bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantum dimer model for the pseudogap metal
Authors: Punk Matthias , Allais Andrea , Sachdev Subir
Published: July 2015

Significance

The most interesting states of the copper oxide compounds are not the superconductors with high critical temperatures. Instead, the novelty lies primarily in the higher temperature metallic “normal” states from which the superconductors descend. Here, we develop a simple, intuitive model for the physics of the metal at low carrier density, in the “pseudogap” regime. This model describes an exotic metal that is similar in many respects to simple metals like silver. However, the simple metallic character coexists with “topological order” and long-range quantum entanglement previously observed only in exotic insulators or fractional quantum Hall states in very high magnetic fields. Our model is compatible with many recent observations, and we discuss more definitive experimental tests.
Conformational propensities of intrinsically disordered proteins influence the mechanism of binding and folding
Authors: Arai Munehito , Sugase Kenji , Dyson H. Jane , Wright Peter E.
Published: July 2015

Significance

Intrinsically disordered proteins play a central role in cellular signaling and regulatory networks. Many regulatory proteins contain disordered recognition motifs that fold upon binding to their cellular targets, by mechanisms that are poorly understood. Here we show that the disordered transactivation domain of the transcription factor c-Myb binds to the KIX domain of the transcriptional coactivator cAMP-response element binding (CREB-binding) protein (CBP) by a mechanism that involves elements of conformational selection and induced fit. In contrast, the phosphorylated kinase-inducible activation domain of CREB binds to the same site on KIX by an induced-fit mechanism. The intrinsic secondary structure propensities of these two disordered proteins determine their binding mechanisms, consistent with their functions as inducible and constitutive transcriptional activators.
The Islamic representation of Tatarstan as an answer to the equalization of the Russian regions
Authors: Yusupova Guzel
Published: July 2015

This article presents a study of Islamic religious symbols involved in maintaining the special status of the Tatars in post-Soviet Tatarstan. It explores how regional ethnic elites in Tatarstan use Islam (the discourse of the history of Islam in the region and Islamic symbols in the representation of the region) as a tool for legitimizing their privileged positions in the region. In addition, the article examines how Islamic culture enters into the everyday life and public space of the region, thereby, in a sense enforcing social borders between different ethnic groups. This study has two aims: a theoretical analysis of religious symbols’ role in the struggle for status in the ethnic hierarchy and the practical application of the developed theoretical framework to the case of post-Soviet Tatarstan. The author concludes that after the system of ethnic federalism was abolished in Russia, Tatars have retained their special status by appealing to Islam.
Ethnic profiling as negotiating: Traffic law enforcement in the Republic of Tatarstan (Russia)
Authors: Khalioullina Leisan
Published: July 2015

Complex and ambiguous relations between state officials and civilians in Russia in general, and in Tatarstan in particular, are best reflected by daily communications between traffic police officers and motorists and pedestrians. These short interactions bring up issues of violence and minority discrimination, bribing, and dominant political values. In this paper based on my field research, I explore the practice of ethnic profiling employed by police officers and analyze its effects. I focus on identity construction and its “quality measurement.” Unlike a standardized system of weights or “brute facts,” law enforcement involves the creation of identities, including selective and sanctioned usage of, and manipulation by, ethnic traits. I conclude that ethnic profiling exists in Tatarstan, but stems not from nationalist inspirations of the controlling agents, but rather as an effect of rational economic decision-making. I also argue that despite its haphazard nature, ethnic minorities in Tatarstan are able to interact with controlling agencies more effectively than the majority, partially due to their alleged ability to employ collective action and partially because of the specific ethnic policy of the Republic.
Basigin is a druggable target for host-oriented antimalarial interventions
Authors: Zenonos Zenon A. , Dummler Sara K. , Müller-Sienerth Nicole , Chen Jianzhu , Preiser Peter R. , Rayner Julian C. , Wright Gavin J.
Published: July 2015

Plasmodium falciparum is the parasite responsible for the most lethal form of malaria, an infectious disease that causes a large proportion of childhood deaths and poses a significant barrier to socioeconomic development in many countries. Although antimalarial drugs exist, the repeated emergence and spread of drug-resistant parasites limit their useful lifespan. An alternative strategy that could limit the evolution of drug-resistant parasites is to target host factors that are essential and universally required for parasite growth. Host-targeted therapeutics have been successfully applied in other infectious diseases but have never been attempted for malaria. Here, we report the development of a recombinant chimeric antibody (Ab-1) against basigin, an erythrocyte receptor necessary for parasite invasion as a putative antimalarial therapeutic. Ab-1 inhibited the PfRH5-basigin interaction and potently blocked erythrocyte invasion by all parasite strains tested. Importantly, Ab-1 rapidly cleared an established P. falciparum blood-stage infection with no overt toxicity in an in vivo infection model. Collectively, our data demonstrate that antibodies or other therapeutics targeting host basigin could be an effective treatment for patients infected with multi-drug resistant P. falciparum.
T cell development involves TRAF3IP3-mediated ERK signaling in the Golgi
Authors: Zou Qiang , Jin Jin , Xiao Yichuan , Hu Hongbo , Zhou Xiaofei , Jie Zuliang , Xie Xiaoping , Li James Y.H. , Cheng Xuhong , Sun Shao-Cong
Published: July 2015

