat color.

Results

There were 90,006 and 74,533 unigenes assembled from the reads obtained from white and black sheep skin, respectively. Genes encoding for the ribosomal proteins and keratin associated proteins were most highly expressed. A total of 2,235 known genes were differentially expressed in black versus white sheep skin, with 479 genes up-regulated and 1,756 genes down-regulated. A total of 845 novel genes were differentially expressed in black versus white sheep skin, consisting of 107 genes which were up-regulated (including 2 highly expressed genes exclusively expressed in black sheep skin) and 738 genes that were down-regulated. There was also a total of 49 known coat color genes expressed in sheep skin, from which 13 genes showed higher expression in black sheep skin. Many of these up-regulated genes, such as DCT, MATP, TYR and TYRP1, are members of the components of melanosomes and their precursor ontology category.

Conclusion

The white and black sheep skin transcriptome profiles obtained provide a valuable resource for future research to understand the network of gene expression controlling skin physiology and melanogenesis in sheep.
Archaeal nucleosome positioning in vivo and in vitro is directed by primary sequence motifs
Authors: Nalabothula Narasimharao , Xi Liqun , Bhattacharyya Sucharita , Widom Jonathan , Wang Ji-Ping , Reeve John N , Santangelo Thomas J , Fondufe-Mittendorf Yvonne N
Published: June 2013

Background

Histone wrapping of DNA into nucleosomes almost certainly evolved in the Archaea, and predates Eukaryotes. In Eukaryotes, nucleosome positioning plays a central role in regulating gene expression and is directed by primary sequence motifs that together form a nucleosome positioning code. The experiments reported were undertaken to determine if archaeal histone assembly conforms to the nucleosome positioning code.

Results

Eukaryotic nucleosome positioning is favored and directed by phased helical repeats of AA/TT/AT/TA and CC/GG/CG/GC dinucleotides, and disfavored by longer AT-rich oligonucleotides. Deep sequencing of genomic DNA protected from micrococcal nuclease digestion by assembly into archaeal nucleosomes has established that archaeal nucleosome assembly is also directed and positioned by these sequence motifs, both in vivo in Methanothermobacter thermautotrophicus and Thermococcus kodakarensis and in vitro in reaction mixtures containing only one purified archaeal histone and genomic DNA. Archaeal nucleosomes assembled at the same locations in vivo and in vitro, with much reduced assembly immediately upstream of open reading frames and throughout the ribosomal rDNA operons. Providing further support for a common positioning code, archaeal histones assembled into nucleosomes on eukaryotic DNA and eukaryotic histones into nucleosomes on archaeal DNA at the same locations. T. kodakarensis has two histones, designated HTkA and HTkB, and strains with either but not both histones deleted grow normally but do exhibit transcriptome differences. Comparisons of the archaeal nucleosome profiles in the intergenic regions immediately upstream of genes that exhibited increased or decreased transcription in the absence of HTkA or HTkB revealed substantial differences but no consistent pattern of changes that would correlate directly with archaeal nucleosome positioning inhibiting or stimulating transcription.

Conclusions

The results obtained establish that an archaeal histone and a genome sequence together are sufficient to determine where archaeal nucleosomes preferentially assemble and where they avoid assembly. We confirm that the same nucleosome positioning code operates in Archaea as in Eukaryotes and presumably therefore evolved with the histone-fold mechanism of DNA binding and compaction early in the archaeal lineage, before the divergence of Eukaryotes.
The effects of endoscopic-guided balloon dilations in esophageal and gastric strictures caused by corrosive injuries
Authors: Chiu Yi-Chun , Liang Chih-Ming , Tam William , Wu Keng-Liang , Lu Long-Sheng , Hu Ming-Luen , Tai Wei-Chen , Chiu King-Wah , Chuah Seng-Kee
Published: June 2013

Background

Esophageal stricture (ES) and gastric outlet obstruction (GOO) can occurred in patients injured by the ingestion of corrosive agents. These complications may occur concurrently but has not been reported in the literature. The aims of this study are to assess the effects and complications of endoscopic-guided balloon dilations (EBD) in patients with corrosive-induced upper gastrointestinal strictures, either ES or GOO alone and simultaneous occurrences of both (ES + GOO).

Methods

From July 2002 to December 2009, 36 patients with corrosive-induced upper gastrointestinal strictures in a tertiary hospital were recruited into this study. The patients were divided into three groups, ES group (n = 18), GOO (n = 7), and ES + GOO group (n = 11). All strictures were dilated under direct visualization by using through-the-scope balloon catheters to the end point of 15 mm. The end-point of treatment was successful ingestion of a solid or semisolid diet without additional dilation for more than 12 months.

