bluuebunny/crossref_metadata_2025 huggingface dataset:
Unified modeling of gene duplication, loss, and coalescence using a locus tree
Authors: Rasmussen Matthew D. , Kellis Manolis
Published: January 2012

Gene phylogenies provide a rich source of information about the way evolution shapes genomes, populations, and phenotypes. In addition to substitutions, evolutionary events such as gene duplication and loss (as well as horizontal transfer) play a major role in gene evolution, and many phylogenetic models have been developed in order to reconstruct and study these events. However, these models typically make the simplifying assumption that population-related effects such as incomplete lineage sorting (ILS) are negligible. While this assumption may have been reasonable in some settings, it has become increasingly problematic as increased genome sequencing has led to denser phylogenies, where effects such as ILS are more prominent. To address this challenge, we present a new probabilistic model, DLCoal, that defines gene duplication and loss in a population setting, such that coalescence and ILS can be directly addressed. Interestingly, this model implies that in addition to the usual gene tree and species tree, there exists a third tree, the locus tree, which will likely have many applications. Using this model, we develop the first general reconciliation method that accurately infers gene duplications and losses in the presence of ILS, and we show its improved inference of orthologs, paralogs, duplications, and losses for a variety of clades, including flies, fungi, and primates. Also, our simulations show that gene duplications increase the frequency of ILS, further illustrating the importance of a joint model. Going forward, we believe that this unified model can offer insights to questions in both phylogenetics and population genetics.
TherolBGene Suppresses Reactive Oxygen Species in Transformed Plant Cells through the Sustained Activation of Antioxidant Defense
Authors: Bulgakov Victor P. , Gorpenchenko Tatiana Y. , Veremeichik Galina N. , Shkryl Yuri N. , Tchernoded Galina K. , Bulgakov Dmitry V. , Aminin Dmitry L. , Zhuravlev Yuri N.
Published: January 2012

The rolB (for rooting locus of Agrobacterium rhizogenes) oncogene has previously been identified as a key player in the formation of hairy roots during the plant-A. rhizogenes interaction. In this study, using single-cell assays based on confocal microscopy, we demonstrated reduced levels of reactive oxygen species (ROS) in rolB-expressing Rubia cordifolia, Panax ginseng, and Arabidopsis (Arabidopsis thaliana) cells. The expression of rolB was sufficient to inhibit excessive elevations of ROS induced by paraquat, menadione, and light stress and prevent cell death induced by chronic oxidative stress. In rolB-expressing cells, we detected the enhanced expression of antioxidant genes encoding cytosolic ascorbate peroxidase, catalase, and superoxide dismutase. We conclude that, similar to pathogenic determinants in other pathogenic bacteria, rolB suppresses ROS and plays a role not only in cell differentiation but also in ROS metabolism.
Poly[tetraamminecopper(II) bis[tris(μ2-cyanido-κ2C,N)dicuprate(I)]]: a unique CuI–CuIImixed-valence complex containing anionic cuprous cyanide layers and [Cu(NH3)4]2+cations
Authors: Jia Li-Na , Hou Lei
Published: January 2012

The title compound, {[Cu(NH3)4][Cu(CN)3]2}n, features a CuI–CuIImixed-valence CuCN framework based on {[Cu2(CN)3]−}nanionic layers and [Cu(NH3)4]2+cations. The asymmetric unit contains two different CuIions and one CuIIion which lies on a centre of inversion. Each CuIion is coordinated to three cyanide ligands with a distorted trigonal–planar geometry, while the CuIIion is ligated by four ammine ligands, with a distorted square-planar coordination geometry. The interlinkage between CuIions and cyanide bridges produces a honeycomb-like {[Cu2(CN)3]−}nanionic layer containing 18-membered planar [Cu(CN)]6metallocycles. A [Cu(NH3)4]2+cation fills each metallocyclic cavity within pairs of exactly superimposed {[Cu2(CN)3]−}nanionic layers, but there are no cations between the layers of adjacent pairs, which are offset. Pairs of N—H...N hydrogen-bonding interactions link the N—H groups of the ammine ligands to the N atoms of cyanide ligands.
Cloning, purification, crystallization and preliminary X-ray diffraction analysis of mouse PACSIN 3 protein
Authors: Bai Xiaoyun , Meng Geng , Zheng Xiaofeng
Published: January 2012

PACSIN-family proteins are cytoplasmic proteins that have vesicle-transport, membrane-dynamics, actin-reorganization and microtubule activities. Here, the N-terminal F-BAR domain of mouse PACSIN 3, which contains 341 amino acids, was successfully cloned, purified and crystallized. The crystal of PACSIN 3 (1–341) diffracted to 2.6 Å resolution and belonged to space groupP21, with unit-cell parametersa= 46.9,b= 54.7,c= 193.7 Å, α = 90, β = 96.9, γ = 90°. These data should provide further information on PACSIN-family protein structures.
Expression, purification, crystallization and preliminary crystallographic analysis of a thermostable DNA ligase from the archaeonThermococcus sibiricus
Authors: Petrova T. E. , Bezsudnova E. Y. , Dorokhov B. D. , Slutskaya E. S. , Polyakov K. M. , Dorovatovskiy P. V. , Ravin N. V. , Skryabin K. G. , Kovalchuk M. V. , Popov V. O.
Published: January 2012

