bluuebunny/crossref_metadata_2025 huggingface dataset:
Experiencing health care service quality: through patient's eyes
Authors: Schembri Sharon
Published: October 2014

Objective The primary aim of the present study was to consider health care service quality from the patients’ perspective, specifically through the patient’s eyes. Method A narrative analysis was performed on 300 patient stories. This rigorous analysis of patient stories is designed to identify and describe health care service quality through patients’ eyes in an authentic and accurate, experiential manner. Results The findings show that there are variant and complex ways that patients experience health care service quality. Conclusion Patient stories offer an authentic view of the complex ways that patients experience health care service quality. Narrative analysis is a useful tool to identify and describe how patients experience health care service quality. Patients experience health care service quality in complex and varying ways. What is known about the topic? Patient satisfaction measures are increasingly used for benchmark and accreditation purposes. Measures of patient satisfaction are considered indicative measures of service quality and quality of care. However, the measurement of patient satisfaction and service quality is not an accurate reflection of what and how patients experience health care. What does this paper add? This paper takes a narrative approach and analyses 300 patient stories to demonstrate the essence of patients’ evaluation of health care service quality. What are the implications for practitioners? Health care service quality is shown to be experienced in various ways. Identifying and describing these different ways of experiencing health care service quality provides practitioners with strategic insight into improving the quality of service they provide outside the realm of objective satisfaction measures. These findings also demonstrate the value in a third-party feedback system.
Development of a mechanistic model of intake, chewing and digestion in cattle in connection with updated feed units
Authors: Sauvant D. , Nozière P. , Baumont R.
Published: October 2014

Recent proposals have updated systems of feed units of energy, protein, structure and rumen fill. However, consistency between the largely independently built units has not been checked, even though energy, structure and fill values of feedstuffs are linked throughout feeding in ruminants. The target of this work was to build a mechanistic model to ensure consistency across equations related to intake, mastication, fill value of feeds and diets, digestion of organic matter and transit times. The first step was to build a large database of published results on digestion, intake and chewing in cattle. This database was studied by meta-analyses to calculate more than 100 empirical regressions; about half of these equations were used to build the new French systems of net energy and metabolisable protein. The other equations were mainly related to mastication (per day or kg dry matter intake, DMI), as well as the sizes and adjacent flows of 12 compartments inside the rumen: neutral detergent fibre (NDF), degradable (D) or not (U), in large or small particles; protein, soluble (S) or D and U; starch, S or D; water; volatile fatty acids; and microbes. The rumen digesta load (RL) was closely linked with the forage NDF intake, but in this dataset, there was no maximum RL, so it does not seem to limit DMI. Close relationships were observed between long-forage intake (NDFI, % of liveweight) and dietary forage NDF (%DM) and between mastication (min/day) and dietary index of mastication (min/kg DMI). Unlike RL, each of these two relationships exhibited obvious asymptotic maximum values for the duration of mastication per day (~1000 min/day) and for the level intake of NDF from long forages (1.35% of liveweight). In these two equations, the slope represented the level of DMI. The two equations were added to the other structural equations. It is therefore possible to use a mechanistic model with 12 compartments to consistently integrate aspects dealing with fill, chewing, DMI and energy value of rations in cattle.
Prediction of nutrient flows with potential impacts on the environment in a rabbit farm: a modelling approach
Authors: Méda Bertrand , Fortun-Lamothe Laurence , Hassouna Mélynda
Published: October 2014

To face the increasing demand for animal products throughout the world, livestock-farming systems have been intensified. This intensification has proven to be economically effective but is noted for its negative impact on the environment through the production of ammonia (NH3) and the greenhouse gases nitrous oxide (N2O) and methane. In this context, dynamic models are useful tools to evaluate the effects of farming practice on nutrient flows and losses to the environment. This paper presents the development of a model simulating the flows of nitrogen (N) and phosphorus (P) in a rabbit production farm. The model is comprised of two submodels. The first submodel simulates the number of animals in the farm (births, deaths, culling of does/fatteners) and their respective performances (growth, feed intake, milk production). The second one simulates the excretion of N and P for each animal category using a mass-balance approach between intake (feed and/or milk intake) and exports (body deposition, milk production, gestation). Specific emission factors are then applied to the excreted N amounts to estimate total N, NH3 and N2O losses in the housing unit and during manure storage. Methane emissions from enteric fermentations and manure are also estimated. A simulation example based on French technico-economic data illustrates how the model could be used to study the dynamics of animal populations within the system and of nutrient flows. Finally, there is a need for new knowledge (experimental data) to improve the model and help design more sustainable rabbit production systems by identifying best practices that minimise environmental impacts.
Bromination of Pyrimidines: A Simple Inexpensive Method
Authors: Delia Thomas J. , Hood Robin J.
Published: October 2014

Although the introduction of halogens into the pyrimidine ring has been accomplished numerous times, the methods usually involve either specialised reagents or very aggressive conditions. This communication paper describes the introduction of bromine into position 5 of the pyrimidine ring using common inorganic salts at room temperature. An evaluation of the substituents required for successful reaction is provided.
LIMP-2 expression is critical for β-glucocerebrosidase activity and α-synuclein clearance
Authors: Rothaug Michelle , Zunke Friederike , Mazzulli Joseph R. , Schweizer Michaela , Altmeppen Hermann , Lüllmann-Rauch Renate , Kallemeijn Wouter W. , Gaspar Paulo , Aerts Johannes M. , Glatzel Markus , Saftig Paul , Krainc Dimitri , Schwake Michael , Blanz Judith
Published: October 2014

