bluuebunny/crossref_metadata_2025 huggingface dataset:
Causal Mediation Analysis for the Cox Proportional Hazards Model With A Smooth Baseline Hazard Estimator
Authors: Wang Wei , Albert Jeffrey M.
Published: October 2016

An important problem within the social, behavioural and health sciences is how to partition an exposure effect (e.g. treatment or risk factor) among specific pathway effects and to quantify the importance of each pathway. Mediation analysis based on the potential outcomes framework is an important tool to address this problem and we consider the estimation of mediation effects for the proportional hazards model. We give precise definitions of the total effect, natural indirect effect and natural direct effect in terms of the survival probability, hazard function and restricted mean survival time within the standard two-stage mediation framework. To estimate the mediation effects on different scales, we propose a mediation formula approach in which simple parametric models (fractional polynomials or restricted cubic splines) are utilized to approximate the baseline log-cumulative-hazard function. Simulation study results demonstrate low bias of the mediation effect estimators and close-to-nominal coverage probability of the confidence intervals for a wide range of complex hazard shapes. We apply this method to the Jackson heart study data and conduct a sensitivity analysis to assess the effect on the mediation effects inference when the no unmeasured mediator–outcome confounding assumption is violated.
Factors associated with utilization of dental services in a long‐term care facility: a descriptive cross‐sectional study
Authors: Scannapieco Frank A. , Amin Summar , Salme Marc , Tezal Mine
Published: October 2016

Purpose

To describe factors associated with the utilization of dental services in a long‐term care facility (LTCF) in Western New York.

Methods and materials

A descriptive cross‐sectional study reviewed the dental and medical records of residents of an LTCF discharged between January 1, 2008 and December 30, 2012. Information on demographic and health variables at admission was extracted from electronic health records. Information on oral health variables was extracted from patient charts.

Results

A total of 2,516 residents were discharged between 2008 and 2012. From those, 259 (10.3%) utilized dental services at least once during their stay. Those who utilized dental services were significantly older at admission (78.5 vs. 82.0 years, p < 0.001), stayed longer (1.6 vs. 3.9 years, p < 0.001), more likely to be female (63.6 vs. 75.6%, p = 0.008), and less likely to be married (37.7 vs. 14.0%, p = < 0.001) compared to those who did not. Patients with endocrine, nutritional, metabolic, and immunity disorders, mental disorders, and circulatory system diseases were more likely to receive dental services.

Conclusions

Dental services appear to be underutilized by residents of LTCF. Significant differences exist in demographic and health variables between residents who utilize these services compared to those who do not.
The World Bank, Organized Hypocrisy, and Women's Health: A Cross‐National Analysis of Maternal Mortality in Sub‐Saharan Africa
Authors: Coburn Carolyn , Reed Holly E. , Restivo Michael , Shandra John M.
Published: October 2016

The theory of organized hypocrisy asserts that an organization depends upon its external environment for both financial support and conferred legitimacy, which can lead to conflicting policy agendas. We apply the theory of organized hypocrisy to World Bank structural adjustment and investment lending for reproductive health, hypothesizing these two lending policies should have differential effects on maternal mortality. We estimate a two‐way fixed effects regression model with robust standard errors clustered by country to examine the effect of World Bank reproductive health lending on maternal mortality within sub‐Saharan African nations over the period 1990–2010. We find that in every model the coefficients for World Bank structural adjustment lending in the health sector are positive and significant while the coefficients for World Bank investment lending in the reproductive health sector are negative and significant. The findings lend support to the theory that the World Bank is pursuing contradictory agendas, embodied by its lending policies, which can have differential effects on maternal mortality.
Smooth estimation of a monotone hazard and a monotone density under random censoring
Authors: Lopuhaä Hendrik P. , Musta Eni
Published: October 2016

We consider kernel smoothed Grenander‐type estimators for a monotone hazard rate and a monotone density in the presence of randomly right censored data. We show that they converge at rate n2/5 and that the limit distribution at a fixed point is Gaussian with explicitly given mean and variance. It is well known that standard kernel smoothing leads to inconsistency problems at the boundary points. It turns out that, also by using a boundary correction, we can only establish uniform consistency on intervals that stay away from the end point of the support (although we can go arbitrarily close to the right boundary).
Taxonomy as a hypothesis: testing the status of the Bermuda buckeye butterfly Junonia coenia bergi (Lepidoptera: Nymphalidae)
Authors: PETERS MELISSA J. , MARCUS JEFFREY M.
Published: October 2016