DNA ligases join single-strand breaks in double-stranded DNA by catalyzing the formation of a phosphodiester bond between adjacent 5′-phosphate and 3′-hydroxyl termini. Their function is essential to maintain the integrity of the genome in DNA replication, recombination and repair. A recombinant ATP-dependent DNA ligase from the hyperthermophilic anaerobic archaeonThermococcus sibiricuswas expressed inEscherichia coliand purified. Crystals were grown by vapour diffusion using the hanging-drop method with 17%(w/v) PEG 4000 and 8.5%(v/v) 2-propanol as precipitants. A diffraction experiment was performed with a single crystal, which diffracted X-rays to 3.0 Å resolution. The crystal belonged to space groupP212121, with unit-cell parametersa = 58.590,b= 87.540,c= 126.300 Å.
A new crystal lattice structure ofHelicobacter pylorineutrophil-activating protein (HP-NAP)
Authors: Tsuruta Osamu , Yokoyama Hideshi , Fujii Satoshi
Published: January 2012

A new crystal lattice structure ofHelicobacter pylorineutrophil-activating protein (HP-NAP) has been determined in two forms: the native state (Apo) at 2.20 Å resolution and an iron-loaded form (Fe-load) at 2.50 Å resolution. The highly solvated packing of the dodecameric shell is suitable for crystallographic study of the metal ion-uptake pathway. Like other bacterioferritins, HP-NAP forms a spherical dodecamer with 23 symmetry including two kinds of channels. Iron loading causes a series of conformational changes of amino-acid residues (Trp26, Asp52 and Glu56) at the ferroxidase centre.
A process‐based approach to modelling impacts of climate change on the damage niche of an agricultural weed
Authors: Stratonovitch Pierre , Storkey Jonathan , Semenov Mikhail A.
Published: January 2012

Predicting the impact of climate change on the damage niche of an agricultural weed at a local scale requires a process‐based modelling approach that integrates local environmental conditions and the differential responses of the crop and weed to change. A simulation model of the growth and population dynamics of winter wheat and a competing weed, Sirius 2010, was calibrated and validated for the most economically damaging weed in UK cereals, Alopecurus myosuroides. The model was run using local‐scale climatic scenarios generated by the LARS‐WG weather generator and based on the HadCM3 projections for the periods 2046–2065 and 2080–2099 to predict the impact of climate change on the population dynamics of the weed and its effect on wheat yields. Owing to rising CO2 concentration and its effect on radiation use efficiency of wheat, weed‐free wheat yields were predicted to increase. The distribution of the weed was predicted to remain broadly similar with a possible northward shift in range. Local‐scale variation in the impact of climate change was apparent owing to variation in soil type and water holding capacity. The competitive balance was shifted in favour of the deeper rooted crop under climate change, particularly on sites with lighter soils, owing to more frequent and severe drought stress events. Although the damage niche of A. myosuroides was predicted to reduce under climate change, it is likely that weeds with contrasting physiology, such as C4 species, will be better adapted to future conditions and pose a more serious threat.
Interannual variability in responses of belowground net primary productivity (NPP) and NPP partitioning to long‐term warming and clipping in a tallgrass prairie
Authors: Xu Xia , Niu Shuli , Sherry Rebecca A. , Zhou Xuhui , Zhou Jizhong , Luo Yiqi
Published: January 2012

The dynamics of belowground net primary productivity (BNPP) is of fundamental importance in understanding carbon (C) allocation and storage in grasslands. However, our knowledge of the interannual variability in response of BNPP to ongoing global warming is limited. In this study, we explored temporal responses of BNPP and net primary productivity (NPP) partitioning to warming and clipping in a tallgrass prairie in Oklahoma, USA. Infrared heaters were used to elevate soil temperature by approximately 2 °C since November 1999. Annual clipping was to mimic hay harvest. On average from 2005 to 2009, warming increased BNPP by 41.89% in the unclipped subplots and 66.93% in the clipped subplots, with significant increase observed in wet years. Clipping also had significant positive impact on BNPP, which was mostly found under warming. Overall, fBNPP, the fraction of BNPP to NPP, increased under both warming and clipping treatments, more in dry years. Water availability (either precipitation or soil moisture) was the most limiting factor for both BNPP and fBNPP. It strongly dominated the interannual variability in NPP, fBNPP, and their responses to warming and clipping. Our results suggest that water availability regulates tallgrass prairie's responses to warming and land use change, which may eventually influence the global C cycle. With increasing variability in future precipitation patterns, warming effects on the vegetation in this region may become less predictable.
Response of butterflies to structural and resource boundaries
Authors: Schultz Cheryl B. , Franco Aldina M. A. , Crone Elizabeth E.
Published: January 2012

1. Two aspects of landscape composition shape the behavioural response of animals to habitat heterogeneity: physical habitat structure and abundance of key resources. In general, within‐habitat movement behaviour has been investigated in relation to resources, and preference at boundaries has been quantified in response to physical structure.

