bluuebunny/crossref_metadata_2025_split huggingface dataset:
Palaeoproxies: botanical monitors and recorders of atmospheric change
Authors: Lomax Barry H. , Fraser Wesley T. 
Published: July 2015

AbstractThe integration of plant and Earth sciences offers the opportunity to develop and test palaeobotanical monitors and recorders (palaeoproxies) of past atmospheric change that are understood from a mechanistic perspective, with the underpinning responses being identified and understood at the genetic level. This review highlights how this approach has been used to deliver two distinct palaeoproxies. The first is based on the negative relationship between stomata (breathing pores found on the leaf surface) and atmospheric CO2 concentration; the second is based on tracking chemical changes seen in the composition of pollen and spores to reconstruct changes in the flux of UV‐B radiation on the Earth's surface and from this infer changes in stratospheric processes linked to the eruption and emplacement of Large Igneous Provinces. Here, we highlight the potential of integrating a new rapid, inexpensive chemical analysis technique with existing, robust palynological methods, opening the door to a deeper understanding of past environments via the palaeobiological record. A look to the future suggests a combined solar radiation–CO2 concentration approach could be readily applied across the geological record.
Influence of body size on fecundity and sperm management in the parasitoid wasp Anisopteromalus calandrae
Authors: Kasamatsu Eiichi , Abe Jun 
Published: July 2015

AbstractA large body size is considered to be advantageous to the reproductive success of females as a result of several factors, such as the allocation of more resources to reproduction and the efficient management of sperm transferred by males. In the present study, the effects of female body size, female mating status and additional food availability on fecundity and the offspring sex ratio are investigated in the parasitoid wasp Anisopteromalus calandrae Howard (Hymenoptera: Pteromalidae). Because of haplodiploid sex determination, females must fertilize eggs to produce female offspring but not to produce male offspring. As predicted, female fecundity and the number of female offspring are positively correlated with body size. However, although the volume of the spermatheca increases with female body size, the amount of sperm stored in the spermatheca is relatively constant, irrespective of body size. Consequently, larger females produce a greater proportion of male offspring, especially at the end of the oviposition sequence, suggesting that larger females that possess more resources for reproduction and produce a larger number of offspring are more likely to suffer sperm depletion. The results of the present study also show that mated females have an increased fecundity compared with virgin females, although the opportunity to feed on honey along with host feeding has no impact upon fecundity or the sex ratio.
Effectiveness of antibacterial prophylaxis with non‐absorbable polymyxin B compared to levofloxacin after allogeneic hematopoietic stem cell transplantation
Authors: Koh S. , Yamada K. , Nishimoto M. , Hayashi Y. , Koh H. , Nakashima Y. , Nakane T. , Hirose A. , Nakamae M. , Kakeya H. , Hino M. , Nakamae H. 
Published: July 2015

AbstractBackgroundFluoroquinolones are widely used for antibacterial prophylaxis during neutropenia following hematopoietic stem cell transplantation (HSCT). Nevertheless, data are inadequate as to whether fluoroquinolones decrease mortality rate compared with other antibiotics.MethodsWe retrospectively compared the efficacy of antibacterial prophylaxis using non‐absorbable polymyxin B (PB) (n = 106) or systemic levofloxacin (LVFX) (n = 140) after allogeneic SCT at our institute between 2004 and 2013.ResultsNo significant difference was observed between the 2 groups in the cumulative incidences of failure of prophylaxis (P = 0.21), clinically documented infections (P = 0.70), or non‐relapse mortality within the first 100 days after transplantation (P = 0.42). With bacteremia, the rate of resistance to LVFX was 82% in the PB group and 100% in the LVFX group (P = 0.41). Also, no significant difference was found in overall survival between the 2 groups (P = 0.78).ConclusionOur results indicate no difference in the effectiveness of antibacterial prophylaxis between systemic antibiotic LVFX and non‐absorbable antibiotic PB.
Trade Liberalisation and Capital Spending by US Manufacturers
Authors: Liebman Benjamin H. , Reynolds Kara M. 
Published: July 2015

