bluuebunny/crossref_metadata_2025 huggingface dataset:
The genome of black raspberry (Rubus occidentalis)
Authors: VanBuren Robert , Bryant Doug , Bushakra Jill M. , Vining Kelly J. , Edger Patrick P. , Rowley Erik R. , Priest Henry D. , Michael Todd P. , Lyons Eric , Filichkin Sergei A. , Dossett Michael , Finn Chad E. , Bassil Nahla V. , Mockler Todd C.
Published: May 2016

Black raspberry (Rubus occidentalis) is an important specialty fruit crop in the US Pacific Northwest that can hybridize with the globally commercialized red raspberry (R. idaeus). Here we report a 243 Mb draft genome of black raspberry that will serve as a useful reference for the Rosaceae and Rubus fruit crops (raspberry, blackberry, and their hybrids). The black raspberry genome is largely collinear to the diploid woodland strawberry (Fragaria vesca) with a conserved karyotype and few notable structural rearrangements. Centromeric satellite repeats are widely dispersed across the black raspberry genome, in contrast to the tight association with the centromere observed in most plants. Among the 28 005 predicted protein‐coding genes, we identified 290 very recent small‐scale gene duplicates enriched for sugar metabolism, fruit development, and anthocyanin related genes which may be related to key agronomic traits during black raspberry domestication. This contrasts patterns of recent duplications in the wild woodland strawberry F. vesca, which show no patterns of enrichment, suggesting gene duplications contributed to domestication traits. Expression profiles from a fruit ripening series and roots exposed to Verticillium dahliae shed insight into fruit development and disease response, respectively. The resources presented here will expedite the development of improved black and red raspberry, blackberry and other Rubus cultivars.
Todos Sacrifican: Immigrant Organizing and the Meanings of (Domestic) Work
Authors: Rosenbaum Susanna
Published: May 2016

Domestic service is one of the few available jobs open to Mexican and Central American immigrant women, individuals who have migrated to the US to escape poverty in their home countries. Economic inequalities between countries are mirrored in a growing split within the US, where immigrant women have become the serving classes that sustain the lifestyles of the (native‐born) professional and managerial workforce. In LA, immigrant women often take up domestic work, remaining in jobs where they do not earn enough and experience daily humiliations. In this paper, I examine two groups that seek to mitigate the most abusive aspects of paid domestic employment in Los Angeles. Although they address significant and enduring issues, neither group is entirely successful. I ask how immigrant domestic workers define themselves, their experiences in the United States, and their jobs—and how these understandings affect the functioning of both groups.
Meshing Efficiency Analysis of Two Degree-of-Freedom Epicyclic Gear Trains
Authors: Lauibi Esmail Essam
Published: May 2016

The concept of potential power efficiency is introduced as the efficiency of an epicyclic gear train (EGT) measured in any moving reference frame. The conventional efficiency can be computed in a carrier-moving reference frame in which the gear carrier appears relatively fixed. In principle, by attaching the reference frame to an appropriate link, torques can be calculated with respect to each input, output, or (relatively) fixed link in the EGT. Once the power flow direction is obtained from the potential power ratio, the torque ratios are obtained from the potential power efficiencies, the particular expression of the efficiency of the EGT is found in a simple manner. A systematic methodology for the efficiency analysis of one and two degree-of-freedom (DOF) EGTs is described, and 14 ready-to-use efficiency formulas are derived for 2DOF gear pair entities (GPEs). This paper includes also a discussion on the redundancy of the efficiency formulas used for 1DOF GPEs. An incomplete in the efficiency formulas in previous literature, which make them susceptible to wrong application, is brought to light.
Configuration Robustness Analysis of the Optimal Design of Cable-Driven Manipulators
Authors: Bryson Joshua T. , Jin Xin , Agrawal Sunil K.
Published: May 2016

Designing an effective cable architecture for a cable-driven robot becomes challenging as the number of cables and degrees of freedom of the robot increase. A methodology has been previously developed to identify the optimal design of a cable-driven robot for a given task using stochastic optimization. This approach is effective in providing an optimal solution for robots with high-dimension design spaces, but does not provide insights into the robustness of the optimal solution to errors in the configuration parameters that arise in the implementation of a design. In this work, a methodology is developed to analyze the robustness of the performance of an optimal design to changes in the configuration parameters. This robustness analysis can be used to inform the implementation of the optimal design into a robot while taking into account the precision and tolerances of the implementation. An optimized cable-driven robot leg is used as a motivating example to illustrate the application of the configuration robustness analysis. Following the methodology, the effect on robot performance due to design variations is analyzed, and a modified design is developed which minimizes the potential performance degradations due to implementation errors in the design parameters. A robot leg is constructed and is used to validate the robustness analysis by demonstrating the predicted effects of variations in the design parameters on the performance of the robot.
Comparison of Three-Dimensional Multidomain and Single-Domain Models for the Horizontal Solidification Problem
Authors: Avnaim M. H. , Levy A. , Mikhailovich B. , Ben-David O. , Azulay A.
Published: May 2016