Species determination and definition in eukaryotes have traditionally been based on morphology, with little focus on genetic differentiation. Molecular methods allow for the independent assessment of morphology‐based taxonomic hypotheses. Three criteria used to define a full species for taxonomic purposes are morphological distinction, formation of a monophyletic lineage, and reproductive isolation. Junonia butterflies (Nymphalidae) are becoming an important experimental model system, but the taxonomy of many New World Junonia species is unclear. One of these species is J. coenia, which contains the subspecies J. coenia coenia, J. coenia grisea and J. coenia bergi. Previous studies suggest that J. coenia grisea may meet the criteria for full species status. Therefore, we evaluated the geographically isolated and rarely studied Bermuda buckeye butterfly J. coenia bergi to determine if it was similarly distinct. Physical examination of specimens and phylogenetic and population genetic analyses of mitochondrial cytochrome c oxidase subunit I, nuclear wingless, and complete mitochondrial genome sequences suggest that while J. coenia bergi is smaller in body size than many Junonia and has distinctive ventral hindwing colouration, it does not form a monophyletic lineage and shows indications of continued gene flow with North American mainland J. coenia coenia populations. Thus, J. coenia bergi does not meet the criteria for full species designation, but geographic isolation, morphological distinctiveness, and cultural importance suggest that it remain recognized as a subspecies of J. coenia. Similar analyses will be useful for addressing further taxonomic questions in Junonia and other taxa, especially where morphology‐based taxonomic determinations are ambiguous.
Changes in cardiovascular responses to chemoreflex activation of rats recovered from protein restriction are not related to AT1 receptors
Authors: Sá Renato Willian Martins , Haibara Andrea Siqueira , Gomes Paula Magalhães , Aguiar Giovana Lopes , Nascimento Rafael Souza Leopoldino , Pedrosa Maria Lucia , Alzamora Andréia Carvalho , de Oliveira Lisandra Brandino , Cardoso Leonardo Máximo
Published: October 2016

New Findings

What is the central question of this study?

In this study, we sought to investigate whether cardiovascular responses to peripheral chemoreflex activation of rats recovered from protein restriction are related to activation of AT1 receptors.

What is the main finding and its importance?

This study highlights the fact that angiotensinergic mechanisms activated by AT1 receptors do not support increased responses to peripheral chemoreflex activation by KCN in rats recovered from protein restriction. Also, we found that protein restriction led to increased resting ventilation in adult rats, even after recovery.

The effects of a low‐protein diet followed by recovery on cardiorespiratory responses to peripheral chemoreflex activation were tested before and after systemic angiotensin II type 1 (AT1) receptor antagonism. Male Fischer rats were divided into control and recovered (R‐PR) groups after weaning. The R‐PR rats were fed a low‐protein (8%) diet for 35 days and recovered with a normal protein (20%) diet for 70 days. Control rats received a normal protein diet for 105 days (CG105). After cannulation surgery, mean arterial pressure, heart rate, respiratory frequency, tidal volume and minute ventilation were acquired using a digital recording system in freely moving rats. The role of angintensin II was evaluated by systemic antagonism of AT1 receptors with losartan (20 mg kg−1
i.v.). The peripheral chemoreflex was elicited by increasing doses of KCN (20–160 μg kg min−1, i.v.). At baseline, R‐PR rats presented increased heart rate and minute ventilation (372 ± 34 beats min−1 and 1.274 ± 377 ml kg−1 min−1) compared with CG105 animals (332 ± 22 beats min−1 and 856 ± 112 ml kg−1 min−1). Mean arterial pressure was not different between the groups. Pressor and bradycardic responses evoked by KCN (60 μg kg−1) were increased in R‐PR (+45 ± 13 mmHg and −77 ± 47 beats min−1) compared with CG105 rats (+25 ± 17 mmHg and −27 ± 28 beats min−1), but no difference was found in the tachypnoeic response. These differences were preserved after losartan. The data suggest that angiotensin II acting on AT1 receptors may not be associated with the increased heart rate, increased minute ventilation and acute cardiovascular responses to peripheral chemoreflex activation in rats that underwent postweaning protein restriction followed by recovery.
Low-Dimensional Modeling of a Pumping Unit to Cope With Multiphase Flow
Authors: Omrani Ala E. , Franchek Matthew A. , Ebrahimi Behrouz , Mutlu Mete , Grigoriadis Karolos
Published: October 2016

Pumping unit efficiency is highly disturbed by the presence of gas influx reducing the productivity and inducing unpredictable system response due to the change of its intrinsic properties such as the natural frequency. A poor estimation of those properties may affect the on-field crew and system safety as well as the production rate. The purpose of this paper is to construct a hydromechanical model describing the coupled multiphase flow-pumping unit system dynamics and to develop a procedure to control the pumping speed for safety assurance and oil production maximization. A coupled mechanical-multiphase flow model capturing the interplay between the gas void fraction (GVF) and the driving harmonic force of the pumping unit is developed. Specifically, the predicted downhole pressure is used to determine the sucker rod effective load. Consequently, a reduced-order model, capturing the dynamics of the sucker rod, is used to estimate the saddle bearings axial displacements which are function of polished rod loading. An error-driven adaptation using the difference between presumed bearing displacement with known GVF and the predicted bearing displacement from the proposed multiphysics model is employed to estimate the unknown downhole GVF. The obtained results prove that the adaptation allows an accurate evaluation of the pumped fluid's GVF, thereby circumventing the need for a costly and inaccurate measurement of the two-phase flow gas fraction. Based on this estimation, a control strategy is then proposed to regulate the pump speed while avoiding the resonance frequency of the sucker-rod system.
On the role of self-adjointness in the continuum formulation of topological quantum phases
Authors: Tanhayi Ahari Mostafa , Ortiz Gerardo , Seradjeh Babak
Published: October 2016

