bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proteomic and Genomic Characterization of a Yeast Model for Ogden Syndrome
Authors: Döerfel Max J. , Fang Han , Crain Jonathan , Klingener Michael , Weiser Jake , Lyon Gholson J. 
Published: March 2016

AbstractNaa10 is a Nα-terminal acetyltransferase that, in a complex with its auxiliary subunit Naa15, co-translationally acetylates the α-amino group of newly synthetized proteins as they emerge from the ribosome. Roughly 40-50% of the human proteome is acetylated by Naa10, rendering this an enzyme with one of the most broad substrate ranges known. Recently, we reported an X-linked disorder of infancy, Ogden syndrome, in two families harboring a c.109T>C (p.Ser37Pro) variant in NAA10. In the present study we performed in-depth characterization of a yeast model of Ogden syndrome. Stress tests and proteomic analyses suggest that the S37P mutation disrupts Naa10 function thereby reducing cellular fitness, possibly due to an impaired functionality of molecular chaperones, Hsp104, Hsp40 and the Hsp70 family. Microarray and RNA-seq revealed a pseudo-diploid gene expression profile in ΔNaa10 cells, likely responsible for a mating defect. In conclusion, the data presented here further support the disruptive nature of the S37P/Ogden mutation and identify affected cellular processes potentially contributing to the severe phenotype seen in Ogden syndrome.
Decoding social media speak: developing a speech act theory research agenda
Authors: Ludwig Stephan , de Ruyter Ko 
Published: March 2016

Purpose– Drawing on the theoretical domain of speech act theory (SAT) and a discussion of its suitability for setting the agenda for social media research, this study aims to explore a range of research directions that are both relevant and conceptually robust, to stimulate the advancement of knowledge and understanding of online verbatim data.Design/methodology/approach– Examining previously published cross-disciplinary research, the study identifies how recent conceptual and empirical advances in SAT may further guide the development of text analytics in a social media context.Findings– Decoding content and function word use in customers’ social media communication can enhance the efficiency of determining potential impacts of customer reviews, sentiment strength, the quality of contributions in social media, customers’ socialization perceptions in online communities and deceptive messages.Originality/value– Considering the variety of managerial demand, increasing and diverging social media formats, expanding archives, rapid development of software tools and fast-paced market changes, this study provides an urgently needed, theory-driven, coherent research agenda to guide the conceptual development of text analytics in a social media context.
Food labels – status and consumers’ attitude on the Serbian food market
Authors: Djekic Ilija , Smigic Nada 
Published: March 2016

Purpose
– This paper aims to present results from a research that analyzed the quality of labels available in the Serbian food market and consumers’ attitudes toward food labels.

Design/methodology/approach
– A total of 899 food labels have been analyzed in relation to the presence of legally required information, their readability to average consumer and presence of nutritional/health claims and/or nutritional information. In parallel, 400 respondents were interviewed in the survey of consumers’ attitudes regarding labels.

Findings
– Results revealed that 38.2 per cent of food products hold labels that are not fully readable to average consumers. Regarding basic label information, 11 per cent of foods have missing information in terms of series/lot identification. The majority of the products (87.4 per cent) have only basic nutritional information with 4.6 per cent of products holding nutritional claims. Consumers with active sport activities showed higher awareness of nutritional information. There were no statistically significant differences between smokers and non-smokers regarding their attitudes toward nutritional information. Age and education play a significant role in ranking nutritional facts. The most important nutritional information is fat content, followed by sugar and vitamins.

Research limitations/implications
– The nature of the study did not allow conclusions regarding causal relationship between food products and consumers as well as if nutritional information affects consumers’ choices and purchasing patronage.

