bluuebunny/crossref_metadata_2025 huggingface dataset:
Chapter 1. Contributions of study abroad research to our understanding of SLA processes and outcomes
Authors: Sanz Cristina
Published: June 2014

Central to research on second language acquisition (SLA) has been the question of the potential effects of learning conditions on rate of acquisition and final attainment, with enough publications to allow for meta-analyses (Norris & Ortega 2000; Spada & Tomita 2010; Li 2010). Typically, the specific learning conditions themselves, whether implicit or explicit, have been motivated either by research on cognitive psychology – memorization vs. rule search, for example – or have been pedagogical in nature – grammar explanation or type of feedback. As of late, however, the field has been reconsidering the breadth of those external conditions to include research on Study Abroad as a special context characterized by an uninstructed (i.e. implicit) component that may or may not combine with an instructed (i.e. explicit) component. With this, research on Study Abroad – the topic of the present volume – has moved to a central place in SLA research. This chapter introduces the SALA Project as an example of the contributions that research on study/stay abroad can make to our understanding of how second languages are learned.
Chapter 12. Contrasting intercultural awareness at home and abroad
Authors: Merino Elena , Avello Pilar
Published: June 2014

This chapter examines the effects of Study Abroad (SA), following Formal Instruction (FI), on a group of Catalan/Spanish English-as-a-foreign-language (EFL) learners (n = 28) regarding changes in their intercultural awareness. Data from this group were compared with data from a group of native speakers of English (n = 26) enrolled in a SA program in Spain. Following one of the main objectives in the SALA Project, we seek to understand to what extent learners’ cultural beliefs may change after a three-month SA program. Results showed that intercultural awareness increased immediately following SA but not FI, and it decreased 15 months upon the EFL learners’ return from the SA period. No statistically significant differences were found between the Catalan/Spanish undergraduates and the English group.
Chapter 13. Research on language development during study abroad
Authors: DeKeyser Robert M.
Published: June 2014

This chapter gives a brief overview of the main findings of the Study Abroad literature and situates the SALA Project against that background. It then provides suggestions for further research on some of the main issues that remain to be resolved: how do variables such as the social context of the Study Abroad experience or the researcher’s focus on specific aspects of language help explain what appears contradictory in the literature so far, how can we get a better grip on individual differences, and how can quantitative and qualitative research methodologies be integrated better to answer these questions?
Bilingual constructions
Authors: Demirçay Derya , Backus Ad
Published: June 2014

Code-switching comes in three major sub-types: insertion, alternation, and congruent lexicalization. Turkish-Dutch code-switching is supposed to feature the first two types but not the third, because when the languages in contact are typologically distinct, there is not enough shared lexicon and structure to make the fine-grained integration of the two languages possible that is the basic requirement for congruent lexicalization. Recent data of third generation Dutch Turks, however, shows some instances of code-switching that do not rely as much on keeping the two languages separate as the prototypical instances of insertion and alternation do. This empirical development lends support to a theoretical approach to linguistics that makes use of an expanded definition of the lexicon. Many of the complex instantiations of code-switching qualify as both insertion and alternation, because the inserted unit is so large that it involves a complete switch to the other language at the same time.
Personal Network Characteristics of Youth in Substance use Treatment: Motivation for and Perceived Difficulty of Positive Network Change
Authors: Chung Tammy , Sealy Lauren , Abraham Margaret , Ruglovsky Cynthia , Schall Jacqueline , Maisto Stephen A.
Published: June 2014

Background

Among youth in substance use treatment, peer substance use consistently predicts worse treatment outcomes. This study characterized personal (egocentric) networks of treated youth and examined predictors of adolescents’ motivation and perceived difficulty in making changes in the peer network to support recovery.

Methods

Adolescents (aged 14–18; N = 155) recruited from substance use treatment reported on substance use severity, motivation to abstain from substance use, abstinence goals such as “temporary abstinence,” motivation and perceived difficulty in reducing contact with substance-using peers, and personal network characteristics. Personal network variables included composition (proportion of abstinent peers) and structure (number of network members, extent of ties among members) for household and nonhousehold (peer) members.

Results

Although a majority of peer network members were perceived as using alcohol or marijuana, youth in treatment had relatively high motivation to abstain from substance use. However, treated youths’ motivation to reduce contact with substance-using peers was relatively low. In particular, a goal of temporary abstinence was associated with lower motivation to change the peer network. For marijuana, specifically, network composition features (proportion of abstinent peers) were associated with motivation and perceived difficulty to change the peer network. For marijuana, in particular, network structural variables (extent of ties among members) were associated only with perceived difficulty of changing the peer network.

Conclusions

Despite high motivation to abstain from substance use during treatment, adolescents reported low motivation to reduce contact with substance-using peers. Personal motivation to abstain and abstinence goal predicted motivation to reduce contact with substance-using peers. In contrast, particularly for marijuana, network structure predicted perceived difficulty of network change. Results highlight the potential utility of addressing motivation and perceived difficulty to change the peer network as part of youth network-based interventions.
Latino Immigrants’ Biological Parents’ Histories of Substance use Problems in Their Country of Origin Predict Their Pre- and Post-Immigration Alcohol use Problems
Authors: Blackson Timothy C. , De La Rosa Mario , Sanchez Mariana , Li Tan
Published: June 2014

Background

No studies to date have assessed whether recent young adult (aged 18–34) Latino immigrants’ biological parents’ histories of substance use problems (BPHSUP) in their country of origin predict their alcohol use problems at pre- and post-immigration to the United States (US).