Significance

Our report highlights, for the first time to our knowledge, a distinct relationship between lysosomal integral membrane protein type-2 (LIMP-2) expression, β-glucocerebrosidase (GC) activity, and clearance of α-synuclein. In LIMP-2–deficient mice, increased levels of endogenous α-synuclein led to severe neurological deficits and premature death. We found that loss of LIMP-2 reduced lysosomal GC activity, resulting in lipid storage, disturbed autophagic/lysosomal function, and α-synuclein accumulation leading to neurotoxicity of dopaminergic neurons as well as apoptotic cell death and inflammation. Furthermore, heterologous overexpression of functional LIMP-2 enhanced α-synuclein clearance and improved lysosomal activity of GC. Our results suggest that lysosomal GC activity can be influenced via its interaction with LIMP-2, which could be a promising strategy for the treatment of synucleinopathies.
Intestinal myofibroblast-specific Tpl2-Cox-2-PGE
2
pathway links innate sensing to epithelial homeostasis
Authors: Roulis Manolis , Nikolaou Christoforos , Kotsaki Elena , Kaffe Eleanna , Karagianni Niki , Koliaraki Vasiliki , Salpea Klelia , Ragoussis Jiannis , Aidinis Vassilis , Martini Eva , Becker Christoph , Herschman Harvey R. , Vetrano Stefania , Danese Silvio , Kollias George
Published: October 2014

Significance

Tumor progression locus-2 (Tpl2) is a proinflammatory gene genetically associated with inflammatory bowel diseases. This study provides a mechanistic interpretation for this association showing a dominant Tpl2-mediated homeostatic mechanism protecting mice from epithelial injury-induced colitis. This function of Tpl2 is mediated specifically by subepithelial intestinal myofibroblasts, a cell type supporting crypt stem cells. Tpl2 in myofibroblasts is essential for the compensatory proliferative response of the epithelium by promoting arachidonic acid metabolism and cyclooxygenase-2 (Cox-2)/prostaglandin E
2
activation. Notably, in Crohn’s Disease patients, Tpl2 is downregulated in myofibroblasts isolated from the inflamed ileum. These results challenge current concepts on a solely proinflammatory function of Tpl2 and highlight the dominant role of subepithelial myofibroblasts in sensing inflammation and tissue damage and promoting intestinal homeostasis through Tpl2-Cox-2-prostaglandin E
2
.
Family Cohesion as a Longevity Factor of Business with Intergenerational Transmission
Authors: Fernández-Roca FCO. Javier , López-Manjón Jesús D. , Gutiérrez-Hidalgo Fernando
Published: October 2014

This article contributes to a line of research in Business History that aims to determine the factors of family business longevity in the long term with the study of individual cases. The literature has identified family cohesion as one of the essential factors for survival. Cohesion may be reinforced or broken at the time of the intergenerational transfer. This study finds that a critical response on the part of the business family to the difficulties associated with intergenerational transfer of control, including modifications to the original plan, is usually based on trust between generations. Within the business family cohesion facilitates intergenerational transfers and, consequently, allows the family to evolve and transform itself into a business dynasty.
The C iv forest as a probe of baryon acoustic oscillations
Authors: Pieri Matthew M.
Published: October 2014

In light of recent successes in measuring baryon acoustic oscillations (BAO) in quasar absorption using the Lyman α (Lyα) transition, I explore the possibility of using the 1548 Å transition of triply ionized carbon (C iv) as a tracer. While the Lyα forest is a more sensitive tracer of intergalactic gas, it is limited by the fact that it can only be measured in the optical window at redshifts z > 2. Quasars are challenging to identify and observe at these high redshifts, but the C iv forest can be probed down to redshifts z ≈ 1.3, taking full advantage of the peak in the redshift distribution of quasars that can be targeted with high efficiency. I explore the strength of the C iv absorption signal and show that the absorbing population on the red side of the Lyα emission line is dominated by C iv (and so will dominate over the potential BAO signal of other metals). As a consequence, I argue that forthcoming surveys may have a sufficient increase in quasar number density to offset the lower sensitivity of the C iv forest and provide competitive precision using both the C iv autocorrelation and the C iv-quasar cross-correlation at 〈z〉 ≈ 1.6.
Early-time polarized optical light curve of GRB 131030A
Authors: King O. G. , Blinov D. , Giannios D. , Papadakis I. , Angelakis E. , Baloković M. , Fuhrmann L. , Hovatta T. , Khodade P. , Kiehlmann S. , Kylafis N. , Kus A. , Myserlis I. , Modi D. , Panopoulou G. , Papamastorakis I. , Pavlidou V. , Pazderska B. , Pazderski E. , Pearson T. J. , Rajarshi C. , Ramaprakash A. N. , Readhead A. C. S. , Reig P. , Tassis K. , Zensus J. A.
Published: October 2014

