bluuebunny/crossref_metadata_2025 huggingface dataset:
The Relation between Living Group Climate and Reactions to Social Problem Situations in Detained Adolescents: “I Stabbed Him Because He Looked Mean at Me”
Authors: Eltink Ellen M. A. , van der Helm Peer , Wissink Inge B. , Stams Geert-Jan J. M.
Published: June 2015

The present study examined the association between living group climate and aversive reactions to social problem situations (e.g., getting angry, bullying or not cooperating with staff) in adolescents in secure residential facilities. The sample consisted of 128 adolescent boys and girls. Results showed an open living group climate—designated as a structured, safe and therapeutic environment—to be associated with less aversive reactions to social problem situations. Living group climate had a negative relation with aversive reactions to social problem situations (β = −.632, p < .001). It is argued that group workers should be trained in providing an open living group climate in order to diminish aversive responses to social problem situations in detained adolescents.
The influence of performance level, age and gender on pacing strategy during a 100‐km ultramarathon
Authors: Renfree Andrew , Crivoi do Carmo Everton , Martin Louise
Published: June 2015

The aim of this study is to analyse the influence of performance level, age and gender on pacing during a 100‐km ultramarathon. Results of a 100‐km race incorporating the World Masters Championships were used to identify differences in relative speeds in each 10‐km segment between participants finishing in the first, second, third and fourth quartiles of overall positions (Groups 1, 2, 3 and 4, respectively). Similar analyses were performed between the top and bottom 50% of finishers in each age category, as well as within male and female categories. Pacing varied between athletes achieving different absolute performance levels. Group 1 ran at significantly lower relative speeds than all other groups in the first three 10‐km segments (all P < 0.01), and significantly higher relative speeds than Group 4 in the 6th and 10th (both P < 0.01), and Group 2 in the 8th (P = 0.04). Group 4 displayed significantly higher relative speeds than Group 2 and 3 in the first three segments (all P < 0.01). Overall strategies remained consistent across age categories, although a similar phenomenon was observed within each category whereby ‘top’ competitors displayed lower relative speeds than ‘bottom’ competitors in the early stages, but higher relative speeds in the later stages. Females showed lower relative starting speeds and higher finishing speeds than males. ‘Top’ and ‘bottom’ finishing males displayed differing strategies, but this was not the case within females. Although pacing remained consistent across age categories, it differed with level of performance within each, possibly suggesting strategies are anchored on direct competitors. Strategy differs between genders and differs depending on performance level achieved in males but not females.
Seek, and ye shall find: Differences between spontaneous and voluntary analogical retrieval
Authors: Trench Máximo , Olguín Valeria , Minervino Ricardo
Published: June 2015

The present study tackles two overlooked aspects of analogical retrieval: (a) whether argumentation activities elicit a spontaneous search for analogical sources, and (b) whether strategic search can relax the superficial bias typically obtained in experimental studies of analogical retrieval. In Experiment 1, participants had to generate arguments for a target situation under three conditions: without indication to use analogies, with indication to use analogies, and with indication to search for sources within domains provided by the experimenters. Results showed that while voluntary search yields analogical retrievals reliably, the argumentation activity seldom elicits spontaneous remindings. A second set of results demonstrated that the superficial bias can be strategically relaxed, leading to a majority of distant retrievals. Experiment 2 replicated this result with the instruction to search within domains different from that of the target, and without providing a list of specific domains. The theoretical and educational implications of these findings are discussed.
How chromosomes shrink to fit
Authors: Leslie Mitch
Published: June 2015

Chromosome length in early embryo reflects the dimensions of the cell and nucleus.
Genetic absence of PD-1 promotes accumulation of terminally differentiated exhausted CD8+ T cells
Authors: Odorizzi Pamela M. , Pauken Kristen E. , Paley Michael A. , Sharpe Arlene , Wherry E. John
Published: June 2015

Programmed Death-1 (PD-1) has received considerable attention as a key regulator of CD8+ T cell exhaustion during chronic infection and cancer because blockade of this pathway partially reverses T cell dysfunction. Although the PD-1 pathway is critical in regulating established “exhausted” CD8+ T cells (TEX cells), it is unclear whether PD-1 directly causes T cell exhaustion. We show that PD-1 is not required for the induction of exhaustion in mice with chronic lymphocytic choriomeningitis virus (LCMV) infection. In fact, some aspects of exhaustion are more severe with genetic deletion of PD-1 from the onset of infection. Increased proliferation between days 8 and 14 postinfection is associated with subsequent decreased CD8+ T cell survival and disruption of a critical proliferative hierarchy necessary to maintain exhausted populations long term. Ultimately, the absence of PD-1 leads to the accumulation of more cytotoxic, but terminally differentiated, CD8+ TEX cells. These results demonstrate that CD8+ T cell exhaustion can occur in the absence of PD-1. They also highlight a novel role for PD-1 in preserving TEX cell populations from overstimulation, excessive proliferation, and terminal differentiation.
FourCSeq: analysis of 4C sequencing data
Authors: Klein Felix A. , Pakozdi Tibor , Anders Simon , Ghavi-Helm Yad , Furlong Eileen E. M. , Huber Wolfgang
Published: June 2015

Motivation: Circularized Chromosome Conformation Capture (4C) is a powerful technique for studying the spatial interactions of a specific genomic region called the ‘viewpoint’ with the rest of the genome, both in a single condition or comparing different experimental conditions or cell types. Observed ligation frequencies typically show a strong, regular dependence on genomic distance from the viewpoint, on top of which specific interaction peaks are superimposed. Here, we address the computational task to find these specific peaks and to detect changes between different biological conditions.