Methods

BPHSUP in their country of origin were assessed via interviews conducted by bilingual Latino researchers with recent Latino immigrants primarily from Cuba and Central and South America recruited through respondent-driven sampling at the time of their immigration to southeastern US. Three waves of data were collected to document Latino immigrants’ severity of alcohol use problems at pre-immigration and 2 annual post-immigration follow-up assessments. BPHSUP+/− status was used as a predictor of Latinos’ ( N = 452; 45.8% female, 54.2% male) Alcohol Use Disorders Identification Test (AUDIT) scores at pre- and post-immigration with age, education, and income as covariates as wells as odds ratios for AUDIT classifications of hazardous use, harmful use, and dependence.

Results

BPHSUP+ status predicted Latino immigrants’ higher AUDIT scores pre- and post-immigration by gender ( P < .01) compared with Latino immigrants of BPHSUP− status, controlling for age, education, and income. BPHSUP+ status predicted odds ratios of 3.45 and 2.91 for AUDIT alcohol dependence classification for men and women, respectively.

Conclusions

This study documents that BPHSUP+/− status in their country of origin predict their young adult Latino offspring's severity of alcohol use problems pre- and post-immigration. These results may inform (1) community-based health care providers to screen recent young adult Latino immigrants for their BPHSUP+/− status and severity of alcohol use problems to redirect trajectories away from alcohol use disorders toward more normative post-immigration outcomes through culturally relevant prevention services and (2) future research advantages of differential susceptibility theory. Implications for future research and the need for replication studies in other geographic regions of the US are discussed.
Human CalDAG-GEFI gene (RASGRP2) mutation affects platelet function and causes severe bleeding
Authors: Canault Matthias , Ghalloussi Dorsaf , Grosdidier Charlotte , Guinier Marie , Perret Claire , Chelghoum Nadjim , Germain Marine , Raslova Hana , Peiretti Franck , Morange Pierre E. , Saut Noemie , Pillois Xavier , Nurden Alan T. , Cambien François , Pierres Anne , van den Berg Timo K. , Kuijpers Taco W. , Alessi Marie-Christine , Tregouet David-Alexandre
Published: June 2014

The nature of an inherited platelet disorder was investigated in three siblings affected by severe bleeding. Using whole-exome sequencing, we identified the culprit mutation (cG742T) in the RAS guanyl-releasing protein-2 (RASGRP2) gene coding for calcium- and DAG-regulated guanine exchange factor-1 (CalDAG-GEFI). Platelets from individuals carrying the mutation present a reduced ability to activate Rap1 and to perform proper αIIbβ3 integrin inside-out signaling. Expression of CalDAG-GEFI mutant in HEK293T cells abolished Rap1 activation upon stimulation. Nevertheless, the PKC- and ADP-dependent pathways allow residual platelet activation in the absence of functional CalDAG-GEFI. The mutation impairs the platelet’s ability to form thrombi under flow and spread normally as a consequence of reduced Rac1 GTP-binding. Functional deficiencies were confined to platelets and megakaryocytes with no leukocyte alteration. This contrasts with the phenotype seen in type III leukocyte adhesion deficiency caused by the absence of kindlin-3. Heterozygous did not suffer from bleeding and have normal platelet aggregation; however, their platelets mimicked homozygous ones by failing to undergo normal adhesion under flow and spreading. Rescue experiments on cultured patient megakaryocytes corrected the functional deficiency after transfection with wild-type RASGRP2. Remarkably, the presence of a single normal allele is sufficient to prevent bleeding, making CalDAG-GEFI a novel and potentially safe therapeutic target to prevent thrombosis.
Computing the torsion of the 𝑝-ramified module of a number field
Authors: Pitoun Frédéric , Varescon Firmin
Published: June 2014

We fix a prime number

p
p

and a number field

K
K

, and denote by

M
M

the maximal abelian

p
p

-extension of

K
K

unramified outside

p
p

. Our aim is to study the

Z

p

\mathbb {Z}_p

-module

X

=

G
a
l

(
M

/

K
)

\mathfrak {X}=\mathrm {Gal}(M/K)

and to give a method to effectively compute its structure as a

Z

p

\mathbb {Z}_p

-module. We also give numerical results, for real quadratic fields, cubic fields and quintic fields, together with their interpretations via Cohen-Lenstra heuristics.
PIWI proteins and their interactors in piRNA biogenesis, germline development and gene expression
Authors: Ku Hsueh-Yen , Lin Haifan
Published: June 2014

PIWI-interacting RNAs (piRNAs) are a complex class of small non-coding RNAs that are mostly 24–32 nucleotides in length and composed of at least hundreds of thousands of species that specifically interact with the PIWI protein subfamily of the ARGONAUTE family. Recent studies revealed that PIWI proteins interact with a number of proteins, especially the TUDOR-domain-containing proteins, to regulate piRNA biogenesis and regulatory function. Current research also provides evidence that PIWI proteins and piRNAs are not only crucial for transposon silencing in the germline, but also mediate novel mechanisms of epigenetic programming, DNA rearrangements, mRNA turnover, and translational control both in the germline and in the soma. These new discoveries begin to reveal an exciting new dimension of gene regulation in the cell.
Pathophysiology of Celiac Disease
Authors: Koning Frits
Published: June 2014

