bluuebunny/crossref_metadata_2025 huggingface dataset:
Genotypic diversity and differentiation among populations of two benthic freshwater diatoms as revealed by microsatellites
Authors: Vanormelingen Pieter , Evans Katharine M. , Mann David G. , Lance Stacey , Debeer Ann‐Eline , D'Hondt Sofie , Verstraete Tine , De Meester Luc , Vyverman Wim
Published: July 2015

Given their large population sizes and presumed high dispersal capacity, protists are expected to exhibit homogeneous population structure over large spatial scales. On the other hand, the fragmented and short‐lived nature of the lentic freshwater habitats that many protists inhabit promotes strong population differentiation. We used microsatellites in two benthic freshwater diatoms,Eunotia bilunaris‘robust’ andSellaphora capitata, sampled from within a pond and connected ponds, through isolated ponds from the same region to western Europe to determine the spatial scale at which differentiation appears. Because periods of low genotypic diversity contribute to population differentiation, we also assessed genotypic diversity. While genotypic diversity was very high to maximal in most samples of both species, some had a markedly lower diversity, with up to half (Eunotia) and over 90% (Sellaphora) of the strains having the same multilocus genotype. Population differentiation showed an isolation‐by‐distance pattern with very low standardizedFSTvalues between samples from the same or connected ponds but high values between isolated ponds, even when situated in the same region. PartialrbcL sequences inEunotiawere consistent with this pattern as isolated ponds in the same region could differ widely in haplotype composition. Populations identified byStructurecorresponded to the source ponds, confirming that ‘pond’ is the main factor structuring these populations. We conclude that freshwater benthic diatom populations are highly fragmented on a regional scale, reflecting either less dispersal than is often assumed or reduced establishment success of immigrants, so that dispersal does not translate into gene flow.
Arabidopsis GERANYLGERANYL DIPHOSPHATE SYNTHASE 11 is a hub isozyme required for the production of most photosynthesis‐related isoprenoids
Authors: Ruiz‐Sola M. Águila , Coman Diana , Beck Gilles , Barja M. Victoria , Colinas Maite , Graf Alexander , Welsch Ralf , Rütimann Philipp , Bühlmann Peter , Bigler Laurent , Gruissem Wilhelm , Rodríguez‐Concepción Manuel , Vranová Eva
Published: July 2015

Most plastid isoprenoids, including photosynthesis‐related metabolites such as carotenoids and the side chain of chlorophylls, tocopherols (vitamin E), phylloquinones (vitamin K), and plastoquinones, derive from geranylgeranyl diphosphate (GGPP) synthesized by GGPP synthase (GGPPS) enzymes. Seven out of 10 functional GGPPS isozymes in Arabidopsis thaliana reside in plastids. We aimed to address the function of different GGPPS paralogues for plastid isoprenoid biosynthesis.

We constructed a gene co‐expression network (GCN) using GGPPS paralogues as guide genes and genes from the upstream and downstream pathways as query genes. Furthermore, knock‐out and/or knock‐down ggpps mutants were generated and their growth and metabolic phenotypes were analyzed. Also, interacting protein partners of GGPPS11 were searched for.

Our data showed that GGPPS11, encoding the only plastid isozyme essential for plant development, functions as a hub gene among GGPPS paralogues and is required for the production of all major groups of plastid isoprenoids. Furthermore, we showed that the GGPPS11 protein physically interacts with enzymes that use GGPP for the production of carotenoids, chlorophylls, tocopherols, phylloquinone, and plastoquinone.

GGPPS11 is a hub isozyme required for the production of most photosynthesis‐related isoprenoids. Both gene co‐expression and protein–protein interaction likely contribute to the channeling of GGPP by GGPPS11.
Breeding timed to maximize reproductive success for a migratory songbird: the importance of phenological asynchrony
Authors: Lany Nina K. , Ayres Matthew P. , Stange Erik E. , Sillett T. Scott , Rodenhouse Nicholas L. , Holmes Richard T.
Published: July 2015

Phenological advances and trophic mismatches are frequently reported ecological consequences of climate warming. Trophic mismatches occur when phenological responses to environmental conditions differ among trophic levels such that the timing of resource demand by consumers becomes decoupled from supply. We used 25 years of demographic measurements of a migratory songbird (the black‐throated blue warbler Setophaga caerulescens) to compare its breeding phenology to the phenology of both its caterpillar prey and the foliage on which caterpillars feed. Caterpillar biomass in this forest did not show a predictable seasonal pulse. Nest initiation by warblers in this northern hardwood forest was therefore not timed to coincide with a peak in food availability for nestlings. Nonetheless, timing of first clutches was strongly associated with spring leaf expansion (slope ± SE = 0.56 ± 0.08 days per day of change in leaf phenology, R2 = 0.66). Warblers adjusted the timing of breeding to early springs mainly by shortening the interval between arrival and clutch initiation, but this likely has limits because recent early springs are approaching the relatively inflexible dates when birds arrive on the breeding grounds. Although the timing of first nests did not match 1:1 with leaf‐out phenology, the adjustments in breeding time maximized mean annual reproductive success. Nest predation had the greatest effect on annual reproductive success, but the ability of nesting warblers to appropriately track leaf phenology accounted for effects on annual reproductive success comparable to the influence of variation in caterpillar abundance and conspecific density. Nesting phenology in black‐throated blue warblers was generally well matched to the timing of leaf‐out, even though the match was not 1:1. Without measurements of reproductive success, these unequal phenological shifts might otherwise have been interpreted as having negative ecological consequences.
High resilience masks underlying sensitivity to algal phase shifts of Pacific coral reefs
Authors: Mumby Peter J. , Steneck Robert S. , Adjeroud Mehdi , Arnold Suzanne N.
Published: July 2015

