bluuebunny/crossref_metadata_2025 huggingface dataset:
The kinetic basis of CRISPR-Cas off-targeting rules
Authors: Klein Misha , Eslami-Mossallam Behrouz , Gonzalez Arroyo Dylan , Depken Martin
Published: May 2017

Cas nucleases are popular tools for genome editing applications due to their ability to introduce DNA breaks at desired genomic locations. Such differential targeting is achieved through loading an RNA guide complimentary to the intended target sequence. As it turns out, sequences with only a partial match to the guide can also be cleaved. A large number of experiments have shed light on this off-targeting, outlining a number of rather peculiar empirical rules that detail the effect of mismatches at various positions and at various relative distances. We construct a kinetic model predicting on-target cleavage efficiency as well as off-target specificity. Our model explains a unified targeting rule for any target harboring mismatches, independent of their abundance and placing, and the observed decoupling between efficiency and specificity when protein-DNA interactions are weakened. We favorably compare our model to published experimental data from CRISPR-Cas9, CRISPR-Cpf1, CRISPR-Cascade, as well as to the human Argonaute 2 systems. Understanding the origins of off-targeting principles is important for the further development of CRISPR-Cas as a precise genome editing tool.
Conserved neural circuit structure acrossDrosophilalarval development revealed by comparative connectomics
Authors: Gerhard Stephan , Andrade Ingrid , Fetter Richard D. , Cardona Albert , Schneider-Mizell Casey M.
Published: May 2017

Throughout an animal’s postembryonic development, neuronal circuits must maintain appropriate output even as the body grows. The contribution of structural adaptation — neuronal morphology and synaptic connectivity — to circuit development remains unclear. In a previous paper (Schneider-Mizellet al., 2016), we measured the detailed neuronal morphological structures subserving neuronal connectivity inDrosophila. Here, we examine how neuronal morphology and connectivity change across postembyronic development. Using new and existing serial section electron microscopy volumes, we reconstructed an identified nociceptive circuit in two larvae, one 1st instar and one 3rd instar. We found extremely consistent, topographically-arranged circuit structure. Five-fold increases in size of interneurons were associated with compensatory structural changes that maintained cell-type-specific synaptic input as a fraction of total inputs. An increase in number of synaptic contacts was accompanied with a disproportionate increase in the number of small dendritic terminal branches relative to other neuronal compartments. We propose that these precise patterns of structural growth act to conserve the computational function of a circuit, for example determining the location of a nociceptive stimulus.
Phylogenomic species delimitation in microendemic frogs of the Brazilian Atlantic Forest
Authors: Pie Marcio R. , Bornschein Marcos R. , Ribeiro Luiz F. , Faircloth Brant C. , McCormack John E.
Published: May 2017

The advent of next-generation sequencing allows researchers to use large-scale datasets for species delimitation analyses, yet one can envision an inflection point where the added accuracy of including more loci does not offset the increased computational burden. One alternative to including all loci could be to prioritize the analysis of loci for which there is an expectation of high informativeness, such as those with higher numbers of parsimony-informative sites. Here, we explore the issue of species delimitation and locus selection with species from two anuran genera:Melanophryniscus(Bufonidae) andBrachycephalus(Brachycephalidae). Montane species in these genera have been isolated in sky islands across the southern Brazilian Atlantic Forest, which led to the formation of a number of microendemic species. To delimit species, we obtained genetic data using target enrichment of ultraconserved elements from 32 populations (13 forMelanophryniscusand 19 forBrachycephalus), and we were able to create datasets that included over 800 loci with no missing data. We ranked loci according to their corresponding number of parsimony-informative sites, and we performed species delimitation analyses using BPP in each genus based on the top 10, 20, 40, 80, 160, 320, and 640 loci. We also conducted several additional analyses using 10 randomly sampled datasets containing the same numbers of loci to discriminate the relative contribution of increasing the number of loci from prioritizing those with higher informativeness. We identified three types of node: nodes with either consistently high or low support regardless of the number of loci or their informativeness, and nodes that were initially poorly supported, but their support became stronger with more data. Adding more loci had a stronger impact on model support than prioritizing loci for their informativeness, but this effect was less apparent in datasets with more than 160 loci. When viewed across all sensitivity analyses, our results suggest that the current species richness in both genera might have been underestimated. In addition, our results provide useful guidelines to the use of different sampling strategies to carry out species delimitation with phylogenomic datasets.
The Human Cytoplasmic Dynein Interactome Reveals Novel Activators of Motility
Authors: Redwine William B. , DeSantis Morgan E. , Hollyer Ian , Htet Zaw Min , Tran Phuoc Tien , Swanson Selene K. , Florens Laurence , Washburn Michael P. , Reck-Peterson Samara L.
Published: May 2017

In human cells, cytoplasmic dynein-1 is essential for long-distance transport of many cargos, including organelles, RNAs, proteins, and viruses, towards microtubule minus ends. To understand how a single motor achieves cargo specificity, we identified the human dynein interactome or “transportome” by attaching a promiscuous biotin ligase (“BioID”) to seven components of the dynein machinery, including a subunit of the essential cofactor dynactin. This method reported spatial information about the large cytosolic dynein/dynactin complex in living cells. To achieve maximal motile activity and to bind its cargos, human dynein/dynactin requires “activators”, of which only five have been described. We developed methods to identify new activators in our BioID data, and discovered that ninein and ninein-like are a new family of dynein activators. Analysis of the protein interactomes for six activators, including ninein and ninein-like, suggests that each dynein activator has multiple cargos.
Anticipating emerging arboviruses: What comes after Zika?
Authors: Evans Michelle V. , Murdock Courtney C. , Drake John M.
Published: May 2017