Generation of T lymphocytes in the thymus is guided by signal transduction from the T cell receptor (TCR), but the underlying mechanism is incompletely understood. Here we have identified a Golgi-associated factor, TRAF3-interacting protein 3 (TRAF3IP3), as a crucial mediator of thymocyte development. TRAF3IP3 deficiency in mice attenuates the generation of mature thymocytes caused by impaired thymocyte-positive selection. TRAF3IP3 mediates TCR-stimulated activation of the mitogen-activated protein kinase (MAPK) extracellular signal-regulated kinase (ERK) and its upstream kinase mitogen/extracellular signal-regulated kinase (MEK). Interestingly, TRAF3IP3 exerts this signaling function through recruiting MEK to the Golgi and, thereby, facilitating the interaction of MEK with its activator BRAF. Transgenic expression of a constitutively active MEK rescues the T cell development block in Traf3ip3 knockout mice. These findings establish TRAF3IP3 as a novel regulator of T cell development and suggest a Golgi-specific ERK signaling mechanism that regulates thymocyte development.
Identification of resolvin D2 receptor mediating resolution of infections and organ protection
Authors: Chiang Nan , Dalli Jesmond , Colas Romain A. , Serhan Charles N.
Published: July 2015

Endogenous mechanisms that orchestrate resolution of acute inflammation are essential in host defense and the return to homeostasis. Resolvin (Rv)D2 is a potent immunoresolvent biosynthesized during active resolution that stereoselectively stimulates resolution of acute inflammation. Here, using an unbiased G protein–coupled receptor-β-arrestin–based screening and functional sensing systems, we identified a receptor for RvD2, namely GPR18, that is expressed on human leukocytes, including polymorphonuclear neutrophils (PMN), monocytes, and macrophages (MΦ). In human MΦ, RvD2-stimulated intracellular cyclic AMP was dependent on GPR18. RvD2-stimulated phagocytosis of Escherichia coli and apoptotic PMN (efferocytosis) were enhanced with GPR18 overexpression and significantly reduced by shRNA knockdown. Specific binding of RvD2 to recombinant GPR18 was confirmed using a synthetic 3H-labeled-RvD2. Scatchard analysis gave a Kd of ∼10 nM consistent with RvD2 bioactive concentration range. In both E. coli and Staphylococcus aureus infections, RvD2 limited PMN infiltration, enhanced phagocyte clearance of bacteria, and accelerated resolution. These actions were lost in GPR18-deficient mice. During PMN-mediated second organ injury, RvD2’s protective actions were also significantly diminished in GPR18-deficient mice. Together, these results provide evidence for a novel RvD2–GPR18 resolution axis that stimulates human and mouse phagocyte functions to control bacterial infections and promote organ protection.
Characteristics of MHD instabilities limiting the beta value in LHD
Authors: Sakakibara S. , Watanabe K.Y. , Takemura Y. , Okamoto M. , Ohdachi S. , Suzuki Y. , Narushima Y. , Ida K. , Yoshinuma M. , Tanaka K. , Tokuzawa T. , Yamada I. , Yamada H. , Takeiri Y.
Published: July 2015

Effects of low-n magnetohydrodynamic instabilities on plasma performance have been assessed in the regime where an achieved beta value is limited by instabilities. The unstable regime of an ideal interchange mode is characterized by enhanced magnetic hill and reduced magnetic shear. Experiments have clarified that (i) low-n modes are significantly destabilized in the ideal-unstable configurations and lead to degradation of central beta by at most 60%, and (ii) the degree of their damages strongly depends on the mode rotation velocity. The occurrence of the minor collapse is independent of an existence of an error field.
Identification of the energetic-particle driven GAM in the LHD
Authors: Ido T. , Osakabe M. , Shimizu A. , Watari T. , Nishiura M. , Toi K. , Ogawa K. , Itoh K. , Yamada I. , Yasuhara R. , Yoshimura Y. , Kato S.
Published: July 2015

n = 0 modes with frequency chirping have been observed by a heavy ion beam probe and Mirnov coils in the large helical device plasmas, where n is the toroidal mode number. The spatial structures of the electrostatic potential fluctuation and the density fluctuation correspond to those of the geodesic acoustic mode (GAM). The modes are observed only during the tangential neutral beam injection with the energy of 175 keV. The energy spectra of fast ions measured by a neutral particle analyzer implies that the modes are excited by the fast ions through the inverse Landau damping. The absolute values and the temperature dependence of the frequency of the mode can be interpreted by the dispersion relation taking into account the measured energy spectra of the fast ions. Therefore, the observed n = 0 modes are identified as the energetic-particle driven GAM.
Experimental turbulence studies for gyro-kinetic code validation using advanced microwave diagnostics
Authors: Stroth U. , Bañón Navarro A. , Conway G.D. , Görler T. , Happel T. , Hennequin P. , Lechte C. , Manz P. , Simon P. , Biancalani A. , Blanco E. , Bottereau C. , Clairet F. , Coda S. , Eibert T. , Estrada T. , Fasoli A. , Guimarais L. , Gürcan Ö. , Huang Z. , Jenko F. , Kasparek W. , Koenen C. , Krämer-Flecken A. , Manso M.E. , Medvedeva A. , Molina D. , Nikolaeva V. , Plaum B. , Porte L. , Prisiazhniuk D. , Ribeiro T. , Scott B.D. , Siart U. , Storelli A. , Vermare L. , Wolf S.
Published: July 2015