Originality/value
– The findings of this study are worthy, as they report the Serbian consumers’ understanding of labels and nutritional information as well as the status food labels sold in the Serbian market.
The influence of traditional stir-frying with oil on acceptability, antioxidant activities, nutrients, and the phytic acid content of fermented soybean (tempeh)
Authors: Setiawan Budhi , Thamtam Sandeep Kumar , Jati Ignasius Radix AP , Purwestri Ratna Chrismiari , Nohr Donatus , Biesalski Hans Konrad 
Published: March 2016

Purpose– The purpose of this paper was to investigate the acceptability of processed tempeh and the effect of stir-frying on uncooked tempeh composition, total phenolic content (TPC), antioxidant (AO) activities and the phytic acid (PA) concentration.Design/methodology/approach– Fermentation was performed in the solid-state using soybean (Glycine max) inoculated withRhizopus oligosporus. The acceptability of tempeh was evaluated by administering a questionnaire. The TPC of uncooked and stir-fried tempeh was examined using Folin-Ciocalteu’s method, and PA was analyzed by high-performance liquid chromatography. AO activities were measured by the thiobarbituric acid reactive substance (TBARS) and ferric ion reducing/antioxidant power methods. The stir-fried tempeh was more acceptable than other preparations to the panelists.Findings– In comparison with the uncooked tempeh, stir-fried tempeh showed higher fat composition, in addition to decreased levels of minerals, PA and TBARS.Originality/value– Soy foods are an important source of protein. However, conventional cooking methods could change the chemical properties in soy foods. To avoid additional oil that adds calories, consumers might opt for other cooking methods, such as steaming.
Quality characteristics and chemical safety of fried and smoked West Africa Ilisha (Ilisha africana) from Ibadan, Oyo State, Nigeria
Authors: Adeyeye Samuel Ayofemi Olalekan , Oyewole Olusola Bandele , Obadina Adewale Olusegun , Omemu Adebukunola M , Oyedele Hakeem A 
Published: March 2016

Purpose
– This study aims to assess and compare the quality and safety of street-vended, ready-to-eat fried and smoked West African Ilisha fish from the major markets in Ibadan, Oyo State, Nigeria.

Design/methodology/approach
– A total of 50 samples each were obtained from ten major markets in Ibadan, Oyo State, Nigeria. Samples were analyzed in the laboratory for proximate, rancidity indices; i.e. peroxide value (PV), thiobarbituric acid (TBA), total volatile base-nitrogen (TVB-N), trimethylamine acid (TMA) and free fatty acid (FFA), polycyclic aromatic hydrocarbon (PAH) and heavy metals.

Findings
– The results showed that the mean PV (meq. peroxide/kg), TBA (mg Mol/kg), TVB-N (mgN/kg), TMA (mgN/kg) and FFA (%) contents within the fried fish samples ranged from 18.86-23.11, 2.08-2.98, 14.89-17.79, 1.98-2.89 and 2.46-5.98, respectively, while in the case of smoked fish samples, the corresponding contents were found to be 9.03-15.96, 1.03-1.59, 17.29-19.36, 2.15-2.68 and 1.13-1.62, respectively. The results also revealed the presence of PAH compounds in the fried and smoked fish samples. However, majority of the PAH compounds were above 5.0 μg/kg B(a)P maximum permissible levels set by EU Regulation 1881/2006. Concentrations of Hg, Pb, Cd and Cr in the fried and smoked fish samples showed that quantities of these trace heavy metals were below the recommended limits set by the World Health Organization and hence posed no risk to the consumers. The study concluded that consumption of fried and smoked fish may expose consumers to high-level PAH.

Research limitations/implications
– The fried and smoked West African Ilisha fish samples used in this study were obtained from major markets in Ibadan, Oyo State, and there were limitations in getting the same samples with the same treatments in time because of poor and non-established uniform methodology of frying and smoking.

Practical implications
– The paper helps in measuring quality and safety standards of fried and smoked fish products to reduce the incidence of food poison and enhance the health of consumers.