Results: We model the overall trend of decreasing interaction frequency with genomic distance by fitting a smooth monotonically decreasing function to suitably transformed count data. Based on the fit, z-scores are calculated from the residuals, and high z-scores are interpreted as peaks providing evidence for specific interactions. To compare different conditions, we normalize fragment counts between samples, and call for differential contact frequencies using the statistical method DESeq2 adapted from RNA-Seq analysis.

Availability and implementation: A full end-to-end analysis pipeline is implemented in the R package FourCSeq available at www.bioconductor.org.

Contact:  felix.klein@embl.de or whuber@embl.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Mango: a bias-correcting ChIA-PET analysis pipeline
Authors: Phanstiel Douglas H. , Boyle Alan P. , Heidari Nastaran , Snyder Michael P.
Published: June 2015

Motivation: Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) is an established method for detecting genome-wide looping interactions at high resolution. Current ChIA-PET analysis software packages either fail to correct for non-specific interactions due to genomic proximity or only address a fraction of the steps required for data processing. We present Mango, a complete ChIA-PET data analysis pipeline that provides statistical confidence estimates for interactions and corrects for major sources of bias including differential peak enrichment and genomic proximity.

Results: Comparison to the existing software packages, ChIA-PET Tool and ChiaSig revealed that Mango interactions exhibit much better agreement with high-resolution Hi-C data. Importantly, Mango executes all steps required for processing ChIA-PET datasets, whereas ChiaSig only completes 20% of the required steps. Application of Mango to multiple available ChIA-PET datasets permitted the independent rediscovery of known trends in chromatin loops including enrichment of CTCF, RAD21, SMC3 and ZNF143 at the anchor regions of interactions and strong bias for convergent CTCF motifs.

Availability and implementation: Mango is open source and distributed through github at https://github.com/dphansti/mango.

Contact:  mpsnyder@standford.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
Agency at the Managerial Interface: Public Sector Reform as Institutional Work
Authors: Cloutier Charlotte , Denis Jean-Louis , Langley Ann , Lamothe Lise
Published: June 2015

This article draws on recent developments in institutional theory to better understand the managerial efforts implicated in the implementation of government-led reforms in public sector services. Based on a longitudinal study of a massive reform effort aimed at transforming the province of Quebec’s publicly-funded healthcare system, the article applies the notion of institutional work to understand how managers responsible for newly formed healthcare organizations defined and carried out their individual missions while simultaneously clarifying and operationalizing the government’s reform mandate. We identify and describe the properties of four types of work implicated in this process and suggest that structural work, conceptual work, and operational work need to be underpinned by relational work to offer chances for successful policy reform. By showing the specific processes whereby top-down reform initiatives are taken up by managers and hybridized with existing institutionalized forms and practices, this article helps us better understand both the importance of managerial agency in enacting reform, and the dynamics that lead to policy slippage in complex reform contexts.
Learning More About Your Eating Pattern
Authors: Apple Robin F. , Agras W. Stewart
Published: June 2015

Chapter 3 covers how the patient can learn about eating patterns, and includes an overview of the session, how to keep records and why they are important, concerns about keeping records, the daily food record, concerns about weight gain, the healthy weighing routine, homework, and self-assessment questions.
Understanding the Binge-Eating Cycle
Authors: Apple Robin F. , Agras W. Stewart
Published: June 2015

Chapter 4 discusses understanding the binge-eating cycle, and includes how to understand the disorders of BN and BED, how the patient can apply this model, to understand why binging and purging don't work to rid the body of calories, how to interrupt the cycle of binge/purge, dieting and deprivation, control issues, how to engage in activities that bring pleasure, homework, and self-assessment questions.
Weight and Shape Concerns
Authors: Apple Robin F. , Agras W. Stewart
Published: June 2015

Chaper 9 discusses weight and shape concerns, including the role of body image in the development of an eating disorder, body-image distortion, heightening patient awareness of body image issues, common types of body-image concerns, avoidance of activities where the body is exposed, homework, and self-assessment questions.
Understanding More About Interpersonal and Emotional Triggers
Authors: Apple Robin F. , Agras W. Stewart
Published: June 2015

Chapter 12 covers how to indentify emotional and interpersonal binge triggers, strategies to manage high-risk situations, what to do if a binge has already occurred, homework, and self-assessment questions.
Maintaining Changes After Treatment
Authors: Apple Robin F. , Agras W. Stewart
Published: June 2015

Chapter 13 discusses maintaining positive change after treatment, including methods and plans to prevent relapse, including homework and self-assessment questions.
Treatment for Hoarding Disorder
Authors: Steketee Gail , Frost Randy O.
Published: June 2015