We report the polarized optical light curve of a gamma-ray burst afterglow obtained using the RoboPol instrument. Observations began 655 s after the initial burst of gamma-rays from GRB 131030A, and continued uninterrupted for 2 h. The afterglow displayed a low, constant fractional linear polarization of p = (2.1 ± 1.6) per cent throughout, which is similar to the interstellar polarization measured on nearby stars. The optical brightness decay is consistent with a forward-shock propagating in a medium of constant density, and the low polarization fraction indicates a disordered magnetic field in the shock front. This supports the idea that the magnetic field is amplified by plasma instabilities on the shock front. These plasma instabilities produce strong magnetic fields with random directions on scales much smaller than the total observable region of the shock, and the resulting randomly-oriented polarization vectors sum to produce a low net polarization over the total observable region of the shock.
Fine-Scale Genetic Structure of Monilinia fructicola During Brown Rot Epidemics Within Individual Peach Tree Canopies
Authors: Everhart S. E. , Scherm H.
Published: October 2014

The purpose of this study was to determine the fine-scale genetic structure of populations of the brown rot pathogen Monilinia fructicola within individual peach tree canopies to better understand within-tree plant pathogen diversity and to complement previous work on spatiotemporal development of brown rot disease at the canopy level. Across 3 years in a total of six trees, we monitored disease development, collected isolates from every M. fructicola symptom during the course of the season, and created high-resolution three-dimensional maps of all symptom and isolate locations within individual canopies using an electromagnetic digitizer. Each canopy population (65 to 173 isolates per tree) was characterized using a set of 13 microsatellite markers and analyzed for evidence of spatial genetic autocorrelation among isolates during the epidemic phase of the disease. Results showed high genetic diversity (average uh = 0.529) and high genotypic diversity (average D = 0.928) within canopies. The percentage of unique multilocus genotypes within trees was greater for blossom blight isolates (78.2%) than for fruit rot isolates (51.3%), indicating a greater contribution of clonal reproduction during the preharvest epidemic. For fruit rot isolates, between 54.2 and 81.7% of isolates were contained in one to four dominant clonal genotypes per tree having at least 10 members. All six fruit rot populations showed positive and significant spatial genetic autocorrelation for distance classes between 0.37 and 1.48 m. Despite high levels of within-tree pathogen diversity, the contribution of locally available inoculum combined with short-distance dispersal is likely the main factor generating clonal population foci and associated spatial genetic clustering within trees.
Quantifying the Effects of Fusarium Head Blight on Grain Yield and Test Weight in Soft Red Winter Wheat
Authors: Salgado Jorge David , Madden Laurence V. , Paul Pierce A.
Published: October 2014

Fusarium head blight (FHB), caused by the fungus Fusarium graminearum, is known to negatively affect wheat grain yield (YLD) and test weight (TW). However, very little emphasis has been placed on formally quantifying FHB–YLD and FHB–TW relationships. Field plots of three soft red winter wheat cultivars—‘Cooper’ (susceptible to FHB), ‘Hopewell’ (susceptible), and ‘Truman’ (moderately resistant)—were grown during the 2009, 2010, 2011, and 2012 seasons, and spray inoculated with spore suspensions of F. graminearum and Parastagonospora nodorum to generate a range of FHB and Stagonospora leaf blotch (SLB) levels. FHB index (IND) and SLB were quantified as percent diseased spike and flag leaf area, respectively, and YLD (kg ha−1) and TW (kg m−3) data were collected. Using IND as a continuous covariate and cultivar (CV) and SLB as categorical fixed effects, linear mixed-model regression analyses (LMMR) were used to model the IND–YLD and IND–TW relationship and to determine whether these relationships were influenced by CV and SLB. The final models fitted to the data were of the generic form y = a + b (IND), where a (intercept) or b (slope) could also depend on other factors. LMMR analyses were also used to estimate a and b by combining the studies from these 4 years with an additional 16 experiments conducted from 2003 to 2013, and bivariate random-effects meta-analysis was used to estimate population mean b ([Formula: see text]) and a (ā) for the IND–YLD relationship. YLD and TW decreased as IND increased, with b ranging from −3.2 to −2.3 kg m−3 %−1 for TW. For the IND–YLD relationship, [Formula: see text] was −51.7 kg ha−1 %IND−1 and ā was 4,426.7 kg ha−1. Neither cultivar nor SLB affected the IND–YLD relationship but SLB affected a of the IND–TW regression lines, whereas cultivar affected b. Plots with the highest levels of SLB (based on ordinal categories for SLB) had the lowest a and Hopewell had the highest b. The level of IND at which a 50-kg m−3 reduction in TW was predicted to occur was 19, 16, and 22% for Cooper, Hopewell, and Truman, respectively. A yield loss of 1 MT ha−1 was predicted to occur at 19% IND. The rate of reduction in relative TW or YLD per unit increase in IND was between −0.39 and −0.32%−1 for TW and −1.17%−1 for YLD. Results from this study could be integrated into more general models to evaluate the economics of FHB management strategies.
Sea otter dental enamel is highly resistant to chipping due to its microstructure
Authors: Ziscovici Charles , Lucas Peter W. , Constantino Paul J. , Bromage Timothy G. , van Casteren Adam
Published: October 2014

