bluuebunny/crossref_metadata_2025 huggingface dataset:
Heart rate and respiration influence on macroscopic blood and CSF flows
Authors: Daouk Joël , Bouzerar Roger , Baledent Olivier
Published: November 2016

Background

Changes in blood volume in the intracranial arteries and the resulting oscillations of brain parenchyma have been presumed as main initiating factors of cerebrospinal fluid (CSF) pulsations. However, respiration has been recently supposed to influence CSF dynamics via thoracic pressure changes.

Purpose

To measure blood and CSF cervical flow and quantify the contribution of cardiac and respiratory cycles on the subsequent signal evolution.

Material and Methods

Sixteen volunteers were enrolled. All participant underwent two-dimensional fast field echo echo planar imaging (FFE-EPI). Regions of interest were placed on internal carotids, jugular veins, and rachidian canal to extract temporal profiles. Spectral analysis was performed to extract respiratory and cardiac frequencies. The contribution of respiration and cardiac activity was assessed to signal evolution by applying a multiple linear model.

Results

Mean respiratory frequency was 14.6 ± 3.9 cycles per min and mean heart rate was 66.8 ± 9 cycles per min. Cardiac contribution was higher than breathing for internal carotids, explaining 74.68% and 10.27% of the signal variance, respectively. For the jugular veins, respiratory component was higher than the cardiac one contributing 44.28% and 6.53% of the signal variance, respectively. For CSF, breathing and cardiac component contributed less than half of signal variance (12.61% and 23.23%, respectively).

Conclusion

Respiration and cardiac activity both influence fluid flow at the cervical level. Arterial inflow is driven by the cardiac pool whereas venous blood aspiration seems more due to thoracic pressure changes. CSF dynamics acts as a buffer between these two blood compartments.
Property study of power transmission system for rotary ultrasonic application
Authors: Chenjun Wu , Shijin Chen , Kai Cheng , Hui Ding
Published: November 2016

Rotary ultrasonic applications are being widely used in machining hard and brittle materials. Conventional conducting ring used as power transmission part limits the ultrasonic applications from rotating at high speed. A high efficiency power transmission system is defined in this article to solve this problem. It consists of a contactless transformer, which was made up of two hollow copper coils, ultrasonic power supply and compensation capacitors. Four compensation methods are proposed and their properties are analyzed through simulations and experiments. The simulations show that S-S compensation is superior to others on the performance of transient and steady circuit parameters and the max transmit efficiency can reach about 97.2% when appropriate compensation method and capacitance are used. Rotary experiments show that speed has little effect on the property of the system.
Nonoperative Versus Operative Treatment of Displaced Ankle Fractures in Diabetics
Authors: Lovy Andrew J. , Dowdell James , Keswani Aakash , Koehler Steven , Kim Jaehon , Weinfeld Steven , Joseph David
Published: November 2016

Background:

Diabetes is a risk factor for complications related to displaced ankle fractures. Limited literature exists comparing complication rates in nonoperative versus operative treatment of displaced ankle fractures in diabetics. No study has highlighted the natural history of nonoperative treatment of displaced ankle fractures in diabetics.

Methods:

We retrospectively reviewed all adult ankle fractures from September 2011 through December 2014. Inclusion was limited to ambulatory adults (>18 years) with closed, displaced (widened mortise) ankle fractures with diabetes mellitus. Nonoperative treatment consisted of closed reduction and casting. Fractures were classified according to the Lauge-Hansen and AO-Weber classification systems. All operative fractures underwent open reduction internal fixation (ORIF) within 3 weeks of injury. Functional outcomes and complication rates were compared. Of 28 displaced diabetic ankle fractures, 20 were treated nonoperatively (closed reduction and casting) and 8 operatively (ORIF within 3 weeks of injury). Mean follow-up was 7 months (range 3-18 months).

Results:

Age, insulin-dependent diabetes, and AO type B fracture rate were similar in nonoperative and operative cohorts, but fracture dislocation rate was significantly higher among operative fractures (87.5% vs 40%; P = .04). Nonoperative treatment was associated with a 21-fold increased odds of complication compared with operative treatment (75% vs 12.5%, OR 21.0, P = .004). Complication rate following unintended ORIF for persistent nonunion or malunion in nonoperatively treated patients was significantly greater compared with immediate ORIF (100% vs 12.5%, P = .005).

Conclusion:

Nonoperative treatment of displaced diabetic ankle fractures was associated with unacceptably high complication rates when compared to operative treatment.

Level of Evidence:

Level III, retrospective comparative series.
Architectural work for modeling and simulation combining the NATO Architecture Framework and C3 Taxonomy
Authors: Hannay Jo Erskine
Published: November 2016

To provide modeling and simulation functionality as services is strategically leveraged in the defense domain and elsewhere. To describe and understand the context, the ecosystem, wherein such services are used and interoperate with other services and capabilities, one needs tools that capture the simulation services themselves as well as the capability landscape they operate in. By using the NATO Consultation, Command, and Control (C3) Taxonomy to structure architecture design in the NATO Architecture Framework (NAF), cohesive descriptions of modeling and simulation capabilities within larger contexts can be given. We show how a basic seven-step approach may benefit architecture work for modeling and simulation at the overarching, reference, and target architectural levels; in particular for (1) hybrid architectures that embed simulation architectures within a larger service-oriented architecture and (2) for architectural design of simulation scenarios. Central to the approach is the use of the C3 Taxonomy as a repository for overarching architecture building blocks and patterns. We conclude that the promotion of technical functionality as capabilities in their own right helps delineate simulation environment boundaries, helps delineate services within and outside the boundary, and is an enabler for defining the service concepts in cloud-based approaches to modeling and simulation as a service (MSaaS).
A Year in Review
Authors: Pritchett Amy R.
Published: November 2016