A single ecosystem can exhibit great biogeographic and environmental variability. While a given ecological driver might have a strong impact in one region, it does not necessarily hold that its importance will extend elsewhere. Coral reefs provide a striking example in that coral communities have low resilience in the Atlantic and remarkable resilience in parts of the species‐rich Pacific. Recent experimental evidence from the Atlantic finds that fishing of large herbivorous fish can be a strong driver of coral resilience. Here, we repeat the Atlantic experiment in the highly resilient forereef of Moorea (French Polynesia), which has repeatedly recovered from disturbances. A combination of cages, fish deterrents (FDs), and controls allowed us to simulate the consequences of fishing large herbivores on algal assemblages, coral recruitment, and the demographic rates of coral juveniles. We find that the impacts of removing large herbivorous reef fish vary with early coral ontogeny. Reduced herbivore access led to a modest macroalgal bloom and reduction in coral recruitment. However, larger juvenile corals (> 1 cm diameter) survived better and grew faster under these conditions because of a reduction in corallivory. To determine the net impact of losing larger herbivorous fish, we combined experimental results with estimated demographic parameters in an individual‐based model. Simulating coral recovery trajectories for five years, we find that protecting larger reef fish led to better recovery in 66–99% of simulations, depending on underlying assumptions (with the more credible assumptions being associated with greater likelihood of net positive impacts). While we find that fishing effects are detrimental to corals in both the Atlantic and Pacific systems studied, the nature of the interactions varied markedly. In the identical previously‐published study in the Atlantic, macroalgae exhibited a rapid bloom and caused a sufficiently large reduction in coral recruitment to force a predicted ecosystem shift to an alternative attractor. The commensurate macroalgal bloom in Moorea was weak yet the corals were two orders of magnitude more sensitive to its presence. We do not suggest that a reduction in recruitment in Moorea will lead to alternative attractors but the long‐term risks of a reduction in recovery rate are cause for concern as rates of coral mortality are projected to increase. The emerging picture is that Pacific reefs are less likely to experience macroalgal blooms but are surprisingly sensitive to such blooms if they occur.
Imiquimod and Photodynamic Therapy Are Useful in the Treatment of Porokeratosis in Children with Bone Marrow Transplantation
Authors: Gracia‐Cazaña Tamara , Vera‐Álvarez Jesús , García‐Patos Vicente , Gilaberte Yolanda
Published: July 2015

Porokeratosis is an uncommon disorder that affects keratinization. Immunosuppression may favor the development of porokeratotic lesions. Patients who receive allogenic transplants represent a therapeutic challenge to dermatologists. We report two cases of porokeratosis in children with bone marrow transplant and their excellent response to imiquimod and photodynamic therapy.
Dunaliella tertiolecta (Chlorophyta) Avoids Cell Death Under Ultraviolet Radiation By Triggering Alternative Photoprotective Mechanisms
Authors: Segovia María , Mata Teresa , Palma Armando , García‐Gómez Candela , Lorenzo Rosario , Rivera Alicia , Figueroa Félix L.
Published: July 2015

The effect of different ultraviolet radiation (UVR) treatments combining PAR (P), UVA (A) and UVB (B) on the molecular physiology of Dunaliella tertiolecta was studied during 6 days to assess the response to chronic UVR exposure. UVR reduced cell growth but did not cause cell death, as shown by the absence of SYTOX Green labeling and cellular morphology. However, caspase‐like enzymatic activities (CLs), (regarded as cell death proteases), were active even though the cells were not dying. Maximal quantum yield of fluorescence (Fv/Fm) and photosynthetic electron transport rate (ETR) dropped. Decreased nonphotochemical quenching (NPQ) paralleled a drop in xanthophyll cycle de‐epoxidation under UVB. Reactive oxygen species (ROS) and D1 protein accumulation were inversely correlated. PAB exhibited elevated ROS production at earlier times. Once ROS decayed, D1 protein recovered two‐fold compared with P and PA at later stages. Therefore, PsbA gene was still transcribed, suggesting ROS involvement in D1 recovery by its direct effect on mRNA‐translation. We add evidence of an UVB‐induced positive effect on the cells when P is present, providing photoprotection and resilience, by means of D1 repair. This allowed cells to survive. The photoprotective mechanisms described here (which are counterintuitive in principle) conform to an important ecophysiological response regarding light stress acclimation.
Changes in the Factors Influencing Public Acceptance of Nuclear Power Generation in Japan Since the 2011 Fukushima Daiichi Nuclear Disaster
Authors: Tsujikawa Norifumi , Tsuchida Shoji , Shiotani Takamasa
Published: July 2015

Public support for nuclear power generation has decreased in Japan since the Fukushima Daiichi nuclear accident in March 2011. This study examines how the factors influencing public acceptance of nuclear power changed after this event. The influence factors examined are perceived benefit, perceived risk, trust in the managing bodies, and pro‐environmental orientation (i.e., new ecological paradigm). This study is based on cross‐sectional data collected from two online nationwide surveys: one conducted in November 2009, before the nuclear accident, and the other in October 2011, after the accident. This study's target respondents were residents of Aomori, Miyagi, and Fukushima prefectures in the Tohoku region of Japan, as these areas were the epicenters of the Great East Japan Earthquake and the locations of nuclear power stations. After the accident, trust in the managing bodies was found to have a stronger influence on perceived risk, and pro‐environmental orientation was found to have a stronger influence on trust in the managing bodies; however, perceived benefit had a weaker positive influence on public acceptance. We also discuss the theoretical and practical implications of these findings.
Developmental Trajectories of Social Justice Values in Adolescence: Relations with Sympathy and Friendship Quality
Authors: Daniel Ella , Dys Sebastian P. , Buchmann Marlis , Malti Tina
Published: July 2015