Topological quantum phases of matter are characterized by an intimate relationship between the Hamiltonian dynamics away from the edges and the appearance of bound states localized at the edges of the system. Elucidating this correspondence in the continuum formulation of topological phases, even in the simplest case of a one-dimensional system, touches upon fundamental concepts and methods in quantum mechanics that are not commonly discussed in textbooks, in particular the self-adjoint extensions of a Hermitian operator. We show how such topological bound states can be derived in a prototypical one-dimensional system. Along the way, we provide a pedagogical exposition of the self-adjoint extension method as well as the role of symmetries in correctly formulating the continuum, field-theory description of topological matter with boundaries. Moreover, we show that self-adjoint extensions can be characterized generally in terms of a conserved local current associated with the self-adjoint operator.
A multi-functional apparatus for α and β spectroscopy utilizing a permanent ring-magnet β spectrometer
Authors: Becchetti F. D. , Febbraro M. , Riggins J. , Torres-Isea R. O.
Published: October 2016

A multi-functional teaching apparatus has been developed for α and β spectroscopy utilizing a solid-state detector and associated electronics. The possible experiments include conventional measurements to determine α and β decay energies, half lives, characteristic energy loss of nuclear particles in matter, and limits on the β-neutrino mass set from endpoints in β-decay spectra. In addition, the relativistic mass increase of β particles is verified using a high-efficiency, axially symmetric permanent ring-magnet β spectrometer. The basic apparatus also can be adapted for experiments in Rutherford scattering and other nuclear measurements.
Pedagogical Techniques Employed by the Television Show “MythBusters”
Authors: Zavrel Erik
Published: October 2016

“MythBusters,” the long-running though recently discontinued Discovery Channel science entertainment television program, has proven itself to be far more than just a highly rated show. While its focus is on entertainment, the show employs an array of pedagogical techniques to communicate scientific concepts to its audience. These techniques include: achieving active learning, avoiding jargon, employing repetition to ensure comprehension, using captivating demonstrations, cultivating an enthusiastic disposition, and increasing intrinsic motivation to learn. In this content analysis, episodes from the show’s 10-year history were examined for these techniques. “MythBusters” represents an untapped source of pedagogical techniques, which science educators may consider availing themselves of in their tireless effort to better reach their students. Physics educators in particular may look to “MythBusters” for inspiration and guidance in how to incorporate these techniques into their own teaching and help their students in the learning process.
Vič Goes to Near Space
Authors: Merhar Vida Kariž , Capuder Rok , Maroševič Timotej , Artač Sonja , Mozer Alenka , Štekovič Maja
Published: October 2016

In the school year 2012-2013 about 50 students (Fig. 1), managed by mentors (teachers from the middle school Gimnazija Vič in Ljubljana, Slovenia) created an atmospheric probe and launched it into an altitude of more than 30 km above Earth’s surface. The aim of this “space expedition” was to take pictures of Earth and to measure how air pressure, the temperature, CO2 and O2 concentrations, the level of UVA and UVB radiation, and the amount of light change with altitude. There was also a yeast sample placed inside and outside of the probe. Here we report on some of the successes and failures of this endeavor.
A New Version of an Old Demonstration Experiment Using the Elihu Thomson Jumping Ring Apparatus
Authors: Foster Theodore , Cary Arthur , Mottmann John , van Wyngaarden Willem
Published: October 2016

The goal of this paper is to make more widely known an eye-catching demonstration experiment in which a hanging conducting can is made to spin when placed near the iron core of an Elihu Thomson “jumping ring” apparatus. An explanation is given based on Faraday’s law of induced voltages and the magnetic forces due to the core’s fields interacting with the induced currents.
Brain stimulation reveals crucial role of overcoming self-centeredness in self-control
Authors: Soutschek Alexander , Ruff Christian C. , Strombach Tina , Kalenscher Tobias , Tobler Philippe N.
Published: October 2016

Self-control in intertemporal choice requires overcoming self-centeredness, a function typically associated with social decisions.
Comment on “Reconciliation of the Devils Hole climate record with orbital forcing”
Authors: Coplen Tyler B.
Published: October 2016

Moseley
et al
.’s (Reports, 8 January 2016, p. 165) preferred-Termination-II age is subjective, as evidenced by variation in their Termination-II ages of 2500 years per meter. Termination-II-age bias decreases to zero at ~1.5 meters below the present-day water table, if one assumes linear variation with core-sample height. Maintaining the required gradient of thorium isotope
230
Th over 3.6 meters for 1000 years, much less 10,000 years, seems exceedingly unlikely.
Observation of a nematic quantum Hall liquid on the surface of bismuth
Authors: Feldman Benjamin E. , Randeria Mallika T. , Gyenis András , Wu Fengcheng , Ji Huiwen , Cava R. J. , MacDonald Allan H. , Yazdani Ali
Published: October 2016

Relating interactions and nematicity

The electronic system in a strongly correlated material can sometimes be less symmetrical than the underlying crystal lattice. This loss of symmetry, caused by interactions and dubbed electronic nematicity, has been observed in a number of exotic materials. However, establishing a direct connection between the interactions and nematicity is tricky. Feldman
et al.
used scanning tunneling microscopy to image the wave functions of electrons on the surface of bismuth placed in an external magnetic field. The exchange interactions in the material caused a loss of symmetry, which was reflected in the orientations of the electrons' elliptical orbits.