2. Habitat preference studies suggest that responses to resources vs. structure should differ, e.g. between male and female animals, and effects of responses to structure and resources may also interact. However, most studies of animal movement combine various aspects of behavioural responses to ‘habitat’, implicitly assuming that resources and structure are broadly equivalent.

3. We conducted a large‐scale experiment of the movement of Fender’s blue (Icaricia icarioides fenderi), an endangered butterfly, to investigate butterfly response to physical structure of the landscape (prairie, open woods and dense woods) and to resources [presence or absence of Kincaid’s lupine, Lupinus oreganus (larval hostplant patches)]. The experiment included 606 butterfly flight paths across four habitat types and nine ecotones.

4. Responses to physical structure and resource patches were not congruent. Butterflies were attracted to resource patches within both prairies and open woods and moved more slowly when in resource patches. Butterflies tended to prefer prairie at prairie‐forest edges but tended to move faster in prairies than in open woods. Physical structure and resources also interacted; butterflies did not respond to physical habitat structure when resource patches spanned prairie – open woods ecotones.

5. Even dense woods were not perfect barriers, in contrast to a large body of literature that assumes insects from open habitats will not enter dense forests.

6. Movement of both males and females responded to resources and structure. However, female butterflies had stronger responses to both resources and structure in most cases. Females had strongest response to resource (hostplant) patches at patch edges, whereas the strongest preference of males was to return to prairie from open forest.

7. If other species behave like Fender’s blue, then combining different definitions of ‘habitat’ (physical structure vs. resources), different aspects of movement (edge preference vs. within‐habitat movement) and/or males and females within species could all lead to misleading conclusions. Our results highlight the importance of investigating these responses, and our study provides a framework for separating them in other systems.
Habitat use throughout migration: linking individual consistency, prior breeding success and future breeding potential
Authors: Hoye Bethany J. , Hahn Steffen , Nolet Bart A. , Klaassen Marcel
Published: January 2012

1. Habitat use can influence individual performance in a wide range of animals, either immediately or through carry‐over effects in subsequent seasons. Given that many animal species also show consistent individual differences in reproductive success, it seems plausible that individuals may have consistent patterns of habitat use representing individual specializations, with concomitant fitness consequences.

2. Stable‐carbon isotope ratios from a range of tissues were used to discern individual consistency in habitat use along a terrestrial–aquatic gradient in a long‐distance migrant, the Bewick’s swan (Cygnus columbianus bewickii). These individual specialisations represented <15% of the isotopic breadth of the population for the majority of individuals and were seen to persist throughout autumn migration and overwintering until aquatic habitats were no longer available.

3. Individual foraging specialisations were then used to demonstrate two consecutive carry‐over effects associated with macroscale habitat segregation: consequences of breeding season processes for autumn habitat use; and consequences of autumn habitat use for future reproductive success. Adults that were successful breeders in the year of capture used terrestrial habitats significantly more than adults that were not successful, revealing a substantial cost of reproduction and extended parental care. Use of aquatic habitats during autumn was, however, associated with increased body condition prior to spring migration; and increased subsequent breeding success in adults that had been unsuccessful the year before. Yet adults that were successful breeders in the year of capture remained the most likely to be successful the following year, despite their use of terrestrial habitats.

4. Our results uniquely demonstrate not only individual foraging specializations throughout the migration period, but also that processes during breeding and autumn migration, mediated by individual consistency, may play a fundamental role in the population dynamics of long‐distance migrants. These findings, therefore, highlight the importance of long‐term consistency to our understanding of habitat function, interindividual differences in fitness, population dynamics and the evolution of migratory strategies.
Successional trends in Floristic Quality
Authors: Spyreas Greg , Meiners Scott J. , Matthews Jeffrey W. , Molano‐Flores Brenda
Published: January 2012

1. Simple, conservation‐relevant, plant community measures are sought by resource managers. In this context, the use of Floristic Quality Assessment (FQA) has increased exponentially over the past 30 years. FQA measures a habitat’s Floristic Quality and conservation value by summarizing the relative anthropogenic disturbance tolerances of its plant species (i.e. their Conservatism). However, despite their widespread use in research, restoration and conservation work, the behaviour of FQA values in communities during succession is not understood.

2. We analysed FQA values in 10 old fields over 50 years of unaltered succession. We determined whether Floristic Quality followed a predictable increasing successional trend, assessing four specific predictions: (i) FQA values will follow an asymptotically increasing, rather than peaked or linearly increasing trajectory; (ii) field initiation treatments (abandoned as hayfield or cropfield) will not lead to long‐term differences in FQA values; (iii) trajectories will be consistent regardless of the particular species composition of fields and (iv) trajectories will be robust to common variations in FQA metric formulations (non‐native species, varied spatial scale).

3. In all cases, a negative exponential rise to an asymptote best described FQA value trajectories over time. Field abandonment treatments did not affect FQA value trajectories. Furthermore, trends were consistent among fields despite differences in species composition among fields. Overall, the results suggest a predictable, deterministic path for FQA values over the early‐ to mid‐successional timeframes studied.