Celiac disease (CD) is strongly associated with HLA‐DQ2 and HLA‐DQ8, HLA‐class II molecules that present antigen‐derived peptides to CD4 T cells. Indeed, proinflammatory CD4 T cells specific for gluten‐derived peptides bound to HLA‐DQ2 or HLA‐DQ8 are present in the lamina propria of patients, and not found in nonceliac controls. While gluten peptides bind poorly to HLA‐DQ2/8, modification by tissue tranglutaminase converts the neutral amino acid glutamine into glutamic acid, introducing a negative charge that allows high affinity binding. Thus, the association between CD and HLA‐DQ2/8 is well understood. What is less clear is why only a small minority of HLA‐DQ2/8 positive individuals develops CD, why disease can develop at any stage in life and present with highly variable symptoms. I discuss this in the framework of the multiple hit model: next to genetic predisposition, multiple other factors—some extrinsic, some intrinsic—can favour or protect from disease development.
Celiac Disease and Autoimmunity
Authors: Troncone Riccardo , Discepolo Valentina
Published: June 2014

Celiac disease (CD) has a multifactorial etiology with complex genetics and frequently occurs in association with other autoimmune disorders. Even though triggered by a dietary antigen, it shows many autoimmune features, the most peculiar being the presence of high titers of anti‐tissue transglutaminase 2 autoantibodies, produced in the small intestinal mucosa since the early stages of the disease. More than 60% of CD‐associated susceptibility loci are shared with at least another autoimmune condition, suggesting common pathogenic mechanisms. In particular, recognition of peptides by HLA molecules, posttranslational modifications required for optimal peptide binding and immune mechanisms leading to tissue damage have been found in CD as well as in other autoimmune diseases. This review briefly summarizes the main autoimmune features of CD, underlining the similarities with other autoimmune disorders, in particular with type 1 diabetes mellitus. Furthermore, the role of gluten and microbiome in driving autoimmunity is discussed.
Genomics of homoploid hybrid speciation: diversity and transcriptional activity of long terminal repeat retrotransposons in hybrid sunflowers
Authors: Renaut Sebastien , Rowe Heather C. , Ungerer Mark C. , Rieseberg Loren H.
Published: June 2014

Hybridization is thought to play an important role in plant evolution by introducing novel genetic combinations and promoting genome restructuring. However, surprisingly little is known about the impact of hybridization on transposable element (TE) proliferation and the genomic response to TE activity. In this paper, we first review the mechanisms by which homoploid hybrid species may arise in nature. We then present hybrid sunflowers as a case study to examine transcriptional activity of long terminal repeat retrotransposons in the annual sunflowersHelianthus annuus,Helianthus petiolarisand their homoploid hybrid derivatives (H. paradoxus,H. anomalusandH. deserticola) using high-throughput transcriptome sequencing technologies (RNAseq). Sampling homoploid hybrid sunflower taxa revealed abundant variation in TE transcript accumulation. In addition, genetic diversity for several candidate genes hypothesized to regulate TE activity was characterized. Specifically, we highlight one candidate chromatin remodelling factor gene with a direct role in repressing TE activity in a hybrid species. This paper shows that TE amplification in hybrid lineages is more idiosyncratic than previously believed and provides a first step towards identifying the mechanisms responsible for regulating and repressing TE expansions.
Adaptive gains through repeated gene loss: parallel evolution of cyanogenesis polymorphisms in the genusTrifolium(Fabaceae)
Authors: Olsen Kenneth M. , Kooyers Nicholas J. , Small Linda L.
Published: June 2014

Variation in cyanogenesis (hydrogen cyanide release following tissue damage) was first noted in populations of white clover more than a century ago, and subsequent decades of research have established this system as a classic example of an adaptive chemical defence polymorphism. Here, we document polymorphisms for cyanogenic components in several relatives of white clover, and we determine the molecular basis of this trans-specific adaptive variation. One hundred and thirty-nine plants, representing 13 of the 14 species withinTrifoliumsectionTrifoliastrum, plus additional species across the genus, were assayed for cyanogenic components (cyanogenic glucosides and their hydrolysing enzyme, linamarase) and for the presence of underlying cyanogenesis genes (CYP79D15andLi, respectively). One or both cyanogenic components were detected in seven species, all within sectionTrifoliastrum; polymorphisms for the presence/absence (PA) of components were detected in six species. In a pattern that parallels our previous findings for white clover, all observed biochemical polymorphisms correspond to gene PA polymorphisms atCYP79D15andLi. Relationships of DNA sequence haplotypes at the cyanogenesis loci and flanking genomic regions suggest independent evolution of gene deletions within species. This study thus provides evidence for the parallel evolution of adaptive biochemical polymorphisms through recurrent gene deletions in multiple species.
Identification of major quantitative trait loci underlying floral pollination syndrome divergence in
Penstemon
Authors: Wessinger Carolyn A. , Hileman Lena C. , Rausher Mark D.
Published: June 2014