This study examined developmental trajectories of social justice values (SJV) in a representative sample of Swiss adolescents (N = 1258) at 15 (Time 1), 18 (Time 2), and 21 years of age (Time 3). SJV and friendship quality were measured via self‐reports. Sympathy was assessed via self‐ and mother‐reports. Latent class growth analysis revealed three developmental trajectories of SJV: high‐stable (80 percent), moderate‐decreasing (17 percent), and low‐increasing (3 percent). Adolescents with low levels of self‐ and mother‐reported sympathy were more likely to be members of the low‐increasing than the high‐stable or moderate decreasing trajectory groups. Adolescents who reported low levels of sympathy and friendship quality at 15 years of age were more likely to be members of the moderate‐decreasing trajectory group than the high‐stable trajectory group. Results are discussed with respect to the potential significance of sympathy and friendship quality for understanding the development of SJV during adolescence.
The Shift from Traditional Marketing to Entrepreneurial Marketing Practices: A Literature Review
Authors: H Abdul Rahim, , K Ab. Wahab, , A Saad,
Published: July 2015

Small and medium enterprise(SME) have always been an interesting subject for research. In comparison to larger business organizations, SMEs faced many challenges including how they manage daily marketing activities and make marketing related decision. This study compiles the related literature review on the issues of traditional marketing and entrepreneurial marketing. Purpose: This study aims to explore the role of marketing practices in small and medium sized enterprises (SMEs) and to evaluate the impact of changes in marketing practices from traditional to entrepreneurial marketing practices will have an impact on the SME performance. Research methodology: A compilation of related literature review on traditional marketing and entrepreneurial marketing was done. An observation on the changes in marketing practices in small and medium enterprises towards a more innovative marketing practice were identified. Findings: Marketing in SMEs is centered on traditional methods such as using print media and hard selling. SME owners should take account of the findings and work towards introducing SME-specific marketing practices in trying to achieve higher sales volume and growth. In the study area which is Klang Valley, Malaysia the shift from traditional marketing to entrepreneurial marketing was observed amongst the SMEs being studied. Research limitations: This study uses a small number of SME companies in one region and therefore the generalizability of the findings may be limited. Further research could extend the number of SME companies and to other regions of Malaysia. Practical Implications: The findings have a bearing on the Malaysian SME performance. This study offers insights into how the marketing practices in Malaysian SMEs needs to be adapted in light of the findings to ensure marketing practices of SMEs are compatible with current digital approaches.
Strange metal without magnetic criticality
Authors: Tomita Takahiro , Kuga Kentaro , Uwatoko Yoshiya , Coleman Piers , Nakatsuji Satoru
Published: July 2015

A mysteriously misbehaving phase

Two electrons in a vacuum repel each other because they carry like charges. But in a metal, with a bunch of other electrons, in some ways they behave as if they didn't interact. This phenomenon, known as the Fermi liquid (FL) behavior, comes with a typical quadratic dependence of the solid's electrical resistance on temperature. Cases where the resistance deviates from the FL dependence are commonly associated with magnetic quantum criticality. Tomita
et al.
measured the resistivity of the heavy-fermion compound β-YbAlB
4
over a range of pressures and temperatures to identify a non-FL phase removed from a magnetic phase by an intervening FL. Explaining the non-FL behavior in the absence of magnetism presents a challenge to theorists.

Science
, this issue p.
506
Forensic labs explore blind testing to prevent errors
Authors: Servick Kelly
Published: July 2015

Evidence examiners get practical about fighting cognitive bias.
Alzheimer's amyloid theory gets modest boost
Authors: Underwood Emily
Published: July 2015

Trials of antibody drugs spawn hopes, doubts—and plans for more tests.
Cosmic convergence
Authors: Cho Adrian
Published: July 2015

Neutrinos from beyond our galaxy could be close kin to other mysterious visitors from space.
Setting the bar
Authors: Servick Kelly
Published: July 2015

As the U.S. military opens ground combat roles to women, it's looking to scientists to help define the standards.
A tale of two states
Authors: Holford Mandë , Nichols Rodney
Published: July 2015

On 20 July 2015, the United States reopened its embassy in Havana, Cuba, after more than 50 years, creating a spirit of engagement between the two Cold War adversaries. This is a welcome addition to the 285 U.S. embassies and consulates in 190 other countries and should encourage Cuban and American scientists to practice “science diplomacy.” Sadly, however, U.S. diplomacy has rarely paid enough attention to science. Given that science and technology (S&T) capabilities affect diplomatic agendas on a global scale, the powerful S&T base of the United States must be better linked to its foreign policy goals.
The structure of the regolith on 67P/Churyumov-Gerasimenko from ROLIS descent imaging
Authors: Mottola S. , Arnold G. , Grothues H.-G. , Jaumann R. , Michaelis H. , Neukum G. , Bibring J.-P. , Schröder S. E. , Hamm M. , Otto K. A. , Pelivan I. , Proffe G. , Scholten F. , Tirsch D. , Kreslavsky M. , Remetean E. , Souvannavong F. , Dolives B.
Published: July 2015