Science
, this issue p.
316
A Silurian maxillate placoderm illuminates jaw evolution
Authors: Zhu Min , Ahlberg Per E. , Pan Zhaohui , Zhu Youan , Qiao Tuo , Zhao Wenjin , Jia Liantao , Lu Jing
Published: October 2016

Jaws from the jawless

Until a fossil called Entelognathus was found to contain a tripartite jaw a few years ago, it was believed that the skeletons of early osteichthyans (bony fish), the ancestors of all vertebrates, were derived independently of those of the earlier placoderms (so-called jawless fish). Zhu
et al.
now describe a second Silurian placoderm that more securely bridges the jawless toothlike plates of placoderms to the development of the jawed condition that ultimately led to the three-boned jaw in ancestors of modern vertebrates (see the Perspective by Long). This finding upends the traditional belief that the two types of jaw were nonhomologous and sheds light on the evolution of the complex maxilla, a key component of diversification across many modern taxa, including humans.

Science
, this issue p.
334
; see also p.
280
Metal-catalyzed reductive coupling of olefin-derived nucleophiles: Reinventing carbonyl addition
Authors: Nguyen Khoa D. , Park Boyoung Y. , Luong Tom , Sato Hiroki , Garza Victoria J. , Krische Michael J.
Published: October 2016

How to turn olefins into nucleophiles

The Grignard reaction has a storied place in the development of organic chemistry. Recognized by the Nobel Prize more than a century ago, this coupling of organomagnesium halides with carbonyl compounds remains a widely used route to carbon-carbon bonds. Nguyen
et al.
review an emerging alternative protocol that replaces the sensitive magnesium reagent with a catalytically activated olefin and a reductant such as hydrogen or an alcohol. In addition to safety and efficiency considerations, this class of reactions benefits from the high abundance and low cost of the olefins.

Science
, this issue p.
300
A pathogenic role for T cell–derived IL-22BP in inflammatory bowel disease
Authors: Pelczar Penelope , Witkowski Mario , Perez Laura Garcia , Kempski Jan , Hammel Anna G. , Brockmann Leonie , Kleinschmidt Dörte , Wende Sandra , Haueis Cathleen , Bedke Tanja , Witkowski Marco , Krasemann Susanne , Steurer Stefan , Booth Carmen J. , Busch Philipp , König Alexandra , Rauch Ursula , Benten Daniel , Izbicki Jakob R. , Rösch Thomas , Lohse Ansgar W. , Strowig Till , Gagliani Nicola , Flavell Richard A. , Huber Samuel
Published: October 2016

Interleukin-22 binding protein (IL-22BP) drives inflammatory bowel disease by sopping up the tissue-protective protein IL-22.
What's in a Name? New Bacterial Species and Changes to Taxonomic Status from 2012 through 2015
Authors: Munson Erik , Carroll Karen C.
Published: October 2016

Technological advancements in fields such as molecular genetics and the human microbiome have resulted in an unprecedented recognition of new bacterial genus/species designations by theInternational Journal of Systematic and Evolutionary Microbiology. Knowledge of designations involving clinically significant bacterial species would benefit clinical microbiologists in the context of emerging pathogens, performance of accurate organism identification, and antimicrobial susceptibility testing. In anticipation of subsequent taxonomic changes being compiled by theJournal of Clinical Microbiologyon a biannual basis, this compendium summarizes novel species and taxonomic revisions specific to bacteria derived from human clinical specimens from the calendar years 2012 through 2015.
Deep-Sequence Identification and Role in Virus Replication of a JC Virus Quasispecies in Patients with Progressive Multifocal Leukoencephalopathy
Authors: Takahashi Kenta , Sekizuka Tsuyoshi , Fukumoto Hitomi , Nakamichi Kazuo , Suzuki Tadaki , Sato Yuko , Hasegawa Hideki , Kuroda Makoto , Katano Harutaka
Published: October 2016

JC virus (JCV) is a DNA virus causing progressive multifocal leukoencephalopathy (PML) in immunodeficient patients. In the present study, 22 genetic quasispecies with more than 1.5% variant frequency were detected in JCV genomes from six clinical samples of PML by next-generation sequencing. A mutation from A to C at nucleotide (nt) 3495 in JCV Mad1 resulting in a V-to-G amino acid substitution at amino acid (aa) position 392 of the large T antigen (TAg) was identified in all six cases of PML at 3% to 19% variant frequencies. Transfection of JCV Mad1 DNA possessing the V392G substitution in TAg into IMR-32 and human embryonic kidney 293 (HEK293) cells resulted in dramatically decreased production of JCV-encoded proteins. The virus DNA copy number was also reduced in supernatants of the mutant virus-transfected cells. Transfection of the IMR-32 and HEK293 cells with a virus genome containing a revertant mutation recovered viral production and protein expression. Cotransfection with equal amounts of wild-type genome and mutated JCV genome did not reduce the expression of viral proteins or viral replication, suggesting that the mutation did not have any dominant-negative function. Finally, immunohistochemistry demonstrated that TAg was expressed in all six pathological samples in which the quasispecies were detected. In conclusion, the V392G amino acid substitution in TAg identified frequently in PML lesions has a function in suppressing JCV replication, but the frequency of the mutation was restricted and its role in PML lesions was limited.IMPORTANCEDNA viruses generally have lower mutation frequency than RNA viruses, and the detection of quasispecies in JCV has rarely been reported. In the present study, a next-generation sequencer identified a JCV quasispecies with an amino acid substitution in the T antigen in patients with PML.In vitrostudies showed that the mutation strongly repressed the expression of JC viral proteins and reduced the viral replication. However, because the frequency of the mutation was low in each case, the total expression of virus proteins was sustainedin vivo. Thus, JC virus replicates in PML lesions in the presence of a mutant virus which is able to repress virus replication.
Naf1 Regulates HIV-1 Latency by Suppressing Viral Promoter-Driven Gene Expression in Primary CD4
+
T Cells
Authors: Li Chuan , Wang Hai-Bo , Kuang Wen-Dong , Ren Xiao-Xin , Song Shu-Ting , Zhu Huan-Zhang , Li Qiang , Xu Li-Ran , Guo Hui-Jun , Wu Li , Wang Jian-Hua
Published: October 2016