AbstractThis is the first paper to study the impact of long‐term tariff reductions on capital spending by US manufacturers. We investigate fluctuations in investment for approximately 400 different four‐digit industries during the period 1974–2005. Our results indicate that the dismantling of tariff and quota protection has had a stimulatory effect on US manufacturing investment, despite the relatively low average tariff rate that existed at the start of our sample period. However, our findings reveal that reductions in input tariffs rather than output tariffs were the source of this effect, suggesting that better access to foreign inputs rather than increased foreign competition at the output level served as the primary stimulus for increased US manufacturing investment.
Sensory initiation of a co‐ordinated motor response: synaptic excitation underlying simple decision‐making
Authors: Buhl Edgar , Soffe Stephen R. , Roberts Alan 
Published: July 2015

Key points
Deciding whether or how to initiate a motor response to a stimulus can be surprisingly slow and the underlying processes are not well understood.
The neuronal circuitry that allows frog tadpoles to swim in response to touch is well characterized and includes excitatory reticulospinal neurons that drive swim circuit neurons.
Build‐up of excitation to reticulospinal neurons is the key decision‐making step for swimming. Asymmetry in this build‐up between the two sides allows bilateral initiation at the same time as avoiding inappropriate co‐activation of motor antagonists.
Following stronger stimuli, reticulospinal neurons are excited through a trigeminal nucleus pathway and swimming starts first on the stimulated side. If this pathway fails or is lesioned, swimming starts later on the unstimulated side.
The mechanisms underlying initiation of a simple tadpole motor response may share similarities with more complex decisions in other animals, including humans.
AbstractAnimals take time to make co‐ordinated motor responses to a stimulus. How can sensory input initiate organized movements, activating all necessary elements at the same time as avoiding inappropriate co‐excitation of antagonistic muscles? In vertebrates, this process usually results in the activation of reticulospinal pathways. Young Xenopus tadpoles can respond to head‐skin touch by swimming, which may start on either side. We investigate how motor networks in the brain are organized, and whether asymmetries in touch sensory pathways avoid co‐activation of antagonists at the same time as producing co‐ordinated movements. We record from key reticulospinal neurons in the network controlling swimming. When the head skin is stimulated unilaterally, excitation builds up slowly and asymmetrically in these neurons such that those on both sides do not fire synchronously. This build‐up of excitation to threshold is the key decision‐making step and determines whether swimming will start, as well as on which side. In response to stronger stimuli, the stimulated side tends to ‘win’ because excitation from a shorter, trigeminal nucleus pathway becomes reliable and can initiate swimming earlier on the stimulated side. When this pathway fails or is lesioned, swimming starts later and on the unstimulated side. Stochasticity in the trigeminal nucleus pathway allows unpredictable turning behaviour to weaker stimuli, conferring potential survival benefits. We locate the longer, commissural sensory pathway carrying excitation to the unstimulated side and record from its neurons. These neurons fire to head‐skin stimuli but excite reticulospinal neurons indirectly. We propose that asymmetries in the sensory pathways exciting brainstem reticulospinal neurons ensure alternating and co‐ordinated swimming activity from the start.
Current Progress in Developing Subunit Vaccines against Enterotoxigenic Escherichia coli-Associated Diarrhea
Authors: Zhang Weiping , Sack David A. 
Published: July 2015

ABSTRACT

Diarrhea continues to be a leading cause of death in children <5 years of age, and enterotoxigenic
Escherichia coli
(ETEC) is the most common bacterial cause of children's diarrhea. Currently, there are no available vaccines against ETEC-associated diarrhea. Whole-cell vaccine candidates have been under development but require further improvements because they provide inadequate protection and produce unwanted adverse effects. Meanwhile, a newer approach using polypeptide or subunit vaccine candidates focusing on ETEC colonization factor antigens (CFAs) and enterotoxins, the major virulence determinants of ETEC diarrhea, shows substantial promise. A conservative CFA/I adhesin tip antigen and a CFA MEFA (multiepitope fusion antigen) were shown to induce cross-reactive antiadhesin antibodies that protected against adherence by multiple important CFAs. Genetic fusion of toxoids derived from ETEC heat-labile toxin (LT) and heat-stable toxin (STa) induced antibodies neutralizing both enterotoxins. Moreover, CFA-toxoid MEFA polypeptides, generated by fusing CFA MEFA to an STa-LT toxoid fusion, induced antiadhesin antibodies that broadly inhibited adherence of the seven most important ETEC CFAs associated with about 80% of the diarrhea cases caused by ETEC strains with known CFAs. This same antigen preparation also induced antitoxin antibodies that neutralized both toxins that are associated with all cases of ETEC diarrhea. Results from these studies suggest that polypeptide or subunit vaccines have the potential to effectively protect against ETEC diarrhea. In addition, novel adhesins and mucin proteases have been investigated as potential alternatives or, more likely, additional antigens for ETEC subunit vaccine development.
Contribution of Reduced Interleukin-10 Levels to the Pathogenesis of Osteomyelitis in Children with Sickle Cell Disease
Authors: Sarray Sameh , Almawi Wassim Y. 
Published: July 2015