Originality/value
– This research is of value to the traditional fish processors, government agencies responsible for food quality control and assurance as well as consumers, as little work has been done on this product.
Reproductive effort alters immune parameters measured post‐partum in European rabbits under semi‐natural conditions
Authors: Rödel Heiko G. , Zapka Manuela , Stefanski Volker , von Holst Dietrich 
Published: March 2016

SummaryReproduction is energetically costly, and females frequently trade off their reproductive effort with allocation to other physiological processes. One of these processes is the maintenance of a functional immune defence. However, such interactions between immunity and reproduction have rarely been explored in mammals under natural conditions.In our study on females of an individually marked European rabbitOryctolagus cuniculuscolony, we measured different components of the maternal immune system from peripheral blood and serum 1 day after parturition, and we associated variation in these measures with differences in mothers' reproductive effort. We used total litter mass as a measure of the mother's current reproductive effort. In addition, we recorded whether or not mothers gave birth and nursed another litter shortly before and considered this a measure of prior reproductive effort.Mothers with higher current or prior reproductive effort showed generally lower concentrations of white blood cells, in particular neutrophils and lymphocytes, but a higher activity of the complement system and higher IgG serum concentrations than females with lower reproductive effort.We obtained similar results when comparing individual changes in immune parameters measured post‐partum across repeated reproductive events. Cell concentrations of neutrophils and lymphocytes increased when individual females decreased their reproductive effort. In contrast, IgG serum concentrations and the activity of the complement system increased when mothers increased their reproductive effort.In conclusion, the results underline differential responses of different branches of the maternal post‐partum immune system to variation in reproductive effort. On the one hand, our study indicates that females might compromise at least some cellular immune parameters for reproduction. On the other hand, the positive association between IgG concentrations and reproductive effort could be adaptive as a higher litter mass and higher number of pups requires an intensified transfer of this immune parameter via placenta or colostrum and milk. This positive association might constitute an additional, immunological component of the energetic costs of reproduction.Alay summaryis available for this article.
Refining mimicry: phenotypic variation tracks the local optimum
Authors: Mérot Claire , Le Poul Yann , Théry Marc , Joron Mathieu 
Published: March 2016

Summary

Müllerian mimicry between chemically defended preys is a textbook example of natural selection favouring phenotypic convergence onto a shared warning signal. Studies of mimicry have concentrated on deciphering the ecological and genetic underpinnings of dramatic switches in mimicry association, producing a well‐known mosaic distribution of mimicry patterns across geography. However, little is known about the accuracy of resemblance between natural comimics when the local phenotypic optimum varies.

In this study, using analyses of wing shape, pattern and hue, we quantify multimodal phenotypic similarity between butterfly comimics sharing the so‐called postman pattern in different localities with varying species composition.

We show that subtle but consistent variation between populations of the localized species, Heliconius timareta thelxinoe, enhance resemblance to the abundant comimics which drive the mimicry in each locality.

Those results suggest that rarer comimics track the changes in the phenotypic optimum caused by gradual changes in the composition of the mimicry community, providing insights into the process by which intraspecific diversity of mimetic pattern may arise. Furthermore, our results suggest a multimodal evolution of similarity, with coordinated convergence in different features of the phenotype such as wing outline, pattern and hue.

Finally, multilocus genotyping allows estimating local hybridization rates between H. timareta and comimic H. melpomene in different populations, raising the hypothesis that mimicry refinement between closely related comimics may be enhanced by adaptive introgression at loci modifying the accuracy of resemblance.
Long‐term impacts of variable retention harvesting on ground‐layer plant communities in Pinus resinosa forests
Authors: Roberts Margaret W. , D'Amato Anthony W. , Kern Christel C. , Palik Brian J. 
Published: March 2016

Summary

Concerns about loss of biodiversity and structural complexity in managed forests have recently increased and led to the development of new management strategies focused on restoring or maintaining ecosystem functions while also providing wood outputs. Variable retention harvest (VRH) systems, in which mature overstorey trees are retained in various spatial arrangements across harvested areas, represent one potential approach to this problem. However, long‐term evaluations of the effectiveness of this strategy at sustaining plant community composition are needed as this strategy is increasingly applied in managed forest landscapes throughout the world.

