bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical factors predicting the therapeutic response to ustekinumab in patients with moderate to severe chronic plaque psoriasis
Authors: Hwang Young Ji , Youn Sang Woong , Kim Bo Ri , Yu Dae Young , Kim Youngdoe , Pires Antonio , Cho Soyun , Seo Seong Jun , Lee Eun So , Roh Joo Young , Choi Gwang Seong , Lee Min Geol ,   the MARCOPOLO investigators
Published: November 2016

AbstractWhile ustekinumab has been widely used as an effective biologic for the treatment of chronic plaque psoriasis, no prospective studies have specifically investigated the clinical factors that may influence treatment outcomes with ustekinumab. This post‐hoc analysis aimed to identify specific clinical factors that may influence treatment outcomes with ustekinumab in psoriasis patients. In the MARCOPOLO study, 102 Korean patients with moderate to severe psoriasis were analyzed to assess the influence of baseline characteristics as clinical factors on clinical response (improvement in Psoriasis Area and Severity Index by ≥75%/90% [PASI75/PASI90]) to ustekinumab. In addition, differences in PASI75 and PASI90 responses between the responder group and non‐responders were evaluated at weeks 28 and 52. Multiple logistic regression analysis was used to determine adjusted clinical factors predicting treatment outcomes among patient characteristics. At week 28, there was a significant difference in PASI75/PASI90 response based on prior biologic experience, although the difference did not persist at week 52. In addition, after adjusting for the effects of relevant clinical factors, biologic experience was significantly associated with less PASI75 (odds ratio [OR] = 0.14, P = 0.001) and PASI90 (OR = 0.22, P = 0.036) responses at week 28. The presence of comorbidities was higher among non‐responders than among PASI75/PASI90 responders at both weeks 28 and 52, but was not statistically significant. Previous biologic use was the only clinical factor predicting less response at week 28, although it did not influence the clinical response after week 52. Further studies are warranted to investigate the association between presence of comorbidities and clinical response.
First‐arrival traveltime tomography with modified total‐variation regularization
Authors: Jiang Wenbin , Zhang Jie 
Published: November 2016

ABSTRACTFirst‐arrival traveltime tomography is a robust tool for near‐surface velocity estimation. A common approach to stabilizing the ill‐posed inverse problem is to apply Tikhonov regularization to the inversion. However, the Tikhonov regularization method recovers smooth local structures while blurring the sharp features in the model solution. We present a first‐arrival traveltime tomography method with modified total‐variation regularization to preserve sharp velocity contrasts and improve the accuracy of velocity inversion. To solve the minimization problem of the new traveltime tomography method, we decouple the original optimization problem into the two following subproblems: a standard traveltime tomography problem with the traditional Tikhonov regularization and a L2 total‐variation problem. We apply the conjugate gradient method and split‐Bregman iterative method to solve these two subproblems, respectively. Our synthetic examples show that the new method produces higher resolution models than the conventional traveltime tomography with Tikhonov regularization, and creates less artefacts than the total variation regularization method for the models with sharp interfaces. For the field data, pre‐stack time migration sections show that the modified total‐variation traveltime tomography produces a near‐surface velocity model, which makes statics corrections more accurate.
Abundant and rare picoeukaryotic sub‐communities present contrasting patterns in the epipelagic waters of marginal seas in the northwestern Pacific Ocean
Authors: Wu Wenxue , Logares Ramiro , Huang Bangqin , Hsieh Chih‐hao 
Published: November 2016

SummaryIn this work, they compared patterns of abundant and rare picoeukaryotic sub‐communities in the epipelagic waters (surface and 40–75 m depth subsurface layers) of the East and South China Seas across seasons via 454 pyrosequencing of the V4 region of 18S rDNA. They also examined the relative effects of environmental filtering, dispersal limitations and seasonality on community assembly. Their results indicated that (i) in the surface layer, abundant taxa are primarily influenced by dispersal limitations and rare taxa are primarily influenced by environmental filtering, whereas (ii) in the subsurface layer, both abundant and rare sub‐communities are only weakly influenced by environmental filtering but are strongly influenced by dispersal limitations. Moreover, (iii) abundant taxa exhibit stronger temporal variability than rare taxa. They also found that abundant and rare sub‐communities display similar spatial richness patterns that are negatively correlated with latitude and chlorophyll a and positively correlated with temperature. In summary, environmental filtering and dispersal limitations have different effects on abundant and rare picoeukaryotic sub‐communities in different layers. Thus, depth appears as an essential variable that governs the structuring patterns of picoeukaryotic communities in the oceans and should be thoroughly considered to develop a more comprehensive understanding of oceanic microbial assemblages.
PAAR‐Rhs proteins harbor various C‐terminal toxins to diversify the antibacterial pathways of type VI secretion systems
Authors: Ma Jiale , Sun Min , Dong Wenyang , Pan Zihao , Lu Chengping , Yao Huochun 
Published: November 2016