In this paper, horizontal solidification of gallium in a rectangular cavity was studied both experimentally and numerically. Two three-dimensional (3D) numerical models related to different numerical approaches were built. The first is a single-domain (SD) model based on the volume-of-fluid (VOF) method. This model also takes into account the presence of a mushy zone. The second model is a multidomain (MD) one; it includes two different meshes for the two phases and uses Stephan's boundary condition to determine the front velocity. The 3D models were tested under various thermal boundary conditions and compared with experimental results obtained in an appropriate experimental setup. The experimental setup included an ultrasonic Doppler velocimeter (UDV) for noninvasive measurements of the velocities in the liquid part of the metal, liquid–solid interface position and profile, its displacement, and longitudinal mean velocity. For determining the boundary influence, both 3D and 2D models were built. The comparison was carried out for the solidification front location and shape and the velocity and temperature fields. In general, the 3D numerical model gave more accurate results than the 2D model with respect to the experiments results. Although the MD model is more complicated to build and requires more computational efforts than the VOF model, the 3D MD model provides the most accurate results in comparison with current experiments.
Shooting for a star
Authors: Merali Zeeya
Published: May 2016

Internet billionaire explains his plan to send very small spaceships a very long way.
The battery builder
Authors: Service Robert F.
Published: May 2016

Yi Cui is pioneering efforts to use nanotechnology to revolutionize battery design, and just perhaps save the world.
New particle formation in the free troposphere: A question of chemistry and timing
Authors: Bianchi F. , Tröstl J. , Junninen H. , Frege C. , Henne S. , Hoyle C. R. , Molteni U. , Herrmann E. , Adamov A. , Bukowiecki N. , Chen X. , Duplissy J. , Gysel M. , Hutterli M. , Kangasluoma J. , Kontkanen J. , Kürten A. , Manninen H. E. , Münch S. , Peräkylä O. , Petäjä T. , Rondo L. , Williamson C. , Weingartner E. , Curtius J. , Worsnop D. R. , Kulmala M. , Dommen J. , Baltensperger U.
Published: May 2016

From neutral to new

Many of the particles in the troposphere are formed in situ, but what fraction of all tropospheric particles do they constitute and how exactly are they made? Bianchi
et al.
report results from a high-altitude research station. Roughly half of the particles were newly formed by the condensation of highly oxygenated multifunctional compounds. A combination of laboratory results, field measurements, and model calculations revealed that neutral nucleation is more than 10 times faster than ion-induced nucleation, that particle growth rates are size-dependent, and that new particle formation occurs during a limited time window.

Science
, this issue p.
1109
Biosynthesis of a broad-spectrum nicotianamine-like metallophore in
Staphylococcus aureus
Authors: Ghssein Ghassan , Brutesco Catherine , Ouerdane Laurent , Fojcik Clémentine , Izaute Amélie , Wang Shuanglong , Hajjar Christine , Lobinski Ryszard , Lemaire David , Richaud Pierre , Voulhoux Romé , Espaillat Akbar , Cava Felipe , Pignol David , Borezée-Durant Elise , Arnoux Pascal
Published: May 2016

A new metal scavenger for bacteria

All cells must find a way to acquire trace metals. Bacteria and plants scavenge iron, for instance, by synthesizing and releasing iron-chelating compounds called siderophores. Ghssein
et al.
describe three enzymes in
Staphylococcus aureus
that are responsible for the biosynthesis of another type of metallophore (see the Perspective by Nolan). Metabolomics and a range of biochemical assays show that this compound, named staphylopine, is involved in the uptake of a range of metals, depending on the growth environment. The genes required for staphylopine biosynthesis are conserved across a number of pathogenic bacteria and are similar to those for a broad-spectrum metallophore produced by plants.

Science
, this issue p.
1105
; see also p.
1055
Serological Monitoring Is Key To Sustain Progress of the Maternal and Neonatal Tetanus Elimination Initiative
Authors: Levine Myron M. , Pasetti Marcela F.
Published: May 2016

In this issue of
Clinical and Vaccine Immunology
, Scobie and colleagues (H. M. Scobie et al., Clin Vaccine Immunol 23:546–554, 2016,
http://dx.doi.org/10.1128/CVI.00052-16
) report a nationwide serosurvey of tetanus immunity in >2,000 Cambodian women of child-bearing age to monitor progress toward maternal and neonatal tetanus elimination. This commentary discusses vaccines as interventions for disease control, elimination, and eradication and emphasizes the importance of the tools needed to monitor the effectiveness of initiatives that deliver the vaccines programmatically.
Genomic and Phenotypic Analyses Reveal the Emergence of an Atypical Salmonella enterica Serovar Senftenberg Variant in China
Authors: Abd El Ghany Moataz , Shi Xiaolu , Li Yinghui , Ansari Hifzur R. , Hill-Cawthorne Grant A. , Ho Y. S. , Naeem Raeece , Pickard Derek , Klena John D. , Xu Xuebing , Pain Arnab , Hu Qinghua
Published: May 2016