ABSTRACTOsteomyelitis is a significant complication of sickle cell disease (SCD), and several factors contribute to its pathogenesis, including altered expression of proinflammatory and anti-inflammatory cytokines. In view of the role of interleukin-10 (IL-10) as an anti-inflammatory cytokine, we tested the notion that SCD osteomyelitis is associated with a reduction in IL-10 secretion and, hence, precipitation of a proinflammatory state. Study subjects comprised 52 SCD patients with confirmed diagnosis of osteomyelitis and 165 age- and gender-matched SCD patients with negative histories of osteomyelitis. Results obtained showed that IL-10 serum levels in SCD osteomyelitis patients were significantly lower than those of control SCD patients. Receiver operating characteristic (ROC) analysis demonstrated that altered IL-10 serum levels predicted the development of osteomyelitis, and the mean area under ROC curves of IL-10 was 0.810 among SCD patients with osteomyelitis. A systematic shift in IL-10 serum levels toward lower values was seen in osteomyelitis cases, with an increased osteomyelitis risk associated with decreased IL-10 levels. Multivariate logistic regression analyses confirmed the independent association of reduced IL-10 with osteomyelitis after controlling for sickle hemoglobin (HbS), fetal hemoglobin (HbF), platelet count, and white blood cell (WBC) count. These data support the strong association of decreased IL-10 levels with osteomyelitis, thereby supporting a role for IL-10 in osteomyelitis follow-up.
The Carbomer-Lecithin Adjuvant Adjuplex Has Potent Immunoactivating Properties and Elicits Protective Adaptive Immunity against Influenza Virus Challenge in Mice
Authors: Wegmann Frank , Moghaddam Amin E. , Schiffner Torben , Gartlan Kate H. , Powell Timothy J. , Russell Rebecca A. , Baart Matthijs , Carrow Emily W. , Sattentau Quentin J. 
Published: July 2015

ABSTRACT

The continued discovery and development of adjuvants for vaccine formulation are important to safely increase potency and/or reduce the antigen doses of existing vaccines and tailor the adaptive immune response to newly developed vaccines. Adjuplex is a novel adjuvant platform based on a purified lecithin and carbomer homopolymer. Here, we analyzed the adjuvant activity of Adjuplex in mice for the soluble hemagglutinin (HA) glycoprotein of influenza A virus. The titration of Adjuplex revealed an optimal dose of 1% for immunogenicity, eliciting high titers of HA-specific IgG but inducing no significant weight loss. At this dose, Adjuplex completely protected mice from an otherwise lethal influenza virus challenge and was at least as effective as the adjuvants monophosphoryl lipid A (MPL) and alum in preventing disease. Adjuplex elicited balanced Th1-/Th2-type immune responses with accompanying cytokines and triggered antigen-specific CD8
+
T-cell proliferation. The use of the peritoneal inflammation model revealed that Adjuplex recruited dendritic cells (DCs), monocytes, and neutrophils in the context of innate cytokine and chemokine secretion. Adjuplex neither triggered classical maturation of DCs nor activated a pathogen recognition receptor (PRR)-expressing NF-κB reporter cell line, suggesting a mechanism of action different from that reported for classical pathogen-associated molecular pattern (PAMP)-activated innate immunity. Taken together, these data reveal Adjuplex to be a potent and well-tolerated adjuvant with application for subunit vaccines.
Mycoplasma hominis, a Rare but True Cause of Infective Endocarditis
Authors: Gagneux-Brunon Amandine , Grattard Florence , Morel Jerome , Suy Florence , Fuzellier Jean-François , Verhoeven Paul , Cazorla Celine , Guglielminotti Claire , Fresard Anne , Lucht Frederic , Botelho-Nevers Elisabeth 
Published: July 2015