New vector-borne diseases have emerged on multiple occasions over the last several decades, raising fears that they may become established within the United States. Here, we provide a watchlist of flaviviruses with high potential to emerge in the US, identified using new statistical techniques for mining the associations in partially observed data, to allow the public health community to better target surveillance.
Masculinity and the mechanisms of human self-domestication
Authors: Gleeson Ben Thomas
Published: May 2017

Objectives

Pre-historic decline in human craniofacial masculinity has been proposed as evidence of selection for elevated sociability and a process of ‘human self-domestication’ thought to have promoted complex capacities including language, culture, and cumulative technological development. This follows experimental observation of similar changes in non-human animals under selection for reduced aggression. Two distinct domestication hypotheses posit developmental explanations, involving hypoplasia of embryonic neural crest cells (NCCs), and declining androgen influence, respectively. Here, I assess the operation and potential interactions between these two mechanisms and consider their role in enhanced human adaptation to a cooperative sociocultural niche.

Methods

I provide a review and synthesis of related literature with a focus on physiological mechanisms effecting domesticated reductions in masculinity and sexual dimorphism. Further, I examine pre-historic modes of socio-sexual selection likely to drive human self-domestication via reduced aggression and masculinity.

Results

I find pluripotent NCCs provide progenitors for a wide range of vertebrate masculine features, acting as regular targets for sexually driven evolutionary change; suggesting domesticated hypoplasia of NCC-derived tissues would be sufficient to explain declines in masculine traits and features. However, lineage specific androgen receptor variability likely moderates these NCC-based effects.

Conclusions

These findings extend theorised mechanisms driving noted physiological, morphological, and behavioural changes thought to indicate enhanced sociability and human and self-domestication. Multiple current explanations for human sociability are consistent with physiological domestication under socio-sexual selection favouring dampened masculine physiology and behaviour as adaptations to an enhanced sociocultural niche. The analysis highlights multiple avenues for further investigation.
Local signals in mouse horizontal cell dendrites
Authors: Chapot Camille A. , Behrens Christian , Rogerson Luke E. , Baden Tom , Pop Sinziana , Berens Philipp , Euler Thomas , Schubert Timm
Published: May 2017

The mouse retina contains a single type of horizontal cell, a GABAergic interneuron that samples from all cone photoreceptors within reach and modulates their glutamatergic output via parallel feedback mechanisms. Because horizontal cells form an electrically-coupled network, they have been implicated in global signal processing, such as large scale contrast enhancement. Recently, it has been proposed that horizontal cells can also act locally at the level of individual cone photoreceptors. To test this possibility physiologically, we used two-photon microscopy to record light stimulus-evoked Ca2+signals in cone axon terminals and horizontal cell dendrites as well as glutamate release in the outer plexiform layer. By selectively stimulating the two mouse cone opsins with green and UV light, we assessed whether signals from individual cones remain “isolated” within horizontal cell dendritic tips, or whether they spread across the dendritic arbour. Consistent with the mouse‘s opsin expression gradient, we found that the Ca2+signals recorded from dendrites of dorsal horizontal cells were dominated by M- and those of ventral horizontal cells by S-opsin activation. The signals measured in neighbouring horizontal cell dendritic tips varied markedly in their chromatic preference, arguing against global processing. Rather, our experimental data and results from biophysically realistic modelling support the idea that horizontal cells can process cone input locally, extending the “classical” view of horizontal cells function. Pharmacologically removing horizontal cells from the circuitry reduced the sensitivity of the cone signal to low frequencies, suggesting that local horizontal cell feedback shapes the temporal properties of cone output.

Highlights

Light-evoked Ca2+signals in horizontal cell dendrites reflect opsin gradient

Chromatic preferences in neighbouring dendritic tips vary markedly

Mouse horizontal cells process cone photoreceptor input locally

Local horizontal cell feedback shapes the temporal properties of cone output

eTOC Blurb

Chapot et al. show that local light responses in mouse horizontal cell dendrites inherit properties, including chromatic preference, from the presynaptic cone photoreceptor, suggesting that their dendrites can provide “private” feedback to cones, for instance, to shape the temporal filtering properties of the cone synapse.
Crystal structure ofN-acetylmannosamine kinase fromFusobacterium nucleatum
Authors: Caing-Carlsson Rhawnie , Goyal Parveen , Sharma Amit , Ghosh Swagatha , Setty Thanuja Gangi , North Rachel A. , Friemann Rosmarie , Ramaswamy S.
Published: May 2017