This online Second Edition of Treatment for Hoarding Disorder is the culmination of more than 20 years of research on understanding hoarding and building an effective intervention to address its myriad components. Thoroughly updated and reflective of changes made to the Fifth Edition of the Diagnostic and Statistical Manual for Mental Disorders (DSM-5), it outlines an empirically supported and effective CBT program for treating hoarding disorder, and provides numerous assessment and intervention forms to help clients use the methods described in the intervention. A major goal of the treatment is to recapture the positive role of possessions in the lives of people with hoarding problems, and strategies are outlined for sustaining gains and making further progress, as well as for managing stressful life events that can provoke problematic acquiring and difficulty discarding.
Evidence for a Hemibiotrophic Association of the Pitch Canker Pathogen Fusarium circinatum with Pinus radiata
Authors: Swett Cassandra L. , Kirkpatrick Sharon C. , Gordon Thomas R.
Published: June 2015

Fusarium circinatum can be a cause of mortality in pine seedlings but it is also possible for infected seedlings to remain symptomless. The results of this study documented a biotrophic phase in symptomless Pinus radiata seedlings that can persist for at least 52 weeks. A strain of F. circinatum, transformed to express the green fluorescent protein, was observed to grow intercellularly in the root cortex, with no evidence of damage to surrounding cells. Under experimental conditions, shoot symptoms developed only following collar infection, and root deterioration was seen only in plants that first expressed aboveground symptoms. This sequence of events implies that damage to the root system was a secondary consequence of girdling. If so, root symptoms may not reliably detect seedlings infected by F. circinatum. Supplemental mineral nutrition increased the incidence of infection and symptom development in seedlings but some infected plants remained symptomless, precluding the use of this approach to detect infected seedlings. Overall, our findings suggest that the ecological activities of F. circinatum may not be limited to a necrotrophic association with pine trees. A more comprehensive understanding of the life history of this fungus may yield insights that contribute to more effective management of pitch canker.
Resistance to Ditylenchus destructor Infection in Sweet Potato by the Expression of Small Interfering RNAs Targeting unc-15, a Movement-Related Gene
Authors: Fan Weijuan , Wei Zhaorong , Zhang Min , Ma Peiyong , Liu Guiling , Zheng Jianli , Guo Xiaoding , Zhang Peng
Published: June 2015

Stem nematode (Ditylenchus destructor) is one of most serious diseases that limit the productivity and quality of sweet potato (Ipomoea batatas), a root crop with worldwide importance for food security and nutrition improvement. Hence, there is a global demand for developing sweet potato varieties that are resistant to the disease. In this study, we have investigated the interference of stem nematode infectivity by the expression of small interfering RNAs (siRNAs) in transgenic sweet potato that are homologous to the unc-15 gene, which affects the muscle protein paramyosin of the pathogen. The production of double-stranded RNAs and siRNAs in transgenic lines with a single transgene integration event was verified by Northern blot analysis. The expression of unc-15 was reduced dramatically in stem nematodes collected from the inoculated storage roots of transgenic plants, and the infection areas of their storage roots were dramatically smaller than that of wild-type (WT). Compared with the WT, the transgenic plants showed increased yield in the stem nematode-infested field. Our results demonstrate that the expression of siRNAs targeting the unc-15 gene of D. destructor is an effective approach in improving stem nematode resistance in sweet potato, in adjunct with the global integrated pest management programs.
Variability of Arctic sea ice thickness and volume from CryoSat-2
Authors: Kwok R. , Cunningham G. F.
Published: June 2015

We present our estimates of the thickness and volume of the Arctic Ocean ice cover from CryoSat-2 data acquired between October 2010 and May 2014. Average ice thickness and draft differences are within 0.16 m of measurements from other sources (moorings, submarine, electromagnetic sensors, IceBridge). The choice of parameters that affect the conversion of ice freeboard to thickness is discussed. Estimates between 2011 and 2013 suggest moderate decreases in volume followed by a notable increase of more than 2500 km
3
(or 0.34 m of thickness over the basin) in 2014, which could be attributed to not only a cooler summer in 2013 but also to large-scale ice convergence just west of the Canadian Arctic Archipelago due to wind-driven onshore drift. Variability of volume and thickness in the multiyear ice zone underscores the importance of dynamics in maintaining the thickness of the Arctic ice cover. Volume estimates are compared with those from ICESat as well as the trends in ice thickness derived from submarine ice draft between 1980 and 2004. The combined ICESat and CryoSat-2 record yields reduced trends in volume loss compared with the 5 year ICESat record, which was weighted by the record-setting ice extent after the summer of 2007.
A seamless approach to understanding and predicting Arctic sea ice in Met Office modelling systems
Authors: Hewitt Helene T. , Ridley Jeff K. , Keen Ann B. , West Alex E. , Peterson K. Andrew , Rae Jamie G. L. , Milton Sean F. , Bacon Sheldon
Published: June 2015

