bluuebunny/crossref_metadata_2025_split huggingface dataset:
A sRNA in a reduced mutualistic symbiont genome regulates its own gene expression
Authors: Thairu Margaret W. , Cheng Siyuan , Hansen Allison K. 
Published: November 2017

AbstractSimilar to other nutritional endosymbionts that are obligate for host survival, the mutualistic aphid endosymbiont, Buchnera, has a highly reduced genome with few regulatory elements. Until recently, it was thought that aphid hosts were primarily responsible for regulating their symbiotic relationship. However, we recently revealed that Buchnera displays differential protein regulation, but not mRNA expression. We also identified a number of conserved small RNAs (sRNAs) that are expressed among Buchnera taxa. In this study, we investigate whether differential protein regulation in Buchnera is the result of post‐transcriptional gene regulation via sRNAs. We characterize the sRNA profile of two Buchnera life stages: (i) when Buchnera is transitioning from an extracellular proliferating state in aphid embryos and (ii) when Buchnera is in an intracellular nonproliferating state in aphid bacteriocytes (specialized symbiont cells). Overall, we identified 90 differentially expressed sRNAs, 97% of which were upregulated in aphid embryos. Of these sRNAs, the majority were predicted to be involved in the regulation of various metabolic processes, including arginine biosynthesis. Using a heterologous dual expression vector, we reveal for the first time that a Buchnera antisense sRNA can post‐transcriptionally interact with its cognate Buchnera coding sequence, carB, a gene involved in arginine biosynthesis. These results corroborate our in vivo RNAseq and proteomic data, where the candidate antisense sRNA carB and the protein CarB are significantly upregulated in aphid embryos. Overall, we demonstrate that Buchnera may regulate gene expression independently from its host by utilizing sRNAs.
Fungal community reveals less dispersal limitation and potentially more connected network than that of bacteria in bamboo forest soils
Authors: Xiao Xian , Liang Yuting , Zhou Sai , Zhuang Shunyao , Sun Bo 
Published: November 2017

AbstractA central aim of this microbial ecology research was to investigate the mechanisms shaping the assembly of soil microbial communities. Despite the importance of bacterial and fungal mediation of carbon cycling in forest ecosystems, knowledge concerning their distribution patterns and underlying mechanisms remains insufficient. Here, soils were sampled from six bamboo forests across the main planting area of Moso bamboo in southern China. The bacterial and fungal diversities were assessed by sequencing 16SrRNAandITSgene amplicons, respectively, with an Illumina MiSeq. Based on structural equation modelling, dispersal limitation had strongest impact on bacterial beta diversity, while the mean annual precipitation had a smaller impact by directly or indirectly mediating the soil organic carbon density. However, only the mean annual temperature and precipitation played direct roles in fungal beta diversity. Moreover, the co‐occurrence network analyses revealed a possibly much higher network connectivity in the fungal network than in the bacteria. With less dispersal limitation, stronger environmental selection and a potentially more connected network, the fungal community had more important roles in the soil carbon metabolisms in bamboo forests. Fungal beta diversity and the clustering coefficient explained approximately 14.4% and 6.1% of the variation in the carbon metabolic profiles among sites, respectively, but that of bacteria only explained approximately 1.7% and 1.8%, respectively. This study explored soil microbial spatial patterns along with the underlying mechanisms of dispersal limitation, selection and connectivity of ecological networks, thus providing novel insights into the study of the distinct functional traits of different microbial taxa.
Biogeography of mutualistic fungi cultivated by leafcutter ants
Authors: Mueller Ulrich G. , Ishak Heather D. , Bruschi Sofia M. , Smith Chad C. , Herman Jacob J. , Solomon Scott E. , Mikheyev Alexander S. , Rabeling Christian , Scott Jarrod J. , Cooper Michael , Rodrigues Andre , Ortiz Adriana , Brandão Carlos R. F. , Lattke John E. , Pagnocca Fernando C. , Rehner Stephen A. , Schultz Ted R. , Vasconcelos Heraldo L. , Adams Rachelle M. M. , Bollazzi Martin , Clark Rebecca M. , Himler Anna G. , LaPolla John S. , Leal Inara R. , Johnson Robert A. , Roces Flavio , Sosa‐Calvo Jeffrey , Wirth Rainer , Bacci Maurício 
Published: November 2017