Sialic acids comprise a varied group of nine-carbon amino sugars that are widely distributed among mammals and higher metazoans. Some human commensals and bacterial pathogens can scavenge sialic acids from their environment and degrade them for use as a carbon and nitrogen source. The enzymeN-acetylmannosamine kinase (NanK; EC 2.7.1.60) belongs to the transcriptional repressors, uncharacterized open reading frames and sugar kinases (ROK) superfamily. NanK catalyzes the second step of the sialic acid catabolic pathway, transferring a phosphate group from adenosine 5′-triphosphate to the C6 position ofN-acetylmannosamine to generateN-acetylmannosamine 6-phosphate. The structure of NanK fromFusobacterium nucleatumwas determined to 2.23 Å resolution by X-ray crystallography. Unlike other NanK enzymes and ROK family members,F. nucleatumNanK does not have a conserved zinc-binding site. In spite of the absence of the zinc-binding site, all of the major structural features of enzymatic activity are conserved.
Crystal structure of recombinant phosphoribosylpyrophosphate synthetase 2 fromThermus thermophilusHB27 complexed with ADP and sulfate ions
Authors: Timofeev Vladimir I. , Sinitsyna Ekaterina V. , Kostromina Maria A. , Muravieva Tatiana I. , Makarov Dmitry A. , Mikheeva Olga O. , Kuranova Inna P. , Esipov Roman S.
Published: May 2017

Phosphoribosylpyrophosphate synthetase (PRPPS) from the thermophilic bacterial strainThermus thermophilusHB27 catalyzes the synthesis of phosphoribosylpyrophosphate from ribose 5-phosphate and ATP, and belongs to the class I PRPPSs. The three-dimensional structure of the recombinant enzyme was solved at 2.2 Å resolution using crystals grown in microgravity from protein solution containing ATP, magnesium and sulfate ions. An ADP molecule was located in the active site of each subunit of the hexameric enzyme molecule and sulfate ions were located in both the active and allosteric sites. It was found that the catalytic loop that restricts the active-site area and is usually missing from the electron-density map of class I PRPPSs adopts different conformations in three independent subunits inT. thermophilusPRPPS. A closed conformation of the active site was found in one of subunits where the highly ordered catalytic β-hairpin delivers the Lys and Arg residues that are essential for activity directly to the ADP molecule, which occupies the ATP-binding site. A comparison of the conformations of the catalytic loop in the three independent subunits reveals a possible mode of transition from the open to the closed state of the active site during the course of the catalyzed reaction.
Bis[6-(cyclopentyliminomethyl)-2-methoxyphenolato]nickel(II). Corrigendum
Authors: Zhao Xiao-Fan
Published: May 2017

In the paper by Zhao [Acta Cryst. (2007), E63, m704–m705], the metal atom was reported incorrectly.
Different intra- and intermolecular hydrogen-bonding patterns in (3S,4aS,8aS)-2-[(2R,3S)-3-(2,5-X
2-benzamido)-2-(2,5-X
2-benzoyloxy)-4-phenylbutyl]-N-tert-butyldecahydroisoquinoline-3-carboxamides (X = H or Cl): compounds with moderate aspartyl protease inhibition activity
Authors: Cunico Wilson , Ferreira Maria de Lourdes G. , Wardell James L. , Harrison William T. A.
Published: May 2017

The crystal structures of (3S,4aS,8aS)-2-[(2R,3S)-3-benzamido-2-benzoyloxy-4-phenylbutyl]-N-tert-butyldecahydroisoquinoline-3-carboxamide, C38H47N3O4, (I), and (3S,4aS,8aS)-2-[(2R,3S)-3-(2,5-dichlorobenzamido)-2-(2,5-dichlorobenzoyloxy)-4-phenylbutyl]-N-tert-butyldecahydroisoquinoline-3-carboxamide, C38H43Cl4N3O4, (II), are described. Despite their chemical similarity, they adopt different conformations in the solid state: (I) features a bifurcated intramolecular N—H...(N,O) hydrogen bond from the tert-butylamide NH group to the piperidine N atom and the benzoate O atom, whereas (II) has an intramolecular N—H...O link from the benzamide NH group to the tert-butylamide O atom. In the crystal of (I), molecules are linked by C(4) amide N—H...O hydrogen bonds into chains propagating in the [010] direction, with both donor and acceptor parts of the benzamide group. In the extended structure of (II), C(11) N—H...O chains propagating in the [010] direction arise, with the donor being the tert-butylamide NH group and the acceptor being the O atom of the benzamide group.
Measuring the impact of beliefs on luxury buying behavior in an emerging market
Authors: Jain Sheetal , Khan Mohd Naved
Published: May 2017

Purpose

Demand for luxury brands is increasing at a very fast pace in emerging markets like India. But very few quantitative studies have been conducted to explore the reasons behind this sudden surge in demand. Thus, the purpose of this paper is to understand the impact of beliefs on consumer buying behavior for luxury fashion brands in the Indian context employing theory of planned behavior and to develop a comprehensive understanding regarding motivating factors behind luxury goods consumption.

Design/methodology/approach

Researcher-controlled sampling techniques (judgment and snowball sampling) were employed to collect data from actual users of luxury fashion brands in New Delhi (India). Statistical tests including confirmatory factor analysis and structural equation modeling were applied for data analysis.

Findings

The findings show that all three beliefs – attitudinal belief, normative belief (NB) and control belief – were positively and significantly related to attitude, subjective norm and perceived behavioral control (PBC). NB was found to have a positive impact on PBC as well as actual consumer purchasing behavior for luxury fashion brands.