HIV-1 latency is characterized by reversible silencing of viral transcription driven by the long terminal repeat (LTR) promoter of HIV-1. Cellular and viral factors regulating LTR activity contribute to HIV-1 latency, and certain repressive cellular factors modulate viral transcription silencing. Nef-associated factor 1 (Naf1) is a host nucleocytoplasmic shuttling protein that regulates multiple cellular signaling pathways and HIV-1 production. We recently reported that nuclear Naf1 promoted nuclear export of unspliced HIV-1
gag
mRNA, leading to increased Gag production. Here we demonstrate new functions of Naf1 in regulating HIV-1 persistence. We found that Naf1 contributes to the maintenance of HIV-1 latency by inhibiting LTR-driven HIV-1 gene transcription in a nuclear factor kappa B-dependent manner. Interestingly, Naf1 knockdown significantly enhanced viral reactivation in both latently HIV-1-infected Jurkat T cells and primary central memory CD4
+
T cells. Furthermore, Naf1 knockdown in resting CD4
+
T cells from HIV-1-infected individuals treated with antiretroviral therapy significantly increased viral reactivation upon T-cell activation, suggesting an important role of Naf1 in modulating HIV-1 latency
in vivo
. Our findings provide new insights for a better understanding of HIV-1 latency and suggest that inhibition of Naf1 activity to activate latently HIV-1-infected cells may be a potential therapeutic strategy.

IMPORTANCE
HIV-1 latency is characterized mainly by a reversible silencing of LTR promoter-driven transcription of an integrated provirus. Cellular and viral proteins regulating LTR activity contribute to the modulation of HIV-1 latency. In this study, we found that the host protein Naf1 inhibited HIV-1 LTR-driven transcription of HIV genes and contributed to the maintenance of HIV-1 latency. Our findings provide new insights into the effects of host modulation on HIV-1 latency, which may lead to a potential therapeutic strategy for HIV persistence by targeting the Naf1 protein.
The Cellular DNA Helicase ChlR1 Regulates Chromatin and Nuclear Matrix Attachment of the Human Papillomavirus 16 E2 Protein and High-Copy-Number Viral Genome Establishment
Authors: Harris Leanne , McFarlane-Majeed Laura , Campos-León Karen , Roberts Sally , Parish Joanna L.
Published: October 2016

In papillomavirus infections, the viral genome is established as a double-stranded DNA episome. To segregate the episomes into daughter cells during mitosis, they are tethered to cellular chromatin by the viral E2 protein. We previously demonstrated that the E2 proteins of diverse papillomavirus types, including bovine papillomavirus (BPV) and human papillomavirus 16 (HPV16), associate with the cellular DNA helicase ChlR1. This virus-host interaction is important for the tethering of BPV E2 to mitotic chromatin and the stable maintenance of BPV episomes. The role of the association between E2 and ChlR1 in the HPV16 life cycle is unresolved. Here we show that an HPV16 E2 Y131A mutant (E2
Y131A
) had significantly reduced binding to ChlR1 but retained transcriptional activation and viral origin-dependent replication functions. Subcellular fractionation of keratinocytes expressing E2
Y131A
showed a marked change in the localization of the protein. Compared to that of wild-type E2 (E2
WT
), the chromatin-bound pool of E2
Y131A
was decreased, concomitant with an increase in nuclear matrix-associated protein. Cell cycle synchronization indicated that the shift in subcellular localization of E2
Y131A
occurred in mid-S phase. A similar alteration between the subcellular pools of the E2
WT
protein occurred upon ChlR1 silencing. Notably, in an HPV16 life cycle model in primary human keratinocytes, mutant E2
Y131A
genomes were established as episomes, but at a markedly lower copy number than that of wild-type HPV16 genomes, and they were not maintained upon cell passage. Our studies indicate that ChlR1 is an important regulator of the chromatin association of E2 and of the establishment and maintenance of HPV16 episomes.