4. Synthesis and applications. Understanding the temporal behaviour(s) of Floristic Quality is necessary for setting realistic restoration goals, evaluating habitat recovery and adapting management to achieve high conservation value natural areas. By illustrating the temporal consistency of Floristic Quality metrics during succession, this article demonstrates the robustness of FQA for such uses. The FQA value trajectory described here also establishes a background trend model for expected values in recovering habitats, which will allow for the assessment of an individual habitat’s progression relative to the background trend. Such comparisons en masse will highlight the constraints of greatest importance to community‐level Floristic Quality restoration. For example, FQA values in this study were ultimately limited by Conservative understorey plant re‐establishment from adjacent old‐growth forest. As this is not unlike species recovery patterns observed in other habitats, it suggests that restoration practitioners would do well to focus on Conservative species.
Utility of Genome‐Wide Association Study findings: prostate cancer as a translational research paradigm
Authors: Turner A. R. , Kader A. K. , Xu J.
Published: January 2012

Abstract.  Turner AR, Kader AK, Xu J (Wake Forest University, Winston‐Salem, NC; and University of California San Diego, La Jolla, CA; USA). Utility of Genome‐Wide Association Study findings: prostate cancer as a translational research paradigm (Review). J Intern Med 2012; 271: 344–352.

Genome‐Wide Association Studies have identified thousands of consistently replicated associations between genetic markers and complex disease risk, including cancers. Alone, these markers have limited utility in risk prediction; however, when several of these markers are used in combination, the predictive performance appears to be similar to that of many currently available clinical predictors. Despite this, there are divergent views regarding the clinical validity and utility of these genetic markers in risk prediction. There are valid concerns, thus providing a direction for new lines of research. Herein, we outline the debate and use the example of prostate cancer to highlight emerging evidence from studies that aim to address potential concerns. We also describe a translational framework that could be used to guide the development of a new generation of comprehensive research studies aimed at capitalizing on these exciting new discoveries.
New(t)s and views from hybridizing MHC genes: introgression rather than trans‐species polymorphism may shape allelic repertoires
Authors: WEGNER K. MATHIAS , EIZAGUIRRE CHRISTOPHE
Published: January 2012

One of the key features of major histocompatibility complex (MHC) genes is the frequent occurrence of trans‐species polymorphism, that is ‘the passage of allelic lineages from ancestral to descendant species’ (Klein et al. 2007). Selectively maintained ancestral polymorphism may, however, be hard to distinguish from introgression of MHC alleles between hybridizing species (Fig. 1). In this issue of Molecular Ecology, Nadachowska‐Brzyska et al. (2012) present data that suggest that the latter can be observed in two closely related species of newts, Lissotriton vulgaris (Lv) and L. montandoni (Lm) from south‐east Europe. Strikingly, allelic MHC variation displayed more structure between geographically separated populations of L. vulgaris than across species in the hybrid zone. This suggests that high MHC variation in L. montadoni may result from mainly unidirectional gene flow between species, while differentiation between northern and southern populations of L. vulgaris might reflect local adaptation.

 Potential mechanisms generating shared repertoires of major histocompatibility complex alleles between southeast European newt species: Trans‐species polymorphism (left side) maintaining ancestral polymorphism across speciation events and introgression (right side) where alleles arising in one species after speciation introgress into the other by hybridization. The study Nadachowska‐Brzyska et al. 2012 suggests that the latter can be observed in two closely related newt species. Photos by Benny Trapp and Magdalena Herdegen.

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Genotype × environment interaction, environmental heterogeneity and the lek paradox
Authors: GREENFIELD M. D. , DANKA R. G. , GLEASON J. M. , HARRIS B. R. , ZHOU Y.
Published: January 2012

Substantial additive genetic variance (VA) often exists for male signalling traits in spite of the directional selection that female choice imposes. One solution to this problem, a conundrum generally termed the ‘lek paradox’, is that genotype × environment interaction (GEI) occurs and generates a ‘crossover’ of reaction norms in which no one genotype performs in a superior manner in all environments. Theoretical work indicates that such crossover can sustain genetic variance provided that either (i) spatial heterogeneity in environmental conditions combined with limited migration among populations or (ii) temporal heterogeneity in environmental conditions combined with occasional generation overlap is present. Whereas some recent studies have revealed the intersection of reaction norms for sexually selected traits in laboratory and in natural populations, associated information on environmental heterogeneity, migration and generation overlap has not been investigated. We studied this question in an acoustic pyralid moth,Achroia grisella, in which previous work indicated GEI and crossover of reaction norms for several parameters of the male song evaluated by females. We measured reaction norms for male song as expressed when development was completed under different environmental conditions in four neighbouring, yet isolated, populations during 1 year and in one of these populations during consecutive years. Crossover occurred for the various song parameters in the several populations, but we did not observe a higher incidence of crossover between genotypes taken from two different populations than from the same population. However, for several key song parameters, crossover between genotypes taken from two different years was higher than that between genotypes from the same year. We suggest that temporal heterogeneity in the form of varying selection could potentially conserve VAinA. grisella, but we also note other factors that might contribute.
Is the physical functioning of older adults with diabetes associated with the processes and outcomes of care? Evidence from Translating Research Into Action for Diabetes (TRIAD)
Authors: Lee P. G. , McEwen L. N. , Waitzfelder B. , Subramanian U. , Karter A. J. , Mangione C. M. , Herman W. H.
Published: January 2012

Diabet. Med. 29, e321–e325 (2012)

Aims  To examine the relationship between physical function limitations and diabetes self‐management, processes of care and intermediate outcomes in adults ≥ 65 years of age with Type 2 diabetes.