Human infections with
Salmonella enterica
subspecies
enterica
serovar Senftenberg are often associated with exposure to poultry flocks, farm environments, or contaminated food. The recent emergence of multidrug-resistant isolates has raised public health concerns. In this study, comparative genomics and phenotypic analysis were used to characterize 14
Salmonella
Senftenberg clinical isolates recovered from multiple outbreaks in Shenzhen and Shanghai, China, between 2002 and 2011. Single-nucleotide polymorphism analyses identified two phylogenetically distinct clades of
S
. Senftenberg, designated SC1 and SC2, harboring variations in
Salmonella
pathogenicity island 1 (SPI-1) and SPI-2 and exhibiting distinct biochemical and phenotypic signatures. Although the two variants shared the same serotype, the SC2 isolates of sequence type 14 (ST14) harbored intact SPI-1 and -2 and hence were characterized by possessing efficient invasion capabilities. In contrast, the SC1 isolates had structural deletion patterns in both SPI-1 and -2 that correlated with an impaired capacity to invade cultured human cells and also the year of their isolation. These atypical SC1 isolates also lacked the capacity to produce hydrogen sulfide. These findings highlight the emergence of atypical
Salmonella
Senftenberg variants in China and provide genetic validation that variants lacking SPI-1 and regions of SPI-2, which leads to impaired invasion capacity, can still cause clinical disease. These data have identified an emerging public health concern and highlight the need to strengthen surveillance to detect the prevalence and transmission of nontyphoidal
Salmonella
species.
Rapid Drug Susceptibility Testing of Drug-Resistant Mycobacterium tuberculosis Isolates Directly from Clinical Samples by Use of Amplicon Sequencing: a Proof-of-Concept Study
Authors: Colman Rebecca E. , Anderson Julia , Lemmer Darrin , Lehmkuhl Erik , Georghiou Sophia B. , Heaton Hannah , Wiggins Kristin , Gillece John D. , Schupp James M. , Catanzaro Donald G. , Crudu Valeriu , Cohen Ted , Rodwell Timothy C. , Engelthaler David M.
Published: May 2016

Increasingly complex drug-resistant tuberculosis (DR-TB) is a major global health concern and one of the primary reasons why TB is now the leading infectious cause of death worldwide. Rapid characterization of a DR-TB patient's complete drug resistance profile would facilitate individualized treatment in place of empirical treatment, improve treatment outcomes, prevent amplification of resistance, and reduce the transmission of DR-TB. The use of targeted next-generation sequencing (NGS) to obtain drug resistance profiles directly from patient sputum samples has the potential to enable comprehensive evidence-based treatment plans to be implemented quickly, rather than in weeks to months, which is currently needed for phenotypic drug susceptibility testing (DST) results. In this pilot study, we evaluated the performance of amplicon sequencing of
Mycobacterium tuberculosis
DNA from patient sputum samples using a tabletop NGS technology and automated data analysis to provide a rapid DST solution (the Next Gen-RDST assay). One hundred sixty-six out of 176 (94.3%) sputum samples from the Republic of Moldova yielded complete Next Gen-RDST assay profiles for 7 drugs of interest. We found a high level of concordance of our Next Gen-RDST assay results with phenotypic DST (97.0%) and pyrosequencing (97.8%) results from the same clinical samples. Our Next Gen-RDST assay was also able to estimate the proportion of resistant-to-wild-type alleles down to mixtures of ≤1%, which demonstrates the ability to detect very low levels of resistant variants not detected by pyrosequencing and possibly below the threshold for phenotypic growth methods. The assay as described here could be used as a clinical or surveillance tool.
Comparison of Two Widely Used Human Papillomavirus Detection and Genotyping Methods, GP5+/6+-Based PCR Followed by Reverse Line Blot Hybridization and Multiplex Type-Specific E7-Based PCR
Authors: Clifford Gary M. , Vaccarella Salvatore , Franceschi Silvia , Tenet Vanessa , Umulisa M. Chantal , Tshomo Ugyen , Dondog Bolormaa , Vorsters Alex , Tommasino Massimo , Heideman Daniëlle A. M. , Snijders Peter J. F. , Gheit Tarik
Published: May 2016

GP5+/6+-based PCR followed by reverse line blot hybridization (GP5+/6+RLB) and multiplex type-specific PCR (E7-MPG) are two human papillomavirus (HPV) genotyping methodologies widely applied in epidemiological research. We investigated their relative analytical performance in 4,662 samples derived from five studies in Bhutan, Rwanda, and Mongolia coordinated by the International Agency for Research on Cancer (IARC). A total of 630 samples were positive by E7-MPG only (13.5%), 24 were positive by GP5+/6+RLB only (0.5%), and 1,014 were positive (21.8%) by both methods. Ratios of HPV type-specific positivity of the two tests (E7-MPG:GP5+/6+RLB ratio) were calculated among 1,668 samples that were HPV positive by one or both tests. E7-MPG:GP5+/6+RLB ratios were >1 for all types and highly reproducible across populations and sample types. E7-MPG:GP5+/6+RLB ratios were highest for HPV53 (7.5) and HPV68 (7.1). HPV16 (1.6) and HPV18 (1.7) had lower than average E7-MPG:GP5+/6+RLB ratios. Among E7-MPG positive infections, median mean fluorescence intensity (MFI; a semiquantitative measure of viral load) tended to be higher among samples positive for the same virus type by GP5+/6+RLB than for those negative for the same type by GP5+/6+RLB. Exceptions, however, included HPV53, -59, and -82, for which the chances of being undetected by GP5+/6+RLB appeared to be MFI independent. Furthermore, the probability of detecting an additional type by E7-MPG was higher when another type was already detected by GP5+/6+RLB, suggesting the existence of masking effects due to competition for GP5+/6+ PCR primers. In conclusion, this analysis is not an evaluation of clinical performance but may inform choices for HPV genotyping methods in epidemiological studies, when the relative merits and dangers of sensitivity versus specificity for individual types should be considered, as well as the potential to unmask nonvaccine types following HPV vaccination.
Multiplex Real-Time PCR Assay with High-Resolution Melting Analysis for Characterization of Antimicrobial Resistance in Neisseria gonorrhoeae
Authors: Donà Valentina , Kasraian Sara , Lupo Agnese , Guilarte Yuvia N. , Hauser Christoph , Furrer Hansjakob , Unemo Magnus , Low Nicola , Endimiani Andrea
Published: May 2016