The structure of the upper layer of a comet is a product of its surface activity. The Rosetta Lander Imaging System (ROLIS) on board Philae acquired close-range images of the Agilkia site during its descent onto comet 67P/Churyumov-Gerasimenko. These images reveal a photometrically uniform surface covered by regolith composed of debris and blocks ranging in size from centimeters to 5 meters. At the highest resolution of 1 centimeter per pixel, the surface appears granular, with no apparent deposits of unresolved sand-sized particles. The thickness of the regolith varies across the imaged field from 0 to 1 to 2 meters. The presence of aeolian-like features resembling wind tails hints at regolith mobilization and erosion processes. Modeling suggests that abrasion driven by airfall-induced particle “splashing” is responsible for the observed formations.
67P/Churyumov-Gerasimenko surface properties as derived from CIVA panoramic images
Authors: Bibring J.-P. , Langevin Y. , Carter J. , Eng P. , Gondet B. , Jorda L. , Le Mouélic S. , Mottola S. , Pilorget C. , Poulet F. , Vincendon M.
Published: July 2015

The structure and composition of cometary constituents, down to their microscopic scale, are critical witnesses of the processes and ingredients that drove the formation and evolution of planetary bodies toward their present diversity. On board Rosetta’s lander Philae, the Comet Infrared and Visible Analyser (CIVA) experiment took a series of images to characterize the surface materials surrounding the lander on comet 67P/Churyumov-Gerasimenko. Images were collected twice: just after touchdown, and after Philae finally came to rest, where it acquired a full panorama. These images reveal a fractured surface with complex structure and a variety of grain scales and albedos, possibly constituting pristine cometary material.
Averting a North American biodiversity crisis
Authors: Yap Tiffany A. , Koo Michelle S. , Ambrose Richard F. , Wake David B. , Vredenburg Vance T.
Published: July 2015

A newly described pathogen poses a major threat to salamanders via trade
Jumping on water: Surface tension–dominated jumping of water striders and robotic insects
Authors: Koh Je-Sung , Yang Eunjin , Jung Gwang-Pil , Jung Sun-Pill , Son Jae Hak , Lee Sang-Im , Jablonski Piotr G. , Wood Robert J. , Kim Ho-Young , Cho Kyu-Jin
Published: July 2015

How to walk and jump on water

Jumping on land requires the coordinated motion of a number of muscles and joints in order to overcome gravity. Walking on water requires specialized legs that are designed to avoid breaking the surface tension during motion. But how do insects, such as water striders and fishing spiders, manage to jump on water, where extra force is needed to generate lift? Koh
et al.
studied water striders to determine the structure of the legs needed to make jumping possible, as well as the limits on the range of motion that avoids breaking the surface tension (see the Perspective by Vella). They then built water-jumping robots to verify the key parameters of leg design and motion.

Science
, this issue p.
517
; see also p.
472
ACD toxin–produced actin oligomers poison formin-controlled actin polymerization
Authors: Heisler David B. , Kudryashova Elena , Grinevich Dmitry O. , Suarez Cristian , Winkelman Jonathan D. , Birukov Konstantin G. , Kotha Sainath R. , Parinandi Narasimham L. , Vavylonis Dimitrios , Kovar David R. , Kudryashov Dmitri S.
Published: July 2015

A little toxin can do a lot

The actin cross-linking domain (ACD) is an actin-specific toxin produced by several bacterial pathogens. Heisler
et al.
discovered that ACD's pathogenic mechanism involves a highly unusual toxicity amplification cascade. Rather than directly inactivating the actin cytoskeleton, ACD blocks the activity of formins, actin regulatory proteins that play crucial roles in numerous cellular activities. ACD is exceptionally potent, even though its substrate is the most abundant protein of a eukaryotic cell: actin.

Science
, this issue p.
535
Ancient planetary dynamos, take two
Authors: Aubert Julien
Published: July 2015

Magnetic studies of Earth and Mercury constrain their ancient core dynamics

[Also see Report by

Tarduno
et al.

]
Spectroscopic observation of resonances in the F + H
2
reaction
Authors: Kim Jongjin B. , Weichman Marissa L. , Sjolander Tobias F. , Neumark Daniel M. , Kłos Jacek , Alexander Millard H. , Manolopoulos David E.
Published: July 2015

Glimpsing resonances as F and H
2
react

The reaction of fluorine atoms with hydrogen molecules has long provided a window into the subtle effects of quantum mechanics on chemical dynamics. Kim
et al.
now show that the system still has some secrets left to reveal. The authors applied photodetachment to FH
2
−
anions and their deuterated analogs. This allowed them to intercept the reaction trajectory in the middle and thereby uncover unanticipated weakly bound resonances. Theoretical calculations explain these observations and predict additional similar features that have yet to be seen.