Recent CMIP5 models predict large losses of summer Arctic sea ice, with only mitigation scenarios showing sustainable summer ice. Sea ice is inherently part of the climate system, and heat fluxes affecting sea ice can be small residuals of much larger air–sea fluxes. We discuss analysis of energy budgets in the Met Office climate models which point to the importance of early summer processes (such as clouds and meltponds) in determining both the seasonal cycle and the trend in ice decline. We give examples from Met Office modelling systems to illustrate how the seamless use of models for forecasting on time scales from short range to decadal might help to unlock the drivers of high latitude biases in climate models.
Recent changes in Antarctic Sea Ice
Authors: Turner John , Hosking J. Scott , Bracegirdle Thomas J. , Marshall Gareth J. , Phillips Tony
Published: June 2015

In contrast to the Arctic, total sea ice extent (SIE) across the Southern Ocean has increased since the late 1970s, with the annual mean increasing at a rate of 186×10
3
 km
2
per decade (1.5% per decade;
p
<0.01) for 1979–2013. However, this overall increase masks larger regional variations, most notably an increase (decrease) over the Ross (Amundsen–Bellingshausen) Sea. Sea ice variability results from changes in atmospheric and oceanic conditions, although the former is thought to be more significant, since there is a high correlation between anomalies in the ice concentration and the near-surface wind field. The Southern Ocean SIE trend is dominated by the increase in the Ross Sea sector, where the SIE is significantly correlated with the depth of the Amundsen Sea Low (ASL), which has deepened since 1979. The depth of the ASL is influenced by a number of external factors, including tropical sea surface temperatures, but the low also has a large locally driven intrinsic variability, suggesting that SIE in these areas is especially variable. Many of the current generation of coupled climate models have difficulty in simulating sea ice. However, output from the better-performing IPCC CMIP5 models suggests that the recent increase in Antarctic SIE may be within the bounds of intrinsic/internal variability.
OPERA-LG: Efficient and exact scaffolding of large, repeat-rich eukaryotic genomes with performance guarantees
Authors: Gao Song , Bertrand Denis , Chia Burton KH , Nagarajan Niranjan
Published: June 2015

The assembly of large, repeat-rich eukaryotic genomes continues to represent a significant challenge in genomics. While long-read technologies have made the high-quality assembly of small, microbial genomes increasingly feasible, data generation can be prohibitively expensive for larger genomes. Advances in assembly algorithms are thus essential to exploit the characteristics of short and long-read sequencing technologies to consistently and reliably provide high-quality assemblies in a cost-efficient manner. OPERA-LG is a scalable, exact algorithm for the scaffold assembly of large, repeat-rich genomes, with consistent improvement over state-of-the-art programs for scaffold correctness and contiguity. It provides a rigorous framework for scaffolding of repetitive sequences and a systematic approach for combining data from different second-generation (Illumina, Ion Torrent) and third-generation (PacBio, ONT) sequencing technologies. OPERA-LG efficiently scaffolds large genomes with provable scaffold properties, providing an avenue for systematic augmentation and improvement of 1000s of existing draft eukaryotic genome assemblies.
Approximately independent linkage disequilibrium blocks in human populations
Authors: Berisa Tomaz , Pickrell Joseph K.
Published: June 2015

We present a method to identify approximately independent blocks of linkage disequilibrium (LD) in the human genome. These blocks enable automated analysis of multiple genome-wide association studies.

Availability (code)http://bitbucket.org/nygcresearch/ldetect

Availability (data):http://bitbucket.org/nygcresearch/ldetect-data
PIK3CA Mutational Analysis in Formalin-Fixed, Paraffin-Embedded Archival Tissues of Urothelial Carcinoma of Urinary Bladder
Authors: Chaux Alcides , Cohen Julie S. , Schultz Luciana , Albadine Roula , Jadallah Sana , Murphy Kathleen M. , Teheri Diana , Schoenberg Mark P. , Netto George J.
Published: June 2015

OBJECTIVE: Urothelial carcinoma of the urinary bladder is the fourth most common cancer in males in the United States. In addition to mutations in FGFR3, TP53, AKT1, TSC1, and PTEN genes, mutations in PIK3CA have been also described in urothelial carcinomas, preferentially in low-grade tumors. Mutations in PIK3CA also has been shown to have implications for prognosis, surveillance and therapeutic response. Thus, determining the PIK3CA status in urothelial carcinomas could potentially improved the clinical management of patients with bladder cancer. Herein, we evaluated the presence of PIK3CA mutations in exons 1, 9, and 20 in 21 urothelial carcinomas of the urinary bladder. METHODS: Patients were treated by radical cystectomy without neoadjuvant chemotherapy. Representative tissue blocks (1 for each case) were selected. We used a pinpoint DNA extraction technique from formalin-fixed, paraffin-embedded and mutational analysis using the polymerase chain reaction (PCR) assay coupled with sequencing of targeted exons. Patients included 15 men and 6 women, with a median age of 68 years (range, 42 to 76 years), with 3 noninvasive and 18 invasive urothelial carcinomas. Noninvasive carcinomas included 1 case each of low-grade papillary urothelial carcinoma, high-grade papillary urothelial carcinoma, and urothelial carcinoma in situ (CIS). Invasive tumors included 3 pT1, 5 pT2, 6 pT3, and 4 pT4 urothelial carcinomas. RESULTS: We did not find mutations in the analyzed exons of the PIK3CA gene, in any of the 21 urothelial carcinomas. The preponderance of invasive high-grade and high-stage tumors could explain the absence of identifiable mutations in our cohort. CONCLUSIONS: PIK3CA mutations as prognosticators of outcome or predictors of therapeutic response await further evaluation.
Mapping Anatomy to Behavior in Thy1:18 ChR2-YFP Transgenic Mice Using Optogenetics
Authors: Fenno Lief E. , Gunaydin Lisa A. , Deisseroth Karl
Published: June 2015