AbstractLeafcutter ants propagate co‐evolving fungi for food. The nearly 50 species of leafcutter ants (Atta,Acromyrmex) range from Argentina to the United States, with the greatest species diversity in southern South America. We elucidate the biogeography of fungi cultivated by leafcutter ants usingDNAsequence and microsatellite‐marker analyses of 474 cultivars collected across the leafcutter range. Fungal cultivars belong to two clades (Clade‐A and Clade‐B). The dominant and widespread Clade‐A cultivars form three genotype clusters, with their relative prevalence corresponding to southern South America, northern South America, Central and North America. Admixture between Clade‐A populations supports genetic exchange within a single species,Leucocoprinus gongylophorus. Some leafcutter species that cut grass as fungicultural substrate are specialized to cultivate Clade‐B fungi, whereas leafcutters preferring dicot plants appear specialized on Clade‐A fungi. Cultivar sharing between sympatric leafcutter species occurs frequently such that cultivars ofAttaare not distinct from those ofAcromyrmex. Leafcutters specialized on Clade‐B fungi occur only in South America. Diversity of Clade‐A fungi is greatest in South America, but minimal in Central and North America. Maximum cultivar diversity in South America is predicted by the Kusnezov–Fowler hypothesis that leafcutter ants originated in subtropical South America and only dicot‐specialized leafcutter ants migrated out of South America, but the cultivar diversity becomes also compatible with a recently proposed hypothesis of a Central American origin by postulating that leafcutter ants acquired novel cultivars many times from other nonleafcutter fungus‐growing ants during their migrations from Central America across South America. We evaluate these biogeographic hypotheses in the light of estimated dates for the origins of leafcutter ants and their cultivars.
Arsenic methylation by a novel ArsM As(III) S‐adenosylmethionine methyltransferase that requires only two conserved cysteine residues
Authors: Huang Ke , Xu Yan , Packianathan Charles , Gao Fan , Chen Chuan , Zhang Jun , Shen Qirong , Rosen Barry P. , Zhao Fang‐Jie 
Published: November 2017

SummaryArsenic (As) biomethylation is an important component of the As biogeochemical cycle that can influence As toxicity and mobility in the environment. Biomethylation of As is catalyzed by the enzyme arsenite (As[III]) S‐adenosylmethionine methyltransferase (ArsM). To date, all identified ArsM orthologs with As(III) methylation activities have four conserved cysteine residues, which are thought to be essential for As(III) methylation. Here, we isolated an As(III)‐methylating bacterium, Bacillus sp. CX‐1, and identified a gene encoding a S‐adenosylmethionine methyltranserase termed BlArsM with low sequence similarities (≤ 39%) to other ArsMs. BlArsM has six cysteine residues (Cys10, Cys11, Cys145, Cys193, Cys195 and Cys268), three of which (Cys10, Cys145 and Cys195) align with conserved cysteine residues found in most ArsMs. BlarsM is constitutively expressed in Bacillus sp. CX‐1. Heterologous expression of BlarsM conferred As(III) resistance. Purified BlArsM methylated both As(III) and methylarsenite (MAs[III]), with a final product of dimethylarsenate (DMAs[V]). When all six cysteines were individually altered to serine residues, only C145S and C195S derivatives lost the ability to methylate As(III) and MAs(III). The derivative C10S/C11S/C193S/C268S was still active. These results suggest that BlArsM is a novel As(III) S‐adenosylmethionine methyltransferase requiring only two conserved cysteine residues. A model of As(III) methylation by BlArsM is proposed.
Multiple plasmid‐borne virulence genes of Clavibacter michiganensis ssp. capsici critical for disease development in pepper
Authors: Hwang In Sun , Oh Eom‐Ji , Kim Donghyuk , Oh Chang‐Sik 
Published: November 2017

Summary

Clavibacter michiganensis ssp. capsici is a Gram‐positive plant‐pathogenic bacterium causing bacterial canker disease in pepper. Virulence genes and mechanisms of C. michiganensis ssp. capsici in pepper have not yet been studied.