Methods  We studied 1796 participants 65 years of age and older in managed care health plans enrolled in Translating Research into Action for Diabetes (TRIAD). Physical functioning was assessed at baseline with the Physical Component Summary of the Short Form‐12 Health Survey. Diabetes self‐management was assessed with follow‐up surveys, and processes of care (eye examinations, urine microalbumin testing, foot examinations, etc.) and intermediate health outcomes (HbA1c, blood pressure, LDL cholesterol) were assessed with medical chart reviews. Multivariate regression models were constructed to examine the associations between physical function limitations and outcomes.

Results  Frequency of eye examinations (odds ratio 0.69, 95% CI 0.49–0.99) was the only process of care that was worse for participants with physical function limitations (n = 573) compared with those without limitations (n = 618). Neither self‐management nor intermediate outcomes differed by whether patients had or did not have physical function limitations.

Conclusion  Limitations in physical functioning as assessed by the Short Form‐12 were not associated with substantial difference in diabetes care in adults ≥ 65 years of age enrolled in managed care health plans.
Hyperbaric oxygen therapy improves peripheral insulin sensitivity in humans
Authors: Wilkinson D. , Chapman I. M. , Heilbronn L. K.
Published: January 2012

Diabet. Med. 29, 986–989 (2012)

Aim  Hyperbaric oxygen therapy is known to reduce fasting blood glucose in individuals with Type 2 diabetes. However, the mechanisms of this effect are not clear. The aim of this study was to determine whether peripheral insulin sensitivity by hyperinsulinaemic euglycaemic clamp is increased in patients presenting for hyperbaric oxygen therapy.

Methods  Participants were non‐obese individuals without Type 2 diabetes (n = 5) or obese patients with Type 2 diabetes (n = 5). Patients were given 100% oxygen at 2.0 absolute atmospheres for 2 h, six sessions per week for 5 weeks.

Results  Peripheral insulin sensitivity was increased in the whole cohort (P = 0.04). Subsequent analysis revealed that this was significant at both treatment 3 (+37.3 ± 12.7%, P = 0.02) and treatment 30 (+40.6 ± 12.6%, P = 0.009). HbA1c was significantly reduced in subjects without diabetes only (P < 0.05).

Conclusion  Insulin sensitivity increased within 3 days of hyperbaric oxygen treatment and this was maintained for 30 sessions. This increase in insulin sensitivity is equivalent to that observed following moderate weight loss. The mechanisms underlying the insulin‐sensitizing effect of hyperbaric oxygen require further elucidation.
HbA1c and glucose intolerance in obese children and adolescents
Authors: Lee H. S. , Park H. K. , Hwang J. S.
Published: January 2012

Diabet. Med. 29, e102–e105 (2012)

Aims  Childhood obesity is associated with an increased likelihood for having impaired glucose tolerance, dyslipidaemia and diabetes. The aim of the study was to evaluate HbA1c as a screening test for impaired glucose tolerance in obese children and adolescents and identify the optimal HbA1c threshold.

Methods  We studied 126 obese and overweight children (BMI > 85th percentile for age and gender) 4–17 years of age referred to the endocrine clinic at Ajou University Hospital in Korea. All subjects underwent HbA1c and oral glucose tolerance test.

Results  Thirty‐four patients (27%) out of 126 had impaired glucose tolerance. Silent diabetes was diagnosed in 10 adolescents (7.9%). Based on the receiver operating characteristic curve, the optimal cut point of HbA1c related to impaired glucose tolerance diagnosed by oral glucose tolerance test was 40 mmol/mol (5.8%), which was associated with a 64.7% sensitivity and 61.6% specificity, with an area under the receiver operating characteristic curve of 0.651 (95% CI 0.529–0.772).

Conclusions  Obesity is associated with an increased risk of impaired glucose tolerance. An HbA1c value of 40 mmol/mol (5.8%) should be used as a screening tool to identify children and adolescents with impaired glucose tolerance.
Movement and habitat use of Australia's largest snake‐necked turtle: implications for water management
Authors: Bower D. S. , Hutchinson M. , Georges A.
Published: January 2012

Hydrological regimes strongly influence ecological processes in river basins. Yet, the impacts of management regimes are unknown for many freshwater taxa in highly regulated rivers. We used radio‐telemetry to monitor the movement and activity of broad‐shelled river turtles Chelodina expansa to infer the impact of current water management practices on turtles in Australia's most regulated river – the Murray River. We radio‐tracked C. expansa to (1) measure the range span and examine the effect of sex, size and habitat type on turtle movement, and (2) examine habitat use within the river channel and its associated backwaters. C. expansa occupied all macro habitats in the river (main channel, backwater, swamp and connecting inlets). Within these habitats, females occupied discrete home ranges, whereas males moved up to 25 km. The extensive movement of male turtles suggests that weirs and other aquatic barriers may interfere with movement and dispersal. Turtles regularly move between backwaters and the main river channel, which highlights the likely disturbance from backwater detachment, a water saving practice in the lower Murray River.
Is spatial variation in food availability an explanation for aBergmannian size pattern in aNorthAmerican hibernating, burrowing mammal? An information‐theoretic approach
Authors: Gür H. , Kart Gür M.
Published: January 2012