Science
, this issue p.
510
Inside the mind of an engineer
Applied Minds: How Engineers Think
Guru Madhavan
Norton, 2015. 267 pp.
Authors: Derrible Sybil
Published: July 2015

Engaging anecdotes offer readers a glimpse into the problem-solving processes employed by engineers
The "Cryptic"
Escherichia
Authors: Walk Seth T.
Published: July 2015

In 2009, five monophyletic
Escherichia
clades were described and referred to as “cryptic” based on the inability to distinguish them from representative
E. coli
isolates using diagnostic biochemical reactions. Since this original publication, a number of studies have explored the genomic, transcriptomic, and phenotypic diversity of cryptic clade isolates to better understand their phylogenetic, physiological, and ecological distinctiveness with respect to previously named
Escherichia
species. This chapter reviews the original discovery of the cryptic clades, discusses available evidence that some are environmentally adapted, and evaluates current support for taxonomic designations of these microorganisms. The importance of these clades to clinical research, epidemiology, population genetics, and microbial speciation is also discussed.
Clonogrouping, a Rapid Multiplex PCR Method for Identification of Major Clones of Listeria monocytogenes
Authors: Chenal-Francisque Viviane , Maury Mylène M. , Lavina Morgane , Touchon Marie , Leclercq Alexandre , Lecuit Marc , Brisse Sylvain
Published: July 2015

Three multiplex PCR assays were developed to identify the 11 most common
Listeria monocytogenes
clones in clinical and food samples; 270 (95.7%) of 282 strains of serogroups IVb, IIb, IIa, and IIc were identified accurately. This novel tool is a rapid and efficient alternative to multilocus sequence typing for identification of
L. monocytogenes
clones.
Allocation of Klebsiella pneumoniae Bloodstream Isolates into Four Distinct Groups byompK36Typing in a Taiwanese University Hospital
Authors: Yan Jing-Jou , Zheng Po-Xing , Wang Ming-Cheng , Tsai Shu-Huei , Wang Li-Rong , Wu Jiunn-Jong
Published: July 2015

The OmpK36 porin plays a role in carbapenem resistance and may contribute to bacterial virulence inKlebsiella pneumoniae. This study aimed to investigate the characteristics of different groups ofK. pneumoniaeseparated byompK36typing. Among 226 nonduplicateK. pneumoniaebloodstream isolates collected at a Taiwanese hospital in 2011, fourompK36types, designated types A, B, C, and D, were identified by PCR in 61, 28, 100, and 36 isolates, respectively; 1 isolate was untypeable. Statistical analysis showed significantly higher rates of antimicrobial resistance (all tested antibiotics except meropenem), extended-spectrum β-lactamases or DHA-1 (47.5% together), Qnr-type quinolone resistance determinants (50.8%), and IncFIIA-type plasmids (49.2%) in group A than in others. Seventeen isolates were identified as belonging to 3 international high-risk clones (4 sequence type 11 [ST11], 10 ST15, and 3 ST147 isolates); all isolates but 1 ST15 isolate were classified in group A. The significant characteristics of group C were hypermucoviscosity (62.0%) and a higher virulence gene content. This group included all serotype K1 (n= 30), K2 (n= 25), and K5 (n= 3) isolates, 6 of 7 K57 isolates, all isolates of major clones associated with pyogenic liver abscesses (29 ST23, 11 ST65, 5 ST86, 7 ST373, and 1 ST375 isolates), and 16 (94.1%) of 17 isolates causing bacteremic liver abscesses. Twelve (42.9%) of the group B isolates were responsible for bacteremic biliary tract infections. Group D was predominant (83.3%) among 12 K20 isolates. This study suggests that most clinicalK. pneumoniaeisolates can be allocated into four groups with distinct characteristics based onompK36types.
Direct Detection of Erythromycin-Resistant Bordetella pertussis in Clinical Specimens by PCR
Authors: Wang Zengguo , Han Ruijun , Liu Ying , Du Quanli , Liu Jifeng , Ma Chaofeng , Li Hengxin , He Qiushui , Yan Yongping
Published: July 2015

Resistance of
Bordetella pertussis
to erythromycin has been increasingly reported. We developed an allele-specific PCR method for rapid detection of erythromycin-resistant
B. pertussis
directly from nasopharyngeal (NP) swab samples submitted for diagnostic PCR. Based on the proven association of erythromycin resistance with the A2047G mutation in the 23S rRNA of
B. pertussis
, four primers, two of which were designed to be specific for either the wild-type or the mutant allele, were used in two different versions of the allele-specific PCR assay. The methods were verified with results obtained by PCR-based sequencing of 16 recent
B. pertussis
isolates and 100 NP swab samples submitted for diagnostic PCR. The detection limits of the two PCR assays ranged from 10 to 100 fg per reaction for both erythromycin-susceptible and -resistant
B. pertussis
. Two amplified fragments of each PCR, of 286 and 112 bp, respectively, were obtained from a mutant allele of the isolates and/or NP swab samples containing
B. pertussis
DNAs. For the wild-type allele, only a 286-bp fragment was visible when the allele-specific PCR assay 1 was performed. No amplification was found when a number of non-
Bordetella
bacterial pathogens and NP swab samples that did not contain the DNAs of
B. pertussis
were examined. This assay can serve as an alternative for PCR-based sequencing, especially for local laboratories in resource-poor countries.
Innate Immune Activity Correlates with CD4 T Cell-Associated HIV-1 DNA Decline during Latency-Reversing Treatment with Panobinostat
Authors: Olesen Rikke , Vigano Selena , Rasmussen Thomas A. , Søgaard Ole S. , Ouyang Zhengyu , Buzon Maria , Bashirova Arman , Carrington Mary , Palmer Sarah , Brinkmann Christel R. , Yu Xu G. , Østergaard Lars , Tolstrup Martin , Lichterfeld Mathias
Published: July 2015