IMPORTANCE
Infections with high-risk human papillomaviruses (HPVs) are a major cause of anogenital and oropharyngeal cancers. During infection, the circular DNA genome of HPV persists within the nucleus, independently of the host cell chromatin. Persistence of infection is a risk factor for cancer development and is partly achieved by the attachment of viral DNA to cellular chromatin during cell division. The HPV E2 protein plays a critical role in this tethering by binding simultaneously to the viral genome and to chromatin during mitosis. We previously showed that the cellular DNA helicase ChlR1 is required for loading of the bovine papillomavirus E2 protein onto chromatin during DNA synthesis. Here we identify a mutation in HPV16 E2 that abrogates interaction with ChlR1, and we show that ChlR1 regulates the chromatin association of HPV16 E2 and that this virus-host interaction is essential for viral episome maintenance.
Biotic Interactions Shape the Ecological Distributions of
Staphylococcus
Species
Authors: Kastman Erik K. , Kamelamela Noelani , Norville Josh W. , Cosetta Casey M. , Dutton Rachel J. , Wolfe Benjamin E.
Published: October 2016

Many metagenomic sequencing studies have observed the presence of closely related bacterial species or genotypes in the same microbiome. Previous attempts to explain these patterns of microdiversity have focused on the abiotic environment, but few have considered how biotic interactions could drive patterns of microbiome diversity. We dissected the patterns, processes, and mechanisms shaping the ecological distributions of three closely related
Staphylococcus
species in cheese rind biofilms. Paradoxically, the most abundant species (
S. equorum
) is the slowest colonizer and weakest competitor based on growth and competition assays in the laboratory. Through
in vitro
community reconstructions, we determined that biotic interactions with neighboring fungi help resolve this paradox. Species-specific stimulation of the poor competitor by fungi of the genus
Scopulariopsis
allows
S. equorum
to dominate communities
in vitro
as it does
in situ
. Results of comparative genomic and transcriptomic experiments indicate that iron utilization pathways, including a homolog of the
S. aureus
staphyloferrin B siderophore operon pathway, are potential molecular mechanisms underlying
Staphylococcus
-
Scopulariopsis
interactions. Our integrated approach demonstrates that fungi can structure the ecological distributions of closely related bacterial species, and the data highlight the importance of bacterium-fungus interactions in attempts to design and manipulate microbiomes.

IMPORTANCE
Decades of culture-based studies and more recent metagenomic studies have demonstrated that bacterial species in agriculture, medicine, industry, and nature are unevenly distributed across time and space. The ecological processes and molecular mechanisms that shape these distributions are not well understood because it is challenging to connect
in situ
patterns of diversity with mechanistic
in vitro
studies in the laboratory. Using tractable cheese rind biofilms and a focus on coagulase-negative staphylococcus (CNS) species, we demonstrate that fungi can mediate the ecological distributions of closely related bacterial species. One of the
Staphylococcus
species studied,
S. saprophyticus
, is a common cause of urinary tract infections. By identifying processes that control the abundance of undesirable CNS species, cheese producers will have more precise control on the safety and quality of their products. More generally,
Staphylococcus
species frequently co-occur with fungi in mammalian microbiomes, and similar bacterium-fungus interactions may structure bacterial diversity in these systems.
The Evolution of Orphan Regions in Genomes of a Fungal Pathogen of Wheat
Authors: Plissonneau Clémence , Stürchler Alessandra , Croll Daniel
Published: October 2016

Fungal plant pathogens rapidly evolve virulence on resistant hosts through mutations in genes encoding proteins that modulate the host immune responses. The mutational spectrum likely includes chromosomal rearrangements responsible for gains or losses of entire genes. However, the mechanisms creating adaptive structural variation in fungal pathogen populations are poorly understood. We used complete genome assemblies to quantify structural variants segregating in the highly polymorphic fungal wheat pathogen
Zymoseptoria tritici
. The genetic basis of virulence in
Z. tritici
is complex, and populations harbor significant genetic variation for virulence; hence, we aimed to identify whether structural variation led to functional differences. We combined single-molecule real-time sequencing, genetic maps, and transcriptomics data to generate a fully assembled and annotated genome of the highly virulent field isolate 3D7. Comparative genomics analyses against the complete reference genome IPO323 identified large chromosomal inversions and the complete gain or loss of transposable-element clusters, explaining the extensive chromosomal-length polymorphisms found in this species. Both the 3D7 and IPO323 genomes harbored long tracts of sequences exclusive to one of the two genomes. These orphan regions contained 296 genes unique to the 3D7 genome and not previously known for this species. These orphan genes tended to be organized in clusters and showed evidence of mutational decay. Moreover, the orphan genes were enriched in genes encoding putative effectors and included a gene that is one of the most upregulated putative effector genes during wheat infection. Our study showed that this pathogen species harbored extensive chromosomal structure polymorphism that may drive the evolution of virulence.

IMPORTANCE
Pathogen outbreak populations often harbor previously unknown genes conferring virulence. Hence, a key puzzle of rapid pathogen evolution is the origin of such evolutionary novelty in genomes. Chromosomal rearrangements and structural variation in pathogen populations likely play a key role. However, identifying such polymorphism is challenging, as most genome-sequencing approaches only yield information about point mutations. We combined long-read technology and genetic maps to assemble the complete genome of a strain of a highly polymorphic fungal pathogen of wheat. Comparisons against the reference genome of the species showed substantial variation in the chromosome structure and revealed large regions unique to each assembled genome. These regions were enriched in genes encoding likely effector proteins, which are important components of pathogenicity. Our study showed that pathogen populations harbor extensive polymorphism at the chromosome level and that this polymorphism can be a source of adaptive genetic variation in pathogen evolution.
Outer Membrane Vesicle Production Facilitates LPS Remodeling and Outer Membrane Maintenance in
Salmonella
during Environmental Transitions
Authors: Bonnington Katherine E. , Kuehn Meta J.
Published: October 2016