Reviewing the articles within this journal in 2016 reveals a diverse set of approaches and applications but consistent themes: first, translating practice to science and, second, translating science to practice. The first theme addresses the difficulty in understanding cognitive performance in complex work environments. For this, we need improved models of the myriad activities of workers in complex operations—recognizing that experts will adapt their behavior and need to respond to unexpected situations. Many of this year’s articles note the need for multiple perspectives, for integrating multiple theories, and for recognizing that all parts of cognitive behavior are independent and, thus, no one factor can be isolated. The second theme, translating science to practice, then addresses the difficulty in applying this knowledge to improved designs. Such designs may focus on the worker (e.g., training), on processes and procedures, or on technology—regardless, they serve to translate understanding into implementation. A range of design approaches and insights are proposed in this year’s articles, in domains ranging from rugby to aviation, health care, accident analysis, and autonomous systems.
Gelsolin expression in liver, spleen and blood plasma provides insights into its function in mice following acute insults
Authors: Fu Haiyan , Du Hongyang , Hu Zhansheng , Ying Xiudong , Zhou Rongbin
Published: November 2016

Background:

Gelsolin (GSN) is an actin-binding plasma protein with a pivotal role in the systemic response to acute tissue damage. The present study investigated GSN expression in the liver, spleen and blood serum in mice after burn.

Method:

A murine model of thermal injury was selected, and the animals were sacrificed at 8, 24, 48 and 72 h after injury. Real-time quantitative polymerase chain reaction (RT-PCR) was performed to determine the messenger RNA (mRNA) expression of GSN, and GSN protein expression was determined by enzyme-linked immunosorbent assay (ELISA).

Results:

We found that GSN mRNA and protein were expressed in the liver, spleen and blood serum of the mice. GSN expression in these tissues was the lowest among the tested time points at 8 h after burn injury. The mortality within 72 h among the mice subjected to burn injury was significantly lower in those treated with GSN than in those not treated with GSN. Treatment with GSN markedly increased the GSN levels in the liver, spleen and blood serum after injury.

Conclusion:

These results indicated that GSN treatment may affect the outcome of thermal injury via changes in the GSN content of multiple tissues.
Sex Differences in Anthropometrics and Heading Kinematics Among Division I Soccer Athletes
Authors: Bretzin Abigail C. , Mansell Jamie L. , Tierney Ryan T. , McDevitt Jane K.
Published: November 2016

Background:

Soccer players head the ball repetitively throughout their careers; this is also a potential mechanism for a concussion. Although not all soccer headers result in a concussion, these subconcussive impacts may impart acceleration, deceleration, and rotational forces on the brain, leaving structural and functional deficits. Stronger neck musculature may reduce head-neck segment kinematics.

Hypothesis:

The relationship between anthropometrics and soccer heading kinematics will not differ between sexes. The relationship between anthropometrics and soccer heading kinematics will not differ between ball speeds.

Study Design:

Pilot, cross-sectional design.

Level of Evidence:

Level 3.

Methods:

Division I soccer athletes (5 male, 8 female) were assessed for head-neck anthropometric and neck strength measurements in 6 directions (ie, flexion, extension, right and left lateral flexions and rotations). Participants headed the ball 10 times (25 or 40 mph) while wearing an accelerometer secured to their head. Kinematic measurements (ie, linear acceleration and rotational velocity) were recorded at 2 ball speeds.

Results:

Sex differences were observed in neck girth ( t = 5.09, P < 0.001), flexor and left lateral flexor strength ( t = 3.006, P = 0.012 and t = 4.182, P = 0.002, respectively), and rotational velocity at both speeds ( t = −2.628, P = 0.024 and t = −2.227, P = 0.048). Neck girth had negative correlations with both linear acceleration ( r = −0.599, P = 0.031) and rotational velocity at both speeds ( r = −0.551, P = 0.012 and r = −0.652, P = 0.016). Also, stronger muscle groups had lower linear accelerations at both speeds ( P < 0.05).

Conclusion:

There was a significant relationship between anthropometrics and soccer heading kinematics for sex and ball speeds.