SummaryThe type VI secretion system (T6SS) of bacteria plays a key role in competing for specific niches by the contact‐dependent killing of competitors. Recently, Rhs proteins with polymorphic C‐terminal toxin‐domains that inhibit or kill neighboring cells were identified. In this report, we identified a novel Rhs with an MPTase4 (Metallopeptidase‐4) domain (designated as Rhs‐CT1) that showed an antibacterial effect via T6SS in Escherichia coli. We managed to develop a specific strategy by matching the diagnostic domain‐architecture of Rhs‐CT1 (Rhs with an N‐terminal PAAR‐motif and a C‐terminal toxin domain) for effector retrieval and discovered a series of Rhs‐CTs in E. coli. Indeed, the screened Rhs‐CT3 with a REase‐3 (Restriction endonuclease‐3) domain also mediated interbacterial antagonism. Further analysis revealed that vgrGO1 and eagR/DUF1795 (upstream of rhs‐ct) were required for the delivery of Rhs‐CTs, suggesting eagR as a potential T6SS chaperone. In addition to chaperoned Rhs‐CTs, neighborless Rhs‐CTs could be classified into a distinct family (Rhs‐Nb) sharing close evolutionary relationship with T6SS2‐Rhs (encoded in the T6SS2 cluster of E. coli). Notably, the Rhs‐Nb‐CT5 was confirmed bioinformatically and experimentally to mediate interbacterial antagonism via Hcp2B‐VgrG2 module. In a further retrieval analysis, we discovered various toxin/immunity pairs in extensive bacterial species that could be systematically classified into eight referential clans, suggesting that Rhs‐CTs greatly diversify the antibacterial pathways of T6SS.
Eye of the Finch: characterization of the ocular microbiome of house finches in relation to mycoplasmal conjunctivitis
Authors: Thomason Courtney A. , Leon Ariel , Kirkpatrick Laila T. , Belden Lisa K. , Hawley Dana M. 
Published: November 2016

SummaryVertebrate ocular microbiomes are poorly characterized and virtually unexplored in wildlife species. Pathogen defense is considered a key function of microbiomes, but determining microbiome stability during disease is critical for understanding the role of resident microbial communities in infectious disease dynamics. Here, we characterize the ocular bacterial microbiome of house finches (Haemorhous mexicanus), prior to and during experimental infection with an inflammatory ocular disease, Mycoplasmal conjunctivitis, caused by Mycoplasma gallisepticum. In ocular tissues of healthy house finches, we identified 526 total bacterial operational taxonomic units (OTUs, 97% similarity), primarily from Firmicutes (92.6%) and Proteobacteria (6.9%), via 16S rRNA gene amplicon sequencing. Resident ocular communities of healthy female finches were characterized by greater evenness and phylogenetic diversity compared to healthy male finches. Regardless of sex, ocular microbiome community structure significantly shifted 11 days after experimental inoculation with M. gallisepticum. A suite of OTUs, including taxa from the genera Methylobacterium, Acinetobacter and Mycoplasma, appear to drive these changes, indicating that the whole finch ocular microbiome responds to infection. Further study is needed to quantify changes in absolute abundance of resident taxa and to elucidate potential functional roles of the resident ocular microbiome in mediating individual responses to this common songbird bacterial pathogen.
Education in a mobile modernity
Authors: Forsey Martin 
Published: November 2016

AbstractThe main contention of this paper is that education helps frame a modernity in which individual progress and achievement are increasingly linked to the sheer physical act of movement. Thinking of modernisation as a trajectory of progress and development symbolised by industrialisation and a reordering of ‘traditional societies’ through rational forms of governance, we can begin to recognise the importance of the disembedding of people and communities from local institutions and relations that these modernising processes continue to require. Individual education stories are filled with movement that often reflect a commitment to the mobility imperatives of modernity. Reflecting the different scales of practice evident in this mobile modernity, the empirical focus ranges from rural settings to urban mobilities and then out to transnational mobilities and the educational choices exercised by the global middle classes. The paper explores the profound and the mundane ways in which educational structures affect family and individual mobilities.
phylodyn: an R package for phylodynamic simulation and inference
Authors: Karcher Michael D. , Palacios Julia A. , Lan Shiwei , Minin Vladimir N. 
Published: November 2016