Originality/value

This research contributes to the extant literature by bringing to light new findings that could help provide meaningful insights to the academicians and marketing practitioners.
Online customer relationship marketing tactics through social media and perceived customer retention orientation of the green retailer
Authors: Kang Ju-Young M. , Kim Jieun
Published: May 2017

Purpose

Despite the importance of incorporating social media with customer relationship management (CRM), the implementation of social CRM is still in its initial stages for a majority of green brands. The purpose of this paper is to examine whether consumers’ perception-based factors of the online CRM tactics through social media (i.e. perceived marketer-dominated information quality, perceived interaction quality, and perceived service content quality in social media) offered by the green brand were related to the perceived customer retention orientation (CRO) of the green fashion retailer, which was related to patronage intention towards the green retailer, and the moderating effect of green consciousness on the link between perceived CRO of the green retailer and patronage intention.

Design/methodology/approach

Data were collected from social media users (n=631) using a consumer panel via an online survey. Structural equation modelling was employed to test the proposed model and research hypotheses.

Findings

This study found that the perceived CRO of the green retailer was positively related to patronage intention. The perceived marketer-dominated information quality and perceived service content quality in social media were positively related to the perceived CRO of the green retailer. Green consciousness moderated the link between perceived CRO and patronage intention.

Originality/value

First, this study contributes to the further theoretical understanding of the underlying factors that influence customer perception of the CRO of the green retailer and green patronage intention. Second, on a managerial level, this proposed model provides green retailers with beneficial insights into the development of successful social CRM.
Self‐employment Dynamics in Australia and the Importance of State Dependence
Authors: Fitzpatrick Darcy
Published: May 2017

Using Australian labour force data, both cross‐sectional and longitudinal, this study examines the dynamics of self‐employment with a particular focus on workers transitioning between self‐employment and salaried employment, and the extent to which self‐employment is the result of workers’ observed and unobserved characteristics or is instead determined by their prior employment experience itself. Probability models of self‐employment using both pooled‐panel probit and dynamic random‐effects panel probit methods are estimated, and the results are found to be extremely sensitive to the differences in the econometric methods. Once unobserved heterogeneity and initial conditions are controlled for in the dynamic model, the importance of observed characteristics in determining self‐employment is greatly diminished. Instead, workers’ past experience in self‐employment (as opposed to salaried employment) is found to have a large favourable effect on their future self‐employment prospects. The influence of this state dependence is also considerably more important in determining self‐employment outcomes than salaried ones. Despite establishing the importance of state dependence, however, what this effect implies about why individuals choose to become self‐employed or the role that self‐employment plays in the labour market remains unresolved.
Regulatory Reforms in Small Energy Systems: Experience from Australia's Northern Territory Electricity Market
Authors: Nepal Rabindra , Menezes Flavio
Published: May 2017

The global experience with regulatory reforms that promote competition in small and isolated energy markets is limited. We contribute to this knowledge and policy gap by analysing the reform experience and policy options in Australia's Northern Territory (NT) electricity market. More private participation in electricity generation and retail in the short‐term and intra‐regional market integration in the medium term may be appropriate policy options as the demand for electricity grows. Reforms in smaller electricity markets such as the NT should be geared towards meeting the environmental and de‐carbonisation objectives from the early stages.
Risk of impaired cognition after prenatal exposure to psychotropic drugs
Authors: Wibroe M. A. , Mathiasen R. , Pagsberg A. K. , Uldall P.
Published: May 2017

Objective

Prenatal exposure to psychotropic drugs may affect the trajectories of brain development. In a register study, we investigated whether such exposure is associated with long‐term impaired cognitive abilities.

Method

Individuals born in Denmark in 1995–2008 were included. As proxies for cognitive impairment, requiring special needs education, attending special needs school, diagnoses of neurological/mental disorder, missed final examinations, and low school grade average were used. We accounted for maternal confounders.

Results

We identified 868 159 individuals of whom 13 983 (1.6%) were prenatally exposed. The adjusted odds ratio (OR) was 0.97[0.92–1.02] for requiring special needs education, 1.28[1.14–1.43] for attending special needs school, 1.32[1.20–1.46] for a neurological/mental disorder diagnosis, 1.37[1.22–1.54] for missing the final examinations, and 1.13[0.82–1.55] for obtaining a low school grade average. Exposure to psycholeptics (primarily antipsychotics and sedatives) was correlated with significantly increased risk for four outcomes. The highest was the risk of missing the primary school examinations (OR: 1.51[1.29–1.76]). The overall highest risk concerned the presence of a neurological/mental disorder after prenatal exposure to psychoanaleptics (primarily antidepressants) (OR: 1.86[1.24–2.78).

Conclusion

Prenatal exposure to psychotropic drugs affects proxy outcomes of cognitive disabilities at school age. Exposure to psycholeptics carries the largest risk. The role of psychoanaleptics is currently unclear.
The intrinsic cause of color fading in sliced cooked cured beef during chilled storage
Authors: Ma Jing , Yu Chensha , Guo Juanjuan , Wu Mengting , Xu Yunqiang , Yi Hongchao , Sun Weiqing
Published: May 2017