The ability of Gram-negative bacteria to carefully modulate outer membrane (OM) composition is essential to their survival. However, the asymmetric and heterogeneous structure of the Gram-negative OM poses unique challenges to the cell’s successful adaption to rapid environmental transitions. Although mechanisms to recycle and degrade OM phospholipid material exist, there is no known mechanism by which to remove unfavorable lipopolysaccharide (LPS) glycoforms, except slow dilution through cell growth. As all Gram-negative bacteria constitutively shed OM vesicles (OMVs), we propose that cells may utilize OMV formation as a way to selectively remove environmentally disadvantageous LPS species. We examined the native kinetics of OM composition during physiologically relevant environmental changes in
Salmonella enterica
, a well-characterized model system for activation of PhoP/Q and PmrA/B two-component systems (TCSs). In response to acidic pH, toxic metals, antimicrobial peptides, and lack of divalent cations, these TCSs modify the LPS lipid A and core, lengthen the O antigen, and upregulate specific OM proteins. An environmental change to PhoP/Q- and PmrA/B-activating conditions simultaneously induced the addition of modified species of LPS to the OM, downregulation of previously dominant species of LPS, greater OMV production, and increased OMV diameter. Comparison of the relative abundance of lipid A species present in the OM and the newly budded OMVs following two sets of rapid environmental shifts revealed the retention of lipid A species with modified phosphate moieties in the OM concomitant with the selective loss of palmitoylated species via vesiculation following exposure to moderately acidic environmental conditions.

IMPORTANCE
All Gram-negative bacteria alter the structural composition of LPS present in their OM in response to various environmental stimuli. We developed a system to track the native dynamics of lipid A change in
Salmonella enterica
serovar Typhimurium following an environmental shift to PhoP/Q- and PmrA/B-inducing conditions. We show that growth conditions influence OMV production, size, and lipid A content. We further demonstrate that the lipid A content of OMVs does not fit a stochastic model of content selection, revealing the significant retention of lipid A species containing covalent modifications that mask their 1- and 4′-phosphate moieties under host-like conditions. Furthermore, palmitoylation of the lipid A to form hepta-acylated species substantially increases the likelihood of its incorporation into OMVs. These results highlight a role for the OMV response in OM remodeling and maintenance processes in Gram-negative bacteria.
Macrophages and Iron Metabolism
Authors: Ganz Tomas
Published: October 2016

Macrophages exert multiple important roles in iron metabolism. As scavengers, splenic and hepatic macrophages phagocytize and degrade senescent and damaged erythrocytes to recycle iron, predominantly for the production of hemoglobin in new erythrocytes. Splenic red pulp macrophages are specialized for iron recycling, with increased expression of proteins for the uptake of hemoglobin, breakdown of heme, and export of iron. Iron release from macrophages is closely regulated by the interaction of hepcidin, a peptide hormone produced by hepatocytes, with the macrophage iron exporter ferroportin. As regulators and effectors of antimicrobial host defense, macrophages employ multiple mechanisms to contain microbial infections by depriving microbes of iron. Macrophages also have an important trophic role in the bone marrow, supporting efficient erythropoiesis.
Molecular Epidemiology of Colonizing and Infecting Isolates of Klebsiella pneumoniae
Authors: Martin Rebekah M. , Cao Jie , Brisse Sylvain , Passet Virginie , Wu Weisheng , Zhao Lili , Malani Preeti N. , Rao Krishna , Bachman Michael A.
Published: October 2016

K. pneumoniae
commonly infects hospitalized patients, and these infections are increasingly resistant to carbapenems, the antibiotics of last resort for life-threatening bacterial infections. To prevent and treat these infections, we must better understand how
K. pneumoniae
causes disease and discover new ways to predict and detect infections. This study demonstrates that colonization with
K. pneumoniae
in the intestinal tract is strongly linked to subsequent infection. This finding helps to identify a potential time frame and possible approach for intervention: the colonizing strain from a patient could be isolated as part of a risk assessment, and antibiotic susceptibility testing could guide empirical therapy if the patient becomes acutely ill.
Neurological complications of sickle cell disease in Africa: protocol for a systematic review
Authors: Mengnjo Michel K , Kamtchum-Tatuene Joseph , Nicastro Nicolas , Noubiap Jean Jacques N
Published: October 2016

Introduction

Sickle cell disease (SCD) is highly prevalent in Africa. Considered as a public health problem, it is associated with high morbidity and mortality. Neurological complications of SCD can cause significant disability with important socioeconomic and psychological impact on the patients and their families, and can even lead to death if not properly managed. There are important knowledge gaps regarding the burden of neurological complications of SCD in African populations. We propose to conduct the first systematic review to summarise the epidemiological data available on neurological complications of SCD in Africa.

Methods and analysis

We will search PubMed, MEDLINE, EMBASE and the African Index Medicus from 1 January 1950 to 31 May 2016 for studies of neurological complications of SCD in Africa. After study selection, full-text paper acquisition, data extraction and synthesis, we will assess all studies for quality, risk of bias and heterogeneity. Appropriate methods of meta-analysis will be used to pool prevalence estimates from studies with similar features, globally and in major subgroups. This protocol complies with the 2015 Preferred Reporting Items for Systematic reviews and Meta-Analysis protocols (PRISMA-P) guidelines.