Clinical Relevance:

Neck girth and neck strength are factors that may limit head impact kinematics.
Oxygen treatment of critically ill children: A lack of evidence
Authors: Soini Ulla Marie , Clarke Sara , Solberg Marianne Trygg
Published: November 2016

In hospitals, oxygen is the most frequently administered medication to pediatric in-patients. Too much oxygen in arterial blood is not a natural occurrence, consequently hyperoxia can be caused by healthcare providers. The aim of this scoping study was to synthesize evidence that could contribute to safe and appropriate oxygen treatment in children 0–3 years of age. The method was in line with Arksey and O’Malley’s framework, and 11 research articles regarding oxygen treatment were included. The main results are presented as three key findings: 1) overview of assessing the need for oxygen based on the use of pulse oximetry, 2) overview of oxygen treatment, and 3) overview of the need for educational intervention. In conclusion, there is a shortage of research literature to guide nurses in assessment of oxygen requirements, and administration of oxygen treatment in critically ill children. Consensus and guidelines are needed, as there are variations in practice regarding oxygen treatment.
Adolescents’ Implicit Theories of Peer Relationships and Their School Adjustment
Authors: Cheung Cecilia S. , Wang Cixin , Monroy Jorge A. , Couch Lauren
Published: November 2016

This research examined the interplay between adolescents’ implicit theories about peer relationships and their academic adjustment; the mediating role of adolescents’ disclosure to parents and the moderating role of their victimization experience were evaluated. Five hundred and forty adolescents (253 girls; mean age = 13.5 years, SD = 0.67) reported on their incremental (vs. entity) views about peer relationships, disclosure to parents about their everyday activities, and their victimization experience in school. Grades were obtained from official school records. Adolescents who held heightened incremental views about peer relationships disclosed more to their parents—especially when they experienced victimization in school. Incremental views were associated with grades, regardless of victimization experience. The association between incremental views and grades was in part explained by adolescents’ disclosure to parents.
Development of Novel Formulas to Determine Hospital and Pharmacy Opportunities to Reduce Extended Length of Stay
Authors: Hansen Kevin N. , Morbitzer Kathryn A. , Waldron Kayla M. , Amerine Lindsey B.
Published: November 2016

Background: Hospital length of stay (LOS) is an important measure to determine resource utilization and efficiency of care for inpatients. No existing objective methodology is available to determine where and how pharmacy departments can have maximal impact on reducing extended LOS. Objective: An objective methodology to guide decisions by hospital pharmacy departments on reducing extended LOS is described. Methods: University of North Carolina Medical Center’s LOS was compared to hospitals with similar inpatient bed size and case mix index. Objective methodology using pharmacy intensity weight, LOS index, and relative number of cases overall and by hospital service was developed to identify targets of impacting LOS for a pharmacy department. Results: The novel Pharmacy Opportunity Length of Stay (POLOS) formula was developed to prioritize each Medicare Severity Diagnosis Related Group (MSDRG) based on the overall impact pharmacy can have on reducing extended LOS at an individual institution. An additional novel formula, Service Specific POLOS (SSPOLOS), was created to strategically target hospital services, as opposed to MSDRGs, allowing for effective deployment of targeted pharmacy interventions to decrease extended LOS. Conclusion: POLOS and SSPOLOS are novel formulas to guide pharmacy departments in objectively prioritizing and targeting resources to reduce extended LOS. The novel formulas can be used to quantify LOS performance at the hospital and pharmacy specific levels, in addition to providing a hospital service approach to launch LOS initiatives at health care institutions. To our knowledge, this represents the first opportunity for hospital pharmacy departments to objectively target and reduce extended LOS.
Comments on: fold change rank ordering statistics: a new method for detecting differentially expressed genes
Authors: Dembélé Doulaye , Kastner Philippe
Published: November 2016

We published a new method (BMC Bioinformatics 2014, 15:14) for searching for differentially expressed genes from two biological conditions datasets. The presentation of theorem 1 in this paper was incomplete. We received an anonymous comment about our publication that motivates the present work. Here, we present a complementary result which is necessary from the theoretical point of view to demonstrate our theorem. We also show that this result has no negative impact on our conclusions obtained with synthetic and experimental microarrays datasets.
Assessing genotype-phenotype associations in three dorsal colour morphs in the meadow spittlebug Philaenus spumarius (L.) (Hemiptera: Aphrophoridae) using genomic and transcriptomic resources
Authors: Rodrigues Ana S. B. , Silva Sara E. , Pina-Martins Francisco , Loureiro João , Castro Mariana , Gharbi Karim , Johnson Kevin P. , Dietrich Christopher H. , Borges Paulo A. V. , Quartau José A. , Jiggins Chris D. , Paulo Octávio S. , Seabra Sofia G.
Published: November 2016

Background

Colour polymorphisms are common among animal species. When combined with genetic and ecological data, these polymorphisms can be excellent systems in which to understand adaptation and the molecular changes underlying phenotypic evolution. The meadow spittlebug, Philaenus spumarius (L.) (Hemiptera, Aphrophoridae), a widespread insect species in the Holarctic region, exhibits a striking dorsal colour/pattern balanced polymorphism. Although experimental crosses have revealed the Mendelian inheritance of this trait, its genetic basis remains unknown. In this study we aimed to identify candidate genomic regions associated with the colour balanced polymorphism in this species.

Results

By using restriction site-associated DNA (RAD) sequencing we were able to obtain a set of 1,837 markers across 33 individuals to test for associations with three dorsal colour phenotypes (typicus, marginellus, and trilineatus). Single and multi-association analyses identified a total of 60 SNPs associated with dorsal colour morphs. The genome size of P. spumarius was estimated by flow cytometry, revealing a 5.3 Gb genome, amongst the largest found in insects. A partial genome assembly, representing 24% of the total size, and an 81.4 Mb transcriptome, were also obtained. From the SNPs found to be associated with colour, 35% aligned to the genome and 10% to the transcriptome. Our data suggested that major loci, consisting of multi-genomic regions, may be involved in dorsal colour variation among the three dorsal colour morphs analysed. However, no homology was found between the associated loci and candidate genes known to be responsible for coloration pattern in other insect species. The associated markers showed stronger differentiation of the trilineatus colour phenotype, which has been shown previously to be more differentiated in several life-history and physiological characteristics as well. It is possible that colour variation and these traits are linked in a complex genetic architecture.