Resistance to antibiotics used against
Neisseria gonorrhoeae
infections is a major public health concern. Antimicrobial resistance (AMR) testing relies on time-consuming culture-based methods. Development of rapid molecular tests for detection of AMR determinants could provide valuable tools for surveillance and epidemiological studies and for informing individual case management. We developed a fast (<1.5-h) SYBR green-based real-time PCR method with high-resolution melting (HRM) analysis. One triplex and three duplex reactions included two sequences for
N. gonorrhoeae
identification and seven determinants of resistance to extended-spectrum cephalosporins (ESCs), azithromycin, ciprofloxacin, and spectinomycin. The method was validated by testing 39 previously fully characterized
N. gonorrhoeae
strains, 19 commensal
Neisseria
species strains, and an additional panel of 193 gonococcal isolates. Results were compared with results of culture-based AMR determination. The assay correctly identified
N. gonorrhoeae
and the presence or absence of the seven AMR determinants. There was some cross-reactivity with nongonococcal
Neisseria
species, and the detection limit was 10
3
to 10
4
genomic DNA (gDNA) copies/reaction. Overall, the platform accurately detected resistance to ciprofloxacin (sensitivity and specificity, 100%), ceftriaxone (sensitivity, 100%; specificity, 90%), cefixime (sensitivity, 92%; specificity, 94%), azithromycin (sensitivity and specificity, 100%), and spectinomycin (sensitivity and specificity, 100%). In conclusion, our methodology accurately detects mutations that generate resistance to antibiotics used to treat gonorrhea. Low assay sensitivity prevents direct diagnostic testing of clinical specimens, but this method can be used to screen collections of gonococcal isolates for AMR more quickly than current culture-based AMR testing.
Targeted Mutagenesis of Guinea Pig Cytomegalovirus Using CRISPR/Cas9-Mediated Gene Editing
Authors: Bierle Craig J. , Anderholm Kaitlyn M. , Wang Jian Ben , McVoy Michael A. , Schleiss Mark R.
Published: May 2016

The cytomegaloviruses (CMVs) are among the most genetically complex mammalian viruses, with viral genomes that often exceed 230 kbp. Manipulation of cytomegalovirus genomes is largely performed using infectious bacterial artificial chromosomes (BACs), which necessitates the maintenance of the viral genome in
Escherichia coli
and successful reconstitution of virus from permissive cells after transfection of the BAC. Here we describe an alternative strategy for the mutagenesis of guinea pig cytomegalovirus that utilizes clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9)-mediated genome editing to introduce targeted mutations to the viral genome. Transient transfection and drug selection were used to restrict lytic replication of guinea pig cytomegalovirus to cells that express Cas9 and virus-specific guide RNA. The result was highly efficient editing of the viral genome that introduced targeted insertion or deletion mutations to nonessential viral genes. Cotransfection of multiple virus-specific guide RNAs or a homology repair template was used for targeted, markerless deletions of viral sequence or to introduce exogenous sequence by homology-driven repair. As CRISPR/Cas9 mutagenesis occurs directly in infected cells, this methodology avoids selective pressures that may occur during propagation of the viral genome in bacteria and may facilitate genetic manipulation of low-passage or clinical CMV isolates.

IMPORTANCE
The cytomegalovirus genome is complex, and viral adaptations to cell culture have complicated the study of infection
in vivo
. Recombineering of viral bacterial artificial chromosomes enabled the study of recombinant cytomegaloviruses. Here we report the development of an alternative approach using CRISPR/Cas9-based mutagenesis in guinea pig cytomegalovirus, a small-animal model of congenital cytomegalovirus disease. CRISPR/Cas9 mutagenesis can introduce the same types of mutations to the viral genome as bacterial artificial chromosome recombineering but does so directly in virus-infected cells. CRISPR/Cas9 mutagenesis is not dependent on a bacterial intermediate, and defined viral mutants can be recovered after a limited number of viral genome replications, minimizing the risk of spontaneous mutation.
Effects of MF59 Adjuvant on Induction of Isotype-Switched IgG Antibodies and Protection after Immunization with T-Dependent Influenza Virus Vaccine in the Absence of CD4
+
T Cells
Authors: Ko Eun-Ju , Lee Young-Tae , Kim Ki-Hye , Jung Yu-Jin , Lee Youri , Denning Timothy L. , Kang Sang-Moo
Published: May 2016