For a comprehensive comparison with theoretical models and advanced numerical turbulence simulations, a large spectrum of fluctuation parameters was measured on the devices ASDEX Upgrade, TCV, and Tore-Supra. Radial profiles of scale-resolved turbulence levels in H-mode discharges are measured and compared with GENE simulations in the transition range from ion-temperature-gradient to trapped-electron-mode turbulence. Correlation reflectometry is used to study the microscopic structure of turbulence and GAMs in discharges where poloidal flow damping was varied by means of variations of the shape of the poloidal plasma cross-section and collisionality. Full-wave codes and synthetic diagnostics are applied for the interpretation of the data.
Sensitivity of Mycosphaerella pinodes to Pyraclostrobin Fungicide
Authors: Bowness Robyne , Gossen Bruce D. , Chang Kan-Fa , Goswani Rubella , Willenborg Christian J. , Holtz Michael , Strelkov Stephen E.
Published: July 2015

Mycosphaerella blight, caused by Mycosphaerella pinodes, is a destructive disease of field pea that is managed using foliar fungicides. Strobilurin fungicides have been used in western Canada for disease management since 2003. To assess the baseline sensitivities of M. pinodes isolates to the strobilurin fungicide pyraclostrobin, the effective concentration to reduce mycelial growth by 50% (EC50) was determined for 70 isolates collected prior to 2003 from Alberta, Saskatchewan, North Dakota, and Washington State. Each of these isolates was sensitive to pyraclostrobin, with EC50 values ranging from 0.03 to 0.29 mg liter−1. The pyraclostrobin concentrations required to reduce conidia germination by 50% was lower, ranging from 0.008 to 0.041 mg liter−1. In all, 324 isolates collected in 2010 and 2011 were tested for high levels of insensitivity by examining mycelial growth using a discriminatory dose of 5 mg liter−1. Nineteen isolates were highly insensitive to pyraclostrobin, with EC50 values of 80 to 216 mg liter−1. Conidia of these isolates germinated when exposed to a discriminatory dose of 0.1 mg liter−1. Insensitive isolates infected field pea plants treated with pyraclostrobin but sensitive isolates did not. The identification of insensitive isolates indicates that insensitivity may be emerging in the pathogen population.
No Significant Association between Anesthesia Group Concentration and Private Insurer Payments in the United States
Authors: Sun Eric C. , Dexter Franklin , Macario Alex , Miller Thomas R. , Baker Laurence C.
Published: July 2015

AbstractAbstract

In a review of payments from private insurers for five commonly billed anesthesia codes in 229 counties in the United States from 2002 through 2010, payments to anesthesiologists in more concentrated markets were not significantly different from payments in less concentrated markets.

Supplemental Digital Content is available in the text.

Background:

Markets for physician services are becoming increasingly concentrated, with many areas being dominated by a few groups. Antitrust authorities are concerned that increasing concentration will lead to inappropriately high payments for physician services from private insurers. The authors examined the association between market concentration and private insurer payments for anesthesia services.

Methods:

The authors obtained data on average payments from private insurers for five commonly used anesthesia Current Procedure Terminology codes for physicians located in 229 counties in the United States between 2002 and 2010. The authors calculated a measure of market concentration (the Herfindahl–Hirschman Index [HHI]) for anesthesiologists in each county using Medicare claims data. The authors then estimated the association between market concentration and private insurer payments using a difference-in-differences approach to minimize confounding.

Results:

Private insurer payments to anesthesiologists in more concentrated markets were not significantly different from payments in less concentrated markets. Compared with the 25% of counties with the least concentration (counties with an HHI in the 0th to 25th percentile), payments in counties in the 25th to 50th percentile of HHI were approximately 0.51% less (95% CI, −2.3 to 1.3%, P = 0.95), whereas payments in counties in the 50th to 75th percentile of HHI were approximately 2.8% less (95% CI, −6.7 to 1.4%, P = 0.41) and payments in counties in the 75th to 100th percentile were approximately 3.1% less (95% CI, −8.1 to 1.2%, P = 0.32).

Conclusion:

Increasing market concentration of anesthesia groups is not associated with significantly greater payments from private insurers.
Clinical Characteristics of 2 Groups of Children With Feeding Difficulties
Authors: Marshall Jeanne , Hill Rebecca J. , Ware Robert S. , Ziviani Jenny , Dodrill Pamela
Published: July 2015

Objectives:

The primary aim of this study was to describe and compare the clinical characteristics of 2 groups of children presenting to a feeding clinic: children with autism spectrum disorder (ASD) and children with a nonmedically complex history (NMC). A secondary aim was to compare participants according to the degree of oral motor impairment, presence of oral hypersensitivity, and clinically significant parent stress.

Methods:

Children with feeding difficulties ages between 2 and 6 years were recruited. Prospective data were collected on dietary intake, general development, mealtime behaviors, oral motor skills, oral sensory processing, and parental stress via parent questionnaire and clinical assessment.