Conclusions

The loci detected to have an association with colour and the genomic and transcriptomic resources developed here constitute a basis for further research on the genetic basis of colour pattern in the meadow spittlebug P. spumarius.
HIV sero-discordance among married HIV patients initiating anti-retroviral therapy in northern Vietnam
Authors: Van Tam Vu , Cuong Do Duy , Alfven Tobias , Phuc Ho Dang , Chuc Nguyen Thi Kim , Hoa Nguyen Phuong , Diwan Vinod , Larsson Mattias
Published: November 2016

Background

In many countries in Asia, the HIV epidemic is in a concentrated phase, with high prevalence in certain risk groups, such as men who inject drugs. There is also a rapid increase of HIV among women. The latter might be due to high levels of sero-discordant couples and increasing transmission from male to female partners over time.

Methods

All adult married patients initiating antiretroviral treatment at four out-patient clinics in Quang Ninh province in north-eastern Vietnam between 2007 and 2009 were asked to participate in the study. Clinical information was extracted from patients’ records, and a structured questionnaire was used to collect social, demographic and economic data.

Results

Two hundred eighty-eight married patients for whom information on the HIV status of their spouse was available were included in the study. Overall, the sero-discordance rate was 58%. The sero-discordance rate was significantly higher among married males, 71% had spouses not infected, than married females, of whom 18% had spouses not infected. Other factors associated with a high rate of sero-discordance were injection drug use (IDU) history, tuberculosis (TB) history and the availability of voluntary counselling and testing (VCT) in residential locations. High sero-concordance was associated with college/university education.

Conclusion

The sero-discordance was significantly higher among married males than married females. Other factors also related to high sero-discordance were history of IDU, history of TB and the availability of VCT in residential locations. In contrast, college/university education and female sex were significantly related to low sero-discordance. To contain the increasing HIV prevalence among women, measures should be taken to prevent transmission among sero-discordant couples.

Trial registrationNCT01433601
Changes in cerebral glucose metabolism after 3 weeks of noninvasive electrical stimulation of mild cognitive impairment patients
Authors: Yun Kyongsik , Song In-Uk , Chung Yong-An
Published: November 2016

Background

Mild cognitive impairment (MCI) is a syndrome that disrupts an individual’s cognitive function but preserves activities of daily living. MCI is thought to be a prodromal stage of dementia, which disrupts patients’ daily lives and causes severe cognitive dysfunction. Although extensive clinical trials have attempted to slow or stop the MCI to dementia conversion, the results have been largely unsuccessful. The purpose of this study was to determine whether noninvasive electrical stimulation of MCI changes glucose metabolism.

Methods

Sixteen MCI patients participated in this study. We used transcranial direct current stimulation (tDCS) (2 mA/day, three times per week for 3 weeks) and assessed positron emission tomography (18 F-FDG) before and after 3 weeks of stimulation.

Results

We showed that regular and relatively long-term use of tDCS significantly increased regional cerebral metabolism in MCI patients. Furthermore, subjective memory satisfaction and improvement of the memory strategies of participants were observed only in the real tDCS group after 3 weeks of stimulation.

Conclusion

Our findings suggest that neurophysiological intervention of MCI could improve glucose metabolism and transient memory function in MCI patients.
What is the effect of prescribed burning in temperate and boreal forest on biodiversity, beyond tree regeneration, pyrophilous and saproxylic species? A systematic review protocol
Authors: Eales Jacqualyn , Haddaway Neal R. , Bernes Claes , Cooke Steven J. , Jonsson Bengt Gunnar , Kouki Jari , Petrokofsky Gill
Published: November 2016

Background

Forests set aside from productive forestry are often considered best conserved by non-intervention. However, biodiversity is often maintained in natural forests by a background level of disturbance, which, in some forests, takes the form of forest fires. Set-aside forests may therefore benefit from continuation of such disturbances, which, in forests under protection, must be managed anthropogenically. While the effects of prescribed burning on tree regeneration and on pyrophilous and/or saproxylic species in some regions are well known, effects on other organisms are less clear and/or consistent. It would be valuable to broaden the knowledge of how prescribed burning affects forest biodiversity, particularly because this practice is increasingly considered as a conservation management intervention. The primary aim of the proposed systematic review is to clarify how biodiversity is affected by prescribed burning in temperate and boreal forests. The ultimate purpose of the review is to investigate whether and how such prescribed burning may be useful as a means of conserving or restoring biodiversity, beyond that of pyrophilous and saproxylic species, in forest set-asides.