Distinct floral pollination syndromes have emerged multiple times during the diversification of flowering plants. For example, in western North America, a hummingbird pollination syndrome has evolved more than 100 times, generally from within insect-pollinated lineages. The hummingbird syndrome is characterized by a suite of floral traits that attracts and facilitates pollen movement by hummingbirds, while at the same time discourages bee visitation. These floral traits generally include large nectar volume, red flower colour, elongated and narrow corolla tubes and reproductive organs that are exerted from the corolla. A handful of studies have examined the genetic architecture of hummingbird pollination syndrome evolution. These studies find that mutations of relatively large effect often explain increased nectar volume and transition to red flower colour. In addition, they suggest that adaptive suites of floral traits may often exhibit a high degree of genetic linkage, which could facilitate their fixation during pollination syndrome evolution. Here, we explore these emerging generalities by investigating the genetic basis of floral pollination syndrome divergence between two related
Penstemon
species with different pollination syndromes—bee-pollinated
P. neomexicanus
and closely related hummingbird-pollinated
P. barbatus
. In an F
2
mapping population derived from a cross between these two species, we characterized the effect size of genetic loci underlying floral trait divergence associated with the transition to bird pollination, as well as correlation structure of floral trait variation. We find the effect sizes of quantitative trait loci for adaptive floral traits are in line with patterns observed in previous studies, and find strong evidence that suites of floral traits are genetically linked. This linkage may be due to genetic proximity or pleiotropic effects of single causative loci. Interestingly, our data suggest that the evolution of floral traits critical for hummingbird pollination was not constrained by negative pleiotropy at loci that show co-localization for multiple traits.
Polyploidy and novelty: Gottlieb's legacy
Authors: Soltis Pamela S. , Liu Xiaoxian , Marchant D. Blaine , Visger Clayton J. , Soltis Douglas E.
Published: June 2014

Nearly four decades ago, Roose & Gottlieb (Roose & Gottlieb 1976Evolution30, 818–830. (doi:10.2307/2407821)) showed that the recently derived allotetraploidsTragopogon mirusandT. miscelluscombined the allozyme profiles of their diploid parents (T. dubiusandT. porrifolius, andT. dubiusandT. pratensis, respectively). This classic paper addressed the link between genotype and biochemical phenotype and documented enzyme additivity in allopolyploids. Perhaps more important than their model of additivity, however, was their demonstration of novelty at the biochemical level. Enzyme multiplicity—the production of novel enzyme forms in the allopolyploids—can provide an extensive array of polymorphism for a polyploid individual and may explain, for example, the expanded ranges of polyploids relative to their diploid progenitors. In this paper, we extend the concept of evolutionary novelty in allopolyploids to a range of genetic and ecological features. We observe that the dynamic nature of polyploid genomes—with alterations in gene content, gene number, gene arrangement, gene expression and transposon activity—may generate sufficient novelty that every individual in a polyploid population or species may be unique. Whereas certain combinations of these features will undoubtedly be maladaptive, some unique combinations of newly generated variation may provide tremendous evolutionary potential and adaptive capabilities.
Description of Klebsiella quasipneumoniae sp. nov., isolated from human infections, with two subspecies, Klebsiella quasipneumoniae subsp. quasipneumoniae subsp. nov. and Klebsiella quasipneumoniae subsp. similipneumoniae subsp. nov., and demonstration that Klebsiella singaporensis is a junior heterotypic synonym of Klebsiella variicola
Authors: Brisse Sylvain , Passet Virginie , Grimont Patrick A. D.
Published: June 2014

Strains previously classified as members ofKlebsiella pneumoniaephylogroups KpI, KpII-A, KpII-B and KpIII were characterized by 16S rRNA (rrs) gene sequencing, multilocus sequence analysis based onrpoB,fusA,gapA,gyrAandleuSgenes, average nucleotide identity and biochemical characteristics. Phylogenetic analysis demonstrated that KpI and KpIII corresponded toK. pneumoniaeandKlebsiella variicola, respectively, whereas KpII-A and KpII-B formed two well-demarcated sequence clusters distinct from other members of the genusKlebsiella. Average nucleotide identity between KpII-A and KpII-B was 96.4 %, whereas values lower than 94 % were obtained for both groups when compared withK. pneumoniaeandK. variicola. Biochemical properties differentiated KpII-A, KpII-B,K. pneumoniaeandK. variicola, with acid production from adonitol andl-sorbose and ability to use 3-phenylproprionate, 5-keto-d-gluconate and tricarballylic acid as sole carbon sources being particularly useful. Based on their genetic and phenotypic characteristics, we propose the namesKlebsiella quasipneumoniaesubsp.quasipneumoniaesubsp. nov. andK. quasipneumoniaesubsp.similipneumoniaesubsp. nov. for strains of KpII-A and KpII-B, respectively. The type strain ofK. quasipneumoniaesp. nov. and ofK. quasipneumoniaesubsp.quasipneumoniaesubsp. nov. is 01A030T( = SB11T = CIP 110771T = DSM 28211T). The type strain ofK. quasipneumoniaesubsp.similipneumoniaesubsp. nov. is 07A044T( = SB30T = CIP 110770T = DSM 28212T). Both strains were isolated from human blood cultures. This work also showed thatKlebsiella singaporensisis a junior heterotypic synonym ofK. variicola.
Chryseobacterium artocarpi sp. nov., isolated from the rhizosphere soil of Artocarpus integer
Authors: Venil Chidambaram Kulandaisamy , Nordin Nordiana , Zakaria Zainul Akmar , Ahmad Wan Azlina
Published: June 2014