Ethics and dissemination

The proposed study will use published data. Therefore, there is no requirement for ethical approval. This review is expected to provide relevant data to help quantify the burden of neurological complications of SCD in African populations, inform policymakers and identify further research topics. The final report of the systematic review will be published in a peer-reviewed journal and presented at conferences.

Review registration number

CRD42016039574.
Improving diagnosis for congenital cataract by introducing NGS genetic testing
Authors: Musleh Mohammud , Ashworth Jane , Black Graeme , Hall Georgina
Published: October 2016

Childhood cataract (CC) has an incidence of 3.5 per 10,000 by age 15 years. Diagnosis of any underlying cause is important to ensure effective and prompt management of multisystem complications, to facilitate accurate genetic counselling and to streamline multidisciplinary care. Next generation sequencing (NGS) has been shown to be effective in providing an underlying diagnosis in 70% of patients with CC in a research setting. This project aimed to integrate NGS testing in CC within six months of presentation and increase the rate of diagnosis.

A retrospective case note review was undertaken to define the baseline efficacy of current care in providing a precise diagnosis. Quality improvement methods were used to integrate and optimize NGS testing in clinical care and measure the improvements made.

The percentage of children receiving an NGS result within six months increased from 26% to 71% during the project period. The mean time to NGS testing and receiving a report decreased and there was a reduction in variation over the study period. Several patients and families had a change in management or genetic counselling as a direct result of the diagnosis given by the NGS test.

The current recommended investigation of patients with bilateral CC is ineffective in identifying a diagnosis. Quality Improvement methods have facilitated successful integration of NGS testing into clinical care, improving time to diagnosis and leading to development of a new care pathway.
Treatment of canine demodicosis
Authors: Cerundolo Rosario
Published: October 2016

Demodicosis is a common canine ectoparasitosis. Recognising the clinical presentation, identifying the parasite and choosing the most appropriate therapy are essential for the successful management of a patient. There are various acaricides and the recent advent of safer and more effective drugs has made the treatment of affected animals much easier than previously. This article aims to help veterinary practitioners choose the safest and most efficient therapy for canine demodicosis and focuses on the treatment options available in the UK.
Systematic reviews: causes of non-adherence to P2Y12 inhibitors in acute coronary syndromes and response to intervention
Authors: Johnston Nina , Weinman John , Ashworth Lucy , Smethurst Peter , El Khoury Jad , Moloney Clare
Published: October 2016

To understand the factors associated with non-adherence to oral antiplatelet (OAP) therapy in acute coronary syndromes (ACS), and where interventions have modified these factors. Linked systematic reviews were undertaken in accordance with the Preferred Reporting Items for Systematic reviews and Meta-analysis guidelines, using CINAHL Plus, MEDLINE, PsycINFO and PubMed databases. The searches were limited to studies available in English and published from 2000 onwards; last run in June 2015. Review 1: factors. Fifteen articles were identified that reported 25 different factors associated with OAP non-adherence. Factors were categorised into: Demographic, Treatment, Healthcare System Processes, Clinical, Opportunity (ie, factors outside the patients, such as cost and healthcare access) and Psychosocial. It was not possible to determine if any of these factors were more impactful than others, either overall or temporally. Review 2: interventions. Six articles were identified that described interventions targeting adherence in patients with acute coronary syndromes (ACS)/coronary artery disease (CAD). Four broad categories of intervention were identified: treatment counselling and education, educational materials, SMS reminders and telephone monitoring and reinforcement delivered different practitioners. Only reminder-based interventions had a consistently successful impact on adherence outcomes at both 3 and 12 months. A number of factors are associated with OAP non-adherence, and encouragingly, there is some evidence of the effectiveness of intervention to modify treatment adherence in patients with ACS/CAD. Future evaluations ensuring a better cohesion between the factors studied as associated with non-adherence and those targeted by intervention would further increase understanding and lead to improved results.
Bisphenol A interferes with swine vascular endothelial cell functions
Authors: Basini Giuseppina , Bussolati Simona , Grolli Stefano , Ramoni Roberto , Grasselli Francesca
Published: October 2016

Several studies have demonstrated that the endocrine disruptor bisphenol A (BPA) negatively affects animal and human health. An angiogenic process has been suggested among the events disrupted by this molecule, but the underlying mechanisms have not yet been clarified. The effect of BPA on angiogenesis was investigated by means of a bioassay previously validated in our laboratory. Using immortalized swine aortic endothelial cell line (AOC), the development of new blood vessels through a three-dimensional in vitro angiogenesis assay was evaluated. Subsequently, since vascular endothelial growth factor (VEGF) and nitric oxide (NO) are key players in the regulation of the angiogenic process, the effect of BPA on the production of these molecules by AOC was examined. BPA (10 μmol/L) stimulated AOC growth (p < 0.05) and VEGF production (p < 0.05), but did not modify NO levels. Our data suggest that the endocrine-disrupting effects of BPA could also be associated with the promotion of vascular growth, thus interfering with a physiologically finely tuned process resulting from a delicate balance of numerous molecular processes. The stimulatory effects of BPA on VEGF production may have negative implications, potentially switching the balance toward uncontrolled neovascularization. Moreover, since angiogenesis is involved in several pathologies, including cancer growth and progression, potential health risks of BPA exposure should be carefully monitored.