Predictable empirical patterns of variation in body size along spatial and environmental gradients have been documented within many species of mammals. Four main hypotheses, heat conservation, heat dissipation, primary productivity and seasonality, have been proposed to explain these patterns of variation in body size. In this study, we reported an analysis of geographic variation in body size of Richardson's ground squirrelsUrocitellus richardsonii, aNorthAmerican hibernating, burrowing mammal. Firstly, we evaluated whether aBergmannian size pattern was exhibited by Richardson's ground squirrels. Secondly, we used an information‐theoretic approach to test which of the four main hypotheses best explain(s) geographic variation in body size of Richardson's ground squirrels or to assess whether, as proposed byMcNab's ‘resource rule’ orHuston andWolverton's ‘eNPPrule’, the primary productivity hypothesis is the only explanation.Richardson's ground squirrels exhibited a pattern of increasing body size towards the colder areas, that is, more productive and seasonal centralAlberta and foothills of the southernAlbertaRockyMountains, indicative of aBergmannian size pattern. Plant productivity and seasonality in plant productivity were likely the primary underlying factors generating the observed pattern of geographic variation in body size. Thus, our results supported primary productivity and seasonality hypotheses. From these results, we see thatMcNab's ‘resource rule’ orHuston andWolverton's ‘eNPPrule’ (i.e. spatial variation in food availability) is an explanation for aBergmannian size pattern inRichardson's ground squirrels, but not the only explanation.
Visual performance and optical quality with soft lenses in keratoconus patients
Authors: Jinabhai Amit , Radhakrishnan Hema , Tromans Cindy , O’Donnell Clare
Published: January 2012

Citation information: Jinabhai A, Radhakrishnan H, Tromans C & O’Donnell C. Visual performance and optical quality with soft lenses in keratoconus patients. Ophthalmic Physiol Opt 2012, 32, 100–116. doi: 10.1111/j.1475‐1313.2011.00889.x

Purpose:  To assess visual performance and ocular aberrations in keratoconic patients using toric soft contact lenses (SCL), rigid‐gas‐permeable (RGP) contact lenses and spectacle lens correction.

Methods:  Twenty‐two keratoconus patients (16 RGP lens wearers and six spectacle wearers) were fitted with toric SCL. Ocular aberrations were measured with and without the patient’s habitual RGP lenses and with the SCL in place. In the spectacle wearers, aberrations were measured with and without the SCL. Visual performance (high‐ and low‐contrast visual acuity) was evaluated with the patient’s habitual correction and with the SCL.

Results:  In the RGP lens wearers both the habitual lenses and the toric SCL significantly reduced coma, trefoil, 3rd‐order, 4th‐order cylinder and higher‐order root‐mean‐square (RMS) aberrations (p ≤ 0.015). In the spectacle wearers the toric SCL significantly reduced coma, 3rd‐order and higher‐order RMS aberrations (p ≤ 0.01). The patients’ habitual RGP lenses gave better low‐contrast acuity (p ≤ 0.006) compared to the toric SCL; however, no significant difference was found between lens types for high‐contrast acuity (p = 0.10). In the spectacle wearers no significant differences in visual performance measurements were found between the patients’ spectacles and the toric SCL (p ≥ 0.06).

Conclusion:  The results show that RGP lenses provided superior visual performances and greater reduction of 3rd‐order aberrations compared to toric SCL in this group of keratoconic patients. In the spectacle‐wearing group, visual performance with the toric SCL was found to be comparable to that measured with spectacles. Nevertheless, with the exception of spherical aberration, the toric SCL were successful in significantly reducing uncorrected higher‐order aberrations.
Inhibition of Apoptosis Protects Mice from Ethanol‐Mediated Acceleration of Early Markers of CCl4‐Induced Fibrosis but not Steatosis or Inflammation
Authors: Roychowdhury Sanjoy , Chiang Dian J. , Mandal Palash , McMullen Megan R. , Liu Xiuli , Cohen Jessica I. , Pollard John , Feldstein Ariel E. , Nagy Laura E.
Published: January 2012

Background:

Correlative evidence indicates that apoptosis is associated with the progression of alcoholic liver disease. If apoptosis contributes to ethanol (EtOH)‐induced steatohepatitis and/or fibrosis, then mice deficient in Bid, a key pro‐apoptotic Bcl‐2 family member, or mice treated with a pan‐caspase inhibitor (VX166) should be resistant to EtOH‐induced liver injury.

Methods:

This hypothesis was tested in mice using a model of chronic, heavy EtOH‐induced liver injury, as well as in a model in which moderate EtOH feeding accelerated the appearance of early markers of hepatic fibrosis in response to acute carbon tetrachloride (CCl4) exposure.