A bacterial strain, designated UTM-3T, isolated from the rhizosphere soil of Artocarpus integer (cempedak) in Malaysia was studied to determine its taxonomic position. Cells were Gram-stain-negative, non-spore-forming rods, devoid of flagella and gliding motility, that formed yellow-pigmented colonies on nutrient agar and contained MK-6 as the predominant menaquinone. Comparative analysis of the 16S rRNA gene sequence of strain UTM-3T with those of the most closely related species showed that the strain constituted a distinct phyletic line within the genus

Chryseobacterium

with the highest sequence similarities to Chryseobacterium lactis NCTC 11390T, Chryseobacterium viscerum 687B-08T, Chryseobacterium tructae 1084-08T, Chryseobacterium arthrosphaerae CC-VM-7T, Chryseobacterium oncorhynchi 701B-08T, Chryseobacterium vietnamense GIMN1.005T, Chryseobacterium bernardetii NCTC 13530T, Chryseobacterium nakagawai NCTC 13529T, Chryseobacterium gallinarum LMG 27808T, Chryseobacterium culicis R4-1AT, Chryseobacterium flavum CW-E2T, Chryseobacterium aquifrigidense CW9T, Chryseobacterium ureilyticum CCUG 52546T, Chryseobacterium indologenes NBRC 14944T, Chryseobacterium gleum CCUG 14555T, Chryseobacterium jejuense JS17-8T, Chryseobacterium oranimense H8T and Chryseobacterium joostei LMG 18212T. The major whole-cell fatty acids were iso-C15 : 0 and iso-C17 : 1ω9c, followed by summed feature 4 (iso-C15 : 0 2-OH and/or C16 : 1ω7t) and iso-C17 : 0 3-OH, and the polar lipid profile consisted of phosphatidylethanolamine and several unknown lipids. The DNA G+C content strain UTM-3T was 34.8 mol%. On the basis of the phenotypic and phylogenetic evidence, it is concluded that the isolate represents a novel species of the genus

Chryseobacterium

, for which the name Chryseobacterium
artocarpi sp. nov. is proposed. The type strain is UTM-3T ( = CECT 8497T = KCTC 32509T).
Plasma Membrane Localization Is Essential for Oryza sativa Pto-Interacting Protein 1a-Mediated Negative Regulation of Immune Signaling in Rice
Authors: Matsui Hidenori , Fujiwara Masayuki , Hamada Satoshi , Shimamoto Ko , Nomura Yuko , Nakagami Hirofumi , Takahashi Akira , Hirochika Hirohiko
Published: June 2014

Oryza sativa Pto-interacting protein 1a (OsPti1a), an ortholog of tomato (Solanum lycopersicum) SlPti1, functions as a negative regulator of innate immunity in rice (Oryza sativa). In ospti1a mutants, the activation of immune responses, including hypersensitive response-like cell death, is caused by loss of the OsPti1a protein; however, it is as yet unclear how OsPti1a suppresses immune responses. Here, we report that OsPti1a localizes to detergent-resistant membrane fractions of the plasma membrane through lipid modification of the protein’s amino terminus, which is highly conserved among Pti1 orthologs in several plant species. Importantly, mislocalization of OsPti1a after deletion of its amino terminus reduced its ability to complement the mutant phenotypes, including hypersensitive response-like cell death. Furthermore, complex formation of OsPti1a depends on its amino terminus-mediated membrane localization. Liquid chromatography-tandem mass spectrometry analysis of OsPti1a complex-interacting proteins identified several defense-related proteins. Collectively, these findings indicate that appropriate complex formation by OsPti1a at the plasma membrane is required for the negative regulation of plant immune responses in rice.
Bacterial periplasmic sialic acid-binding proteins exhibit a conserved binding site
Authors: Gangi Setty Thanuja , Cho Christine , Govindappa Sowmya , Apicella Michael A. , Ramaswamy S.
Published: June 2014

Sialic acids are a family of related nine-carbon sugar acids that play important roles in both eukaryotes and prokaryotes. These sialic acids are incorporated/decorated onto lipooligosaccharides as terminal sugars in multiple bacteria to evade the host immune system. Many pathogenic bacteria scavenge sialic acids from their host and use them for molecular mimicry. The first step of this process is the transport of sialic acid to the cytoplasm, which often takes place using a tripartite ATP-independent transport system consisting of a periplasmic binding protein and a membrane transporter. In this paper, the structural characterization of periplasmic binding proteins from the pathogenic bacteriaFusobacterium nucleatum,Pasteurella multocidaandVibrio choleraeand their thermodynamic characterization are reported. The binding affinities of several mutations in the Neu5Ac binding site of theHaemophilus influenzaeprotein are also reported. The structure and the thermodynamics of the binding of sugars suggest that all of these proteins have a very well conserved binding pocket and similar binding affinities. A significant conformational change occurs when these proteins bind the sugar. While the C1 carboxylate has been identified as the primary binding site, a second conserved hydrogen-bonding network is involved in the initiation and stabilization of the conformational states.
Controllable assembly of a three-dimensional metal–organic supramolecular framework displaying hydrogen-bonding and π–π stacking interactions
Authors: Cai Hua , Xiao Yan-Ling , Guo Ying , Li Jian-Gang
Published: June 2014