Results:

In total, 68 children (ASD = 33 and NMC = 35) participated in the study. Both groups presented with a large number of difficult mealtime behaviors. Although stress was elevated in both groups, parents of children in the ASD group reported significantly higher stress levels than those with children in the NMC group (mean difference 27.3 on a percentile scale, 95% confidence interval [CI] 15.5–39.2, P < 0.01). Across both groups, the majority of children presented with mild‐to‐moderate oral motor impairments (ASD = 28, 85%; NMC = 28, 80%). Children with heightened oral sensory sensitivity consumed significantly fewer unprocessed fruits and vegetables (mean difference 3.3 foods, 95% CI 1.3–5.3, P < 0.01), and their parents reported a significantly greater frequency of difficult mealtime behaviors (mean difference 5.8 behaviors, 95% CI 3.4–8.1, P < 0.01).

Conclusions:

Features of feeding difficulty presented similarly across the ASD and NMC groups in this study. Oral motor impairment, oral sensory sensitivity, and parental stress should not be overlooked in the management of children with feeding difficulties, regardless of etiology.
Pilot Study Evaluating Efficacy of 2 Regimens for Hypovitaminosis D Repletion in Pediatric Inflammatory Bowel Disease
Authors: Simek Robert Z. , Prince Jarod , Syed Sana , Sauer Cary G. , Martineau Bernadette , Hofmekler Tanya , Freeman Alvin J. , Kumar Archana , McElhanon Barbara O. , Schoen Bess T. , Tenjarla Gayathri , McCracken Courtney , Ziegler Thomas R. , Tangpricha Vin , Kugathasan Subra
Published: July 2015

Objectives:

Vitamin D is critical for skeletal health; hypovitaminosis D is common in pediatric inflammatory bowel disease (IBD), yet optimal repletion therapy is not well studied. We aimed to conduct a pilot trial comparing the efficacy of 2 vitamin D regimens of weekly dosing for the repletion of hypovitaminosis D in pediatric IBD.

Methods:

Subjects identified from our IBD clinic with 25‐hydroxyvitamin D (25[OH]D) concentrations <30 ng/mL were randomized to 10,000 (n = 18) or 5000 (n = 14) IU of oral vitamin D3/10 kg body weight per week for 6 weeks. Serum 25(OH)D, Ca, and parathyroid hormone concentrations were measured at baseline, week 8, and week 12.

Results:

In the higher dosing group, serum 25(OH)D increased from 23.7 ± 8.5 ng/mL at baseline to 49.2 ± 13.6 ng/mL at 8 weeks; P < 0.001. In the lower dosing group, serum 25(OH)D increased from 24.0 ± 7.0 ng/mL at baseline to 41.5 ± 9.6 ng/mL at 8 weeks; P < 0.001. At 12 weeks, serum 25(OH)D concentrations were 35.1 ± 8.4 and 30.8 ± 4.2 ng/mL for the higher and lower dose regimens, respectively. Mean serum Ca and parathyroid hormone concentrations did not significantly change during the study. No patient exhibited hypercalcemia, and no serious adverse events occurred.

Conclusions:

Both treatment arms were safe and effective at normalizing vitamin D nutriture in pediatric IBD. Although significant repletion of 25(OH)D concentration was achieved in both dosing groups at 8 weeks, this effect was lost by the 12‐week follow‐up. Maintenance vitamin D therapy following initial repletion is likely required to maintain long‐term normalized vitamin D status.
A Rare Cause of Metabolic Acidosis
Authors: Sahbudak Bal Zumrut , Can Fulya Kamit , Anil Ayse Berna , Bal Alkan , Anil Murat , Gokalp Gamze , Yavascan Onder , Aksu Nejat
Published: July 2015

Oral methanol intoxication is common, but dermal intoxication is rare. We report a previously healthy 19-month-old female infant admitted to the emergency department (ED) with vomiting and tonic-clonic seizure. On physical examination, she was comatose and presented signs of decompensated shock with Kussmaul breathing. Her left thigh was edematous, with purple coloration. Methanol intoxication was suspected due to high anion gap metabolic acidosis (pH, 6.89; HCO3, <3 meq/L) and exposure to spirit-soaked bandages (%96 methanol) for 24 hours and 3 days. The patient's serum methanol level was 20.4 mg/dL. She was treated with fomepizole and continuous venovenous hemodialysis (CVVHD) in the pediatric intensive care unit, and methanol levels decreased to 0 mg/dL after 12 hours. During follow-up, massive edema and subarachnoid hemorrhage in the occipital lobe were detected by computed tomography of the brain. The patient died after 7 days.

Although methanol intoxication occurs predominantly in adults, it must be considered in children with high-anion gap metabolic acidosis. This case report demonstrates that fatal transdermal methanol intoxication can occur in children, and it is the second report in the English literature of transdermal methanol intoxication in an infant.
Dynamics of immunoglobulin sequence diversity in HIV-1 infected individuals
Authors: Hoehn Kenneth B. , Gall Astrid , Bashford-Rogers Rachael , Fidler S. J. , Kaye S. , Weber J. N. , McClure M. O. ,   SPARTAC Trial Investigators, Kellam Paul , Pybus Oliver G.
Published: July 2015