Linking the activity of defined neural populations with behavior is a key goal of neuroscience. In the context of controlling behavior, electrical stimulation affords researchers precision in the temporal domain with gross regional specificity, whereas pharmacology allows for more specific manipulation of cell types, but in the absence of temporal precision. The use of microbial opsins—light activated, genetically encoded ion channels and pumps—to control mammalian neurons now allows researchers to “sensitize” genetically and/or topologically defined populations of neurons to light to induce either depolarization or hyperpolarization in both a cell-type-specific and temporally precise manner not achievable with previous techniques. Here, we describe the use of transgenic mice expressing the blue-light gated cation channel Channelrhodopsin-2 (ChR2) under control of the Thy1 promoter for the purpose of linking neuronal activity to behavior through restricted delivery of light to an anatomic region of interest. The surgical procedure for implanting a fiber-optic light delivery guide into the mouse brain, the process of optically stimulating the brain in a behaving animal, and post hoc evaluation are given, along with necessary reagents and discussion of common technical problems and their solutions.
Culturing Primary Mouse Pancreatic Ductal Cells
Authors: Reichert Maximilian , Rhim Andrew D. , Rustgi Anil K.
Published: June 2015

The most common subtype of pancreatic cancer is pancreatic ductal adenocarcinoma (PDAC). PDAC resembles ductal cells morphologically. To study pancreatic ductal cell (PDC) and pancreatic intraepithelial neoplasia (PanIN)/PDAC biology, it is essential to have reliable in vitro culture conditions. Here we describe a methodology to isolate, culture, and passage PDCs and duct-like cells from the mouse pancreas. It can be used to isolate cells from genetically engineered mouse models (GEMMs), providing a valuable tool to study disease models in vitro to complement in vivo findings. The culture conditions allow epithelial cells to outgrow fibroblast and other “contaminating” cell types within a few passages. However, the resulting cultures, although mostly epithelial, are not completely devoid of fibroblasts. Regardless, this protocol provides guidelines for a robust in vitro culture system to isolate, maintain, and expand primary pancreatic ductal epithelial cells. It can be applied to virtually all GEMMs of pancreatic disease and other diseases and cancers that arise from ductal structures. Because most carcinomas resemble ductal structures, this protocol has utility in the study of other cancers in addition to PDAC, such as breast and prostate cancers.
Nucleotide Analog Interference Mapping
Authors: Nilsen Timothy W.
Published: June 2015

Methods collectively known as modification interference are exceptionally powerful approaches used to identify functionally important chemical groups in the phosphodiester backbone or nucleobases of an RNA. In a modification interference assay, end-labeled RNAs that have been modified at different positions are allowed to participate in a reaction of interest, and then functional RNA molecules (e.g., those bound by protein or that successfully participate in a processing reaction) are separated from nonfunctional RNA molecules (e.g., those not bound by protein or unable to participate in a processing reaction). Nucleotide analog interference mapping (NAIM) involves the incorporation of α-thionucleotides containing a modified base into the RNA molecule of interest. The sites containing the modified base are identified by cleavage with iodoethanol. NAIM is useful whenever the thiophosphate substitution on its own does not prevent or inhibit a specific reaction. To perform NAIM, it is first necessary to perform a thiophosphate interference analysis. Any positions that are not affected by thiophosphate substitution can then be analyzed by NAIM.
Terminal Deoxynucleotidyl Transferase (TdT)-Mediated dUTP Nick-End Labeling (TUNEL) for Detection of Apoptotic Cells in Drosophila
Authors: Denton Donna , Kumar Sharad
Published: June 2015

A characteristic feature of apoptosis is DNA fragmentation. This fragmentation can be detected by terminal deoxynucleotidyl transferase (TdT)-mediated dUTP nick-end labeling (TUNEL) of DNA in dying cells. Here, we present a protocol for TUNEL detection of apoptosis in Drosophila larval tissue, but these techniques can be adapted for other tissues and developmental stages.
Time-Domain Fluorescence Lifetime Imaging Microscopy: A Quantitative Method to Follow Transient Protein–Protein Interactions in Living Cells
Authors: Padilla-Parra Sergi , Audugé Nicolas , Tramier Marc , Coppey-Moisan Maïté
Published: June 2015