The complex poly[[aqua(μ2-phthalato-κ2O1:O2){μ3-2-[3-(pyridin-2-yl)-1H-pyrazol-1-yl]acetato-κ4N2,N3:O:O′}{μ2-2-[3-(pyridin-2-yl)-1H-pyrazol-1-yl]acetato-κ3N2,N3:O}dizinc(II)] dihydrate], {[Zn2(C10H8N3O2)2(C8H4O4)(H2O)]·2H2O}n, has been prepared by solvothermal reaction of 2-[3-(pyridin-2-yl)-1H-pyrazol-1-yl]acetonitrile (PPAN) with zinc(II). Under hydrothermal conditions, PPAN is hydrolyzed to 2-[3-(pyridin-2-yl)-1H-pyrazol-1-yl]acetate (PPAA−). The structure determination reveals that the complex is a one-dimensional double chain containing cationic [Zn4(PPAA)4]4+structural units, which are further extended by bridging phthalate ligands. The one-dimensional chains are extended into a three-dimensional supramolecular architectureviahydrogen-bonding and π–π stacking interactions.
Burning for biodiversity: highly resilient ant communities respond only to strongly contrasting fire regimes in Australia's seasonal tropics
Authors: Andersen Alan N. , Ribbons Relena R. , Pettit Magen , Parr Catherine L.
Published: June 2014

According to the pyrodiversity paradigm, a wide range of fire regimes is required to maintain biodiversity in fire‐prone landscapes. However, the requisite level of pyrodiversity has seldom been tested and may actually be very low.

Here, we examine the sensitivity of tropical savanna ants to variation in fire regimes using results from a long‐term fire experiment near Darwin, Australia. Six experimental fire regimes, with varying fire frequency and seasonality, have been applied to 18 one‐ha plots in three replicated blocks since 2004, with ants sampled prior to experimental burning and then annually after up to 2009. Our primary focus is on the extent to which different patterns of ant richness and composition are associated with each of the six treatment regimes, or whether there is such high overlap that differences only become apparent when experimental treatments are grouped to provide strongly contrasting fire regimes.

When treating each of the six fire treatments separately, we were unable to detect a significant influence of fire on any ant community response variable. We were only able to detect significant ant responses when we grouped the experimental treatments into two contrasting fire frequency classes, low (burnt at most once over the 5 years) vs. high (burnt every 1 or 2 years). Even then, these responses were only evident after 3 years of fire treatment.

Our findings demonstrate that ant communities have very high resilience in relation to fire, with differences evident only between strongly contrasting regimes. Such resilience appears to be characteristic of savanna ants throughout the world.

Synthesis and applications. A large range of finely tuned fire regimes is unlikely to promote regional ant diversity. Rather, only very limited pyrodiversity (a combination of frequently and infrequently burnt areas) would appear to be sufficient for maintaining diversity at a landscape scale. It is important that fire management for biodiversity conservation focuses on the demonstrated requirements of target species, rather than be based on an assumption that ‘pyrodiversity begets biodiversity’.
Testing predictions of the Janzen–Connell hypothesis: a meta‐analysis of experimental evidence for distance‐ and density‐dependent seed and seedling survival
Authors: Comita Liza S. , Queenborough Simon A. , Murphy Stephen J. , Eck Jenalle L. , Xu Kaiyang , Krishnadas Meghna , Beckman Noelle , Zhu Yan
Published: June 2014

The Janzen–Connell hypothesis proposes that specialist natural enemies, such as herbivores and pathogens, maintain diversity in plant communities by reducing survival rates of conspecific seeds and seedlings located close to reproductive adults or in areas of high conspecific density. Variation in the strength of distance‐ and density‐dependent effects is hypothesized to explain variation in plant species richness along climatic gradients, with effects predicted to be stronger in the tropics than the temperate zone and in wetter habitats compared to drier habitats.

We conducted a comprehensive literature search to identify peer‐reviewed experimental studies published in the 40+ years since the hypothesis was first proposed. Using data from these studies, we conducted a meta‐analysis to assess the current weight of evidence for the distance and density predictions of the Janzen–Connell hypothesis.

Overall, we found significant support for both the distance‐ and density‐dependent predictions. For all studies combined, survival rates were significantly reduced near conspecifics compared to far from conspecifics, and in areas with high densities of conspecifics compared to areas with low conspecific densities. There was no indication that these results were due to publication bias.

The strength of distance and density effects varied widely among studies. Contrary to expectations, this variation was unrelated to latitude, and there was no significant effect of study region. However, we did find a trend for stronger distance and density dependence in wetter sites compared to sites with lower annual precipitation. In addition, effects were significantly stronger at the seedling stage compared to the seed stage.