To identify virulence genes of C. michiganensis ssp. capsici, comparative genome analyses with C. michiganensis ssp. capsici and its related C. michiganensis subspecies, and functional analysis of its putative virulence genes during infection were performed.

The C. michiganensis ssp. capsici type strain PF008 carries one chromosome (3.056 Mb) and two plasmids (39 kb pCM1Cmc and 145 kb pCM2Cmc). The genome analyses showed that this bacterium lacks a chromosomal pathogenicity island and celA gene that are important for disease development by C. michiganensis ssp. michiganensis in tomato, but carries most putative virulence genes in both plasmids. Virulence of pCM1Cmc‐cured C. michiganensis ssp. capsici was greatly reduced compared with the wild‐type strain in pepper. The complementation analysis with pCM1Cmc‐located putative virulence genes showed that at least five genes, chpE, chpG, ppaA1, ppaB1 and pelA1, encoding serine proteases or pectate lyase contribute to disease development in pepper.

In conclusion, C. michiganensis ssp. capsici has a unique genome structure, and its multiple plasmid‐borne genes play critical roles in virulence in pepper, either separately or together.
Identification of perivascular and stromal mesenchymal stem/progenitor cells in porcine endometrium
Authors: Wiater J , Niedziela M , Posmysz A , Wartalski K , Gajda B , Smorąg Z , Rajfur Z , Karasiński J 
Published: November 2017

ContentsMammalian uterus contains a population of mesenchymal stem/progenitor cells that likely contribute to endometrial regeneration during each reproductive cycle. In human and mouse, they reside in perivascular, epithelial and stromal compartments of the endometrial functionalis and basalis. Here, we aimed to identify tissue resident cells expressing mesenchymal stem cell markers CD29, CD44, CD90, CD105, CD140b and CD146 in the porcine endometrium. We used single immunofluorescence and Western blotting. Each of these markers was detected in small cells surrounding endometrial blood vessels. CD105 and CD146 were also expressed in single stromal cells. A few stromal and perivascular cells showed the presence of pluripotency marker Oct4 in the cytoplasm, but not in the nucleus, which may imply they are not truly pluripotent. Endometrial cell cultures were examined for the expression of CD29, CD44, CD90, CD105 and CD140b proteins and tested in wound‐healing assay and culture model of chemotaxis. In conclusion, our results demonstrate perivascular location of prospective mesenchymal stem/progenitor cells in the porcine endometrium and may suggest that stromal CD105+ and CD146+ cells represent more mature precursors originating from their perivascular ancestors.
Estimating the Size and Impact of Affirmative Action in Undergraduate Admissions at the University of Cape Town
Authors: Kerr Andrew , Piraino Patrizio , Ranchhod Vimal 
Published: November 2017

AbstractIn this paper, we estimate the extent and targeting of affirmative action at the University of Cape Town (UCT), a large public university in South Africa. To do this we use admissions data from the UCT, as well as South African population census data and administrative enrolment and graduation data from the South African Department of Higher Education. We find that affirmative action does have a significant effect on the racial distribution of who is made an offer by the university. We also find that affirmative action is well targeted, with those who we estimate to be beneficiaries being of much lower socioeconomic status than those who we estimate are displaced by affirmative action. Beneficiaries of affirmative action have low graduation rates on average, with those beneficiaries who attend UCT being less likely to graduate than those beneficiaries who enrol at other public universities.
Experiences of people with Parkinson's disease and their views of physical activity interventions: a qualitative systematic review protocol
Authors: Hunter Heather , Lovegrove Christopher , Haas Bernhard , Freeman Jennifer , Gunn Hilary 
Published: November 2017

Review question/objectives:
: This review aims to explore the experiences of people with Parkinson's disease (pwPD) participation in physical activity and their views of interventions designed to engage and sustain engagement. Synthesis of the best available evidence will be used to determine any gaps in the research literature and make recommendations on approaches to increase and maintain engagement in physical activity in pwPD living in a community setting. The specific objectives are to:Explore pwPD experiences and preference(s) for physical activity.Explore pwPD perceptions of barriers and enablers to physical activity.Identify, from the perspective of pwPD, the impact of support mechanisms and behavior change interventions in maintaining participation in physical activity.
Emotional intelligence in nurse management and nurse job satisfaction and retention: a scoping review protocol
Authors: Phillips Jacqueline , Harris Janet 
Published: November 2017

Objective:
The objective of this review is to map what is known about emotional intelligence (EI) in relation to staff job satisfaction and retention in nursing, and the tools that are used to measure EI in this context.