Quantitative analysis in Förster resonance energy transfer (FRET) imaging studies of protein–protein interactions within live cells is still a challenging issue. Many cellular biology applications aim at the determination of the space and time variations of the relative amount of interacting fluorescently tagged proteins occurring in cells. This relevant quantitative parameter can be, at least partially, obtained at a pixel-level resolution by using fluorescence lifetime imaging microscopy (FLIM). Indeed, fluorescence decay analysis of a two-component system (FRET and no FRET donor species), leads to the intrinsic FRET efficiency value (E) and the fraction of the donor-tagged protein that undergoes FRET (fD). To simultaneously obtain fD and E values from a two-exponential fit, data must be acquired with a high number of photons, so that the statistics are robust enough to reduce fitting ambiguities. This is a time-consuming procedure. However, when fast-FLIM acquisitions are used to monitor dynamic changes in protein–protein interactions at high spatial and temporal resolutions in living cells, photon statistics and time resolution are limited. In this case, fitting procedures are unreliable, even for single lifetime donors. We introduce the concept of a minimal fraction of donor molecules involved in FRET (mfD), obtained from the mathematical minimization of fD. Here, we discuss different FLIM techniques and the compromises that must be made between precision and time invested in acquiring FLIM measurements. We show that mfD constitutes an interesting quantitative parameter for fast FLIM because it gives quantitative information about transient interactions in live cells.
Pairwise correlations in layered close-packed structures
Authors: Riechers P. M. , Varn D. P. , Crutchfield J. P.
Published: June 2015

Given a description of the stacking statistics of layered close-packed structures in the form of a hidden Markov model, analytical expressions are developed for the pairwise correlation functions between the layers. These may be calculated analytically as explicit functions of model parameters or the expressions may be used as a fast, accurate and efficient way to obtain numerical values. Several examples are presented, finding agreement with previous work as well as deriving new relations.
Topological crystallography of gas hydrates
Authors: Gudkovskikh Sergey V. , Kirov Mikhail V.
Published: June 2015

A new approach to the investigation of the proton-disordered structure of clathrate hydrates is presented. This approach is based on topological crystallography. The quotient graphs were built for the unit cells of the cubic structure I and the hexagonal structure H. This is a very convenient way to represent the topology of a hydrogen-bonding network under periodic boundary conditions. The exact proton configuration statistics for the unit cells of structure I and structure H were obtained using the quotient graphs. In addition, the statistical analysis of the proton transfer along hydrogen-bonded chains was carried out.
Crystal structure of (4Z)-4-[(dimethylamino)methylidene]-3,5-dioxo-2-phenylpyrazolidine-1-carbaldehyde
Authors: Mague Joel T. , Mohamed Shaaban K. , Akkurt Mehmet , Ahmed Eman A. , Khodairy Ahmed
Published: June 2015

In the title compound, C13H13N3O3, the pyrazolidine ring adopts a shallow envelope conformation, with the carbonyl C atom closest to the benzene ring as the flap [deviation of 0.126 (1) Å from the plane through the remaining atoms (r.m.s. deviation = 0.011 Å)]. The dihedral angle between the pyrazolidine ring (all atoms) and the benzene ring is 51.09 (4)°. An extremely short (2.08 Å) intramolecular C—H...O contact is seen. In the crystal, molecules are linked by C—H...O bonds, generating [010] chains. Extremely weak C—H...π interactions are also observed.
Crystal structure of 1-[(2,4,6-triisopropylphenyl)sulfonyl]aziridine
Authors: Knauer Lena , Golz Christopher , Strohmann Carsten
Published: June 2015

The title compound, C17H27NO2S, exhibits a distorted geometry of the aromatic ring with elongated bonds at theipso-C atom. The S atom deviates from the aromatic ring plane by 0.393 (4) Å. Similar to this, the adjacent isopropyl groups are bent out of the aromatic ring plane by −0.125 (4) and −0.154 (4) Å. Even the distant isopropyl group inpara-position to the sulfonyl moiety shows a slight deviation from the ring plane of 0.111 (5) Å. These distortions, which are caused by the bulky substituents, can also be observed in related sulfonylaziridine structures.
Crystal structures of 4-chlorophenylN-(3,5-dinitrophenyl)carbamate and phenylN-(3,5-dinitrophenyl)carbamate
Authors: Raja Rajamani , Sathiyaraj Subramaniyan , Ali B. Mohamad , Nasar A. Sultan
Published: June 2015

The title compounds, C13H8ClN3O6, (I), and C13H9N3O6, (II), differ in the orientation of the two aromatic rings. In (I), they are essentially coplanar, making a dihedral angle of 8.2 (1)°, while in (II), they are inclined to one another by 76.2 (1)°. The two nitro groups are essentially coplanar with the attached benzene rings, as indicated by the dihedral angles of 1.4 (2) and 2.3 (2)° in (I), and 4.96 (18) and 5.4 (2)° in (II). The carbamate group is twisted slightly from the attached benzene ring, with a C—N—C—O torsion angle of −170.17 (15)° for (I) and 168.91 (13)° for (II). In the crystals of of both compounds, molecules are linkedviaN—H...O hydrogen bonds, forming chains propagating along [010]. In (I), C—H...O hydrogen bonds also link molecules within the chains. The crystal packing in (I) also features a very weak π–π interaction [centroid–centroid distance = 3.7519 (9) Å].
Crystal structure of the co-crystalline adduct 1,3,6,8-tetraazatricyclo[4.4.1.13,8]dodecane (TATD)–4-chloro-3,5-dimethylphenol (1/1)
Authors: Rivera Augusto , Rojas Jicli José , Ríos-Motta Jaime , Bolte Michael
Published: June 2015