Synthesis. Our study provides support for the idea that distance‐ and density‐dependent mortality occurs in plant communities world‐wide. Available evidence suggests that natural enemies are frequently the cause of such patterns, consistent with the Janzen–Connell hypothesis, but additional studies are needed to rule out other mechanisms (e.g. intraspecific competition). With the widespread existence of density and distance dependence clearly established, future research should focus on assessing the degree to which these effects permit species coexistence and contribute to the maintenance of diversity in plant communities.
‘Realms so barbarous and cruell’: Writing Violence in Early ModernIreland andEngland
Authors: Covington Sarah
Published: June 2014

In their tendency to avoid theory and interdisciplinary approaches, anglophone historians have frequently neglected to pay attention to questions of genre, form and narrative in the sources they consult. Such an oversight is unfortunate, for it results in partial readings of those sources, and overlooks the fact that the past itself − even as it is expressed in the most apparently neutral of documents − can never be separable from the telling of it. This essay will begin from the premise of genre to argue thatEnglish writings which represented the violence of early modernIreland andEngland were significant in revealing the fraught relationship between historical developments and aesthetic representations; if writings on Ireland remained assured and stylistically stable, even when describing the worst of atrocities, the pamphlets, memoirs, or poetry of theEnglishCivilWar, decades later, became fragmented as the writing of a more internecine and incomprehensible violence could no longer be contained within traditional formal perimeters. Violence in the 1640s was thus questioned in a way it never had been in Ireland, where the certainty embedded inEnglish writings only conveyed the acceptance of that violence as well. By contrast, language which failed in the face ofEnglishCivilWar violence was also productive, raising questions that would ultimately influence emerging conceptions of human rights in the face of atrocity.
‘The Character of Contemporary History’: Human Rights History and Early Modern Violence
Authors: Mitoma Glenn
Published: June 2014

This essay considers the significance of this special issue ofHistoryfor modern historians of human rights with regard to three aspects of that history. First, there has been a division between those who seek to chronicle the history of human rights movements and those who focus on the history of human rights violations. The essays in this volume present a view of the early modernBritish empire that seems defined by the absence of human rights movements and a ubiquity of human rights violations. Second, modern historians of human rights have pursued two approaches: deploying a standard definition of human rights as a ‘plumb line’ by which past movements and violations are assessed, or mapping the genealogy of ‘human rights’ as an empty signifier whose content is indeterminate. This edited collection approaches the violence of the period with genealogical care. Nevertheless, these contributions are also marked by a concern with the conceptual categorization of different forms of violence, which while less bound to a specific legal code, are perhaps normative across period and geography. Third, this special issue illuminates, but does not resolve, the tension between historicism and universality that characterizes the history of human rights. Each of the authors, by engaging with the assumptions and preoccupations of the human rights field, presents evidence that for both themselves and their subjects there is often an aspiration to conceptual and moral standards by which local circumstances and contingencies might be judged.
The Deep Roots of Albion's Fatal Tree: The Tudor State and the Monopoly of Violence
Authors: Wood Andy
Published: June 2014

Building upon some classical debates in historical materialism, this essay proceeds to a critical appreciation of the coercive capacities of the Tudor state. Balancing evidence for coercion against that for more subtle processes of negotiation and persuasion, it shows that when faced with substantial opposition, the Tudor state was capable of exercising massive organized violence. From this flow two key points: first, that the extreme violence of which the Tudor state was capable needs to be read alongside tentative evidence suggesting that in the mid‐ and late sixteenth century very high levels of capital punishment were quite normal; and second, that in its reaction to popular rebellion, the Tudor state fell back upon extra‐legal, informal but nonetheless tightly focused repression. In all these ways, then, there is a profound need for English historians to consider the Tudor state as not only the institutional focus of class power, but also to appreciate it as labouring at its worst: within the theatre of Ireland, the English state worked in the late sixteenth century as a repressive monster, gaining the potential to crush the interests, livelihoods and lives of people of Ireland into the bloody earth. Not for the last time, then, the repressive habits of the English ruling class found their most brutal expression in the things they did to Irish people. There are lessons here, Wood implies, for the present. Studies of the internal repressive capacities of the English state need – historically – always to be tied to its conduct within the island of Ireland.
Ordinary Violence? Ireland as Emergency in the Tudor State
Authors: Kane Brendan
Published: June 2014

This essay urges comparative study of violence in early modern Ireland and England. Ireland was colonized by the English in this period, and thus violence there is primarily studied through the lens of colonialism and in comparison with overseas colonial settings. Additionally, as argued below, scholars should be attentive to links with violence found in the other Tudor and Stuart realms, here focusing on England. To that end, the essay starts out by looking briefly at differences in the characterization and conceptualization of England's Irish and American colonial projects, the point being to make a case for seeing Ireland's centrality to the Tudor and Stuart states. From there, it offers a series of observations on similarities and points of contact between violence and its meanings in these two realms governed (at least in theory) by the same monarchy. In doing so, it claims that while the ‘extraordinary’, i.e. colonial, nature of violence in early modern Ireland is crucial for understanding the period, equally crucial is an understanding of the ‘ordinary’ aspects of that violence – defined as aspects of a more general state of terrific, quotidian violence experienced commonly within the realms. Analysis of both these colonial and the domestic contexts is necessary for assessing early modern Irish−English relations and their place in larger historical inquiries concerned with state/empire formation, modern imperialism and human rights.
Organized Violence in the Elizabethan Monarchical Republic
Authors: Smuts Malcolm
Published: June 2014