CD4
+
T cells play a central role in orchestrating adaptive immunity. To better understand the roles of CD4
+
T cells in the effects of adjuvants, we investigated the efficacy of a T-dependent influenza virus split vaccine with MF59 or alum in CD4 knockout (CD4KO) and wild-type (WT) mice. CD4
+
T cells were required for the induction of IgG antibody responses to the split vaccine and the effects of alum adjuvant. In contrast, MF59 was found to be highly effective in raising isotype-switched IgG antibodies to a T-dependent influenza virus split vaccine in CD4KO mice or CD4-depleted WT mice equivalent to those in intact WT mice, thus overcoming the deficiency of CD4
+
T cells in helping B cells and inducing immunity against influenza virus. Vaccination with the MF59-adjuvanted influenza virus vaccine was able to induce protective CD8
+
T cells and long-lived antibody-secreting cells in CD4KO mice. The effects of MF59 adjuvant in CD4KO mice might be associated with uric acid, inflammatory cytokines, and the recruitment of multiple immune cells at the injection site, but their cellularity and phenotypes were different from those in WT mice. These findings suggest a new paradigm of CD4-independent adjuvant mechanisms, providing the rationales to improve vaccine efficacy in infants, the elderly, immunocompromised patients, as well as healthy adults.

IMPORTANCE
MF59-adjuvanted influenza vaccines were licensed for human vaccination, but the detailed mechanisms are not fully elucidated. CD4
+
T cells are required to induce antibody isotype switching and long-term memory responses. In contrast, we discovered that MF59 was highly effective in inducing isotype-switched IgG antibodies and long-term protective immune responses to a T-dependent influenza vaccine independent of CD4
+
T cells. These findings are highly significant for the following reasons: (i) MF59 can overcome a defect of CD4
+
T cells in inducing protective immunity to vaccination with a T-dependent influenza virus vaccine; (ii) a CD4-independent pathway can be an alternative mechanism for certain adjuvants such as MF59; and (iii) this study has significant implications for improving vaccine efficacies in young children, the elderly, and immunocompromised populations.
A Genome-Wide RNA Interference Screen Identifies a Role for Wnt/β-Catenin Signaling during Rift Valley Fever Virus Infection
Authors: Harmon Brooke , Bird Sara W. , Schudel Benjamin R. , Hatch Anson V. , Rasley Amy , Negrete Oscar A.
Published: May 2016

Rift Valley fever virus (RVFV) is an arbovirus within the
Bunyaviridae
family capable of causing serious morbidity and mortality in humans and livestock. To identify host factors involved in bunyavirus replication, we employed genome-wide RNA interference (RNAi) screening and identified 381 genes whose knockdown reduced infection. The Wnt pathway was the most represented pathway when gene hits were functionally clustered. With further investigation, we found that RVFV infection activated Wnt signaling, was enhanced when Wnt signaling was preactivated, was reduced with knockdown of β-catenin, and was blocked using Wnt signaling inhibitors. Similar results were found using distantly related bunyaviruses La Crosse virus and California encephalitis virus, suggesting a conserved role for Wnt signaling in bunyaviral infection. We propose a model where bunyaviruses activate Wnt-responsive genes to regulate optimal cell cycle conditions needed to promote efficient viral replication. The findings in this study should aid in the design of efficacious host-directed antiviral therapeutics.

IMPORTANCE
RVFV is a mosquito-borne bunyavirus that is endemic to Africa but has demonstrated a capacity for emergence in new territories (e.g., the Arabian Peninsula). As a zoonotic pathogen that primarily affects livestock, RVFV can also cause lethal hemorrhagic fever and encephalitis in humans. Currently, there are no treatments or fully licensed vaccines for this virus. Using high-throughput RNAi screening, we identified canonical Wnt signaling as an important host pathway regulating RVFV infection. The beneficial role of Wnt signaling was observed for RVFV, along with other disparate bunyaviruses, indicating a conserved bunyaviral replication mechanism involving Wnt signaling. These studies supplement our knowledge of the fundamental mechanisms of bunyavirus infection and provide new avenues for countermeasure development against pathogenic bunyaviruses.
Improving documentation of clinical care within a clinical information network: an essential initial step in efforts to understand and improve care in Kenyan hospitals
Authors: Tuti Timothy , Bitok Michael , Malla Lucas , Paton Chris , Muinga Naomi , Gathara David , Gachau Susan , Mbevi George , Nyachiro Wycliffe , Ogero Morris , Julius Thomas , Irimu Grace , English Mike
Published: May 2016

In many low income countries health information systems are poorly equipped to provide detailed information on hospital care and outcomes. Information is thus rarely used to support practice improvement. We describe efforts to tackle this challenge and to foster learning concerning collection and use of information. This could improve hospital services in Kenya.

We are developing a Clinical Information Network, a collaboration spanning 14 hospitals, policy makers and researchers with the goal of improving information available on the quality of inpatient paediatric care across common childhood illnesses in Kenya. Standardised data from hospitals' paediatric wards are collected using non-commercial and open source tools. We have implemented procedures for promoting data quality which are performed prior to a process of semi-automated analysis and routine report generation for hospitals in the network.

In the first phase of the Clinical Information Network, we collected data on over 65 000 admission episodes. Despite clinicians' initial unfamiliarity with routine performance reporting, we found that, as an initial focus, both engaging with each hospital and providing them information helped improve the quality of data and therefore reports. The process has involved mutual learning and building of trust in the data and should provide the basis for collaborative efforts to improve care, to understand patient outcome, and to evaluate interventions through shared learning.