The forest ground layer plays a central role in forest ecosystem functioning, and we evaluated the long‐term (11+ year) dynamics in ground‐layer plant communities in response to VRH study in Pinus resinosa Aiton. forests. This large‐scale, manipulative study included four overstorey (control, small gap‐aggregated, large gap‐aggregated and dispersed) and two understorey (ambient and reduced shrubs) treatments replicated four times in 16‐ha stands.

Changes in ground‐layer community composition were apparent 11 years following harvest, regardless of live‐tree retention pattern. Richness and diversity increased and were driven by introduction and colonization of ruderal species, while forest interior species continued to persist across treatments. All life‐forms responded positively to harvest with the exception of moss and clubmoss species.

The lack of effect of spatial pattern of retention on ground‐layer plant communities was likely related to the presence of a dense and persistent shrub layer, a result of decades of fire suppression. In particular, the greatest responses to overstorey retention pattern occurred in areas receiving shrub reduction treatments, indicating this recalcitrant layer likely filtered response to retention pattern.

Synthesis and applications. Overall, this work highlights flexibility in choosing a variable retention harvest approach when sustaining ground‐layer plant community diversity and composition are goals, but altered disturbance regimes (e.g. fire suppression, timber harvesting) that have facilitated the presence or formation of recalcitrant understories, need to be considered. The legacy effects of historical land use and alterations to natural disturbance regimes on the understorey in northern temperate forests are of equal, if not greater, importance to overstorey retention patterns in eliciting desired responses to variable retention harvest and need to be more carefully considered in future applications of this method.
Phylogenetic and functional mechanisms of direct and indirect interactions among alien and native plants
Authors: Feng Yanhao , van Kleunen Mark 
Published: March 2016

Summary

Disentangling direct and indirect interactions among alien and native plants is essential to understanding the success of alien plants in multispecies communities, but studies have only focused on direct pairwise interactions. Moreover, it is also essential to explore phylogenetic and functional mechanisms driving these interactions.

In a greenhouse experiment, we selected nine groups of alien and native plant species from the herbaceous flora of Germany to disentangle their direct and indirect interactions. Each group had an alien (A) that is common or rare in Germany (i.e. non‐native range), two natives that are phylogenetically closely related (Nclose) and distantly related (Ndist) to A respectively, and a distantly related “target” native (T). We grew the four species of each group alone, and in two‐species and three‐species combinations. Specifically, we tested whether competition is greater between A and Nclose than between A and Ndist, whether presence of Nclose rather than Ndist indirectly alleviates competition of A on T, and whether these interaction patterns depend on commonness of A. Moreover, we tested how intensity of these interactions is explained by phylogenetic distance, functional traits (height, seed mass, SLA, leaf size, specific root length, leaf area ratio, root length ratio (root length/plant mass), shoot weight ratio) and traits‐based functional distance.

We found A had stronger competition on Nclose than on Ndist. In turn, A was more suppressed by Nclose than by Ndist, but this was only true for rare rather than common A. The presence of Ndist rather than Nclose indirectly reduced competition of A on T. The intensity of these interactions was not explained by phylogenetic or functional distance, but by some of the functional traits. Specifically, a plant experienced stronger competition when it was shorter and had smaller leaves and lower shoot weight ratio, and when its neighbours were taller, had greater SLA, leaf area ratio and shoot weight ratio, and had a lower root length ratio.

Synthesis. Functional traits can help explain competitive interactions. While direct competition tended to be stronger between more closely related alien and native plants, this did not indirectly facilitate other co‐occurring native plants.
An update on the pharmacokinetics and pharmacodynamics of alisertib, a selective Aurora kinase A inhibitor
Authors: Durlacher Cameron T , Li Zhi‐Ling , Chen Xiao‐Wu , He Zhi‐Xu , Zhou Shu‐Feng 
Published: March 2016