Dental enamel is prone to damage by chipping with large hard objects at forces that depend on chip size and enamel toughness. Experiments on modern human teeth have suggested that some ante-mortem chips on fossil hominin enamel were produced by bite forces near physiological maxima. Here, we show that equivalent chips in sea otter enamel require even higher forces than human enamel. Increased fracture resistance correlates with more intense enamel prism decussation, often seen also in some fossil hominins. It is possible therefore that enamel chips in such hominins may have formed at even greater forces than currently envisaged.
Raison d’être of insulin resistance: the adjustable threshold hypothesis
Authors: Wang Guanyu
Published: October 2014

The epidemics of obesity and diabetes demand a deeper understanding of insulin resistance, for which the adjustable threshold hypothesis is formed in this paper. To test the hypothesis, mathematical modelling was used to analyse clinical data and to simulate biological processes at both molecular and organismal levels. I found that insulin resistance roots in the thresholds of the cell's bistable response. By assuming heterogeneity of the thresholds, single cells' all-or-none response can collectively produce a graded response at the whole-body level—conforming to existing data. The thresholds have to be adjustable to adapt to extreme conditions. During pregnancy, for example, the thresholds increase consistently to strengthen the mother's insulin resistance to meet the increasing glucose demand of the expanding fetal brain. I also found that hysteresis, a key element of the adjustable threshold hypothesis, can explain reactive hypoglycaemia, which is characteristic of diabetes complications but remains poorly understood. Contrary to the common belief that insulin promotes glucose disposal, the results imply that insulin is the body's ‘ration stamp’ to restricting glucose utilization by peripheral tissues and that insulin resistance is primarily a well-evolved mechanism. The hypothesis provides an intuitive and dynamical description of the previously formless insulin resistance, which may make the detection of pre-diabetes possible and may shed light on the optimal timing of therapeutic intervention. It also provides valuable clues to defining subtypes of type 2 diabetes that might respond differently to specific prevention and intervention strategies.
Social insect colony as a biological regulatory system: modelling information flow in dominance networks
Authors: Nandi Anjan K. , Sumana Annagiri , Bhattacharya Kunal
Published: October 2014

Social insects provide an excellent platform to investigate flow of information in regulatory systems since their successful social organization is essentially achieved by effective information transfer through complex connectivity patterns among the colony members. Network representation of such behavioural interactions offers a powerful tool for structural as well as dynamical analysis of the underlying regulatory systems. In this paper, we focus on the dominance interaction networks in the tropical social waspRopalidia marginata—a species where behavioural observations indicate that such interactions are principally responsible for the transfer of information between individuals about their colony needs, resulting in a regulation of their own activities. Our research reveals that the dominance networks ofR. marginataare structurally similar to a class of naturally evolved information processing networks, a fact confirmed also by the predominance of a specific substructure—the ‘feed-forward loop’—a key functional component in many other information transfer networks. The dynamical analysis through Boolean modelling confirms that the networks are sufficiently stable under small fluctuations and yet capable of more efficient information transfer compared to their randomized counterparts. Our results suggest the involvement of a common structural design principle in different biological regulatory systems and a possible similarity with respect to the effect of selection on the organization levels of such systems. The findings are also consistent with the hypothesis that dominance behaviour has been shaped by natural selection to co-opt the information transfer process in such social insect species, in addition to its primal function of mediation of reproductive competition in the colony.
The influence of mitonuclear genetic variation on personality in seed beetles
Authors: Løvlie Hanne , Immonen Elina , Gustavsson Emil , Kazancioğlu Erem , Arnqvist Göran
Published: October 2014

There is a growing awareness of the influence of mitochondrial genetic variation on life-history phenotypes, particularly via epistatic interactions with nuclear genes. Owing to their direct effect on traits such as metabolic and growth rates, mitonuclear interactions may also affect variation in behavioural types or personalities (i.e. behavioural variation that is consistent within individuals, but differs among individuals). However, this possibility is largely unexplored. We used mitonuclear introgression lines, where three mitochondrial genomes were introgressed into three nuclear genetic backgrounds, to disentangle genetic effects on behavioural variation in a seed beetle. We found within-individual consistency in a suite of activity-related behaviours, providing evidence for variation in personality. Composite measures of overall activity of individuals in behavioural assays were influenced by both nuclear genetic variation and by the interaction between nuclear and mitochondrial genomes. More importantly, the degree of expression of behavioural and life-history phenotypes was correlated and mitonuclear genetic variation affected expression of these concerted phenotypes. These results show that mitonuclear genetic variation affects both behavioural and life-history traits, and they provide novel insights into the maintenance of genetic variation in behaviour and personality.
Changing dynamics of Caribbean reef carbonate budgets: emergence of reef bioeroders as critical controls on present and future reef growth potential
Authors: Perry Chris T. , Murphy Gary N. , Kench Paul S. , Edinger Evan N. , Smithers Scott G. , Steneck Robert S. , Mumby Peter J.
Published: October 2014