We have found that hospitals are willing to support the development of a clinically focused but geographically dispersed Clinical Information Network in a low-income setting. Such networks show considerable promise as platforms for collaborative efforts to improve care, to provide better information for decision making, and to enable locally relevant research.
Reactions and coping strategies in lay rescuers who have provided CPR to out-of-hospital cardiac arrest victims: a qualitative study
Authors: Mathiesen Wenche Torunn , Bjørshol Conrad Arnfinn , Braut Geir Sverre , Søreide Eldar
Published: May 2016

Objective

Cardiopulmonary resuscitation (CPR) provided by community citizens is of paramount importance for out-of-hospital cardiac arrest (OHCA) victims' survival. Fortunately, CPR rates by community citizens seem to be rising. However, the experience of providing CPR is rarely investigated. The aim of this study was to explore reactions and coping strategies in lay rescuers who have provided CPR to OHCA victims.

Methods, participants

This is a qualitative study of 20 lay rescuers who have provided CPR to 18 OHCA victims. We used a semistructured interview guide focusing on their experiences after providing CPR.

Setting

The study was conducted in the Stavanger region of Norway, an area with very high bystander CPR rates.

Results

Three themes emerged from the interview analysis: concern, uncertainty and coping strategies. Providing CPR had been emotionally challenging for all lay rescuers and, for some, had consequences in terms of family and work life. Several lay rescuers experienced persistent mental recurrences of the OHCA incident and had concerns about the outcome for the cardiac arrest victim. Unknown or fatal outcomes often caused feelings of guilt and were particularly difficult to handle. Several reported the need to be acknowledged for their CPR attempts. Health-educated lay rescuers seemed to be less affected than others. A common coping strategy was confiding in close relations, preferably the health educated. However, some required professional help to cope with the OHCA incident.

Conclusions

Lay rescuers experience emotional and social challenges, and some struggle to cope in life after providing CPR in OHCA incidents. Experiencing a positive patient outcome and being a health-educated lay rescuer seem to mitigate concerns. Common coping strategies are attempts to reduce uncertainty towards patient outcome and own CPR quality. Further studies are needed to determine whether an organised professional follow-up can mitigate the concerns and uncertainty of lay rescuers.
School and seasonality in youth suicide: evidence from Japan
Authors: Matsubayashi Tetsuya , Ueda Michiko , Yoshikawa Kanako
Published: May 2016

Background

Seasonality in youth suicide has been speculated to be associated with the school calendar, as it tends to increase at the beginning of the academic year or after a long break, but robust empirical evidence remains scarce.

Methods

We examined the nationwide death records in the Vital Statistics of Japan to investigate the seasonal patterns of suicide among youth. Our data set included 108 968 suicides by individuals who died at 6–26 years of age between 1974 and 2014 in Japan. The daily frequencies of death were plotted against the Japanese school calendar, which has little regional and temporal variations. We also estimated a Poisson regression model to uncover the cyclical patterns of suicide deaths.

Results

We found that the frequencies of suicide by middle school students (ages 12–15 years) and high school students (ages 15–18 years) sharply increased around the dates when a school session began in April and September. These tended to be low during school breaks. The results of regression analysis suggested middle school students were more than twice as likely to die by suicide when the summer break ended and the second semester began, compared with the baseline week in July. Similarly, the frequency of suicide for high school students also increased by ∼40% at the end of the summer break. Importantly, no such pattern was found for those aged 18–26 years.

Conclusions

Our findings strongly indicate that the cyclical pattern of youth suicide is closely related to the school calendar.
What is nature capable of? Evidence, ontology and speculative medical humanities
Authors: Savransky Martin , Rosengarten Marsha
Published: May 2016

Expanding on the recent call for a ‘critical medical humanities’ to intervene in questions of the ontology of health, this article develops a what we call a ‘speculative’ orientation to such interventions in relation to some of the ontological commitments on which contemporary biomedical cultures rest. We argue that crucial to this task is an approach to ontology that treats it not as a question of first principles, but as a matter of the consequences of the images of nature that contemporary biomedical research practices espouse when they make claims to evidence, as well as the possible consequences of imagining different worlds in which health and disease processes partake. By attending to the implicit ontological assumptions involved in the method par excellence of biomedical research, namely the randomised controlled trial (RCT), we argue that the mechanistic ontology that tacitly informs evidence-based biomedical research simultaneously authorises a series of problematic consequences for understanding and intervening practically in the concrete realities of health. As a response, we develop an alternative ontological proposition that regards processes of health and disease as alwayssituatedachievements. We show that, without disqualifying RCT-based evidence, such a situated ontology enables one to resist the reduction of the realities of health and disease to biomedicine's current forms of explanation. In so doing, we call for medical humanities scholars to actively engage in the speculative question of what nature may be capable of.
Seismic performance comparison between force-based and performance-based design as per Canadian Highway Bridge Design Code (CHBDC) 2014
Authors: Zhang Qi , Alam M. Shahria , Khan Saqib , Jiang Jianping
Published: May 2016