The pharmaceutical reactivation of dormant HIV-1 proviruses by histone deacetylase inhibitors (HDACi) represents a possible strategy to reduce the reservoir of HIV-1-infected cells in individuals treated with suppressive combination antiretroviral therapy (cART). However, the effects of such latency-reversing agents on the viral reservoir size are likely to be influenced by host immune responses. Here, we analyzed the immune factors associated with changes in proviral HIV-1 DNA levels during treatment with the potent HDACi panobinostat in a human clinical trial involving 15 cART-treated HIV-1-infected patients. We observed that the magnitude, breadth, and cytokine secretion profile of HIV-1-specific CD8 T cell responses were unrelated to changes in HIV-1 DNA levels in CD4 T cells during panobinostat treatment. In contrast, the proportions of CD3
−
CD56
+
total NK cells and CD16
+
CD56
dim
NK cells were inversely correlated with HIV-1 DNA levels throughout the study, and changes in HIV-1 DNA levels during panobinostat treatment were negatively associated with the corresponding changes in CD69
+
NK cells. Decreasing levels of HIV-1 DNA during latency-reversing treatment were also related to the proportions of plasmacytoid dendritic cells, to distinct expression patterns of interferon-stimulated genes, and to the expression of the
IL28B
CC genotype. Together, these data suggest that innate immune activity can critically modulate the effects of latency-reversing agents on the viral reservoir and may represent a target for future immunotherapeutic interventions in HIV-1 eradication studies.

IMPORTANCE
Currently available antiretroviral drugs are highly effective in suppressing HIV-1 replication, but the virus persists, despite treatment, in a latent form that does not actively express HIV-1 gene products. One approach to eliminate these cells, colloquially termed the “shock-and-kill” strategy, focuses on the use of latency-reversing agents that induce active viral gene expression in latently infected cells, followed by immune-mediated killing. Panobinostat, a histone deacetylase inhibitor, demonstrated potent activities in reversing HIV-1 latency in a recent pilot clinical trial and reduced HIV-1 DNA levels in a subset of patients. Interestingly, we found that innate immune factors, such as natural killer cells, plasmacytoid dendritic cells, and the expression patterns of interferon-stimulated genes, were most closely linked to a decline in the HIV-1 DNA level during treatment with panobinostat. These data suggest that innate immune activity may play an important role in reducing the residual reservoir of HIV-1-infected cells.
Bub1 in Complex with LANA Recruits PCNA To Regulate Kaposi's Sarcoma-Associated Herpesvirus Latent Replication and DNA Translesion Synthesis
Authors: Sun Zhiguo , Jha Hem Chandra , Robertson Erle S.
Published: July 2015

Latent DNA replication of Kaposi's sarcoma-associated herpesvirus (KSHV) initiates at the terminal repeat (TR) element and requires
trans
-acting elements, both viral and cellular, such as ORCs, MCMs, and latency-associated nuclear antigen (LANA). However, how cellular proteins are recruited to the viral genome is not very clear. Here, we demonstrated that the host cellular protein, Bub1, is involved in KSHV latent DNA replication. We show that Bub1 constitutively interacts with proliferating cell nuclear antigen (PCNA) via a highly conserved PIP box motif within the kinase domain. Furthermore, we demonstrated that Bub1 can form a complex with LANA and PCNA in KSHV-positive cells. This strongly indicated that Bub1 serves as a scaffold or molecular bridge between LANA and PCNA. LANA recruited PCNA to the KSHV genome via Bub1 to initiate viral replication in S phase and interacted with PCNA to promote its monoubiquitination in response to UV-induced damage for translesion DNA synthesis. This resulted in increased survival of KSHV-infected cells.

IMPORTANCE
During latency in KSHV-infected cells, the viral episomal DNA replicates once each cell cycle. KSHV does not express DNA replication proteins during latency. Instead, KSHV LANA recruits the host cell DNA replication machinery to the replication origin. However, the mechanism by which LANA mediates replication is uncertain. Here, we show that LANA is able to form a complex with PCNA, a critical protein for viral DNA replication. Furthermore, our findings suggest that Bub1, a spindle checkpoint protein, serves as a scaffold or molecular bridge between LANA and PCNA. Our data further support a role for Bub1 and LANA in PCNA-mediated cellular DNA replication processes as well as monoubiquitination of PCNA in response to UV damage. These data reveal a therapeutic target for inhibition of KSHV persistence in malignant cells.
Virulence and Fitness Determinants of Uropathogenic
Escherichia coli
Authors: Subashchandrabose Sargurunathan , Mobley Harry L. T.
Published: July 2015

Urinary tract infection (UTI) caused by uropathogenic
Escherichia coli
(UPEC) is a major global public health concern. Increasing antibiotic resistance found in clinical UPEC isolates underscores the immediate need for development of novel therapeutics against this pathogen. Better understanding of the fitness and virulence mechanisms that are integral to the pathogenesis of UTI will facilitate identification of novel strategies to prevent and treat infection with UPEC. Working towards that goal, the global UPEC research community has made great strides at unraveling various virulence and fitness genes. Here, we summarize major findings on virulence and fitness determinants that enable UPEC to successfully survive and colonize the urinary tract of mammalian hosts. Major sections of this chapter are devoted to the role of iron acquisition systems, metabolic pathways, fimbriae, flagella, toxins, biofilm formation, capsule, and strain-specific genes in the initiation and progression of UTIs. Transcriptomes of UPEC during experimental UTI in a murine model and naturally occurring UTI in women are compared to elucidate virulence mechanisms specifically involved in human UTI. Capitalizing on the advances in molecular pathogenesis research by translating these findings will help develop better clinical strategies for prevention and management of UTIs.
Retrospective study using MRI to measure depths of acupuncture points in neck and shoulder region
Authors: Chou Pei-Chi , Huang Yu-Chuen , Hsueh Chun-Jen , Lin Jaung-Geng , Chu Heng-Yi
Published: July 2015

Objectives

There are safety issues associated with acupuncture treatment. Previous studies regarding needling depth of acupuncture points revealed inconsistent results due to vague depth definition, acupuncture point localisation and measuring tools. The objective of this study is to find and compare the differences of the mean depths of 11 acupuncture points in the neck and shoulder region between subjects, with variables including gender and body mass index (BMI).