Coral cover has declined rapidly on Caribbean reefs since the early 1980s, reducing carbonate production and reef growth. Using a cross-regional dataset, we show that widespread reductions in bioerosion rates—a key carbonate cycling process—have accompanied carbonate production declines. Bioerosion by parrotfish, urchins, endolithic sponges and microendoliths collectively averages 2 G (where G = kg CaCO
3
m
−2
yr
−1
) (range 0.96–3.67 G). This rate is at least 75% lower than that reported from Caribbean reefs prior to their shift towards their present degraded state. Despite chronic overfishing, parrotfish are the dominant bioeroders, but erosion rates are reduced from averages of approximately 4 to 1.6 G. Urchin erosion rates have declined further and are functionally irrelevant to bioerosion on most reefs. These changes demonstrate a fundamental shift in Caribbean reef carbonate budget dynamics. To-date, reduced bioerosion rates have partially offset carbonate production declines, limiting the extent to which more widespread transitions to negative budget states have occurred. However, given the poor prognosis for coral recovery in the Caribbean and reported shifts to coral community states dominated by slower calcifying taxa, a continued transition from production to bioerosion-controlled budget states, which will increasingly threaten reef growth, is predicted.
Rapid scavenging of jellyfish carcasses reveals the importance of gelatinous material to deep-sea food webs
Authors: Sweetman Andrew K. , Smith Craig R. , Dale Trine , Jones Daniel O. B.
Published: October 2014

Jellyfish blooms are common in many oceans, and anthropogenic changes appear to have increased their magnitude in some regions. Although mass falls of jellyfish carcasses have been observed recently at the deep seafloor, the dense necrophage aggregations and rapid consumption rates typical for vertebrate carrion have not been documented. This has led to a paradigm of limited energy transfer to higher trophic levels at jelly falls relative to vertebrate organic falls. We show from baited camera deployments in the Norwegian deep sea that dense aggregations of deep-sea scavengers (more than 1000 animals at peak densities) can rapidly form at jellyfish baits and consume entire jellyfish carcasses in 2.5 h. We also show that scavenging rates on jellyfish are not significantly different from fish carrion of similar mass, and reveal that scavenging communities typical for the NE Atlantic bathyal zone, including the Atlantic hagfish, galatheid crabs, decapod shrimp and lyssianasid amphipods, consume both types of carcasses. These rapid jellyfish carrion consumption rates suggest that the contribution of gelatinous material to organic fluxes may be seriously underestimated in some regions, because jelly falls may disappear much more rapidly than previously thought. Our results also demonstrate that the energy contained in gelatinous carrion can be efficiently incorporated into large numbers of deep-sea scavengers and food webs, lessening the expected impacts (e.g. smothering of the seafloor) of enhanced jellyfish production on deep-sea ecosystems and pelagic–benthic coupling.
Psychroserpens jangbogonensis sp. nov., a psychrophilic bacterium isolated from Antarctic marine sediment
Authors: Baek Kiwoon , Lee Yung Mi , Hwang Chung Yeon , Park Hyun , Jung You-Jung , Kim Mi-Kyeong , Hong Soon Gyu , Kim Ji Hee , Lee Hong Kum
Published: October 2014

A Gram-staining-negative, yellow-pigmented, aerobic, rod-shaped and non-motile bacterium, PAMC 27130T, was isolated from the marine sediment of the Ross Sea, Antarctica. The temperature, pH and NaCl tolerance ranges for growth were 4–20 °C, pH 6.0–9.0 and 0.5–5.0 % (w/v) NaCl, respectively. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain PAMC 27130T belonged to the genus

Psychroserpens

and was closely related to

Psychroserpens mesophilus

,

Psychroserpens damuponensis

and

Psychroserpens burtonensis

with 97.2, 94.7 and 94.2 % sequence similarities, respectively. Genomic relatedness analyses based on average nucleotide identity and genome-to-genome distance showed that strain PAMC 27130T could be clearly distinguished from other species of the genus

Psychroserpens

. The genomic DNA G+C content was 32.7 mol%. The major fatty acids (>10 %) were C20 : 4ω6c (13.2 %), iso-C15 : 0 (12.3 %), iso-C15 : 1 G (11.7 %) and iso-C15 : 0 3-OH (10.0 %). The major respiratory isoprenoid quinone was menaquinone-6 (MK-6) and the polar lipids were phosphatidylethanolamine, two unidentified aminolipids, an unidentified phospholipid, an unidentified aminophospholipid and three unidentified lipids. On the basis of genotypic and phenotypic data collected in this study, it is proposed that strain PAMC 27130T represents a novel species of the genus

Psychroserpens

, for which the name Psychroserpens jangbogonensis sp. nov. is proposed. The type strain is PAMC 27130T ( = KCTC 42128T = JCM 30228T).
How predator hunting-modes affect prey behaviour: Capture deterrence inDrosophila melanogaster
Authors: Parigi Abhijna , Porter Cody , Cermak Megan , Pitchers William R. , Dworkin Ian
Published: October 2014