Methods

The review will examine primary field studies of how prescribed burning affects biodiversity in boreal and temperate forests. We will consider studies made in such forests anywhere in the world, and will include forests both in protected areas and under commercial management. Non-intervention will be used as a comparator. Relevant outcomes will include a range of measures of biodiversity, including abundance and diversity, but not of pyrophilous and saproxylic species. Relevant studies will be taken from a recent systematic map of the evidence on biodiversity impacts of active management in forests set aside for conservation or restoration. Additional searches and a search update will be undertaken in a subset of databases from the systematic map, using a search string targeted to identify studies focused on prescribed burning interventions. Searches for additional literature will be made in the bibliographies of existing reviews of forest burning. Traditional academic literature and grey literature in English, French, Swedish and Finnish will be considered. Stakeholders who engage in prescribed burning will be asked to provide relevant grey literature.
One-and-a-half nostril endoscopic transsphenoidal approach for pituitary adenomas—a technical report
Authors: Wen Guodao , Tang Chao , Zhong Chunyu , Li Junyang , Cong Zixiang , Zhou Yuan , Liu Kaidong , Zhang Yong , Tohti Mamatemin , Ma Chiyuan
Published: November 2016

Background

Binostril endoscopic transsphenoidal approach (BETA) provides sufficient manipulation space and wide endoscopic vision, although it increases the trauma of nose. Mononostril endoscopic transsphenoidal approach (META) has minimal trauma of nose, at the expense of space within the operation. We describe a one-and-a-half nostril endoscopic transsphenoidal approach (OETA) that combines the advantages of BETA and META.

Methods

We introduced OETA for pituitary adenomas with a detailed technical description. A retrospective analysis was also performed on 57 consecutive patients who underwent one-and-a-half nostril endoscopic transsphenoidal surgery between March 2014 and June 2015 at Jinling hospital.

Results

The gross total resection rate was 79%. The gross complete resection rate of Knosp grade 3 tumors were 63.6, and 27.3% in grade 4 tumors. Postoperative hormone remission was achieved in 14 out of 18 (77.8%) patients with secreting adenomas. Postoperative abnormal visual function improvement was achieved in 23 out of 32 patients (73%) with preoperative visual dysfunction. The overall intra-operative CSF leak was 17.5%, with the postoperative CSF leak decreased to 3.5% after the sellar reconstruction with the unilateral “rescue” nasoseptal flap procedure. The main sinonasal complaints 2 weeks after surgery were: loss of sense of smell (28%), decrease in sense of taste (4%), trouble breathing during the day (18%), thick nasal discharge (36%), post nasal discharge (8%), dried nasal material (6%), and headache (6%). Three months after surgery, there were no reports of decrease of taste, post nasal discharge, or dried nasal material. Other complaints were decreased significantly. Six months after surgery, the main complaints of sinonasal quality of life were negligible, and overall health status was near complete recovery to preoperative status.

Conclusions

The one-and-a-half nostril endoscopic transsphenoidal approach for pituitary adenomas is a simple and reliable technique. It provides not only a sufficient surgical corridor for a 2-surgeon/4 or 3-hands technique, but also ensures minimal invasion of the nasal canal.
The impact of transposable elements on mammalian development
Authors: Garcia-Perez Jose L. , Widmann Thomas J. , Adams Ian R.
Published: November 2016

Despite often being classified as selfish or junk DNA, transposable elements (TEs) are a group of abundant genetic sequences that have a significant impact on mammalian development and genome regulation. In recent years, our understanding of how pre-existing TEs affect genome architecture, gene regulatory networks and protein function during mammalian embryogenesis has dramatically expanded. In addition, the mobilization of active TEs in selected cell types has been shown to generate genetic variation during development and in fully differentiated tissues. Importantly, the ongoing domestication and evolution of TEs appears to provide a rich source of regulatory elements, functional modules and genetic variation that fuels the evolution of mammalian developmental processes. Here, we review the functional impact that TEs exert on mammalian developmental processes and discuss how the somatic activity of TEs can influence gene regulatory networks.
SIRT1 inhibits EV71 genome replication and RNA translation by interfering with the viral polymerase and 5′UTR RNA
Authors: Han Yang , Wang Lvyin , Cui Jin , Song Yu , Luo Zhen , Chen Junbo , Xiong Ying , Zhang Qi , Liu Fang , Ho Wenzhe , Liu Yingle , Wu Kailang , Wu Jianguo
Published: November 2016

Enterovirus 71 (EV71) possesses a single-stranded positive RNA genome that contains a single open reading frame (ORF) flanked by a 5′ untranslated region (5′UTR) and a polyadenylated 3′UTR. Here, we demonstrated that EV71 activates the production of silent mating type information regulation 2 homolog 1 (SIRT1), a histone deacetylase (HDAC). EV71 further stimulates SIRT1 sumoylation and deacetylase activity, and enhances SIRT1 translocation from the nucleus to the cytoplasm. More interestingly, activated SIRT1 subsequently binds with the EV71 3Dpol protein (a viral RNA-dependent RNA polymerase, RdRp) to repress the acetylation and RdRp activity of 3Dpol, resulting in the attenuation of viral genome replication. Moreover, SIRT1 interacts with the cloverleaf structure of the EV71 RNA 5′UTR to inhibit viral RNA transcription, and binds to the internal ribosome entry site (IRES) of the EV71 5′UTR to attenuate viral RNA translation. Thus, EV71 stimulates SIRT1 production and activity, which in turn represses EV71 genome replication by inhibiting viral polymerase, and attenuates EV71 RNA transcription and translation by interfering with viral RNA. These results uncover a new function of SIRT1 and reveal a new mechanism underlying the regulation of EV71 replication.
SeqPlots - Interactive software for exploratory data analyses, pattern discovery and visualization in genomics
Authors: Stempor Przemyslaw , Ahringer Julie
Published: November 2016