Setting

This study was conducted at a single medical center in Taiwan.

Participants

Three hundred and ninety-four participants were included in this study. Participants were grouped according to gender and BMI. Acupuncture points were localised by WHO standard and measured by MRI.

Outcome measures

The distance from the needle insertion point (surface of the skin) to any tissues that would cause possible/severe complications.

Results

Mean depths of 11 points were obtained in groups of different BMI and gender. Mean depths of all participants regardless of BMI and gender are as follows, in centimetres: GB21=5.6, SI14=5.2, SI15=8.8, GV15=4.9, GV16=4.6, GB20=5.0, ST9=1.6, SI16=1.8, SI17=2.4, TE16=3.1, LI18=1.3. Participants with higher BMI had greater measured depths in both gender groups. Male participants had larger mean depths than female participants regardless of BMI except in SI17 and LI18. When taking BMI into consideration, depths in male participants are greater than in female participants in most of the points except the following: GB21, TE16 in obesity group; ST9 in underweight and obesity group; SI16 in ideal body weight, overweight and obesity group; SI17, LI18 in each group.

Conclusions

Participants with higher BMI had greater measured depths and males tended to have greater depths in most of the points. Clinical practitioners are recommended to consider this information to prevent complications when applying acupuncture treatment to their patients.
Prevalence and determinants of excessive daytime sleepiness in hypertensive patients: a cross-sectional study in Douala, Cameroon
Authors: Mbatchou Ngahane Bertrand Hugo , Nganda Motto Malea , Dzudie Anastase , Luma Henry , Kamdem Félicité , Ngote Henri Roger , Monkam Yves , Kuaban Christopher
Published: July 2015

Objective

To determine the prevalence and determinants of excessive daytime sleepiness (EDS) among a group of sub-Saharan Africans living with hypertension.

Design

A cross-sectional study.

Setting

Cardiology outpatient unit of the Douala General Hospital in Cameroon.

Participants

Patients aged 15 years and over, being followed for hypertension between 1st January and 31st July 2013. Patients with unstable heart failure, stroke and head trauma were excluded.

Main outcome measure

EDS was the outcome of interest. It was defined as an Epworth sleeping scale greater or equal to 10. Logistic regression was used to identify factors associated with EDS.

Results

A total of 411 patients participated in this study, with a sex ratio (male/female) of 0.58 and a mean age of 55.56 years. No patient was underweight and the mean body mass index was 30 kg/m2. Controlled blood pressure was found in 92 (22.4%) patients. The prevalence of EDS was 62.78% (95% CI 58.08 to 67.47). The factors independently associated with EDS were: type 2 diabetes (OR 2.51; 95% CI 1 to 6.29), obesity (OR 2.75; 95% CI 1.52 to 4.97), snoring (OR 7.92; 95% CI 4.43 to 14.15) and uncontrolled blood pressure (OR 4.34; 95% CI 2.24 to 8.40).

Conclusions

A significant proportion of hypertensive patients suffer from EDS and present a high risk of sleep apnoea. Preventive measures targeted on weight loss, type 2 diabetes and snoring should be considered among these patients.
The persistent clustering of adult body mass index by school attended in adolescence
Authors: Evans Clare Rosenfeld , Lippert Adam M , Subramanian SV
Published: July 2015

Background

It is well known that adolescent body mass index (BMI) shows school-level clustering. We explore whether school-level clustering of BMI persists into adulthood.

Methods

Multilevel models nesting young adults in schools they attended as adolescents are fit for 3 outcomes: adolescent BMI, self-report adult BMI and measured adult BMI. Sex-stratified and race/ethnicity-stratified (black, Hispanic, white, other) analyses were also conducted.

Results

School-level clustering (wave 1 intraclass correlation coefficient (ICC)=1.3%) persists over time (wave 4 ICC=2%), and results are comparable across stratified analyses of both sexes and all racial/ethnic groups (except for Hispanics when measured BMIs are used). Controlling for BMI in adolescence partially attenuates this effect.

Conclusions

School-level clustering of BMI persists into young adulthood. Possible explanations include the salience of school environments in establishing behaviours and trajectories, the selection of adult social networks that resemble adolescent networks and reinforce previous behaviours, and characteristics of school catchment areas associated with BMI.
Tree-growth response to climatic variability in two climatically contrasting treeline ecotone areas, central Himalaya, Nepal
Authors: Shrestha Krishna B. , Hofgaard Annika , Vandvik Vigdis
Published: July 2015