Review questions:
The primary question of this review is: What is known about nurse managers’ EI as it relates to staff job satisfaction and retention in nursing?
Sub-question 1: What tools are being used to measure nurse managers’ EI and what theoretical frameworks are they based on?
Sub-question 2: What gaps exist in the research related to nurse managers’ EI as it relates to staff job satisfaction and retention in nursing?
Factors influencing self-management in adults with diabetes: an umbrella review protocol
Authors: Alexandre Ketia , Desrichard Olivier , Burnand Bernard , Peytremann-Bridevaux Isabelle 
Published: November 2017

Review objectives:
The aim of this umbrella review is to identify and describe factors influencing diabetes self-management (DSM) in adults with diabetes. More specifically, we will address DSM-related factors and their relationships, considering both qualitative and quantitative components of available literature.
The review question for the qualitative component of the umbrella review is:i) Which are the factors which act as barriers to, or facilitators of, DSM among adults with diabetes?

The review questions for the quantitative component of the umbrella review are:ii) What are the factors associated with DSM of adults with diabetes?iii) What is the association between the identified factors and DSM in terms of strength and direction?

An additional question will be applied to both the qualitative and quantitative components of the overview:iv) Do the identified factors (barriers or facilitators) vary according to patients’ sociodemographic, illness and treatment characteristics, in terms of type of factors, direction and strength of association?
Regulation of TMEM16A/ANO1 and TMEM16F/ANO6 ion currents and phospholipid scrambling by Ca2+ and plasma membrane lipid
Authors: Schreiber Rainer , Ousingsawat Jiraporn , Wanitchakool Podchanart , Sirianant Lalida , Benedetto Roberta , Reiss Karina , Kunzelmann Karl 
Published: November 2017

Key points
TMEM16 proteins can operate as Ca2+‐activated Cl− channels or scramble membrane phospholipids, which are both highly relevant mechanisms during disease.
Overexpression of TMEM16A and TMEM16F were found to be partially active at 37°C and at resting intracellular Ca2+ concentrations.
We show that TMEM16 Cl− currents and phospholipid scrambling can be activated by modification of plasma membrane phospholipids, through reactive oxygen species and phospholipase A2.
While phospholipids and Cl− ions are likely to use the same pore within TMEM16F, TMEM16A only conducts Cl− ions.
Lipid regulation of TMEM16 proteins is highly relevant during inflammation and regulated cell death such as apoptosis and ferroptosis.
AbstractTMEM16/anoctamin (ANO) proteins form Ca2+‐activated ion channels or phospholipid scramblases. We found that both TMEM16A/ANO1 and TMEM16F/ANO6 produced Cl− currents when activated by intracellular Ca2+, but only TMEM16F was able to expose phosphatidylserine to the outer leaflet of the plasma membrane. Mutations within TMEM16F or TMEM16A/F chimeras similarly changed Cl− currents and phospholipid scrambling, suggesting the same intramolecular pathway for Cl− and phospholipids. When overexpressed, TMEM16A and TMEM16F produced spontaneous Cl− currents at 37°C even at resting intracellular Ca2+ levels, which was abolished by inhibition of phospholipase A2 (PLA2). Connversely, activation of PLA2 or application of active PLA2, as well as lipid peroxidation induced by reactive oxygen species (ROS) using staurosporine or tert‐butyl hydroperoxide, enhanced ion currents by TMEM16A/F and in addition activated phospholipid scrambling by TMEM16F. Thus, TMEM16 proteins are activated by an increase in intracellular Ca2+, or independent of intracellular Ca2+, by modifications occurring in plasma and intracellular membrane phospholipids. These results may help to explain why regions distant to the TMEM16 pore and the Ca2+ binding sites control Cl− currents and phospholipid scrambling. Regulation of TMEM16 proteins through modification of membrane phospholipids occurs during regulated cell death such as apoptosis and ferroptosis. It contributes to inflammatory and nerve injury‐induced hypersensitivity and generation of pain and therefore provides a regulatory mechanism that is particularly relevant during disease.
Systematic Feature Selection Process Applied in Short-Term Data-Driven Building Energy Forecasting Models: A Case Study of a Campus Building
Authors: Zhang Liang , Wen Jin , Chen Yimin 
Published: November 2017