AbstractWe introduce phylodyn, an r package for phylodynamic analysis based on gene genealogies. The package's main functionality is Bayesian nonparametric estimation of effective population size fluctuations over time. Our implementation includes several Markov chain Monte Carlo‐based methods and an integrated nested Laplace approximation‐based approach for phylodynamic inference that have been developed in recent years. Genealogical data describe the timed ancestral relationships of individuals sampled from a population of interest. Here, individuals are assumed to be sampled at the same point in time (isochronous sampling) or at different points in time (heterochronous sampling); in addition, sampling events can be modelled with preferential sampling, which means that the intensity of sampling events is allowed to depend on the effective population size trajectory. We assume the coalescent and the sequentially Markov coalescent processes as generative models of genealogies. We include several coalescent simulation functions that are useful for testing our phylodynamics methods via simulation studies. We compare the performance and outputs of various methods implemented in phylodyn and outline their strengths and weaknesses. r package phylodyn is available at https://github.com/mdkarcher/phylodyn.
Resolving microsatellite genotype ambiguity in populations of allopolyploid and diploidized autopolyploid organisms using negative correlations between allelic variables
Authors: Clark Lindsay V. , Schreier Andrea Drauch 
Published: November 2016

AbstractA major limitation in the analysis of genetic marker data from polyploid organisms is non‐Mendelian segregation, particularly when a single marker yields allelic signals from multiple, independently segregating loci (isoloci). However, with markers such as microsatellites that detect more than two alleles, it is sometimes possible to deduce which alleles belong to which isoloci. Here, we describe a novel mathematical property of codominant marker data when it is recoded as binary (presence/absence) allelic variables: under random mating in an infinite population, two allelic variables will be negatively correlated if they belong to the same locus, but uncorrelated if they belong to different loci. We present an algorithm to take advantage of this mathematical property, sorting alleles into isoloci based on correlations, then refining the allele assignments after checking for consistency with individual genotypes. We demonstrate the utility of our method on simulated data, as well as a real microsatellite data set from a natural population of octoploid white sturgeon (Acipenser transmontanus). Our methodology is implemented in the R package polysat version 1.6.
Policy Diffusion: A Regime‐sensitive Conceptual Framework
Authors: Tosun Jale , Croissant Aurel 
Published: November 2016

AbstractThe analysis of diffusion processes is an expanding field of research in the social and economic sciences. However, prolific scholarship has highlighted the transnational diffusion of policy innovations, but the insights provided – at least for policies – are limited by a ‘democracy bias’, that is, the focus of most studies is on democracies. This limitation concerns both the empirical scope of most diffusion studies and their theoretical underpinning. Furthermore, the emphasis placed on the diffusion mechanisms has hindered the development of conceptual frameworks that systematically account for political regime characteristics and their role for policy diffusion. To take a first step towards reducing this gap, we propose an alternative conceptual framework. It builds on the existing literature on policy diffusion, but shifts the perspective from the international to the national context. In the subsequent discussion we put forward a theoretical framework that explicitly accounts for the role of political regime types in policy diffusion and shifts the analytical focus from mechanisms to ‘routes’ of diffusion.
Patterns of Diffusion: Comparing Democratic and Autocratic Waves
Authors: Weyland Kurt 
Published: November 2016

AbstractThis essay examines why the diffusion of autocratic rule tends to unfold more slowly, yet with greater effectiveness (‘success’) than pro‐democratic waves often do. A precedent of progressive regime change often inspires fairly unorganized crowds in many other countries to initiative spontaneous emulation efforts, as it happened in the revolutions of 1848 and the Arab Spring of 2011. Yet this lack of organization creates a high risk of failure. By contrast, the overthrow of democracy, which can also stimulate imitation attempts, is usually spearheaded by well‐established organizations, such as the military, which jump on the bandwagon less rashly, but pursue their goals more effectively. Therefore, autocratic waves advance with lower speed, yet greater ‘success’ than pro‐democratic riptides often do, as was evident in the diffusion of authoritarianism and fascism during the interwar years and the spread of military dictatorships in Latin America during the 1960s and 1970s.
Inferring diet from dental morphology in terrestrial mammals
Authors: Pineda‐Munoz Silvia , Lazagabaster Ignacio A. , Alroy John , Evans Alistair R. 
Published: November 2016

Summary

Dietary inferences are a key foundation for paleoecological, ecomorphological and macroevolutionary studies because they inform us about the direct relationships between the components of an ecosystem. However, we need to consider the range of dietary variation we want to investigate and characterize before choosing a proxy. The goal of the present work is to evaluate the differences in dietary discrimination power between our new method, the multidimensional multi‐proxy dental morphology analysis (MPDMA) and unidimensional dental morphology proxies such as orientation patch count (OPCR), relief index (RI) or slope.

In order to do that, we three‐dimensionally scanned the dentitions of 134 extant mammals including 28 marsupials (order Diprotodontia) and 106 placentals (orders Carnivora, Primates and Rodentia) and classified their diets using a new classification scheme that emphasizes the primary resource in a given diet. Diet categories included herbivory, carnivory, frugivory, granivory, insectivory, fungivory, gumivory and generalist.