Hunting mode, the distinct set of behavioural strategies that a predator employs while hunting, can be an important determinant of the prey organism’s behavioural response. However, few studies have considered how a predator’s hunting mode influences anti-predatory behaviours of a prey species. Here we document the influence of active hunters (zebra jumping spiders,Salticus scenicus) and ambush predators (Chinese praying mantids,Tenodera aridifolia sinensis) on the capture deterrence anti-predatory behavioural repertoire of the model organism,Drosophila melanogaster. We hypothesized thatD. melanogasterwould reduce overall locomotory activity in the presence of ambush predators, and increase activity with active hunters. First we observed and described the behavioural repertoire ofD. melanogasterin the presence of the predators. We documented three previously undescribed behaviours-abdominal lifting, stopping and retreat-which were performed at higher frequency byD. melanogasterin the presence of predators, and may aid in capture deterrence. Consistent with our predictions, we observed an increase in the overall activity ofD. melanogasterin the presence of jumping spiders (active hunter). However, counter to our prediction, mantids (ambush hunter) had only a modest influence on activity. We also observed considerable intra and inter-individual variation in response to both predator types. Given these new insights intoDrosophilabehaviour, and with the genetic tools available, dissecting the molecular mechanisms of anti-predator behaviours may now be feasible in this system.
RBBP6 isoforms regulate the human polyadenylation machinery and modulate expression of mRNAs with AU-rich 3′ UTRs
Authors: Di Giammartino Dafne Campigli , Li Wencheng , Ogami Koichi , Yashinskie Jossie J. , Hoque Mainul , Tian Bin , Manley James L.
Published: October 2014

Polyadenylation of mRNA precursors is mediated by a large multisubunit protein complex. Here we show that RBBP6 (retinoblastoma-binding protein 6), identified initially as an Rb- and p53-binding protein, is a component of this complex and functions in 3′ processing in vitro and in vivo. RBBP6 associates with other core factors, and this interaction is mediated by an unusual ubiquitin-like domain, DWNN (“domain with no name”), that is required for 3′ processing activity. The DWNN is also expressed, via alternative RNA processing, as a small single-domain protein (isoform 3 [iso3]). Importantly, we show that iso3, known to be down-regulated in several cancers, competes with RBBP6 for binding to the core machinery, thereby inhibiting 3′ processing. Genome-wide analyses following RBBP6 knockdown revealed decreased transcript levels, especially of mRNAs with AU-rich 3′ untranslated regions (UTRs) such as c-Fos and c-Jun, and increased usage of distal poly(A) sites. Our results implicate RBBP6 and iso3 as novel regulators of 3′ processing, especially of RNAs with AU-rich 3′ UTRs.
Crystal structure of a Fanconi anemia-associated nuclease homolog bound to 5′ flap DNA: basis of interstrand cross-link repair by FAN1
Authors: Gwon Gwang Hyeon , Kim Youngran , Liu Yaqi , Watson Adam T. , Jo Aera , Etheridge Thomas J. , Yuan Fenghua , Zhang Yanbin , Kim YoungChang , Carr Anthony M. , Cho Yunje
Published: October 2014

Fanconi anemia (FA) is an autosomal recessive genetic disorder caused by defects in any of 15 FA genes responsible for processing DNA interstrand cross-links (ICLs). The ultimate outcome of the FA pathway is resolution of cross-links, which requires structure-selective nucleases. FA-associated nuclease 1 (FAN1) is believed to be recruited to lesions by a monoubiquitinated FANCI–FANCD2 (ID) complex and participates in ICL repair. Here, we determined the crystal structure of Pseudomonas aeruginosa FAN1 (PaFAN1) lacking the UBZ (ubiquitin-binding zinc) domain in complex with 5′ flap DNA. All four domains of the right-hand-shaped PaFAN1 are involved in DNA recognition, with each domain playing a specific role in bending DNA at the nick. The six-helix bundle that binds the junction connects to the catalytic viral replication and repair (VRR) nuclease (VRR nuc) domain, enabling FAN1 to incise the scissile phosphate a few bases distant from the junction. The six-helix bundle also inhibits the cleavage of intact Holliday junctions. PaFAN1 shares several conserved features with other flap structure-selective nucleases despite structural differences. A clamping motion of the domains around the wedge helix, which acts as a pivot, facilitates nucleolytic cleavage. The PaFAN1 structure provides insights into how archaeal Holliday junction resolvases evolved to incise 5′ flap substrates and how FAN1 integrates with the FA complex to participate in ICL repair.
Environmentally responsive genome-wide accumulation of de novoArabidopsis thalianamutations and epimutations
Authors: Jiang Caifu , Mithani Aziz , Belfield Eric J. , Mott Richard , Hurst Laurence D. , Harberd Nicholas P.
Published: October 2014

Evolution is fueled by phenotypic diversity, which is in turn due to underlying heritable genetic (and potentially epigenetic) variation. While environmental factors are well known to influence the accumulation of novel variation in microorganisms and human cancer cells, the extent to which the natural environment influences the accumulation of novel variation in plants is relatively unknown. Here we use whole-genome and whole-methylome sequencing to test if a specific environmental stress (high-salinity soil) changes the frequency and molecular profile of accumulated mutations and epimutations (changes in cytosine methylation status) in mutation accumulation (MA) lineages ofArabidopsis thaliana. We first show that stressed lineages accumulate ∼100% more mutations, and that these mutations exhibit a distinctive molecular mutational spectrum (specific increases in relative frequency of transversion and insertion/deletion [indel] mutations). We next show that stressed lineages accumulate ∼45% more differentially methylated cytosine positions (DMPs) at CG sites (CG-DMPs) than controls, and also show that while many (∼75%) of these CG-DMPs are inherited, some can be lost in subsequent generations. Finally, we show that stress-associated CG-DMPs arise more frequently in genic than in nongenic regions of the genome. We suggest that commonly encountered natural environmental stresses can accelerate the accumulation and change the profiles of novel inherited variants in plants. Our findings are significant because stress exposure is common among plants in the wild, and they suggest that environmental factors may significantly alter the rates and patterns of incidence of the inherited novel variants that fuel plant evolution.
Structural basis for the recognition of muramyltripeptide byHelicobacter pyloriCsd4, aD,L-carboxypeptidase controlling the helical cell shape
Authors: Kim Hyoun Sook , Kim Jieun , Im Ha Na , An Doo Ri , Lee Mijoon , Hesek Dusan , Mobashery Shahriar , Kim Jin Young , Cho Kun , Yoon Hye Jin , Han Byung Woo , Lee Byung Il , Suh Se Won
Published: October 2014