Results

These 36 patients included 15 males and 21 females with average age of 47 years ranging from 25 to 79 years. The success rates for ES group is significantly better than GOO and ES + GOO group (83.3% vs. 57.1% vs. 36.4% p = 0.035). Less complications were observed in ES group than in GOO and ES + GOO group (16.7% vs. 42.9% vs. 36.4%, p = 0.041). GOO group needed more sessions of dilations in order to achieve success dilations than ES and GOO groups (13.7 ± 4.9 vs. 6.1 ± 4.7 vs. 5.5 ± 2.1, p = 0.011).

Conclusions

Corrosive injuries complicated with ES can be effectively and safely treated by EBD. However, the success rates declined significantly in patients with GOO with or without ES and amore complications occurred.
Area-level risk factors for adverse birth outcomes: trends in urban and rural settings
Authors: Kent Shia T , McClure Leslie A , Zaitchik Ben F , Gohlke Julia M
Published: June 2013

Background

Significant and persistent racial and income disparities in birth outcomes exist in the US. The analyses in this manuscript examine whether adverse birth outcome time trends and associations between area-level variables and adverse birth outcomes differ by urban–rural status.

Methods

Alabama births records were merged with ZIP code-level census measures of race, poverty, and rurality. B-splines were used to determine long-term preterm birth (PTB) and low birth weight (LBW) trends by rurality. Logistic regression models were used to examine differences in the relationships between ZIP code-level percent poverty or percent African-American with either PTB or LBW. Interactions with rurality were examined.

Results

Population dense areas had higher adverse birth outcome rates compared to other regions. For LBW, the disparity between population dense and other regions increased during the 1991–2005 time period, and the magnitude of the disparity was maintained through 2010. Overall PTB and LBW rates have decreased since 2006, except within isolated rural regions. The addition of individual-level socioeconomic or race risk factors greatly attenuated these geographical disparities, but isolated rural regions maintained increased odds of adverse birth outcomes. ZIP code-level percent poverty and percent African American both had significant relationships with adverse birth outcomes. Poverty associations remained significant in the most population-dense regions when models were adjusted for individual-level risk factors.

Conclusions

Population dense urban areas have heightened rates of adverse birth outcomes. High-poverty African American areas have higher odds of adverse birth outcomes in urban versus rural regions. These results suggest there are urban-specific social or environmental factors increasing risk for adverse birth outcomes in underserved communities. On the other hand, trends in PTBs and LBWs suggest interventions that have decreased adverse birth outcomes elsewhere may not be reaching isolated rural areas.
Peripapillary choroidal thickness in healthy Chinese subjects
Authors: Huang Wenbin , Wang Wei , Zhou Minwen , Chen Shida , Gao Xinbo , Fan Qian , Ding Xiaoyan , Zhang Xiulan
Published: June 2013

Background

To evaluate the peripapillary choroidal thickness of a healthy Chinese population, and to determine its influencing factors.

Methods

A total of 76 healthy volunteers (76 eyes) without ophthalmic or systemic symptoms were enrolled. Choroidal scans (360-degree 3.4 mm diameter peripapillary circle scans) were obtained for all eyes using enhanced depth imaging spectral-domain optical coherence tomography. Choroid thickness was measured at the temporal, superotemporal, superior, superonasal, nasal, inferonasal, inferior, and inferotemporal segments.

Results

The average peripapillary choroidal thicknesses were 165.03 ± 40.37 μm. Inferonasal, inferior, and inferotemporal thicknesses were significantly thinner than temporal, superotemporal, superior, superonasal, nasal thicknesses (p < 0.05). No statistically significant difference was found among inferonasal, inferior, and inferotemporal thicknesses. The average peripapillary choroidal thickness decreased linearly with age (β = −1.33, 95% CI −1.98, -0.68, P < 0.001). No correlation was noted between average choroidal thickness and other factors (gender, refractive error, axial length, average retinal nerve fiber layer thickness, intraocular pressure, diastolic blood pressure, systolic blood pressure, mean blood pressure, diastolic ocular perfusion pressure, systolic ocular perfusion pressure, and mean ocular perfusion pressure).

Conclusions

The inferonasal, inferior, inferotemporal peripapillary choroidal thicknesses were significantly thinner than temporal, superotemporal, superior, superonasal, and nasal thicknesses. A thinner peripapillary choroid is associated with increasing age.