An accurate building energy forecasting model is a key component for real-time and advanced control of building energy system and building-to-grid integration. With the fast deployment and advancement of building automation systems, data are collected by hundreds and sometimes thousands of sensors every few minutes in buildings, which provide great potential for data-driven building energy forecasting.
To develop building energy forecasting models from a large number of potential inputs, feature selection is a critical procedure to ensure model accuracy and computation efficiency. Though the theory of feature selection is well developed in statistics and machine learning fields, it is not well studied in the application of building energy modeling.
In this paper, a feature selection framework proposed in an earlier study is examined using a real campus building in Philadelphia. This feature selection framework combines domain knowledge and statistical methods and is developed for short-term data-driven building energy forecasting. In this case study, the feasibilities of using this feature selection framework in developing whole building energy forecasting model and chiller energy forecasting model are studied.
Results show that, for both whole building and chiller energy forecasting applications, the model with systematic feature selection process presents better performance (in terms of cross validation error of forecasted output) than other models including that with conventional inputs and that uses only single feature selection technique.
Frequency Separation Control of Series Sequential Boosting System With Electric Supercharger and Turbocharger
Authors: Xiao Baitao , Buckland Julia H. , Karnik Amey 
Published: November 2017

To improve transient torque response of an aggressively downsized turbocharged SI engine a series sequential boosting configuration that utilizes an electrically driven supercharger to assist the main turbocharger compressor is controlled in this paper. A frequency separation controller is designed to decouple the dynamics of the multiple-input-single-output (MISO) system. The controller separates the electric supercharger and turbocharger control actions into different frequency bands that are well suited for the characteristics of each device. The controller can be easily implemented with traditional decentralized single input single output (SISO) control loops.
Significant improvements to the baseline turbocharger only system in transient boost pressure response are observed both in simulation and in vehicle test results. Transitions between the electric supercharger and turbocharger are smooth, without noticeable disturbances, with good coordination between electric supercharger and wastegate control actions.
Optimisation of intravenous fluid prescribing: framework for changing practice through education and audits
Authors: Forryan James , Mishra Vinita 
Published: November 2017

IntroductionIntravenous fluids are one of the most commonly prescribed drugs in the hospital setting and yet the practice continues to fall short of National Institute for Health and Care Excellence (NICE) guidelines, with significant gaps in staff knowledge exposing patients to heightened morbidity and mortality.AimFollowing the 2013 publishing of updated NICE guidelines on intravenous fluid prescribing, an intravenous fluid team was formed within the Royal Liverpool University Hospital (RLUH). Their role has been (and continues to be) to overhaul the culture of suboptimal intravenous fluid prescribing within the hospital and, ultimately, to improve patient outcomes. A framework to engender this change has been developed and is offered as an example to other Trusts within which improvement of guideline-compliant intravenous fluid prescribing remains stagnant.MethodThere have been three principal stages of the project to this point which are best demonstrated in a chronological manner. The period of 2010–2014 allowed for assessment of the issue of intravenous fluid prescribing and analysis of its causes through serial audits and a staff-wide survey. From 2015, there has been implementation of several measures (educative, managerial, administrative and technological) within the hospital to foster reproducible and positive change with regards to intravenous fluid prescribing. Finally, between 2016 and 2017, three cycles of a rolling audit based on NICE guidelines have been completed to allow measurement of improvement in intravenous fluid prescribing practice.ConclusionResults have demonstrated a significant improvement in the appropriateness of the intravenous maintenance and replacement fluids prescribed in the hospital since the March 2016 audit. Moreover, a 29-fold increase has been observed in the use of 4% dextrose/0.18% sodium chloride as maintenance fluid (gold standard as per NICE guidelines) since the staff-wide survey of 2015. Despite progress however, adherence to NICE guidelines remains below the recommended 100% and therefore further work remains to be done.