Tree growth at the treeline ecotone is known to be sensitive to climate variability and is thus considered to be a worldwide biomonitor of climate change. However, our understanding of within-region variation in growth responses through space and time is limited. A dry south-facing slope dominated by Pinus wallichiana A.B. Jacks. and a wet north-facing slope dominated by Abies spectabilis (D. Don) Spach in Nepal, central Himalaya, were used to analyze the intersite (i.e., dry vs. wet sites) and intrasite (i.e., treeline vs. forest line elevations) tree-growth relationships, as well as response to monthly and seasonal temperature and precipitation at annual and bidecadal time scales. At both study sites and at two elevations within each site, growth can be strongly affected by growing-season and nongrowing-season factors; however, there are inconsistencies in terms of the climate–growth relationship across space and over time. At the dry site, only a weak positive growth response to summer temperature is observed. At both sites, there is a negative growth response to winter precipitation at both high and low elevations, and this response is markedly independent of the summer and winter temperature trends of the respective site. At the wet site, growth at the higher elevation is negatively correlated to the early summer temperature, whereas a positive growth response to spring precipitation is observed at the lower elevation, indicating a possible drought effect. The results illustrate how different climatic drivers may govern tree-growth responses both between sites with contrasting climates within a region and along elevational gradients within the treeline ecotone. This underlines the need for multiscale studies and a focus on multiple climate variables when analyzing treeline ecotone responses to climate change.
Inhibitory Effects of Epimedium Herb on the Inflammatory ResponseIn VitroandIn Vivo
Authors: Oh You-Chang , Jeong Yun Hee , Cho Won-Kyung , Ha Jeong-Ho , Lee Sang-Joon , Ma Jin Yeul
Published: July 2015

Epimedium Herb (EH) is a medicinal herb used in traditional Eastern Asia. In this study described, we investigated the biological effects of Epimedium Herb water extract (EHWE) on lipopolysaccharide (LPS)-mediated inflammation in macrophages and local inflammation in vivo. We also investigated the biological effects of EHWE on the production of inflammatory mediators, pro-inflammatory cytokines and related products, as well as nuclear factor κB (NF-κB) and mitogen-activated protein kinase (MAPK) activation in LPS-stimulated macrophages. The analgesic effect of the acetic acid-induced writhing response and inhibitory activity on xylene-induced ear edema was also evaluated in mice. EHWE exhibited anti-inflammatory effects by inhibiting the production of nitric oxide (NO), interleukin (IL)-6 and IL-1β. In addition, EHWE strongly suppressed inducible nitric oxide synthase (iNOS), a NO synthesis enzyme, induced heme oxygenase-1 (HO-1) expression, and inhibited NF-κB activation as well as MAPK pathway phosphorylation. Furthermore, EHWE exhibited an analgesic effect on the writhing response and an inhibitory effect on ear edema in mice. For the first time, we demonstrated the anti-inflammatory effects and inhibitory mechanism in macrophages, as well as the inhibitory activity of EHWE in vivo. Our results indicate a potential use of EHWE as an inflammatory therapeutic agent developed from a natural substance.
GUP-corrected thermodynamics for all black objects and the existence of remnants
Authors: Faizal Mir , Khalil Mohammed M.
Published: July 2015

Based on the universality of the entropy-area relation of a black hole, and the fact that the generalized uncertainty principle (GUP) adds a logarithmic correction term to the entropy in accordance with most approaches to quantum gravity, we argue that the GUP-corrected entropy-area relation is universal for all black objects. This correction to the entropy produces corrections to the thermodynamics. We explicitly calculate these corrections for three types of black holes: Reissner–Nordström, Kerr and charged AdS black holes, in addition to spinning black rings. In all cases, we find that they produce a remnant. Even though the GUP-corrected entropy-area relation produces the logarithmic term in the series expansion, we need to use the full form of the GUP-corrected entropy-area relation to get remnants for these black holes.
Sudden transitions of trace distance discord of dipole–dipole coupled two qubits
Authors: Hu Zheng-Da , Wang Jicheng , Zhang Yixin , Zhang Ye-Qi
Published: July 2015

We investigate the exact dynamics of trace distance discord (TDD) by considering two qubits under dephasing whose states belong to a class of X states beyond Bell diagonal form. The necessary condition for the occurrence of freezing TDD is found and compared with that of entropic discord. For an illustration, we consider two interacting qubits coupled to independent reservoirs and demonstrate these dynamical properties of TDD. It is interesting to find that the freezing TDD exists even for X states without maximally mixed marginals and can be tuned by dipole–dipole coupling of two qubits. Moreover, we consider the initial extended Werner-like (EWL) states and investigate the differences between TDD and entanglement. The influences of initial state and the dipole–dipole coupling of the two qubits on the dynamics of nonclassical correlations are explored.
Parallel lattice Boltzmann simulation of bubble rising and coalescence in viscous flows
Authors: Shi Dongyan , Wang Zhikai
Published: July 2015

A parallel three-dimensional lattice Boltzmann scheme for multicomponent immiscible fluids is proposed to simulate bubble rising and coalescence process in viscous flows. The lattice Boltzmann scheme is based on the free-energy model and is parallelized in the share-memory model by using the OpenMP. Bubble interface is described by a diffusion interface method solving the Cahn–Hilliard equation and both the surface tension force and the buoyancy are introduced in a form of discrete body force. To avoid the numerical instability caused by the interface deformation, the 18 point finite difference scheme is utilized to calculate the first- and second-order space derivative. The correction of the parallel scheme handling three-dimensional interfaces is verified by the Laplace law and the dynamic characteristics of an isolated bubble in stationary flows. Subsequently, effects of the initially relative position, accompanied by the size ratio on bubble–bubble interaction are studied. The results show that the present scheme can effectively describe the bubble interface dynamics, even if rupture and restructure occurs. In addition to the repulsion and coalescence phenomenon due to the relative position, the size ratio also plays an insignificant role in bubble deformation and trajectory.