Helicobacter pyloriinfection causes a variety of gastrointestinal diseases, including peptic ulcers and gastric cancer. Its colonization of the gastric mucosa of the human stomach is a prerequisite for survival in the stomach. Colonization depends on its motility, which is facilitated by the helical shape of the bacterium. InH. pylori, cross-linking relaxation or trimming of peptidoglycan muropeptides affects the helical cell shape. Csd4 has been identified as one of the cell shape-determining peptidoglycan hydrolases inH. pylori. It is a Zn2+-dependent D,L-carboxypeptidase that cleaves the bond between the γ-D-Glu and themDAP of the non-cross-linked muramyltripeptide (muramyl-L-Ala-γ-D-Glu-mDAP) of the peptidoglycan to produce the muramyldipeptide (muramyl-L-Ala-γ-D-Glu) andmDAP. Here, the crystal structure ofH. pyloriCsd4 (HP1075 in strain 26695) is reported in three different states: the ligand-unbound form, the substrate-bound form and the product-bound form.H. pyloriCsd4 consists of three domains: an N-terminal D,L-carboxypeptidase domain with a typical carboxypeptidase fold, a central β-barrel domain with a novel fold and a C-terminal immunoglobulin-like domain. The D,L-carboxypeptidase domain recognizes the substrate by interacting primarily with the terminalmDAP moiety of the muramyltripeptide. It undergoes a significant structural change upon binding eithermDAP or themDAP-containing muramyltripeptide. It it also shown that Csd5, another cell-shape determinant inH. pylori, is capable of interacting not only withH. pyloriCsd4 but also with the dipeptide product of the reaction catalyzed by Csd4.
Structure, mechanism and ensemble formation of the alkylhydroperoxide reductase subunits AhpC and AhpF fromEscherichia coli
Authors: Dip Phat Vinh , Kamariah Neelagandan , Subramanian Manimekalai Malathy Sony , Nartey Wilson , Balakrishna Asha Manikkoth , Eisenhaber Frank , Eisenhaber Birgit , Grüber Gerhard
Published: October 2014

Hydroperoxides are reactive oxygen species (ROS) that are toxic to all cells and must be converted into the corresponding alcohols to alleviate oxidative stress. InEscherichia coli, the enzyme primarily responsible for this reaction is alkylhydroperoxide reductase (AhpR). Here, the crystal structures of both of the subunits ofEcAhpR,EcAhpF (57 kDa) andEcAhpC (21 kDa), have been solved. TheEcAhpF structures (2.0 and 2.65 Å resolution) reveal an open and elongated conformation, while that ofEcAhpC (3.3 Å resolution) forms a decameric ring. Solution X-ray scattering analysis ofEcAhpF unravels the flexibility of its N-terminal domain, and its binding toEcAhpC was demonstrated by isothermal titration calorimetry. These studies suggest a novel overall mechanistic model of AhpR as a hydroperoxide scavenger, in which the dimeric, extended AhpF prefers complex formation with the AhpC ring to accelerate the catalytic activity and thus to increase the chance of rescuing the cell from ROS.
Effects of employees’ career competencies development on their organizations
Authors: Fleisher Chen , N. Khapova Svetlana , G.W. Jansen Paul
Published: October 2014

Purpose

– This paper examines the effects of the development of employees’ career competencies (knowing-why, knowing-how, and knowing-whom) on the employing organization and assesses the role of career satisfaction in this relationship. The purpose of this paper is to contribute to research on the consequences of employees’ boundaryless careers.

Design/methodology/approach

– The study involves a two-wave quantitative investigation of alumni of a large public university in the Netherlands.

Findings

– The results suggest that by investing in the development of their career competencies, employees contribute to organizational culture, capabilities, and connections. However, these contributions depend on employees’ level of perceived career satisfaction. If employees are satisfied with their careers, they contribute more to their organizations.

Research limitations/implications

– Further longitudinal research, strengthened by an additional, third wave of data collection, is needed to replicate the present findings.

Practical implications

– The study highlights the importance of employees’ career development for organizations.

Originality/value

– This study is the first empirical investigation of the link between the development of employees’ career competencies and employees’ contributions to their employers and one of a few studies that examines career satisfaction as a moderating variable.
A review of AWOL policy in use across London; a case for greater standardisation
Authors: Patel Sachin
Published: October 2014

Purpose

– The purpose of this paper is to appraise local absent without leave/missing persons policy in use across the nine NHS mental health trusts providing services across the Greater London region.

Design/methodology/approach

– A review of the literature on best practice management was conducted, evidence collated and an appraisal tool produced. This tool was used to systematically appraise individual policies.