In the crystal of the title co-crystalline adduct, C8H16N4·C8H9ClO, (I), prepared by solid-state reaction, the molecules are linked by intermolecular O—H...N hydrogen bonds, forming aDmotif. The azaadamantane structure in (I) is slightly distorted, with N—CH2—CH2—N torsion angles of 10.4 (3) and −9.0 (3)°. These values differ slightly from the corresponding torsion angles in the free aminal cage (0.0°) and in related co-crystalline adducts, which are not far from a planar geometry and consistent with aD2dmolecular symmetry in the tetraazatricyclo structure. The structures also differ in that there is a slight elongation of the N—C bond lengths about the N atom that accepts the hydrogen bond in (I) compared with the other N—C bond lengths. In the crystal, the two molecules are not only linked by a classical O—H...N hydrogen bond but are further connected by weak C—H...π interactions, forming a two-dimensional supramolecular network parallel to thebcplane.
Crystal structure of tetramethyltetrathiafulvalenium (1S)-camphor-10-sulfonate dihydrate
Authors: Sommer Mathieu , Allain Magali , Mézière Cécile , Pop Flavia , Giffard Michel
Published: June 2015

Electro-oxidation of tetramethyltetrathiafulvalene (TMTTF) in the presence of the chiral anion (1S)-camphor-10-sulfonate (S-camphSO3−) in tetrahydrofuran/water medium afforded a 1/1 salt formulated as TMTTF·S-camphSO3·2H2O or 2-(4,5-dimethyl-1,3-dithiol-2-ylidene)-4,5-dimethyl-1,3-dithiole radical ion (1+) [(1S)-7,7-dimethyl-2-oxobicyclo[2.2.1]heptan-1-yl]methanesulfonate dihydrate, C10H12S4+·C10H15O4S−·2H2O. In this salt, two independent TMTTF units are present but, in both cases, the observed bond lengths and especially the central C=C distance [1.392 (6) and 1.378 (6) Å] are in agreement with a complete oxidation of TMTTF which is thus present as TMTTF.+radical cations. These cations form one-dimensional stacks in which they are associated two by two, forming dimers with short [3.472 (1) to 3.554 (2) Å] S...S contacts. The two S-camphSO3anions present also form stacks and are connected with each otherviathe water molecules with many O—H...O hydrogen bonds ranging from 1.86 (3) to 2.15 (4) Å; the O—H...O hydrogen-bonding network can be described as being constituted ofC22(6) chains bearingR33(11) lateral rings. On the other hand, the columns of cations and anions are connected through C—H...O hydrogen bonds, forming a system expanding in three directions; finally, the result is a three-dimensional network of O—H...O and C—H...O hydrogen bonds.
Editorial
Authors: Ogliastri Enrique
Published: June 2015

This issue includes six research papers originating from ten different institutions across four countries: Chile, Spain, the USA and Portugal. The first paper deals with staff turnover in service companies. The second is a study into life-work interaction for executives who have to take short but frequent international trips as part of their job. The third paper investigates how being self-employed (or alternatively, a salaried employee) affects the relationship between life and job satisfaction. The fourth paper looks at the impact of information technology (IT) on hotel marketing. The fifth examines marketing strategies for the growing segment of people with high purchasing power. And the sixth and final paper studies the impact of IT on the relationship between environmental practices and companies’ actual environmental performance.

Se incluyen seis artículos de investigación procedentes de diez instituciones en cuatro países: Chile, España, Estados Unidos y Portugal. El primero trata sobre la rotación de personal en empresas de servicios. El segundo es un estudio exploratorio sobre la interacción entre vida y trabajo de ejecutivos que deben realizar breves pero frecuentes viajes internacionales como parte de su trabajo. El tercero, estudia el efecto de trabajar por cuenta propia (o asalariado) en la relación entre la satisfacción con la vida y con el trabajo. El cuarto sobre el impacto de las tecnologías de información en el mercadeo de hoteles. El quinto sobre estrategias de mercadeo para el creciente segmento de personas en sectores de alto poder adquisitivo. El sexto estudia el impacto de la tecnología de información en la relación entre prácticas ambientales y el efectivo desempeño ambiental de las empresas.
Evolution of nutrient acquisition: when space matters
Authors: Barot Sébastien , Bornhofen Stefan , Boudsocq Simon , Raynaud Xavier , Loeuille Nicolas
Published: June 2015

Evolution of nutrient acquisition by plants should depend on two forces: local competition is based on the capacity to exploit the local nutrient resource, and regional competition is based on the capacity to occupy the whole landscape through seed production and dispersal.

We build a spatially explicit simulation model where a limiting nutrient is recycled in each local patch of a lattice by individual plants. The model includes both local and regional competition.

Heterogeneity in nutrient availability and dispersal limitation mitigate the effect of competition for the local nutrient resource and allow the evolution of lower rates of nutrient uptake. Our spatially explicit model suggests that evolution in richer ecosystems selects ‘expensive’ strategies (high acquisition, low conservation of resources) compared to poor ecosystems.