Experiments involving high-throughput sequencing are widely used for analyses of chromatin function and gene expression. Common examples are the use of chromatin immunoprecipitation for the analysis of chromatin modifications or factor binding, enzymatic digestions for chromatin structure assays, and RNA sequencing to assess gene expression changes after biological perturbations. To investigate the pattern and abundance of coverage signals across regions of interest, data are often visualized as profile plots of average signal or stacked rows of signal in the form of heatmaps. We found that available plotting software was either slow and laborious or difficult to use by investigators with little computational training, which inhibited wide data exploration. To address this need, we developed SeqPlots, a user-friendly exploratory data analysis (EDA) and visualization software for genomics. After choosing groups of signal and feature files and defining plotting parameters, users can generate profile plots of average signal or heatmaps clustered using different algorithms in a matter of seconds through the graphical user interface (GUI) controls. SeqPlots accepts all major genomic file formats as input and can also generate and plot user defined motif densities. Profile plots and heatmaps are highly configurable and batch operations can be used to generate a large number of plots at once. SeqPlots is available as a GUI application for Mac or Windows and Linux, or as an R/Bioconductor package. It can also be deployed on a server for remote and collaborative usage. The analysis features and ease of use of SeqPlots encourages wide data exploration, which should aid the discovery of novel genomic associations.
A new Plasmodium vivax reference sequence with improved assembly of the subtelomeres reveals an abundance of pir genes
Authors: Auburn Sarah , Böhme Ulrike , Steinbiss Sascha , Trimarsanto Hidayat , Hostetler Jessica , Sanders Mandy , Gao Qi , Nosten François , Newbold Chris I. , Berriman Matthew , Price Ric N. , Otto Thomas D.
Published: November 2016

Plasmodium vivaxis now the predominant cause of malaria in the Asia-Pacific, South America and Horn of Africa. Laboratory studies of this species are constrained by the inability to maintain the parasite in continuousex vivoculture, but genomic approaches provide an alternative and complementary avenue to investigate the parasite’s biology and epidemiology. To date, molecular studies ofP. vivaxhave relied on the Salvador-I reference genome sequence, derived from a monkey-adapted strain from South America. However, the Salvador-I reference remains highly fragmented with over 2500 unassembled scaffolds.  Using high-depth Illumina sequence data, we assembled and annotated a new reference sequence, PvP01, sourced directly from a patient from Papua Indonesia. Draft assemblies of isolates from China (PvC01) and Thailand (PvT01) were also prepared for comparative purposes. The quality of the PvP01 assembly is improved greatly over Salvador-I, with fragmentation reduced to 226 scaffolds. Detailed manual curation has ensured highly comprehensive annotation, with functions attributed to 58% core genes in PvP01 versus 38% in Salvador-I. The assemblies of PvP01, PvC01 and PvT01 are larger than that of Salvador-I (28-30 versus 27 Mb), owing to improved assembly of the subtelomeres.  An extensive repertoire of over 1200Plasmodiuminterspersed repeat (pir) genes were identified in PvP01 compared to 346 in Salvador-I, suggesting a vital role in parasite survival or development. The manually curated PvP01 reference and PvC01 and PvT01 draft assemblies are important new resources to study vivax malaria. PvP01 is maintained at GeneDB and ongoing curation will ensure continual improvements in assembly and annotation quality.
RNF4 interacts with multiSUMOylated ETV4
Authors: Aguilar-Martinez Elisa , Guo Baoqiang , Sharrocks Andrew D.
Published: November 2016

Protein SUMOylation represents an important regulatory event that changes the activities of numerous proteins. Recent evidence demonstrates that polySUMO chains can act as a trigger to direct the ubiquitin ligase RNF4 to substrates to cause their turnover through the ubiquitin pathway. RNF4 uses multiple SUMO interaction motifs (SIMs) to bind to these chains. However, in addition to polySUMO chains, a multimeric binding surface created by the simultaneous SUMOylation of multiple residues on a protein or complex could also provide a platform for the recruitment of multi-SIM proteins like RNF4. Here we demonstrate that multiSUMOylated ETV4 can bind to RNF4 and that a unique combination of SIMs is required for RNF4 to interact with this multiSUMOylated platform. Thus RNF4 can bind to proteins that are either polySUMOylated through a single site or multiSUMOylated on several sites and raises the possibility that such multiSIM-multiSUMO interactions might be more widespread.
Hierarchical Bayesian inference for ion channel screening dose-response data
Authors: Johnstone Ross H , Bardenet Rémi , Gavaghan David J , Mirams Gary R
Published: November 2016