Findings

– Despite some core consistency in policy, there was some notable variability in guidance. Novel and unique approaches to management were also identified.

Research limitations/implications

– It is recognised that policies often arise from pragmatic approaches using local multi-agency agreements and therefore some variability across London was expected. It is also recognised that the audit tool produced is unvalidated but does reflect the best available evidence.

Practical implications

– The authors have shown policy variability in the management of what is a common psychiatric problem across a relatively homogenous population. Standardisation of policy is likely to improve the efficiency in managing these incidents as well as encourage sharing of innovative practice. The authors also illustrate practical implications for local policy benchmarking in the absence of clearly defined national standards.

Originality/value

– This study has shown the variability of policy in managing a common problem faced on psychiatric wards. It also highlights issues related to policy development on a local and regional level.
Systematic characterization of the bZIP transcription factor gene family in the rice blast fungus, Magnaporthe oryzae
Authors: Kong Sunghyung , Park Sook‐Young , Lee Yong‐Hwan
Published: October 2014

Regulatory roles of the basic leucine zipper (bZIP) transcription factors (TFs) in fungi have been identified in diverse cellular processes such as development, nutrient utilization and various stress responses. In this study, the 22 Magnaporthe oryzae genes encoding bZIP TFs were systematically characterized. Phylogenetic analysis of fungal bZIP TFs revealed that seven MobZIPs are Magnaporthe‐specific, while others belongs to 15 clades of orthologous Ascomycota genes. Expression patterns of MobZIPs under various conditions showed that they are highly stress responsive. We generated deletion mutants for 13 MobZIPs: nine with orthologues in other fungal species and four Magnaporthe‐specific ones. Seven of them exhibited defects in mycelial growth, development and/or pathogenicity. Consistent with the conserved functions of the orthologues, MobZIP22 and MobZIP13 played a role in sulfur metabolism and iron homeostasis respectively. Along with MobZIP22 and MobZIP13, one Magnaporthe‐specific gene, MobZIP11 is essential for pathogenicity in a reactive oxygen species‐dependent manner. Taken together, our results will contribute to understanding the regulatory mechanisms of the bZIP TF gene family in fungal development, adaptation to environmental stresses and pathogenicity in the rice blast fungus.
Evidence of an immunosuppressive effect of progesterone upon in vitro secretion of proinflammatory and prodegradative factors in a model of choriodecidual infection
Authors: Pineda‐Torres M , Flores‐Espinosa P , Espejel‐Nunez A , Estrada‐Gutierrez G , Flores‐Pliego A , Maida‐Claros R , Zaga‐Clavellina V
Published: October 2014

Objective

To evaluate whether progesterone (P4) is able to modulate the secretion of tumour necrosis factor α (TNF‐α), interleukin‐1β (IL‐1β), IL‐6, IL‐8, IL‐10 and matrix metalloproteinase‐9 (MMP‐9) after choriodecidual stimulation with lipopolysaccharide (LPS).

Design

Chorioamnionitis‐elicited preterm delivery is associated with an uncontrolled secretion of proinflammatory cytokines that may induce MMPs, which modify the fine immunological and structural equilibrium at the fetal–maternal interface.

Setting

Instituto Nacional de Perinatología ‘Isidro Espinosa de los Reyes’, Mexico City.

Sample

Twelve human fetal membranes at term from healthy patients were placed in a two‐chamber culture system.

Methods

Choriodecidual and amniotic regions were preincubated with 1.0, 0.1, or 0.01 μmol/l P4 for 24 hours; after which the choriodecidual region was costimulated with 1000 ng/ml of LPS for 24 hours.

Main outcome measures

Descriptive statistics were obtained for each variable. Data distribution was tested for normality using Kolmogorov–Smirnoff and Shapiro–Wilk tests. When distribution was normal, Student's t test was used to analyse for differences among groups. Mann–Whitney's U test was used when data were not normally distributed.

Results

Pretreatment with 1.0 μmol/l P4 significantly blunted the secretion of TNF‐α, IL‐1β, IL‐6, IL‐8 and IL‐10. MMP‐9 was inhibited with 0.1 μmol/l P4. Mifepristone (RU486) blocked the immunosuppressive effect of P4, suggesting a P4 effect mediated by its receptor.

Conclusion

These results offer evidence to support the concept that P4 can protect the fetal–placental unit through a compensatory mechanism that partially limits the secretion of proinflammatory and prodegradative modulators.
The vaginal microbiome, vaginal anti‐microbial defence mechanisms and the clinical challenge of reducing infection‐related preterm birth
Authors: Witkin SS
Published: October 2014

Ascending bacterial infection is implicated in about 40–50% of preterm births. The human vaginal microbiota in most women is dominated by lactobacilli. In women whose vaginal microbiota is not lactobacilli‐dominated anti‐bacterial defence mechanisms are reduced. The enhanced proliferation of pathogenic bacteria plus degradation of the cervical barrier increase bacterial passage into the endometrium and amniotic cavity and trigger preterm myometrial contractions. Evaluation of protocols to detect the absence of lactobaciili dominance in pregnant women by self‐measuring vaginal pH, coupled with measures to promote growth of lactobacilli are novel prevention strategies that may reduce the occurrence of preterm birth in low‐resource areas.