ABSTRACT

Mycoplasma spp. are rarely recognized agents of infective endocarditis. We report a case of
Mycoplasma hominis
prosthetic valve endocarditis diagnosed by 16S ribosomal DNA (rDNA) PCR and culture of valves in a 74-year-old man. We reviewed the literature and found only 8 other cases reported.
Characterization of Third-Generation-Cephalosporin-Resistant Shiga Toxin-Producing Strains of Escherichia coli O157:H7 in Japan
Authors: Kawahara Ryuji , Seto Kazuko , Taguchi Masumi , Nakajima Chie , Kumeda Yuko , Suzuki Yasuhiko 
Published: July 2015

ABSTRACTWe isolated Shiga toxin-producingEscherichia coliO157:H7 strains resistant to third-generation cephalosporins. The resistant strains harboredblaCMY-2, a plasmid-mediated AmpC β-lactamase. Genotyping of isolates revealed the possible spread of this problematic bacterium. Results suggested the importance of the investigation and surveillance of enterobacteria with plasmids harboringblaCMY-2.
Use of Alignment-Free Phylogenetics for Rapid Genome Sequence-Based Typing of Helicobacter pylori Virulence Markers and Antibiotic Susceptibility
Authors: van Vliet Arnoud H. M. , Kusters Johannes G. 
Published: July 2015

ABSTRACT

Whole-genome sequencing is becoming a leading technology in the typing and epidemiology of microbial pathogens, but the increase in genomic information necessitates significant investment in bioinformatic resources and expertise, and currently used methodologies struggle with genetically heterogeneous bacteria such as the human gastric pathogen
Helicobacter pylori
. Here we demonstrate that the alignment-free analysis method feature frequency profiling (FFP) can be used to rapidly construct phylogenetic trees of draft bacterial genome sequences on a standard desktop computer and that coupling with
in silico
genotyping methods gives useful information for comparative and clinical genomic and molecular epidemiology applications. FFP-based phylogenetic trees of seven gastric
Helicobacter
species matched those obtained by analysis of 16S rRNA genes and ribosomal proteins, and FFP- and core genome single nucleotide polymorphism-based analysis of 63
H. pylori
genomes again showed comparable phylogenetic clustering, consistent with genomotypes assigned by using multilocus sequence typing (MLST). Analysis of 377
H. pylori
genomes highlighted the conservation of genomotypes and linkage with phylogeographic characteristics and predicted the presence of an incomplete or nonfunctional
cag
pathogenicity island in 18/276 genomes.
In silico
analysis of antibiotic susceptibility markers suggests that most
H. pylori
hspAmerind and hspEAsia isolates are predicted to carry the T
2812
C mutation potentially conferring low-level clarithromycin resistance, while levels of metronidazole resistance were similar in all multilocus sequence types. In conclusion, the use of FFP phylogenetic clustering and
in silico
genotyping allows determination of genome evolution and phylogeographic clustering and can contribute to clinical microbiology by genomotyping for outbreak management and the prediction of pathogenic potential and antibiotic susceptibility.
Impact of Mutations at Amino Acid 70 in Hepatitis C Virus (HCV) Genotype 1b Core Region on Hepatocarcinogenesis following Eradication of HCV RNA
Authors: Akuta Norio , Suzuki Fumitaka , Kobayashi Masahiro , Sezaki Hitomi , Kawamura Yusuke , Hosaka Tetsuya , Kobayashi Mariko , Saitoh Satoshi , Suzuki Yoshiyuki , Arase Yasuji , Ikeda Kenji , Kumada Hiromitsu 
Published: July 2015