Advances in immunoglobulin (Ig) sequencing technology are leading to new perspectives on immune system dynamics. Much research in this nascent field has focused on resolving immune responses to viral infection. However, the dynamics of B-cell diversity in early HIV infection, and in response to anti-retroviral therapy, are still poorly understood. Here, we investigate these dynamics through bulk Ig sequencing of samples collected over 2 years from a group of eight HIV-1 infected patients, five of whom received anti-retroviral therapy during the first half of the study period. We applied previously published methods for visualizing and quantifying B-cell sequence diversity, including the Gini index, and compared their efficacy to alternative measures. While we found significantly greater clonal structure in HIV-infected patients versus healthy controls, within HIV patients, we observed no significant relationships between statistics of B-cell clonal expansion and clinical variables such as viral load and CD4
+
count. Although there are many potential explanations for this, we suggest that important factors include poor sampling resolution and complex B-cell dynamics that are difficult to summarize using simple summary statistics. Importantly, we find a significant association between observed Gini indices and sequencing read depth, and we conclude that more robust analytical methods and a closer integration of experimental and theoretical work is needed to further our understanding of B-cell repertoire diversity during viral infection.
Inferring processes underlying B-cell repertoire diversity
Authors: Elhanati Yuval , Sethna Zachary , Marcou Quentin , Callan Curtis G. , Mora Thierry , Walczak Aleksandra M.
Published: July 2015

We quantify the VDJ recombination and somatic hypermutation processes in human B cells using probabilistic inference methods on high-throughput DNA sequence repertoires of human B-cell receptor heavy chains. Our analysis captures the statistical properties of the naive repertoire, first after its initial generation via VDJ recombination and then after selection for functionality. We also infer statistical properties of the somatic hypermutation machinery (exclusive of subsequent effects of selection). Our main results are the following: the B-cell repertoire is substantially more diverse than T-cell repertoires, owing to longer junctional insertions; sequences that pass initial selection are distinguished by having a higher probability of being generated in a VDJ recombination event; somatic hypermutations have a non-uniform distribution along the V gene that is well explained by an independent site model for the sequence context around the hypermutation site.
Quantifying evolutionary constraints on B-cell affinity maturation
Authors: McCoy Connor O. , Bedford Trevor , Minin Vladimir N. , Bradley Philip , Robins Harlan , Matsen Frederick A.
Published: July 2015

The antibody repertoire of each individual is continuously updated by the evolutionary process of B-cell receptor (BCR) mutation and selection. It has recently become possible to gain detailed information concerning this process through high-throughput sequencing. Here, we develop modern statistical molecular evolution methods for the analysis of B-cell sequence data, and then apply them to a very deep short-read dataset of BCRs. We find that the substitution process is conserved across individuals but varies significantly across gene segments. We investigate selection on BCRs using a novel method that side-steps the difficulties encountered by previous work in differentiating between selection and motif-driven mutation; this is done through stochastic mapping and empirical Bayes estimators that compare the evolution of in-frame and out-of-frame rearrangements. We use this new method to derive a per-residue map of selection, which provides a more nuanced view of the constraints on framework and variable regions.
Masking of antigenic epitopes by antibodies shapes the humoral immune response to influenza
Authors: Zarnitsyna Veronika I. , Ellebedy Ali H. , Davis Carl , Jacob Joshy , Ahmed Rafi , Antia Rustom
Published: July 2015

The immune responses to influenza, a virus that exhibits strain variation, show complex dynamics where prior immunity shapes the response to the subsequent infecting strains. Original antigenic sin (OAS) describes the observation that antibodies to the first encountered influenza strain, specifically antibodies to the epitopes on the head of influenza's main surface glycoprotein, haemagglutinin (HA), dominate following infection with new drifted strains. OAS suggests that responses to the original strain are preferentially boosted. Recent studies also show limited boosting of the antibodies to conserved epitopes on the stem of HA, which are attractive targets for a ‘universal vaccine’. We develop multi-epitope models to explore how pre-existing immunity modulates the immune response to new strains following immunization. Our models suggest that the masking of antigenic epitopes by antibodies may play an important role in describing the complex dynamics of OAS and limited boosting of antibodies to the stem of HA. Analysis of recently published data confirms model predictions for how pre-existing antibodies to an epitope on HA decrease the magnitude of boosting of the antibody response to this epitope following immunization. We explore strategies for boosting of antibodies to conserved epitopes and generating broadly protective immunity to multiple strains.
Redefining the differences in gene content between Yersinia pestis and Yersinia pseudotuberculosis using large-scale comparative genomics
Authors: Califf Katy J. , Keim Paul S. , Wagner David M. , Sahl Jason W.
Published: July 2015

Yersinia pestis, the causative agent of plague, is best known for historical pandemics, but still actively causes disease in many parts of the world. Y. pestis is a recently derived clone of the pathogenic species Yersinia pseudotuberculosis, but is more associated with human infection. Numerous studies have documented genomic changes since the two species differentiated, although all of these studies used a relatively small sample set for defining these differences. In this study, we compared the complete genomic content between a diverse set of Y. pestis and Y. pseudotuberculosis genomes, and identified unique loci that could serve as diagnostic markers or for better understanding the evolution and pathogenesis of each group. Comparative genomics analyses also identified subtle variations in gene content between individual monophyletic clades within these species, based on a core genome single nucleotide polymorphism phylogeny that would have been undetected in a less comprehensive genome dataset. We also screened loci that were identified in other published studies as unique to either species and generally found a non-uniform distribution, suggesting that the assignment of these unique genes to either species should be re-evaluated in the context of current sequencing efforts. Overall, this study provides a high-resolution view into the genomic differences between Y. pestis and Y. pseudotuberculosis, demonstrating fine-scale differentiation and unique gene composition in both species.
Tools and techniques for computational reproducibility
Authors: Piccolo Stephen R. , Frampton Michael B.
Published: July 2015