Dose-response (or ‘concentration-effect’) relationships commonly occur in biological and pharmacological systems and are well characterised by Hill curves. These curves are described by an equation with two parameters: the inhibitory concentration 50% (IC50); and the Hill coefficient. Typically just the ‘best fit’ parameter values are reported in the literature. Here we introduce a Python-based software tool, PyHillFit, and describe the underlying Bayesian inference methods that it uses, to infer probability distributions for these parameters as well as the level of experimental observation noise. The tool also allows for hierarchical fitting, characterising the effect of inter-experiment variability. We demonstrate the use of the tool on a recently published dataset on multiple ion channel inhibition by multiple drug compounds. We compare the maximum likelihood, Bayesian and hierarchical Bayesian approaches. We then show how uncertainty in dose-response inputs can be characterised and propagated into a cardiac action potential simulation to give a probability distribution on model outputs.
Hepitopes: A live interactive database of HLA class I epitopes in hepatitis B virus
Authors: Lumley Sheila , Noble Howard , Hadley Martin J. , Callow Liz , Malik Amna , Chua Yi Yi , Duffey Owen J. , Grolmusova Natalia , Kumar Arvind , Ravenscroft Samuel , Spencer Jonathan I. , Neumann-Haefelin Christoph , Thimme Robert , Andersson Monique , Klenerman Paul , Barnes Eleanor , Matthews Philippa C.
Published: November 2016

Increased clinical and scientific scrutiny is being applied to hepatitis B virus (HBV), with focus on the development of new therapeutic approaches, ultimately aiming for cure. Defining the optimum natural CD8+ T cell immune responses that arise in HBV, mediated by HLA class I epitope presentation, may help to inform novel immunotherapeutic strategies. Therefore, we have set out to develop a comprehensive database of these epitopes in HBV, coined ‘Hepitopes’. This undertaking has its foundations in a systematic literature review to identify the sites and sequences of all published class I epitopes in HBV. We also collected information regarding the methods used to define each epitope, and any reported associations between an immune response to this epitope and disease outcome. The results of this search have been collated into a new open-access interactive database that is available athttp://www.expmedndm.ox.ac.uk/hepitopes. Over time, we will continue to refine and update this resource, as well as inviting contributions from others in the field to support its development. This unique new database is an important foundation for ongoing investigations into the nature and impact of the CD8+ T cell response to HBV.
Identifying genes required for respiratory growth of fission yeast
Authors: Malecki Michal , Bähler Jürg
Published: November 2016

We have used both auxotroph and prototroph versions of the latest deletion-mutant library to identify genes required for respiratory growth on solid glycerol medium in fission yeast. This data set complements and enhances our recent study on functional and regulatory aspects of energy metabolism by providing additional proteins that are involved in respiration. Most proteins identified in this mutant screen have not been implicated in respiration in budding yeast. We also provide a protocol to generate a prototrophic mutant library, and data on technical and biological reproducibility of colony-based high-throughput screens.
The process of change in nursing audit
Authors: Malby Rebecca
Published: November 2016

This article reviews the current literature on change in nursing audit in order to develop a strategy for nursing staff. It suggests that the model for change will affect the nature of the measurement phase of audit, and proposes that an open systems model be adopted and a change agent incorporated to manage the audit cycle.
Em busca da integração de ações governamentais no planejamento regional: o caso do Promeso
Authors: Rocha Neto João Mendes
Published: November 2016

As políticas públicas têm sido estudadas a partir de diferentes aspectos teóricos e técnicos, mas ainda persiste uma lacunaenvolvendo questões diversas relacionadas à intersetorialidade e à integração de ações das agências governamentais. Esteartigo buscou identificar onde esse caráter disjunto se manifesta, partindo da literatura sobre intersetorialidade para entãoexplicitar, através de pesquisa documental, a dissociação entre a oficialidade da ação coordenada e a prática da implementaçãofragmentada. Para tanto, além do debate teórico que incorpora categorias diversas da ciência política, da administraçãopública, das políticas públicas, da geografia e da economia, debruçou-se sobre fontes secundárias, utilizando bases dedados das diferentes agências governamentais para o levantamento de dados. Assim, a proposta deste artigo é contribuirpara a construção de uma metodologia que possibilite compreender alguns limites dessa atuação intersetorial partindo dedimensões pouco tratadas nos estudos.
Especialização versus diversificação: economias de aglomeração e seus impactos sobre os salários industriais em Minas Gerais
Authors: Dalberto Cassiano Ricardo , Cirino Jader Fernandes , Staduto Jefferson Andronio Ramundo
Published: November 2016

Este trabalho investiga a relação entre as economias de aglomeração – subdivididas em economias de especialização e urbanização – e os salários industriais dos municípios do estado de Minas Gerais entre 2001 e 2011. A análise se utilizou da regressão econométrica espacial e da análise exploratória de dados espaciais a fim de verificar a importância do caráter geográfico e os padrões regionais da distribuição das variáveis. Encontraram-se evidências da presença de economias de aglomeração, principalmente de especialização, de forma que salários mais elevados tendem a estar associados às cidades onde a indústria é mais especializada.
A experiência e mais dez: uma estratégia para vencer na Champions League
Authors: Scharf Edson Roberto , Sousa Richard Perassi Luiz de , Sarquis Aléssio Bessa , Belz Elton
Published: November 2016

O objetivo deste estudo é analisar as relações entre a marca Ford e a competição europeia de futebol Champions League do ponto de vista da experiência, tendo por base a Teoria do Comportamento Planejado, de Ajzen. Foram realizadas entrevistas com executivos responsáveis pela operação que envolve a Ford e a Champions League, analisadas por meio da técnica de análise de conteúdo. Os resultados demonstraram que a Ford concentra a quase totalidade de seu budget no patrocínio desse grande evento esportivo anual do mundo, sendo compreendido como ação central em sua estratégia de branding, e que a experiência tem sido o mote utilizado para obter reconhecimento da marca e aperfeiçoar seu capital de marca e seu relacionamento.
Gestão colaborativa em cadeias de suprimentos: um estudo bibliométrico
Authors: Vitorino Filho Valdir Antonio , Pires Silvio Roberto Ignácio , Argoud Ana Rita Tiradentes Terra , Simon Alexandre Tadeu
Published: November 2016