ABSTRACT
The impact of the HCV genotype 1b core amino acid (aa) 70 mutant on the cumulative rate of hepatocellular carcinoma following eradication of HCV RNA by antiviral therapy was investigated with the Q-Invader assay. Multivariate analysis based on 649 patients indicated that a core aa70 Q-Invader mutant level ≥20% is a predictor of hepatocellular carcinoma.
Comparison of Three Commercial Molecular Assays for Detection of Rifampin and Isoniazid Resistance among Mycobacterium tuberculosis Isolates in a High-HIV-Prevalence Setting
Authors: Strydom K. , Ismail F. , Matabane M. M. Z. , Onwuegbuna O. , Omar S. V. , Ismail N. 
Published: July 2015

ABSTRACT

In a head-to-head comparison of the MTBDR
plus
version 2.0 (Hain Lifescience), the Xpert MTB/RIF (Cepheid), and the Anyplex MTB/NTM (Seegene) assays, we demonstrated equal sensitivity (59/61; 96.7%) and specificity (53/54; 98.1%) for detecting rifampin resistance with further analysis of discordances. The Xpert assay does not detect isoniazid resistance while the Anyplex assay showed high false positivity.
Evolution of Influenza B Virus in Kuala Lumpur, Malaysia, between 1995 and 2008
Authors: Sam I-Ching , Su Yvonne C. F. , Chan Yoke Fun , Nor'E Siti Sarah , Hassan Ardalinah , Jafar Faizatul Lela , Joseph Udayan , Halpin Rebecca A. , Ghedin Elodie , Hooi Poh Sim , Fourment Mathieu , Hassan Hamimah , AbuBakar Sazaly , Wentworth David E. , Smith Gavin J. D. 
Published: July 2015

ABSTRACT
Influenza B virus causes significant disease but remains understudied in tropical regions. We sequenced 72 influenza B viruses collected in Kuala Lumpur, Malaysia, from 1995 to 2008. The predominant circulating lineage (Victoria or Yamagata) changed every 1 to 3 years, and these shifts were associated with increased incidence of influenza B. We also found poor lineage matches with recommended influenza virus vaccine strains. While most influenza B virus lineages in Malaysia were short-lived, one circulated for 3 to 4 years.
Exploring the Balance between DNA Pressure and Capsid Stability in Herpesviruses and Phages
Authors: Bauer D. W. , Li D. , Huffman J. , Homa F. L. , Wilson K. , Leavitt J. C. , Casjens S. R. , Baines J. , Evilevitch A. 
Published: July 2015

ABSTRACT
We have recently shown in both herpesviruses and phages that packaged viral DNA creates a pressure of tens of atmospheres pushing against the interior capsid wall. For the first time, using differential scanning microcalorimetry, we directly measured the energy powering the release of pressurized DNA from the capsid. Furthermore, using a new calorimetric assay to accurately determine the temperature inducing DNA release, we found a direct influence of internal DNA pressure on the stability of the viral particle. We show that the balance of forces between the DNA pressure and capsid strength, required for DNA retention between rounds of infection, is conserved between evolutionarily diverse bacterial viruses (phages λ and P22), as well as a eukaryotic virus, human herpes simplex 1 (HSV-1). Our data also suggest that the portal vertex in these viruses is the weakest point in the overall capsid structure and presents the Achilles heel of the virus's stability. Comparison between these viral systems shows that viruses with higher DNA packing density (resulting in higher capsid pressure) have inherently stronger capsid structures, preventing spontaneous genome release prior to infection. This force balance is of key importance for viral survival and replication. Investigating the ways to disrupt this balance can lead to development of new mutation-resistant antivirals.

IMPORTANCE
A virus can generally be described as a nucleic acid genome contained within a protective protein shell, called the capsid. For many double-stranded DNA viruses, confinement of the large DNA molecule within the small protein capsid results in an energetically stressed DNA state exerting tens of atmospheres of pressures on the inner capsid wall. We show that stability of viral particles (which directly relates to infectivity) is strongly influenced by the state of the packaged genome. Using scanning calorimetry on a bacterial virus (phage λ) as an experimental model system, we investigated the thermodynamics of genome release associated with destabilizing the viral particle. Furthermore, we compare the influence of tight genome confinement on the relative stability for diverse bacterial and eukaryotic viruses. These comparisons reveal an evolutionarily conserved force balance between the capsid stability and the density of the packaged genome.