When reporting research findings, scientists document the steps they followed so that others can verify and build upon the research. When those steps have been described in sufficient detail that others can retrace the steps and obtain similar results, the research is said to be reproducible. Computers play a vital role in many research disciplines and present both opportunities and challenges for reproducibility. Computers can be programmed to execute analysis tasks, and those programs can be repeated and shared with others. Due to the deterministic nature of most computer programs, the same analysis tasks, applied to the same data, will often produce the same outputs. However, in practice, computational findings often cannot be reproduced due to complexities in how software is packaged, installed, and executed—and due to limitations in how scientists document analysis steps. Many tools and techniques are available to help overcome these challenges. Here we describe seven such strategies. With a broad scientific audience in mind, we describe strengths and limitations of each approach, as well as circumstances under which each might be applied. No single strategy is sufficient for every scenario; thus we emphasize that it is often useful to combine approaches.
Scalable multi whole-genome alignment using recursive exact matching
Authors: Linthorst Jasper , Hulsman Marc , Holstege Henne , Reinders Marcel
Published: July 2015

The emergence of third generation sequencing technologies has brought near perfectde-novogenome assembly within reach. This clears the way towards reference-free detection of genomic variations.

In this paper, we introduce a novel concept for aligning whole-genomes which allows the alignment of multiple genomes. Alignments are constructed in a recursive manner, in which alignment decisions are statistically supported. Computational performance is achieved by splitting an initial indexing data structure into a multitude of smaller indices.

We show that our method can be used to detect high resolution structural variations between two human genomes, and that it can be used to obtain a high quality multiple genome alignment of at least nineteen Mycobacterium tuberculosis genomes.

An implementation of the outlined algorithm called REVEAL is available on:https://github.com/jasperlinthorst/REVEAL
A comparative study of SVDquartets and other coalescent-based species tree estimation methods
Authors: Chou Jed , Gupta Ashu , Yaduvanshi Shashank , Davidson Ruth , Nute Mike , Mirarab Siavash , Warnow Tandy
Published: July 2015

Background

Species tree estimation is challenging in the presence of incomplete lineage sorting (ILS), which can make gene trees different from the species tree. Because ILS is expected to occur and the standard concatenation approach can return incorrect trees with high support in the presence of ILS, “coalescent-based” summary methods (which first estimate gene trees and then combine gene trees into a species tree) have been developed that have theoretical guarantees of robustness to arbitrarily high amounts of ILS. Some studies have suggested that summary methods should only be used on “c-genes” (i.e., recombination-free loci) that can be extremely short (sometimes fewer than 100 sites). However, gene trees estimated on short alignments can have high estimation error, and summary methods tend to have high error on short c-genes. To address this problem, Chifman and Kubatko introduced SVDquartets, a new coalescent-based method. SVDquartets takes multi-locus unlinked single-site data, infers the quartet trees for all subsets of four species, and then combines the set of quartet trees into a species tree using a quartet amalgamation heuristic. Yet, the relative accuracy of SVDquartets to leading coalescent-based methods has not been assessed.

Results

We compared SVDquartets to two leading coalescent-based methods (ASTRAL-2 and NJst), and to concatenation using maximum likelihood. We used a collection of simulated datasets, varying ILS levels, numbers of taxa, and number of sites per locus. Although SVDquartets was sometimes more accurate than ASTRAL-2 and NJst, most often the best results were obtained using ASTRAL-2, even on the shortest gene sequence alignments we explored (with only 10 sites per locus). Finally, concatenation was the most accurate of all methods under low ILS conditions.

Conclusions

ASTRAL-2 generally had the best accuracy under higher ILS conditions, and concatenation had the best accuracy under the lowest ILS conditions. However, SVDquartets was competitive with the best methods under conditions with low ILS and small numbers of sites per locus. The good performance under many conditions of ASTRAL-2 in comparison to SVDquartets is surprising given the known vulnerability of ASTRAL-2 and similar methods to short gene sequences.
Crystal structure ofrac-(3aR*,9aS*)-4,4,4-trichloro-1,2,3,3a,4,9a-hexahydro-4λ5,9λ4-cyclopenta[4,5][1,3]tellurazolo[3,2-a]pyridine
Authors: Askerov Rizvan K. , Lukiyanova Julia M. , Matsulevich Zhanna V. , Borisov Alexander V. , Khrustalev Victor N.
Published: July 2015