Low rates of nutrient acquisition can be considered as a form of altruism because they leave more resource available for other individuals. Our model thus suggests that the influence of spatial processes on the evolution of altruism is pervasive and is linked to key aspects of ecosystem functioning.

Because our model includes both regional and local competition, evolution does not minimize the availability of mineral nutrient, although evolution or species replacement is often thought to minimize the availability of nutrient. Taken together, our work confirms that the interplay between local and regional competition is critical for the evolution of plant nutrient strategies and its effect on ecosystem properties.
Tougher and thornier: general patterns in the induction of physical defence traits
Authors: Barton Kasey E.
Published: June 2015

Most plants rely at least in part on physical defence traits to deter herbivores, and yet, very little is known about the inducibility of these traits.

A meta‐analysis was conducted on data extracted from 57 publications from 1982 to 2014, including 53 species in 20 plant families in which the induction of physical defence traits was examined. Log response ratio effect sizes were calculated for 112 separate responses and analysed to characterize general patterns and test whether induction differed between physical and chemical defence traits (in the same study), among defence traits, and in response to the damage type (artificial, herbivore, jasmonates).

Physical defence traits are generally inducible, showing a mean increase of 52% in damaged compared to control plants. The magnitude of increase did not differ between physical and chemical defence traits measured within the same experiments, and nutrients showed no overall response. Physical defence traits varied significantly in their responses, with non‐glandular trichomes showing the greatest magnitude of increase, and no induction detected for leaf toughness. Responses induced by real herbivores or by jasmonate application were significantly greater than responses elicited by mechanical damage alone. This suggests that specificity in physical trait induction in response to different kinds of damage may occur.

Induction of physical defence traits is common and widespread, but the ecological and evolutionary consequences of this response remain unknown. Future studies examining genetic variation in the inducibility of physical defence traits and their fitness consequences for plants would be particularly informative.
Facilitation and sustainable agriculture: a mechanistic approach to reconciling crop production and conservation
Authors: Brooker Rob W. , Karley Alison J. , Newton Adrian C. , Pakeman Robin J. , Schöb Christian
Published: June 2015

Food security is currently considered a major global problem. However, increasing intensity of food production in agricultural systems has driven reductions in farmland biodiversity. A major challenge is to enable biodiversity conservation whilst addressing the problem of food security.

Here we describe how facilitative plant–plant interactions in crop systems could be used to help strike this balance. An obvious example is that of intercropping systems, where combinations of crop species can – under some circumstances – deliver reduced inputs of agrochemicals (fertilizers, pesticides) per unit yield, with potential knock‐on benefits for biodiversity conservation.

Other facilitative processes can also play a role in biodiversity conservation. Increased intraspecific crop genetic diversity can help protect crops from pests and diseases. Although overlooked in facilitation research, we argue that the mechanisms operate in a manner which is directly analogous to associational defence against herbivores, a process well recognized in the facilitation literature. As with intercropping, the benefits to nature conservation arise from reduced pesticide use per unit harvested crop.

Crops may have facilitative effects on some arable weed species, particularly those that are currently considered rare in intensive farming systems. Work is in its early stages to understand the underlying mechanisms, but it appears that crops might create niche space to which some weed species are adapted. Increasing plant species diversity through niche space creation may then have cascading benefits for other components of farmland biodiversity.

Our new understanding of facilitative processes arising from work on crop systems has lessons for the study of facilitative interactions in natural and semi‐natural communities. We argue that, although easier to identify and quantify in crop systems, some of these facilitative processes have to date been overlooked in studies of non‐crop systems and certainly deserve further consideration.

Finally, we discuss what steps may be needed to move from our understanding of the role of facilitation to the development of new agricultural practice. In some cases the challenge may be one of the encouraging uptake of existing practices, and in others more research is needed to understand how new ecological understanding might deliver more sustainable agricultural practice.
Phage–bacteria interaction network in human oral microbiome
Authors: Wang Jinfeng , Gao Yuan , Zhao Fangqing
Published: June 2015

Although increasing knowledge suggests that bacteriophages play important roles in regulating microbial ecosystems, phage–bacteria interaction in human oral cavities remains less understood. Here we performed a metagenomic analysis to explore the composition and variation of oral dsDNA phage populations and potential phage–bacteria interaction. A total of 1,711 contigs assembled with more than 100 Gb shotgun sequencing data were annotated to 104 phages based on their best BLAST matches against the NR database. Bray–Curtis dissimilarities demonstrated that both phage and bacterial composition are highly diverse between periodontally healthy samples but show a trend towards homogenization in diseased gingivae samples. Significantly, according to the CRISPR arrays that record infection relationship between bacteria and phage, we found certain oral phages were able to invade other bacteria besides their putative bacterial hosts. These cross‐infective phages were positively correlated with commensal bacteria while were negatively correlated with major periodontal pathogens, suggesting possible connection between these phages and microbial community structure in oral cavities. By characterizing phage–bacteria interaction as networks rather than exclusively pairwise predator–prey relationships, our study provides the first insight into the participation of cross‐infective phages in forming human oral microbiota.