The relationship between color change and other physical and chemical characteristics of sliced cooked cured beef (SCCB) during chilled storage were investigated using principal components analysis (PCA) to determine the color fading causes. Samples were prepared and stored at 8°C for up to 35 days in a vacuum package to simulate a supermarket storage environment; related indicators were measured periodically every week. The results showed that the first PC explained 59.82% of the total variation, and the second explained 22.28%.PC1 was a concentrated reflection of color changes ofSCCBduring storage andPC2 was an environment factor causing the change of color. The change in apparent redness is mainly caused by redox reaction of the nitroso hemochromogen (NH) (eigenvectors ofa*,CandNHinPC1 were all the maximum value of 0.28);a*was correlated withNH(0.96), free sulfhydryls (0.98), carbonyl derivatives (−0.95) formed during protein oxidation, and malondialdehyde (−0.98) and dienes (−0.92) formed by lipid oxidation. Color fading was significantly correlated with oxidizing and reducing power, existing forms of nitrogen and with thepHof the meat matrix. Changes in the internal environment of the sample initially influencedL*andb*values, and subsequentlya*.
Can we improve the efficacy of modern cataract surgery by using different tip designs? A comparison of balanced and tapered tip in femtosecond laser‐assisted cataract surgery and manual phacoemulsification
Authors: Pahlitzsch Milena , Pahlitzsch Marie‐Luise , Sumarni Uly , Pahlitzsch Thomas
Published: May 2017

Importance

Different tip designs in modern cataract surgery have not been studied between the reported systems.

Background

Aim of this study is to assess the efficacy of two tip designs, Intrepid® balanced tip (BT) and Kelman tapered tip (TT), in femtosecond laser assisted cataract surgery (FLACS) and the microcoaxial torsional phacoemulsification.

Design

Prospective randomized unmasked cohort outcome study (hospital setting).

Participants

Threehundert‐forty‐three eyes of 343 patientes underwent cataract surgery.

Methods

Data of n = 196 FLACS and n = 147 manual phacoemulsification were analysed. Intrepid® balanced tip and Kelman tapered tip, Alcon, USA, were tested in FLACS (LenSx Alcon, USA) und manual phaco (Alcon Centurion System, USA). Four study cohorts were formed; FLACS BT (n = 90, 70.2 years), FLACS TT (n = 106, 68.1years), Manual BT (n = 70, 71.3 years), Manual TT (n = 77, 71.8 years). The nuclei were graded in Lens Opacities Classification System (LOCS) II,III and IV.

Main Outcome Measures

Cumulative dissipated energy (CDE%s), balanced salt solution volume (BSSml), total longitudinal energy (%s) and torsional amplitude (%s).

Results

Lower CDE values were seen in FLACS compared to manual phacoemulsification (CDE %s median FLACS BT 3.28, FLACS TT 4.07, Manual BT 5.57, Manual TT 6.27). There was a significant difference between CDE FLACS BT and FLACS TT (p = 0.038), and between FLACS BT and Manual TT (p = 0.001).

Conclusions and Relevance

The right choice of tip designs in advanced phacoemulsification systems is a key factor in increasing efficacy in cataract surgery. The balanced tip showed a considerable energy‐saving advantage in FLACS and manual phacoemulsification compared to the tapered tip.
Kidney transplantation from donors with rhabdomyolysis and acute renal failure
Authors: Chen Chuan‐bao , Zheng Yi‐tao , Zhou Jian , Han Ming , Wang Xiao‐ping , Yuan Xiao‐peng , Wang Chang‐xi , He Xiao‐shun
Published: May 2017

Rhabdomyolysis in deceased donors usually causes acute renal failure (ARF), which may be considered a contraindication for kidney transplantation. From January 2012 to December 2016, 30 kidneys from 15 deceased donors with severe rhabdomyolysis and ARF were accepted for transplantation at our center. The peak serum creatinine (SCr) kinase, myoglobin, and SCr of the these donors were 15 569±8597 U/L, 37 092±42 100 μg/L, and 422±167 μmol/L, respectively. Two donors received continuous renal replacement therapy due to anuria. Six kidneys exhibited a discolored appearance (from brown to glossy black) due to myoglobin casts. The kidney transplant results from the donors with rhabdomyolysis donors were compared with those of 90 renal grafts from standard criteria donors (SCD). The estimated glomerular filtration rate at 2 years was similar between kidney transplants from donors with rhabdomyolysis and SCD (70.3±14.6 mL/min/1.73 m2 vs 72.3±15.1 mL/min/1.73 m2). We conclude that excellent graft function can be achieved from kidneys donors with ARF caused by rhabdomyolysis.
Extreme and complex variation in range‐wide abundances across a threatened Neotropical bird community
Authors: Devenish Christian , Buchanan Graeme M. , Smith Graham R. , Marsden Stuart J.
Published: May 2017

Aim

Understanding patterns and drivers of variation in abundance across full species ranges is crucial in conservation science, but our knowledge of these forms and processes is limited, especially in the tropics. This study aims to: (1) identify patterns in variation of abundance across sites; (2) examine congruence of abundance hotspots across species and spatial autocorrelation of abundance within species; and (3) assess the nature and strength of environmental correlates of abundance (topography, habitat and human pressure).

Location

Twenty‐six sites across the full ranges of 14 dry forest bird species in northern Peru.

Methods

Study sites in this patchy habitat were selected within strata derived from species distribution models, while also ensuring geographic representation. Species abundance data from variable‐width transects were compared across sites and across range core versus edge; relationships between abundance and environmental variables were examined usingGAMs, and spatial autocorrelation was examined with multivariate Mantel tests.

Results

Although most species were recorded at most sites, local abundance varied by one or two orders of magnitude. Several species showed a humped rather than the classic skewed abundance distribution, with abundance not necessarily highest at the centre of species’ ranges. Spatial autocorrelation in species’ local abundance was evident only at distances less than 55 km. Sites of maximum abundance for individual species did not coincide—nine different sites held highest densities of at least one species. Relationships between local abundance and almost all environmental correlates were non‐linear.