Performance-based design (PBD) was first introduced in Canadian Highway Bridge Design Code (CHBDC) in 2014. Performance-based design is the design that meets multiple performance criteria under different earthquake hazards. To investigate the impact of changes in CHBDC 2014, a four-span concrete highway bridge is designed and evaluated using force-based design (FBD) and PBD methods as per CHBDC 2014, and FBD method as per CHBDC 2006. By incorporating soil–structure interaction (using p–y curves) nonlinear pushover and dynamic time history analyses are conducted to assess the seismic performance of these bridges. Maximum strains of concrete and reinforcing steel are compared among the three designs to determine their performance levels. It is concluded that PBD (CHBDC 2014) is highly conservative compared to FBD (for both CHBDC 2014 and 2006). For the three-level PBD approach, the design is governed by the criterion of reinforcing steel not yielding under the design earthquake (with 475 years return period).
Nest defense behaviour of four raptor species (osprey, bald eagle, ferruginous hawk, and red-tailed hawk) to a novel aerial intruder – a small rotary-winged drone
Authors: Junda James H. , Greene Erick , Zazelenchuk Dan , Bird David M.
Published: May 2016

A small rotary-winged unmanned aerial vehicle (UAV) was flown above the nests of four raptor species: osprey (Pandion haliaetus), bald eagle (Haliaeetus leucocephalus), ferruginous hawk (Buteo regalis), and red-tailed hawk (B. jamaicensis) to document the parental nest defense response to the aircraft. Adult behaviour was documented with a voice recorder and an ethogram, starting ~100 m distant from the nest and continuing until the base of the nest was reached, the survey completed, and the nest area exited. All adult movements and vocalizations were recorded with distance of bird and researchers from the nest when a given behaviour occurred. Ospreys showed the strongest nest defense response followed by ferruginous hawks and red-tailed hawks with bald eagles showing the least aggressive response. Ospreys showed no greater response to the UAV in the air near the nest than to researchers simply standing at the base of the nest structure, while bald eagles showed a significantly higher response to the aircraft than researchers at the nest base. Although aggression varied, no species showed aggression at levels that would discourage the use of UAVs to survey raptor nests. When a proper flight technique is adopted, UAVs can offer a useful tool for surveying raptor nests.
CAPITAL FLOW SURGES AS BUBBLES: BEHAVIORAL FINANCE AND MCKINNON’S OVER-BORROWING SYNDROME EXTENDED
Authors: EFREMIDZE LEVAN , RUTLEDGE JOHN , WILLETT THOMAS D.
Published: May 2016

This paper explores how behavioral finance and complexity economics, along with imperfect information, faulty mental models and perverse incentive structures can cast light on the factors that generate the international capital flow surges and sudden stops that McKinnon described as the over-borrowing syndrome. While there has been a great deal of empirical research on this topic in recent years, there has been much less theoretical analysis of why these flows too often behave in such a volatile manner. Developing a better understanding of the forces driving capital flows should help us identify situations where capital flow surges are particularly likely to end in costly sudden stops and help policy makers decide how best to respond to such flows.
REGIONAL DEVELOPMENT DYNAMICS IN INDONESIA BEFORE AND AFTER THE ‘BIG BANG’ DECENTRALIZATION
Authors: HILL HAL , VIDYATTAMA YOGI
Published: May 2016

Decentralization is in vogue. However, the relationship between decentralization and local-level development dynamics remains unclear. Does decentralization lead to a ‘reform dividend’ of more rapid development in better-governed regions, with attendant national benefits? What is the impact on spatial inequality? In particular, do poorer regions lag further behind as equalizing fiscal policies at the national level weaken? We address these issues with reference to Indonesia, the world’s largest archipelagic nation, which implemented a ‘big bang’ decentralization program in 2001. Our main conclusion, perhaps counterintuitive, is that decentralization had a minimal impact on regional development dynamics, although its political impacts have been far-reaching.
De Rham–Hodge decomposition and vanishing of harmonic forms by derivation operators on the Poisson space
Authors: Privault Nicolas
Published: May 2016

We construct differential forms of all orders and a covariant derivative together with its adjoint on the probability space of a standard Poisson process, using derivation operators. In this framewok we derive a de Rham–Hodge–Kodaira decomposition as well as Weitzenböck and Clark–Ocone formulas for random differential forms. As in the Wiener space setting, this construction provides two distinct approaches to the vanishing of harmonic differential forms.
The ups and downs of geology in Portugal: the Geological Survey, a historical perspective
Authors: Mota Teresa Salomé , Carneiro Ana
Published: May 2016

The Geological Survey of Portugal was created in 1857 in the context of a liberal monarchy within a general policy implemented by the state to effectively control Portuguese territory. Throughout the nineteenth century, despite the structural problems faced by the Survey, it developed a consistent geological research programme, which led to the publication of two editions of the geological map of Portugal on a scale of 1:500 000, together with a considerable number of related scientific articles and monographs. During the first three decades of the twentieth century, however, the Survey and the production of maps were no longer a priority for the State and the institution progressively declined. Only with the establishment of the dictatorial regime known as the Estado Novo (New State) and, in particular, the implementation of its industrializing policies in the context of development plans, did the Geological Survey recover its original purpose of producing geological maps and assert itself as a reference scientific institution.
Fluid transport by the cornea endothelium is dependent on buffering lactic acid efflux
Authors: Li Shimin , Kim Edward , Bonanno Joseph A.
Published: May 2016