Results:

Chronic EtOH feeding to mice increased TUNEL‐ and cytokeratin‐18‐positive cells in the liver, as well as the expression of receptor‐interacting protein kinase 3 (RIP3), a marker of necroptosis. In this model, Bid−/− mice or wild‐type mice treated with VX166 were protected from EtOH‐induced apoptosis, but not EtOH‐induced RIP3 expression. Bid deficiency or inhibition of caspase activity did not protect mice from EtOH‐induced increases in plasma alanine and aspartate amino transferase activity, steatosis, or mRNA expression of some inflammatory cytokines. Moderate EtOH feeding to mice enhanced the response of mice to acute CCl4 exposure, resulting in increased expression of α‐smooth muscle actin and accumulation of extracellular matrix protein. VX166‐treatment attenuated EtOH‐mediated acceleration of these early indicators of CCl4‐induced hepatic fibrosis, decreasing the expression of α‐smooth muscle actin, and the accumulation of extracellular matrix protein.

Conclusions:

EtOH‐induced apoptosis of hepatocytes was mediated by Bid. Apoptosis played a critical role in the accelerating the appearance of early markers of CCl4‐induced fibrosis by moderate EtOH but did not contribute to EtOH‐induced hepatocyte injury, steatosis, or expression of mRNA for some inflammatory cytokines.
Imaging Spectrum of Pediatric Corpus Callosal Pathology: A Pictorial Review
Authors: Hyun Yoo Jeong , Hunter Jill
Published: January 2012

A wide spectrum of pediatric corpus callosal diseases can occur in the pediatric age group. Cross‐sectional magnetic resonance imaging plays an important role in the diagnosis of these patients. We reviewed our imaging record and collected cases of corpus callosal pathology. The purpose of this review is to illustrate the imaging features of various corpus callosal lesions encountered in children.
Use of spinosad and predatory mites for the management of Frankliniella occidentalis in low tunnel‐grown strawberry
Authors: Rahman Touhidur , Spafford Helen , Broughton Sonya
Published: January 2012

Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae) is a major pest of strawberry. The efficacy of three species of predatory mites, Typhlodromips montdorensis (Schicha), Neoseiulus cucumeris (Oudemans) (both: Acari: Phytoseiidae), and Hypoaspis miles (Berlese) (Acari: Laelapidae), and their compatibility with spinosad for the control of this thrips was evaluated in commercial strawberry in spring. Low tunnel‐grown strawberry was treated with ‘water then mites’, ‘spinosad then mites’, or ‘mites then spinosad’. Predatory mites were released as single‐, two‐ and three‐species combinations. Overall, spinosad‐treated plants had fewer thrips than water‐treated plants (control). In all treatment regimes, each species of predatory mite reduced the number of thrips relative to those plants that received no mites. Predatory mites were most effective in reducing thrips when released after spinosad was applied. Any multiple‐species combination of predatory mites reduced thrips numbers more than single‐species releases. The two‐species combination of T. montdorensis (foliage inhabiting) and H. miles (soil dwelling) was the most effective in suppressing thrips. The next most effective combination was a three‐species release. Of multiple‐species combinations, the two‐species combination of T. montdorensis and N. cucumeris was the least effective in suppressing thrips numbers. The spinosad and mites only temporarily reduced the numbers of F. occidentalis. This suggests that further application of predatory mites, spinosad, or both is required to maintain F. occidentalis populations below an economically damaging level.
Diagnosis and treatment of rectovaginal endometriosis: an overview
Authors: KRUSE CHRISTINA , SEYER‐HANSEN MIKKEL , FORMAN AXEL
Published: January 2012

Rectovaginal endometriosis can be a cause of severe pain, dyspareunia and intestinal problems. A thorough examination is needed and should include diagnostic imaging, such as transvaginal or transrectal ultrasound or magnetic resonance imaging. Medical therapies, such as oral contraceptives, progestins and levonorgestrel‐releasing intrauterine devices, all seem to reduce pain and should always be considered. Surgical treatment is challenging and implies a risk of severe complications. It is preferable to treat endometriotic lesions with superficial infiltration into the rectal wall by local laparoscopic excision, while segmental rectal resection is needed in the case of severe intestinal infiltration. This review describes available diagnostic tools, the possibilities for medical treatment and the alternative surgical approaches.
The human hair follicle, a bistable organ?
Authors: Bernard Bruno A.
Published: January 2012

Abstract:  The hair cycle and its control remain today an object of debate. A number of factors, which can modulate this process, have been identified but its choreography remains elusive. For years, the hunt for the conductor has been on, but nobody ever caught him. Intuitively, the process being considered as cyclic, an automaton controlling this cycle should be looked for, by analogy with a clock. However, the putative hair follicle oscillator that would control hair cycle failed to be identified and characterized. In fact, we have revealed that human hair follicle has an autonomous behaviour and that the transitions from one phase to the next occur independently for each follicle, after time intervals given stochastically by a lognormal distribution characterized by a mean and a variance. From this analysis, one can conclude that instead of a cyclical behaviour with an intrinsic automaton, a bistable steady state controls human hair follicle behaviour, which under a stochastic way jumps from the dormant to the active steady state and vice versa.
Using Recovery Data to Extend the Effective Duration of Pumping Tests
Authors: Neville Christopher J. , van der Kamp Garth
Published: January 2012