Main conclusions

The extreme variation in species abundances and the complexity in their relationships with environmental variables have important implications, both for design of conservation‐motivated surveys for which we offer some recommendations, and for the need for multiple reserves to capture high local abundances of key species.
Will climate change increase hybridization risk between potential plant invaders and their congeners in Europe?
Authors: Klonner Günther , Dullinger Iwona , Wessely Johannes , Bossdorf Oliver , Carboni Marta , Dawson Wayne , Essl Franz , Gattringer Andreas , Haeuser Emily , van Kleunen Mark , Kreft Holger , Moser Dietmar , Pergl Jan , Pyšek Petr , Thuiller Wilfried , Weigelt Patrick , Winter Marten , Dullinger Stefan
Published: May 2017

Aim

Interspecific hybridization can promote invasiveness of alien species. In many regions of the world, public and domestic gardens contain a huge pool of non‐native plants. Climate change may relax constraints on their naturalization and hence facilitate hybridization with related species in the resident flora. Here, we evaluate this possible increase in hybridization risk by predicting changes in the overlap of climatically suitable ranges between a set of garden plants and their congeners in the resident flora.

Location

Europe.

Methods

From the pool of alien garden plants, we selected those which (1) are not naturalized in Europe, but established outside their native range elsewhere in the world; (2) belong to a genus where interspecific hybridization has been previously reported; and (3) have congeners in the native and naturalized flora of Europe. For the resulting set of 34 alien ornamentals as well as for 173 of their European congeners, we fitted species distribution models and projected suitable ranges under the current climate and three future climate scenarios. Changes in range overlap between garden plants and congeners were then assessed by means of the true skill statistic.

Results

Projections suggest that under a warming climate, suitable ranges of garden plants will increase, on average, while those of their congeners will remain constant or shrink, at least under the more severe climate scenarios. The mean overlap in ranges among congeners of the two groups will decrease. Variation among genera is pronounced; however, and for some congeners, range overlap is predicted to increase significantly.

Main conclusions

Averaged across all modelled species, our results do not indicate that hybrids between potential future invaders and resident species will emerge more frequently in Europe when climate warms. These average trends do not preclude, however, that hybridization risk may considerably increase in particular genera.
THE OPTIMAL TAXATION OF ASSET INCOME WHEN GOVERNMENT CONSUMPTION IS ENDOGENOUS: THEORY, ESTIMATION AND WELFARE
Authors: Ben‐Gad Michael
Published: May 2017

This paper derives the Ramsey optimal fiscal policy for taxing asset income in a model where government expenditure is a function of net output or the inputs that produce it. Extending work by Kenneth L. Judd, I demonstrate that the canonical result that the optimal tax on capital income is zero in the medium to long term is a special case of a more general model. Employing a vector error correction model to estimate the relationship between government consumption and net output or the factor inputs that generate it for the United States between 1948Q1 and 2015Q4, I demonstrate that this special case is empirically implausible, and show how a cointegrating vector can be used to determine the optimal tax schedule. I simulate a version of the model using the empirical estimates to measure the welfare implications of changing the tax rate on asset income, and contrast these results with those generated in a version of the model where government consumption is purely exogenous. The shifting pattern of welfare measurements confirms the theoretical results. I calculate that the prevailing effective tax rate on net asset income in the United States between 1970 and 2014 averaged 0.449. Hence abolishing the tax completely does generate welfare improvements, though only by the equivalent of between 1.103% and 1.616% permanent increase in consumption—well under half the implied welfare benefit when the endogeneity of the government consumption is ignored. The maximum welfare improvement from shifting part of the burden of tax from capital to labor is the equivalent of a permanent increase in consumption of between only 1.491% and 1.858%, and is attained when the tax rate on asset income is lowered to between 0.148 and 0.186. Allowing the tax rate to vary over time raises the maximum welfare benefit to 1.865%. All the results are very robust to a wide range of elasticities of labor supply. (JEL E62, H21, H50)
Spinocerebellar ataxia type 10: common haplotype and disease progression rate in Peru and Brazil
Authors: Gheno T. C. , Furtado G. V. , Saute J. A. M. , Donis K. C. , Fontanari A. M. V. , Emmel V. E. , Pedroso J. L. , Barsottini O. , Godeiro‐Junior C. , van der Linden H. , Ternes Pereira E. , Cintra V. P. , Marques W. , de Castilhos R. M. , Alonso I. , Sequeiros J. , Cornejo‐Olivas M. , Mazzetti P. , Leotti V. B. , Jardim L. B. , Saraiva‐Pereira M. L. ,   Rede Neurogenetica
Published: May 2017

Background and purpose

Spinocerebellar ataxia type 10 is a neurodegenerative disorder that is due to an expanded ATTCT repeat tract in the ATXN10 gene. Our aim was to describe clinical characteristics and intragenic haplotypes of patients with spinocerebellar ataxia type 10 from Brazil and Peru.

Methods

Expanded alleles were detected by repeat‐primed polymerase chain reaction. Disease progression was measured by the Scale for the Assessment and Rating of Ataxia, and the Neurological Examination Score for Spinocerebellar Ataxias when possible. Haplotypes were constructed based on polymorphic markers within and outside the gene.