Maintenance of corneal hydration is dependent on the active transport properties of the corneal endothelium. We tested the hypothesis that lactic acid efflux, facilitated by buffering, is a component of the endothelial fluid pump. Rabbit corneas were perfused with bicarbonate-rich (BR) or bicarbonate-free (BF) Ringer of varying buffering power, while corneal thickness was measured. Perfusate was collected and analyzed for lactate efflux. In BF with no added HEPES, the maximal corneal swelling rate was 30.0 ± 4.1 μm/h compared with 5.2 ± 0.9 μm/h in BR. Corneal swelling decreased directly with [HEPES], such that with 60 mM HEPES corneas swelled at 7.5 ± 1.6 μm/h. Perfusate [lactate] increased directly with [HEPES]. Similarly, reducing the [HCO3−] increased corneal swelling and decreased lactate efflux. Corneal swelling was inversely related to Ringer buffering power (β), whereas lactate efflux was directly related to β. Ouabain (100 μM) produced maximal swelling and reduction in lactate efflux, whereas carbonic anhydrase inhibition and an monocarboxylic acid transporter 1 inhibitor produced intermediate swelling and decreases in lactate efflux. Conversely, 10 μM adenosine reduced the swelling rate to 4.2 ± 0.8 μm/h and increased lactate efflux by 25%. We found a strong inverse relation between corneal swelling and lactate efflux ( r = 0.98, P < 0.0001). Introducing lactate in the Ringer transiently increased corneal thickness, reaching a steady state (0 ± 0.6 μm/h) within 90 min. We conclude that corneal endothelial function does not have an absolute requirement for bicarbonate; rather it requires a perfusing solution with high buffering power. This facilitates lactic acid efflux, which is directly linked to water efflux, indicating that lactate flux is a component of the corneal endothelial pump.
Possible role for brain prostanoid pathways in the development of angiotensin II-salt hypertension in rats
Authors: Asirvatham-Jeyaraj Ninitha , Fink Gregory D.
Published: May 2016

Prostanoids generated by the cyclooxygenase (COX) pathway appear to contribute to the neurogenic hypertension (HTN) in rats. The first goal of this study was to establish the time frame during which prostanoids participate in ANG II-salt HTN. We induced HTN using ANG II (150 ng·kg−1·min−1sc) infusion for 14 days in rats on a high-salt (2% NaCl) diet. When ketoprofen pretreatment was combined with treatment during the first 7 days of ANG II infusion, development of HTN and increased neurogenic pressor activity (indexed by the depressor response to ganglion blockade) were significantly attenuated for the entire ANG II infusion period. This suggests that prostanoid generation caused by administration of ANG II and salt leads to an increase in neurogenic pressor activity and blood pressure (BP) via a mechanism that persists without the need for continuing prostanoid input. The second goal of this study was to determine whether prostanoid products specifically in the brain contribute to HTN development. Expression of prostanoid pathway genes was measured in brain regions known to affect neurogenic BP regulation. ANG II-treated rats exhibited changes in gene expression of phospholipase A2 (upregulated in organum vasculosum of the lamina terminalis, paraventricular nucleus, nucleus of the solitary tract, and middle cerebral artery) and lipocalin-type prostaglandin D synthase (upregulated in the organum vasculosum of the lamina terminalis). On the basis of our results, we propose that activation of the brain prostanoid synthesis pathway both upstream and downstream from COX at early stages plays an important role in the development of the neurogenic component of ANG II-salt HTN.
Neural and neurochemical basis of reinforcement-guided decision making
Authors: Khani Abbas , Rainer Gregor
Published: May 2016

Decision making is an adaptive behavior that takes into account several internal and external input variables and leads to the choice of a course of action over other available and often competing alternatives. While it has been studied in diverse fields ranging from mathematics, economics, ecology, and ethology to psychology and neuroscience, recent cross talk among perspectives from different fields has yielded novel descriptions of decision processes. Reinforcement-guided decision making models are based on economic and reinforcement learning theories, and their focus is on the maximization of acquired benefit over a defined period of time. Studies based on reinforcement-guided decision making have implicated a large network of neural circuits across the brain. This network includes a wide range of cortical (e.g., orbitofrontal cortex and anterior cingulate cortex) and subcortical (e.g., nucleus accumbens and subthalamic nucleus) brain areas and uses several neurotransmitter systems (e.g., dopaminergic and serotonergic systems) to communicate and process decision-related information. This review discusses distinct as well as overlapping contributions of these networks and neurotransmitter systems to the processing of decision making. We end the review by touching on neural circuitry and neuromodulatory regulation of exploratory decision making.
Message Passing Based Time Synchronization in Wireless Sensor Networks: A Survey
Authors: Sarvghadi Mohammad Ali , Wan Tat-Chee
Published: May 2016

Various protocols have been proposed in the area of wireless sensor networks in order to achieve network-wide time synchronization. A large number of proposed protocols in the literature employ a message passing mechanism to make sensor node clocks tick in unison. In this paper, we first classify Message Passing based Time Synchronization (MPTS) protocols and then analyze them based on different metrics. The classification is based on the following three criteria: structure formation of the network affected by the synchronization protocol, frequency of synchronization process (synchronization interval), and synchronization message overhead. Proposed protocols are analyzed and evaluated from different perspectives based on available data. A comparison table of the reviewed protocols is presented according to the evaluation metrics. Finally, some potential methods will be proposed to improve the synchronization process.