The title compound, C10H12Cl3NTe, crystallizes with two crystallographically independent molecules (AandB) in the asymmetric unit. In each case, the coordination around the Te atom is distorted square-pyramidal, with the equatorial plane composed of the three Cl atoms and the C atom of the pyridinium ring. The Te atom is displaced from the mean-square plane by 0.1926 (7) and 0.1981 (8) Å, in moleculesAandB, respectivly, away from the apical C atom. The bond lengths from the Te atom to the two Cl atoms arrangedtransto each other [2.5009 (7)/2.5145 (7) and 2.5184 (7)/2.5220 (8) Å in moleculesAandB, respectivly] are substantially shorter than the third Te—Cl distance [2.8786 (7) and 2.8763 (7) Å in moleculesAandB, respectivly]. The 1,3-tellurazole ring is almost planar (r.m.s. deviations of 0.042 and 0.045 Å in moleculesAandB, respectivly). The cyclopentane rings in both moleculesAandBadopt envelope conformations with the carbon atom opposed to the (Te)C—C(N) bond as the flap. In the crystal, molecules form centrosymmetric 2 + 2 associatesviaTe...Cl interactions [3.3993 (7) and 3.2030 (7) Å]. As a result of these secondary interactions, the Te atom attains a strongly distorted 5 + 1 octahedral environment. Further, the 2 + 2 associates are bound by weak C—H...Cl hydrogen bonds into a three–dimensional framework.
Crystal structures of 4-phenylpiperazin-1-ium 6-chloro-5-ethyl-2,4-dioxopyrimidin-1-ide and 4-phenylpiperazin-1-ium 6-chloro-5-isopropyl-2,4-dioxopyrimidin-1-ide
Authors: Al-Alshaikh Monirah A. , El-Emam Ali A. , Al-Deeb Omar A. , Abdelbaky Mohammed S. M. , Garcia-Granda Santiago
Published: July 2015

The title molecular salts, C10H15N2+·C6H6ClN2O2−, (I), and C10H15N2+·C7H8ClN2O2−, (II), consist of 4-phenylpiperazin-1-ium cations with a 6-chloro-5-ethyl-2,4-dioxopyrimidin-1-ide anion in (I) and a 6-chloro-5-isopropyl-2,4-dioxopyrimidin-1-ide anion in (II). Salt (I) crystallizes with two independent cations and anions in the asymmetric unit. In the crystal structures of both salts, the ions are linkedviaN—H...O and N—H...N hydrogen bonds, forming sheets which are parallel to (100) in (I) and to (001) in (II). In (I), the sheets are linkedviaC—H...Cl hydrogen bonds, forming a three-dimensional framework.
Antecedents of attitudes toward the website
Authors: Alcántara-Pilar Juan Miguel , Del Barrio-García Salvador
Published: July 2015

Purpose

– The purpose of this paper is to analyze the moderating role of the cultural dimensions of long-term orientation (LTO) and individualism (IND) on the relationships between satisfaction online, message involvement (MI) and perceived usefulness (PU) of the web site on attitude toward the web site.

Design/methodology/approach

– The authors chose a between-subjects experimental design, using culture (Spanish vs British) as the independent variable. Two versions of a web site for a fictitious tourist destination were created – one written in Spanish and the other in English. The sample comprised 491 users.

Findings

– The findings indicate that the LTO dimension moderates the relationship between satisfaction online and PU on attitude toward the web site. The relationships between MI and attitude toward the web site could not be confirmed.

Research limitations/implications

– The main limitation of this study is the comparison of only two cultures, Spain vs the UK.

Practical implications

– The key implication is that if marketers and web site designers can better understand how national cultural differences moderate the attitude formation and change process among tourists, this will enable them to market their destinations and services more effectively. National cultural differences explain the differences found in the effect of satisfaction and PU on attitude toward the web site.

Originality/value

– This study is one of the few analyzing the moderating effect of LTO and IND on three antecedents of attitude toward the web site. The original cultural values established by Hofstede (2001) were tested among the present sample to establish the extent to which they remain true today. To create an authentic browsing scenario for the experiment, a web site was specially designed for a fictitious tourist destination, with its own domain name (buyada.org). Subjects were invited to browse the site freely while carrying out the task assigned to them. This approach contributed added value to the research by simulating the real behavior of tourists who are faced with a range of choices when putting together a tourism package for a given destination.
Brand personality and purchase intention
Authors: Toldos-Romero María de la Paz , Orozco-Gómez Ma. Margarita
Published: July 2015

Purpose

– The purpose of this paper is to analyze the effects of brand personality dimensions on purchase intention. Furthermore, the brand personality dimensions are compared to study the differences between users and non-users of 12 brands.

Design/methodology/approach

– An estimated 400 undergraduate students participated. They were given a questionnaire divided into two sessions (six brands of think products in one session and six brands of feel products in another session). In the end, 313 participants completed the questionnaire on the six brands of think products, and 320 completed the questionnaire on the six brands of feel products.

Findings

– Multiple regression analysis revealed that Hipness/Vivacity, Success, Sincerity and Sophistication brand personality dimensions are significant predictors of purchase intention. In addition, Domesticity/Emotionality and Professionalism also explain purchase intention but with a negative weight. The results are also broken down into product categories. Compared with non-users of the brands, the users rate the brands higher in all the brand personality dimensions.

Practical implications

– This paper should prove useful to marketing practitioners to understand how Mexican customers perceive their brands and those of their competitors and, therefore, to understand what competitors of these brands can do to increase purchase intention.