Results

Thirteen new families were diagnosed (three from Peru). Patients from three Brazilian families diagnosed previously were also reassessed. In total, 25 individuals (16 families) were evaluated. Mean (± SD) age at onset and disease duration were 34.8 ± 10.2 and 12 ± 8 years, respectively. Common findings were ataxia, dysarthria/dysphagia, nystagmus, pyramidal signs, ophthalmoparesis and seizures. No associations were found between clinical findings and geographical origins. Twelve patients living in remote regions were examined only once. In the remaining individuals, the Scale for the Assessment and Rating of Ataxia score, and Neurological Examination Score for Spinocerebellar Ataxias worsened by 0.444 (95% CI, −0.088 to 0.800) and 0.287 (95% CI, −0.061 to 0.635) points/year, respectively. A common haplotype, 19CGGC14, was found in 11/13 of Brazilian and in 1/3 of Peruvian families.

Conclusions

The progression rate was slower than in other spinocerebellar ataxias. A consistently recurrent intragenic haplotype was found, suggesting a common ancestry for most, if not all, patients.
Clinicopathological characteristics of KIT and protein kinase C‐δ expression in adenoid cystic carcinoma: comparison with chromophobe renal cell carcinoma and gastrointestinal stromal tumour
Authors: Park Cheol Keun , Kim Won Kyu , Kim Hoguen
Published: May 2017

Aims

KIT overexpression is frequently observed in adenoid cystic carcinomas (AdCCs), chromophobe renal cell carcinomas (ChRCCs), and gastrointestinal stromal tumours (GISTs). Persistent KIT activation has been reported to be mediated by protein kinase C (PKC)‐δ in a subset of colon cancers with wild‐type KIT overexpression, and by PKC‐θ in GISTs with mutant KIT overexpression. To elucidate the clinical implications of PKC‐δ and PKC‐θ expression in KIT‐expressing tumours, we investigated the expression of KIT, PKC‐δ and PKC‐θ in AdCCs and ChRCCs in comparison with GISTs.

Methods and results

KIT expression, PKC‐δ expression and PKC‐θ expression were analysed in whole sections from 41 AdCCs, 40 ChRCCs and 56 GISTs by immunohistochemistry. Membranous expression of KIT was found in 34 AdCCs and all ChRCCs, whereas cytoplasmic expression of KIT was found in 46 GISTs. In AdCCs, PKC‐δ expression was associated with histological grade (P = 0.049), lymphovascular invasion (P = 0.004), perineural invasion (P = 0.002), and KIT positivity (P = 0.002). PKC‐δ positivity was associated with shorter relapse‐free survival (RFS) (P = 0.017) and a tendency for there to be shorter overall survival (OS) (P = 0.090) in patients with AdCCs. No clinicopathological associations were observed between PKC‐δ and KIT expression in ChRCCs. In GISTs, PKC‐θ expression was associated with higher mitotic count (P = 0.011) and high grade according to the modified National Institutes of Health criteria (P < 0.001). PKC‐θ positivity was associated with shorter RFS (P = 0.016) and a tendency for there to be shorter OS (P = 0.051) in patients with GISTs.

Conclusions

PKC‐δ expression is associated with KIT expression and the prognosis of patients with AdCCs, suggesting that PKC‐δ may be a potential therapeutic target for AdCCs.
Development of an epitope panel for consistent identification of antigen‐specific T‐cells in humans
Authors: Fløe Andreas , Løppke Caroline , Hilberg Ole , Wejse Christian , Brix Liselotte , Jacobsen Kivin
Published: May 2017

We aimed to establish a panel of MHC–peptide multimers suitable as a positive control in the detection of HLA A*0201 restricted antigen specific T cells (ASTC) by flow cytometry. MHC Dextramers were loaded with HLA A*0201 binding peptides from viral antigens and melanoma targets identified from a literature search and in silico prediction. Peripheral blood mononuclear cells (PBMC) from healthy donors were analysed with the MHC Dextramers using flow cytometry. The best performing epitopes were tested on PBMC from patients undergoing testing for Mycobacterium tuberculosis infection to assess the coverage of this epitope panel. Of 21 candidate epitopes, ASTC could be detected against 12 (57·1%) in at least one of 18 healthy blood donors. Reactivity to two or more epitopes was seen in 17 of the 18 donors (94·4%). We selected the six best‐performing epitopes and demonstrated a positive response in 42 (97·7%) of 43 patient samples (healthy, latent and active M. tuberculosis infection). The selected panel of six antigenic epitopes sufficed as a positive control in the detection of ASTC in HLA A*0201. Performance was robust in different stages of latent and active M. tuberculosis infection, indicating reliability also during infection.
Medication compliance and clinical outcomes of fixed‐dose combinations vs free combinations of an angiotensin II receptor blocker and a calcium channel blocker in hypertension treatment
Authors: Tung Ying‐Chang , Huang Yu‐Chang , Wu Lung‐Sheng , Chang Chee‐Jen , Chu Pao‐Hsien
Published: May 2017

Using the National Health Insurance Research Database of Taiwan, the authors identified 1136 patients taking fixed‐dose combination and 4544 patients taking free combinations of an angiotensin II receptor blocker and a dihydropyridine calcium channel blocker from January 2009 to December 2012. At a mean follow‐up of 2.1 years, the fixed‐dose combination was associated with improved medication adherence and persistence and better survival free from major adverse cardiac events and hospitalization for heart failure compared with the free combination regimens.
Lipoprotein ratios are better than conventional lipid parameters in predicting arterial stiffness in young men
Authors: Wen Jianghua , Zhong Yuyu , Kuang Chaoqun , Liao Jierong , Chen Zhijin , Yang Qiong
Published: May 2017