Collection of water‐level recovery data is a common practice for pumping tests. The resulting data can provide some of the most useful information from the tests, but are rarely used to their full value. van der Kamp (1989) proposed a general method that uses recovery data to extend the effective duration of pumping. The method is straightforward to implement and applicable for simple or complex hydrogeologic settings. The only assumption invoked is that the response remains linear such that the principle of superposition can be applied. No other assumptions about the properties of the aquifer are required. The method can greatly increase the value of pumping tests by extending the effective duration of the tests for as long as significant residual drawdowns are observed.
FOBT Completion in FQHCs: Impact of Physician Recommendation, FOBT Information, or Receipt of the FOBT Kit
Authors: Davis Terry C. , Arnold Connie L. , Rademaker Alfred W. , Platt Daci J. , Esparza Julia , Liu Dachao , Wolf Michael S.
Published: January 2012

Purpose: To determine the effect of common components of primary care‐based colorectal cancer (CRC) screening interventions on fecal occult blood test (FOBT) completion within rural and urban community clinics, including: (1) physician's spoken recommendation, (2) providing information or education about FOBTs, and (3) physician providing the FOBT kit; to determine the relative effect of these interventions; and to compare the effect of each intervention between rural and urban clinics.

Methods: We conducted structured interviews with patients aged 50 years and over receiving care at community clinics that were noncompliant with CRC screening. Self‐report of ever receiving a physician's recommendation for screening, FOBT information or education, physician providing an FOBT kit, and FOBT completion were collected.

Findings: Participants included 849 screening‐eligible adults; 77% were female and 68% were African American. The median age was 57; 33% lacked a high school diploma and 51% had low literacy. In multivariable analysis, all services were predictive of rural participants completing screening (physician recommendation: P= .002; FOBT education: P= .001; physician giving FOBT kit: P < .0001). In urban clinics, only physician giving the kit predicted FOBT completion (P < .0001). Compared to urban patients, rural patients showed a stronger relationship between FOBT completion and receiving a physician recommendation (risk ratio [RR]: 5.3 vs 2.1; P= .0001), receiving information or education on FOBTs (RR: 3.8 vs 1.9; P= .0002), or receiving an FOBT kit from their physician (RR: 22.3 vs 10.1; P= .035).

Conclusions: Participants who receive an FOBT kit from their physician are more likely to complete screening.
Birds in space and time: genetic changes accompanying anthropogenic habitat fragmentation in the endangered black‐capped vireo (Vireo atricapilla)
Authors: Athrey Giridhar , Barr Kelly R. , Lance Richard F. , Leberg Paul L.
Published: January 2012

Anthropogenic alterations in the natural environment can be a potent evolutionary force. For species that have specific habitat requirements, habitat loss can result in substantial genetic effects, potentially impeding future adaptability and evolution. The endangered black‐capped vireo (Vireo atricapilla) suffered a substantial contraction of breeding habitat and population size during much of the 20th century. In a previous study, we reported significant differentiation between remnant populations, but failed to recover a strong genetic signal of bottlenecks. In this study, we used a combination of historical and contemporary sampling from Oklahoma and Texas to (i) determine whether population structure and genetic diversity have changed over time and (ii) evaluate alternate demographic hypotheses using approximate Bayesian computation (ABC). We found lower genetic diversity and increased differentiation in contemporary samples compared to historical samples, indicating nontrivial impacts of fragmentation. ABC analysis suggests a bottleneck having occurred in the early part of the 20th century, resulting in a magnitude decline in effective population size. Genetic monitoring with temporally spaced samples, such as used in this study, can be highly informative for assessing the genetic impacts of anthropogenic fragmentation on threatened or endangered species, as well as revealing the dynamics of small populations over time.
Classifying Ischemic Stroke, from TOAST to CISS
Authors: Chen Pei‐Hao , Gao Shan , Wang Yong‐Jun , Xu An‐Ding , Li Yan‐Sheng , Wang David
Published: January 2012

SUMMARY  Ischemic stroke classification is critical in conducting basic research and clinical practice. A precise analysis of stroke subtypes requires the integration of clinical features, findings from diagnostic tests, and knowledge about potential etiologic factors by competent diagnostic investigators. We performed a literature review of the published stroke classification systems and examined each for its benefits and limitations in the evaluation of the stroke etiology. Two major approaches to etiologic classifications of ischemic stroke are currently being used: the causative and phenotypic subtyping. The most widely used causative system is the Trial of Org 10172 in acute stroke treatment (TOAST) classification. With the advances in modern diagnostic technology, new stroke subclassification systems, such as the causative classification system (CCS) and Chinese ischemic stroke subclassification (CISS) system, have been developed to enhance the accuracy of TOAST. The A‐S‐C‐O (Atherosclerosis, Small‐vessel disease, Cardiac source, Other cause) phenotypic classification system makes efforts to identify the most likely etiology but not neglecting the possibility of other potential multiple causes. We conclude that the ideal stroke classification system needs to be valid, easy to use, evidence‐based, and incorporate new information as it emerges.