Este artigo tem como objetivo principal analisar a produção acadêmica internacional sobre a gestão colaborativa em cadeias de suprimentos em artigos publicados em periódicos internacionais indexados no ISI Web of Knowledge. A pesquisa abrangeu um período de dez anos (2005-2014), com 63 artigos analisados, utilizando técnicas bibliométricas para analisar ano de publicação, periódicos em que esses artigos foram publicados, autores com maior número de publicação, artigos mais acessados, e a identificação das principais obras em gestão colaborativa em cadeias de suprimentos. Os resultados da pesquisa indicam que não há predominância de publicações em poucos periódicos, e que há muitos autores com apenas um artigo publicado sobre o tema.
Cenários do ramo de materiais de construção civil na cidade de Toledo/PR: percepções frente à crise de 2015
Authors: Carvalho Leonardo de , Endo Gustavo Yuho , Rojo Claudio Antonio
Published: November 2016

O presente estudo objetivou analisar a percepção de cenários de dois empresários do ramo de materiais de construção civil na cidade de Toledo, oeste do Paraná, por meio das cinco forças competitivas de Porter e da matriz SWOT. Empregou-se a análise de conteúdo temática de duas entrevistas semiestruturadas, utilizando-se para isso o software ATLAS.ti. Este estudo permitiu demonstrar que ambos tiveram uma perspectiva realista e otimista quanto aos cenários futuros no ramo de materiais de construção civil para a cidade de Toledo, diferente da perspectiva pessimista que vem se desenvolvendo no cenário econômico e político nacional. É importante ressaltar que, nos dois casos, o que corrobora para esta visão está vinculado à percepção de que a economia regional, baseada no agronegócio e na indústria farmacêutica, ainda não foi diretamente afetada pela crise.
Phylogenetic analysis of Indonesian gandaria (Bouea) using molecular markers of cpDNA trnL-F intergenic spacer
Authors: HARSONO TRI , PASARIBU NURSAHARA , SOBIR SOBIR , FITMAWATI FITMAWATI , PRASETYA EKO
Published: November 2016

Abstract. Harsono T, Pasaribu N, Sobir, Fitmawati, Prasetya E.2017. Phylogenetic analysis of Indonesian gandaria (Bouea) using molecular markers of cpDNA trnL-F intergenic spacer. Biodiversitas 18: 51-57.Genus Bouea is a member of the Family Anacardiaceae which is widespread in Malesia region. Genus Bouea consists of two types, namely, B. oppositifolia (Roxb.) Adelb. and B. macrophylla Griffit. This study aims to uncover the genetic diversity of Bouea in Indonesia based on molecular markers of cpDNA trnL-F intergenic spacer. The samples of genetic material analyzed are 7 accessions of B. oppositifolia and 8 accessions of B. macrophylla coming from the collection of the Bogor Botanical Gardens and the field exploration activity in Sumatra, Java, Kalimantan and Ambon, and Anacardium occidentale and Mangifera indica are also used as an out-group comparator. Based on phylogenetic analysis using the maximum parsimony and neighbor-joining method, genus Bouea is a monophyletic group or is derived from the same ancestor. Bouea derived from Gunung Tua, North Sumatra, has the longest branch and showed up earlier than the other sample so it can be considered that the ancestor of genus Bouea. B. oppositifolia has branches longer and show up early so it can be considered the ancestor of B. macrophylla. Both types of genera Bouea grouped separately in the phylogenetic tree and supports grouping types in genera Bouea. The results of phylogenetic tree construction do not indicate a geographical grouping of accession. Based on the phylogenetic tree, genus Bouea has a closer relationship with Anacardium occidentale compared with Mangifera indica. The results showed that the markers cpDNA trnL-F intergenic spacer effectively used to determine relationship in genus Bouea.

Keywords: Bouea, cpDNA, gandaria, phylogenetic, trnL-F intergenic spacer
Estimating Mill Residue Surplus in Canada: A Spatial Forest Fiber Cascade Modeling Approach
Authors: Ghafghazi Saeed , Lochhead Kyle , Mathey Anne-Helen , Forsell Nicklas , Leduc Sylvain , Mabee Warren , Bull Gary
Published: November 2016

The potential development of a Canadian forest-based bioeconomy requires an assessment of both fiber availability and associated marginal supply costs. To a large extent, the bioeconomy is expected to rely on wood fiber made available through primary products, sawnwood, and pulp production processing streams. Therefore, it is important to understand the regional wood fiber flows and mill residue availability through various processing streams. In this study, we developed a spatially explicit Forest Fiber Cascade Model (FCM) to estimate regional fiber flows and availability of untapped residue surplus. The FCM was calibrated to 2013 production levels, and we evaluated the wood fiber cascade through existing forest industry in Canada. The results show that, under current conditions, there is limited availability of surplus mill residues in Canada, especially in the Eastern provinces. It is therefore critical to consider the impacts on regional fiber flows and feedstock availability to the secondary industries when designing feedstock supply strategies and policies for the emerging forest-based industries.