Although dyslipidemia is associated with cardiovascular disease, there are conflicting data about the role of serum lipids and their ratios in promoting arterial stiffness. The authors aimed to compare serum lipid profiles to predict arterial stiffness, which was assessed by brachial‐ankle pulse wave velocity in young Chinese men. A total of 1015 participants aged 18 to 44 years without serious comorbidities were recruited for conventional detection. Anthropometrics, brachial‐ankle pulse wave velocity, serum lipids, and other laboratory data were measured. Univariate analysis and multivariate logistic regression were performed to examine the relationship between serum lipid profiles and brachial‐ankle pulse wave velocity. Participants with high brachial‐ankle pulse wave velocity exhibited higher levels of total cholesterol, triglyceride (TG), low‐density lipoprotein cholesterol, non–high‐density lipoprotein cholesterol (HDL‐C), total cholesterol/HDL‐C, TG/HDL‐C, low‐density lipoprotein cholesterol/HDL‐C, and non–HDL‐C/HDL‐C. The subsequent multivariable logistic regression showed that TG/HDL‐C, total cholesterol/HDL‐C, non–HDL‐C/HDL‐C, and TG significantly increased the risk for arterial stiffness after adjustment for confounding factors. Results indicate that lipid ratios are superior to conventional lipid parameters for predicting arterial stiffness in young men and that the TG/HDL‐C ratio has the strongest association with arterial stiffness.
Evaluation of the skeletal and dental effects in orthodontic patients with maxillary lateral incisor agenesis
Authors: Buyuk Suleyman K. , Ozkan Serkan , Benkli Y. Atakan , Arslan Akif , Celik Ersan
Published: May 2017

Objective

The purpose of this study was to evaluate the transverse dimension of the dentoalveolar and skeletal widths in both unilateral (UMLIA) and bilateral (BMLIA) maxillary lateral incisor agenesis groups.

Materials and Methods

The study sample consisted of 59 patients (34 females and 25 males) divided into three groups as UMLIA group (16 patients; 14.94 ± 1.37 years), BMLIA group (21 patients; 14.46 ± 1.53 years) and control group (22 patients; 15.28 ± 1.70 years) without tooth agenesis. Transversal measurements (maxillary and mandibular intercanine, interpremolar, intermolar, intercanine alveolar, interpremolar alveolar, intermolar alveolar widths) were done on dental casts. Craniofacial skeletal measurements were done with posteroanterior cephalometric radiographs. Statistical testing was performed with the one‐way variance analysis, Kruskal‐Wallis and post hoc tests.

Results

UMLIA and BMLIA groups had statistically significantly narrower skeletal apical base of the maxilla, maxillary intercanine and intercanine alveolar widths compared with the control group (P < .05). Moreover, UMLIA and BMLIA groups had statistically significantly similar dental, alveolar and skeletal features (P > .05).

Conclusions

The UMLIA and BMLIA groups showed statistically significantly smaller values for maxillary intercanine, maxillary intercanine alveolar and skeletal maxillary widths compared with the control group.

CLINICAL SIGNIFICANCE

This study provides information the transverse dimension of the dental, alveolar and skeletal widths with maxillary lateral incisor agenesis patients. Knowledge of transverse dimension of the dental, alveolar and skeletal widths with maxillary lateral incisor agenesis patients is important for diagnosis and treatment planning.
A modified colorectal screening score for prediction of advanced neoplasia: A prospective study of 5744 subjects
Authors: Sung Joseph J Y , Wong Martin C S , Lam Thomas Y T , Tsoi Kelvin K F , Chan Victor C W , Cheung Wilson , Ching Jessica Y L
Published: May 2017

Background and Aim

We validated a modified risk algorithm based on the Asia‐Pacific Colorectal Screening (APCS) score that included body mass index (BMI) for prediction of advanced neoplasia.

Methods

Among 5744 Chinese asymptomatic screening participants undergoing a colonoscopy in Hong Kong from 2008 to 2012, a random sample of 3829 participants acted as the derivation cohort. The odds ratios for significant risk factors identified by binary logistic regression analysis were used to build a scoring system ranging from 0 to 6, divided into “average risk” (AR): 0; “moderate risk” (MR): 1–2; and “high risk” (HR): 3–6. The other 1915 subjects formed a validation cohort, and the performance of the score was assessed.

Results

The prevalence of advanced neoplasia in the derivation and validation cohorts was 5.4% and 6.0%, respectively (P = 0.395). Old age, male gender, family history of colorectal cancer, smoking, and BMI were significant predictors in multivariate regression analysis. A BMI cut‐off at > 23 kg/m2 had better predictive capability and lower number needed to screen than that of > 25 kg/m2. Utilizing the score developed, 8.4%, 57.4%, and 34.2% in the validation cohort were categorized as AR, MR, and HR, respectively. The corresponding prevalence of advanced neoplasia was 3.8%, 4.3%, and 9.3%. Subjects in the HR group had 2.48‐fold increased prevalence of advanced neoplasia than the AR group. The c‐statistics of the modified score had better discriminatory capability than that using predictors of APCS alone (c‐statistics = 0.65 vs 0.60).

Conclusions

Incorporating BMI into the predictors of APCS score was found to improve risk prediction of advanced neoplasia and reduce colonoscopy resources.