This article argues that the Tudor concept of England as a Protestant commonwealth normally implied a belief in the legitimacy and necessity of armed violence against enemies of God and the public good. In the absence of a standing army the instruments of such violence had to be mobilized partly through the voluntary efforts of subjects who regarded warfare as a form of public service. The article goes on to explore how ideas and practices of armed violence shaped government policies in England and Ireland. In England the privy council constructed a system of county militias under the control of a cohort deemed loyal to the Protestant state, and toyed with schemes for using martial law against vagrants and other groups who threatened public order. But in the absence of a successful invasion or major rebellion, this machinery of military control was never fully mobilized and a reaction eventually set in against its potential abuse. By contrast in Ireland linguistic and cultural divisions, weaker institutions of civil government and the preponderance of Catholicism created situations in which brutal military coercion sometimes appeared the only effective method of maintaining ‘civil’ governance and Protestant control. The weakness of royal supervision over the captains who carried out government policy on the ground also enabled freelance violence. Elizabethan brutality in Ireland was not simply a product of colonial rule; it reflected the dark underside of commonwealth ideals of civility, political initiative and godly rule.
Retropharyngeal Hematoma Secondary to Cervical Spine Surgery: Report of One Fatal Case
Authors: Dedouit Fabrice , Grill Stéphane , Guilbeau‐Frugier Céline , Savall Frédéric , Rougé Daniel , Telmon Norbert
Published: June 2014

A 53‐year‐old woman suffering from radicular pain due to cervical herniation underwent a spinal surgery consisting of anterior cervical discectomy and fusion with an implantable titanium cage. Five hours after the procedure, the patient developed cervical swelling and dyspnea. An emergency surgery permitted evacuation of a deep cervical hematoma and intubation of the patient, who died some minutes later. The family of the deceased lodged a complaint with the public prosecutor because of unclear circumstances of death. After analysis of the medical records by two forensic pathologists, a medicolegal autopsy was ordered. Massive retropharyngeal and mediastinal hematomas were diagnosed. Pathological study confirmed acute cervical hemorrhage, but failed to detect the source of bleeding. The forensic pathologists concluded that death was due to mechanical asphyxia secondary to pharyngeal compression by the cervical hematoma. To the best of our knowledge, death secondary to retropharyngeal hematoma in this neurosurgical context is rarely encountered.
Molecular cloning and characterization of the putative Halloween gene Phantom from the small brown planthopper Laodelphax striatellus
Authors: Jia Shuang , Wan Pin‐Jun , Li Guo‐Qing
Published: June 2014

Ecdysteroid hormone 20‐hydroxyecdysone plays fundamental roles in insect postembryonic development and reproduction. Several cytochrome P450 mono‐oxygenases (CYPs), encoded by the Halloween genes, have been documented to be involved in ecdysteroidogenesis in representative insects in Diptera, Lepidoptera and Orthoptera. Here the putative Halloween gene Phantom (Phm, cyp306a1) from a hemipteran insect species, the small brown planthopper Laodelphax striatellus, was cloned. LsPHM shows five insect conserved P450 motifs, that is, Helix‐C, Helix‐I, Helix‐K, PERF and heme‐binding motifs. Temporal and spatial expression patterns of LsPhm were evaluated by quantitative polymerase chain reaction. Through the fourth‐instar and the early fifth‐instar stages, LsPhm showed two expression peaks in day 2 and days 4−5 fourth‐instar nymphs, and three troughs in day 1 and 3 fourth instars and day 1 fifth instars. On day 5 of the fourth‐instar nymphs, LsPhm clearly had a high transcript level in the thorax where the prothoracic glands were located. Dietary introduction of double‐stranded RNA (dsRNA) of LsPhm at the nymph stage successfully knocked down the target gene, decreased expression level of ecdysone receptor (LsEcR) gene and caused a higher nymphal mortality rate and delayed development. Ingestion of 20‐hydroxyecdysone on LsPhm‐dsRNA‐exposed nymphs did not increase LsPhm expression level, but almost completely rescued the LsEcR mRNA level, and relieved the negative effects on survival and development. Thus, our data suggest that the putative LsPhm encodes a functional 25‐hydroxylase that catalyzes the biosynthesis of ecdysteroids in L. striatellus.
Increase in the Dosage Amount of Vitamin D3 Preparations by Switching From Calcium Carbonate to Lanthanum Carbonate
Authors: Hyodo Toru , Kawakami Junko , Mikami Noriko , Wakai Haruki , Ishii Daisuke , Yoshida Kazunari , Iwamura Masatsugu , Hida Miho , Kurata Yasuhisa
Published: June 2014

It is widely known that dialysis patients who are administered vitamin D preparations have a better prognosis than patients who are not. In this study, of 22 patients on maintenance dialysis who had been administered calcium (Ca) carbonate in our hospital, we investigated the dosage amount of vitamin D3 preparations after the phosphorus (P) binder was switched from Ca carbonate to the newly developed lanthanum carbonate (LC). After completely switching to LC, the dosage amount of oral vitamin D3 preparation (alfacalcidol equivalent) was significantly increased from 0.094 μg/day to 0.375 μg/day (P = 0.0090). No significant changes were observed in the values of serum corrected Ca, alkaline phosphatase, intact parathyroid hormone and P after switching. The administration of LC enabled complete cessation of the administration of Ca carbonate preparations, and increased the dosage amount of vitamin D3 preparations. Therefore, LC may be a useful P binder to improve patient prognosis.