Originality/value

– The results found regarding purchase intention are important, as they can be used to identify those personality brand dimensions that appear to be most important in explaining consumer preferences.
Conceptualising the influence of the cultural orientation of Latin Americans on consumers’ choice of US brands
Authors: Gaur Sanjaya S. , Bathula Hanoku , Diaz Carolina Valcarcel
Published: July 2015

Purpose

– The purpose of this study is to identify the main cultural factors that influence Latin American consumers’ intentions to purchase US brands. Although culture and cultural orientation have been well researched in international business and marketing literature, there is a lack of research on the relationship between consumers’ cultural orientation and their bias towards foreign and domestic products.

Design/methodology/approach

– The paper reviews the extant literature with a particular emphasis on the key constructs of consumer ethnocentrism, consumer xenocentrism, conspicuous consumption and consumers’ national characteristics. Based on this review, the authors propose a conceptual model showing the influence of cultural orientation on the selection of US brands in Latin America.

Findings

– The review of the literature shows that previous studies support the proposition of cultural orientation and preferences for foreign versus domestic products among Latin American consumers. Accordingly, in their conceptual framework, the authors posit that consumer ethnocentrism negatively influences the selection of US brands, while xenocentrism does the opposite. Conspicuous consumption is posited as moderating the influence of consumer xenocentrism on purchase intentions of the US brands. On the other hand, national characteristics of consumers in Latin America are posited as moderating the influence of both consumer ethnocentrism and consumer xenocentrism on the selection of US brands.

Practical implications

– The authors also present important theoretical and practical implications that contribute to the growing body of research on consumer acculturation and country of origin effects, providing a better interpretation of consumer behaviour in the context of international and domestic markets.

Originality/value

– This study fills a significant gap in the understanding of the impact of cultural orientation and conspicuous consumption on selection of US brands in Latin America. Its conceptual framework can provide the basis for future empirical studies and also improve understanding of emerging markets.
Critical characteristics for the implementation of mass-customized services
Authors: Vidor Gabriel , Medeiros Janine Fleith de , Fogliatto Flavio Sanson , Tseng Mitchel M.
Published: July 2015

Purpose

– This paper aims to propose a method to determine which mass customization (MC) characteristics should be prioritized in mass-customized service design.

Design/methodology/approach

– Looking at manufacturing MC systems and conducting a literature review, it is not possible to observe a methodological step to define customized service design as the one we propose in this work. Results show a systematic classification of MC characteristics based on MC enablers and service enablers. These enablers are related by a quality function deployment (QFD) matrix and rewritten using a reverse QFD procedure.

Findings

– In the end, it was possible to determine which characteristics should be prioritized in mass-customized services.

Research limitations/implications

– Two case studies were performed: one with an electric power supplier and another one with a university.

Practical implications

– It shows that despite easy customization, organization is not always interest in service features customization. The explanation in these two cases is customization cost, which compared to the benefit does not seem advantageous for the organization.

Originality/value

– This paper creates a methodology to design a first phase in customized services in Latin American services and that is the original contribution.
Subsidiary strategy processes in Latin America
Authors: Ljung Anna , Pahlberg Cecilia
Published: July 2015

Purpose

– The purpose of this paper is to discuss how network relationships, with business as well as with non-business actors, affect each other and have an impact on strategy processes in subsidiaries in Latin America.

Design/methodology/approach

– A qualitative approach is used in which a new strategy in a European multinational company (MNC) is studied at the subsidiary level in Brazil and Argentina. The authors discuss why the strategic processes are so different within the same MNC. During 2009-2011, 50 interviews were conducted with respondents in Latin America and at headquarters.

Findings

– The results point to the importance of including relationships with both business and non-business actors to understand the subsidiary strategy processes. The authors suggest that such processes can be explained by interdependent relationships in a wider network context characterised by commitment and trust, leading to increased legitimacy among the actors involved.

Practical implications

– Managers need to invest in relationships not only with business counterparts but also with non-business actors, as they are interdependent and vital for the strategy development.

Originality/value

– Relationships between firms and actors such as governments and civil society are still under-researched, although they are essential, especially in emerging economies. The paper puts focus on network relationships in strategy research and contributes to the development of business network theory by extending the network to also include relationships with such non-business actors and relate it to strategy processes. There is also a contribution to research on corporate social responsibility activities with a specific focus on Latin America.
The effects of gender differences on the use of annotatable multimedia e-readers
Authors: Liu Yi-Fan , Hwang Wu-Yuin , Chen Sherry
Published: July 2015

Purpose

– This paper aims to examine how gender differences influence students’ reactions to the use of the annotatable multimedia e-reader (AME). To reach this aim, we develop an AME where various annotation tools are provided to help students learn English in-class and after-class.

Design/methodology/approach

– An empirical study was conducted with 63 fifth-grade students from an elementary school. A pre-test and post-test were used to identify their prior knowledge and learning achievement, respectively. A questionnaire was applied to identify participants’ perceptions towards the AME.

Findings

– The results show that students’ post-test scores are significantly related to after-class behaviour, instead of in-class behaviour. Females prefer to use the text annotation and teachers’ voice, but it is voice annotation that is beneficial to improve their learning achievement. Conversely, males prefer to use the text-to-speech only, but it is text annotation that is helpful to improve their learning achievement. Additionally, the ease of use affects males’ intention to use the AME to learn English after-class while it has no effects on females.

Originality/value

– This study not only shows the importance of gender differences but also demonstrates the essence of after-class learning behaviour. More importantly, a framework is proposed to support designers to develop e-readers that can accommodate the preferences of females and males.