Unidimensional proxies significantly discriminate (P < 0·05) between one or two diet categories on the one hand and the rest on the other. For example, OPCR discriminates well between carnivorous and non‐carnivorous species. However, none of the individual proxies discriminate all eight dietary categories. Multi‐proxy dental morphology analysis demonstrates significant morphological differences across diets (MANOVA, d.f. = 7; F = 7·56; P < 0·05) and correctly discriminates diet for 67–82% of the specimens in the data set including and excluding rodents respectively.

Combining different morphological variables makes it possible to draw better dietary inferences and fully represent the multidimensional nature of dental morphology and dietary specializations. Our results have important applications in ecological, paleoecological and evolutionary research.
Infections and exposure to anti‐infective agents and the risk of severe mental disorders: a nationwide study
Authors: Köhler O. , Petersen L. , Mors O. , Mortensen P. B. , Yolken R. H. , Gasse C. , Benros M. E. 
Published: November 2016

ObjectiveSevere infections are associated with increased risks of mental disorders; however, this is the first large‐scale study investigating whether infections treated with anti‐infective agents in the primary care setting increase the risks of schizophrenia and affective disorders.MethodWe identified all individuals born in Denmark 1985–2002 (N = 1 015 447) and studied the association between infections treated with anti‐infective agents and the subsequent risk of schizophrenia and affective disorders during 1995–2013. Cox regression analyses were adjusted for important confounders.ResultsInfections treated with anti‐infective agents were associated with increased risks of schizophrenia by a hazard rate ratio (HRR) of 1.37 (95%‐CI = 1.20–1.57) and affective disorders by a HRR of 1.64 (95%‐CI = 1.48–1.82), fitting a dose–response and temporal relationship (P < 0.001). The excess risk was primarily driven by infections treated with antibiotics, whereas infections treated with antivirals, antimycotics, and antiparasitic agents were not significant after mutual adjustment. Individuals with infections requiring hospitalization had the highest risks for schizophrenia (HRR = 2.05; 95%‐CI = 1.77–2.38) and affective disorders (HRR = 2.59; 95%‐CI = 2.31–2.89).ConclusionInfections treated with anti‐infective agents and particularly infections requiring hospitalizations were associated with increased risks of schizophrenia and affective disorders, which may be mediated by effects of infections/inflammation on the brain, alterations of the microbiome, genetics, or other environmental factors.
When the neighbourhood goes bad: can endangered black robins adjust nest‐site selection in response to the risk of an invasive predator?
Authors: Lawrence C. , Paris D. , Briskie J. V. , Massaro M. 
Published: November 2016

AbstractThe introduction of exotic predators into new areas has had significant impacts on naïve prey species, which initially lack behavioural mechanisms to avoid predation. Understanding a species’ ability to respond appropriately to novel threats may inform in situ management options for threatened island populations. In the presence of nest predators, physical characteristics of the nest site can influence the likelihood that eggs or chicks are lost to predation. Some birds that evolved under high nest predation pressure show predictable changes in nest‐site selection following nest predation, but the ability of naïve island birds to alter nest‐site decisions based on experience with novel nest predators has not been well studied. We examined nest‐site choices of re‐nesting Chatham Island black robins Petroica traversi following nest predation by invasive European starlings Sturnus vulgaris. Robins whose first nests were depredated re‐nested in a new location that was significantly lower to the ground than pairs whose first nests were lost through other causes. As predation risk increases with nest height, the lower placement of re‐nests is consistent with a movement towards safer nest sites. The cause of nest failure did not influence the choice of substrate for a replacement nest, nor did individual pairs re‐nest further away from depredated nests. Changes in nest‐site selection did not carry over into subsequent nesting seasons. Our results suggest that some evolutionarily naïve species may be capable of assessing immediate risk through individual experience with novel predators, and modifying their nest‐site decisions accordingly.
Potential risks of orthodontic therapy: a critical review and conceptual framework
Authors: Wishney M 
Published: November 2016

AbstractThis review examines some of the potential risks of orthodontic therapy along with their evidence base. The risks of orthodontic treatment include periodontal damage, pain, root resorption, tooth devitalization, temporomandibular disorder, caries, speech problems and enamel damage. These risks can be understood to arise from a synergy between treatment and patient factors. In general terms, treatment factors that can influence risk include appliance type, force vectors and duration of treatment whilst relevant patient factors are both biological and behavioural. Hence, the natural variation between orthodontic treatment plans and patients gives rise to variations in risk. A good understanding of these risks is required for clinicians to obtain informed consent before starting treatment as well as to reduce the potential for harm during treatment. After considering each of these risks, a conceptual framework is presented to help clinicians better understand how orthodontic risks arise and may therefore be mitigated.