SummaryHuman Aurora kinases, including Aurora kinase A (AURKA), B (AURKB), and C (AURKC), play an essential role in mitotic events such as monitoring of the mitotic checkpoint, creation of bipolar mitotic spindle and alignment of centrosomes on it, also regulating centrosome separation, bio‐orientation of chromosomes and cytokinesis. AURKA and AURKB are key regulators of mitosis and centrosome via polymerizing microfilaments and controlling chromatid segregation. In particular, AURKA plays critical roles in the regulation of mitotic entry, centrosome function, bipolar spindle assembly, and chromosome segregation. AURKA has been found to be overexpressed in various solid and haematological cancers and has been linked with poor prognosis. Its important role in cancer initiation, growth, and metastasis has brought the focus to search for potent and selective AURKA inhibitors for cancer treatment. MLN8237, also known as alisertib, is one selective AURKA inhibitor that has shown remarkable anticancer effects in preclinical studies. Alisertib exhibits favourable pharmacokinetic properties. Alisertib has generally showed good partial response rates of 4–52% and good safety profiles in Phase I and II trials when it is solely administered as well as combined with cytotoxic chemotherapeutic drugs. Recently, the multicentre, randomized Phase III study of alisertib in patients with relapsed or refractory peripheral T‐cell lymphoma has been discontinued due to unsatisfactory efficacy. The low risk of side effects, accessibility, and effectiveness of alisertib makes it a new promising anticancer therapy and further mechanistic and clinical studies are warranted.
RpoS is required for natural transformation of Vibrio cholerae through regulation of chitinases
Authors: Dalia* Ankur B. 
Published: March 2016

SummaryVibrio species naturally reside in the aquatic environment and a major metabolite in this habitat is the chitinous exoskeletons of crustacean zooplankton. In addition to serving as a nutrient, chitin‐derived oligosaccharides also induce natural genetic competence in many Vibrio spp., a physiological state in which bacteria take up DNA from the extracellular environment and can integrate it into their chromosome by homologous recombination. Another inducing cue required for competence are quorum‐sensing autoinducers. The alternative sigma factor RpoS is critical for natural transformation in Vibrio cholerae, and it was previously presumed to exert this effect through regulation of quorum sensing. Here, we show that RpoS does not affect quorum sensing‐dependent regulation of competence. Instead, we show that an rpoS mutant has reduced chitinase activity, which is required to liberate the soluble chitin oligosaccharides that serve as an inducing cue for competence. Consistent with this, we demonstrate that RpoS is required for growth of V. cholerae on insoluble chitin. RpoS also regulates the mucosal escape response in pathogenic strains of V. cholerae. Thus, in addition to promoting egress from its human host, RpoS may also prime this pathogen for successful reentry into the aquatic environment.
Anthropogenic effects on bacterial diversity and function along a river‐to‐estuary gradient in Northwest Greece revealed by metagenomics
Authors: Meziti Alexandra , Tsementzi Despina , Ar. Kormas Konstantinos , Karayanni Hera , Konstantinidis Konstantinos T. 
Published: March 2016

SummaryStudies assessing the effects of anthropogenic inputs on the taxonomic and functional diversity of bacterioplankton communities in lotic ecosystems are limited. Here, we applied 16S rRNA gene amplicon and whole‐genome shotgun sequencing to examine the microbial diversity in samples from the Kalamas River (Northwest Greece), a mid‐size river that runs through agricultural and NATURA‐protected areas, but also receives urban sewage from a large city through a manmade ditch. Samples from three different locations between the exit of the ditch and the estuary, during three different months showed that temporal differences of taxonomic and functional diversity were more pronounced than spatial ones, and <1% of total taxa were shared among all samples, revealing a highly dynamic ecosystem. Comparisons of gene diversity with other aquatic habitats showed that only the high flow winter samples resembled more to freshwater environments while samples during the decreased water flow months were dominated by sewage inputs and soil‐related organisms. Notably, microbial human gut signals were detectable over background freshwater and soil/runoff related signals, even at tens of kilometers downstream the city. These findings revealed the significance of allochthonous inputs on the composition and dynamics of river bacterial communities, and highlighted the potential of metagenomics for source tracking purposes.