bluuebunny/crossref_metadata_2025_split huggingface dataset:
Designing perfect linear polarization converters using perfect electric and magnetic conducting surfaces
Authors: Zhou Gaochao , Tao Xudong , Shen Ze , Zhu Guanghao , Jin Biaobing , Kang Lin , Xu Weiwei , Chen Jian , Wu Peiheng 
Published: December 2016

AbstractWe propose a kind of general framework for the design of a perfect linear polarization converter that works in the transmission mode. Using an intuitive picture that is based on the method of bi-directional polarization mode decomposition, it is shown that when the device under consideration simultaneously possesses two complementary symmetry planes, with one being equivalent to a perfect electric conducting surface and the other being equivalent to a perfect magnetic conducting surface, linear polarization conversion can occur with an efficiency of 100% in the absence of absorptive losses. The proposed framework is validated by two design examples that operate near 10 GHz, where the numerical, experimental and analytic results are in good agreements.
System-specific periodicity in quantitative real-time polymerase chain reaction data questions threshold-based quantitation
Authors: Spiess Andrej-Nikolai , Rödiger Stefan , Burdukiewicz Michał , Volksdorf Thomas , Tellinghuisen Joel 
Published: December 2016

AbstractReal-time quantitative polymerase chain reaction (qPCR) data are found to display periodic patterns in the fluorescence intensity as a function of sample number for fixed cycle number. This behavior is seen for technical replicate datasets recorded on several different commercial instruments; it occurs in the baseline region and typically increases with increasing cycle number in the growth and plateau regions. Autocorrelation analysis reveals periodicities of 12 for 96-well systems and 24 for a 384-well system, indicating a correlation with block architecture. Passive dye experiments show that the effect may be from optical detector bias. Importantly, the signal periodicity manifests as periodicity in quantification cycle (Cq) values when these are estimated by the widely applied fixed threshold approach, but not when scale-insensitive markers like first- and second-derivative maxima are used. Accordingly, any scale variability in the growth curves will lead to bias in constant-threshold-based Cqs, making it mandatory that workers should either use scale-insensitive Cqs or normalize their growth curves to constant amplitude before applying the constant threshold method.
Non-canonical integration events in Pichia pastoris encountered during standard transformation analysed with genome sequencing
Authors: Schwarzhans Jan-Philipp , Wibberg Daniel , Winkler Anika , Luttermann Tobias , Kalinowski Jörn , Friehs Karl 
Published: December 2016

AbstractThe non-conventional yeast Pichia pastoris is a popular host for recombinant protein production in scientific research and industry. Typically, the expression cassette is integrated into the genome via homologous recombination. Due to unknown integration events, a large clonal variability is often encountered consisting of clones with different productivities as well as aberrant morphological or growth characteristics. In this study, we analysed several clones with abnormal colony morphology and discovered unpredicted integration events via whole genome sequencing. These include (i) the relocation of the locus targeted for replacement to another chromosome (ii) co-integration of DNA from the E. coli plasmid host and (iii) the disruption of untargeted genes affecting colony morphology. Most of these events have not been reported so far in literature and present challenges for genetic engineering approaches in this yeast. Especially, the presence and independent activity of E. coli DNA elements in P. pastoris is of concern. In our study, we provide a deeper insight into these events and their potential origins. Steps preventing or reducing the risk for these phenomena are proposed and will help scientists working on genetic engineering of P. pastoris or similar non-conventional yeast to better understand and control clonal variability.
Analysis of complete genomes of the rubella virus genotypes 1E and 2B which circulated in China, 2000–2013
Authors: Zhu Zhen , Chen Min-hsin , Abernathy Emily , Icenogle Joseph , Zhou Shujie , Wang Changyin , Zhao Chunfang , Wang Yan , Chen Haiyun , Si Yuan , Xu Wenbo 
Published: December 2016

AbstractRubella viruses of genotypes 1E and 2B are currently the most frequently detected wild-type viruses in the world. Genotype 1E viruses from China have been genetically distinct from genotype 1E viruses found elsewhere, while genotype 2B viruses found in China are not distinguishable from genotype 2B viruses from other areas. Genetic clusters of viruses of both genotypes were defined previously using sequences of the 739-nt genotyping window. Here we report phylogenic analysis using whole genomic sequences from seven genotype 1E and three genotype 2B viruses which were isolated in China between 2000 and 2013 and confirm the subgrouping of current circulating genotypes 1E and 2B viruses. In addition, the whole genomic characterization of Chinese rubella viruses was clarified. The results indicated that the Chinese rubella viruses were highly conserved at the genomic level, and no predicted amino acid variations were found at positions where functional domains of the proteins were identified. Therefore, it gives us the idea that the rubella control and elimination goal should be achieved if vaccine immunization coverage continues maintaining at the high level.
Deficiency of AXL in Bone Marrow-Derived Cells Does Not Affect Advanced Atherosclerotic Lesion Progression
Authors: Subramanian Manikandan , Proto Jonathan D. , Matsushima Glenn K. , Tabas Ira 
Published: December 2016

AbstractAXL, a member of the TAM (Tyro3, Axl, MerTK) family of receptors, plays important roles in cell survival, clearance of dead cells (efferocytosis), and suppression of inflammation, which are processes that critically influence atherosclerosis progression. Whereas MerTK deficiency promotes defective efferocytosis, inflammation, and plaque necrosis in advanced murine atherosclerosis, the role of Axl in advanced atherosclerosis progression is not known. Towards this end, bone marrow cells from Axl−/− or wild-type mice were transplanted into lethally irradiated Ldlr−/− mice. These chimeric mice were then fed the Western-type diet (WD) for 17 weeks. We demonstrate that lesional macrophages in WT mice express Axl but that Axl deficiency in bone marrow-derived cells does not affect lesion size, cellularity, necrosis, or inflammatory parameters in advanced atherosclerotic plaques. Moreover, apoptosis of lesional cells was unaffected, and we found no evidence of defective lesional efferocytosis. In contrast to previously reported findings with MerTK deficiency, hematopoietic cell-Axl deficiency in WD-fed Ldlr−/− mice does not affect the progression of advanced atherosclerosis or lesional processes associated with TAM receptor signaling. These findings suggest a heretofore unappreciated TAM receptor hierarchy in advanced atherosclerosis.
Cortical grey matter volume reduction in people with schizophrenia is associated with neuro-inflammation
Authors: Zhang Y , Catts V S , Sheedy D , McCrossin T , Kril J J , Shannon Weickert C 
Published: December 2016

AbstractCortical grey matter volume deficits and neuro-inflammation exist in patients with schizophrenia, although it is not clear whether elevated cytokines contribute to the cortical volume reduction. We quantified cortical and regional brain volumes in fixed postmortem brains from people with schizophrenia and matched controls using stereology. Interleukin (IL)-6, IL-1β, IL-8 and SERPINA3 messenger RNAs (mRNAs) were quantified in the contralateral fresh frozen orbitofrontal cortex. We found a small, but significant reduction in cortical grey matter (1.3%; F(1,85)=4.478, P=0.037) and superior frontal gyrus (6.5%; F(1,80)=5.700, P=0.019) volumes in individuals with schizophrenia compared with controls. Significantly reduced cortical grey matter (9.2%; F(1,24)=8.272, P=0.008) and superior frontal gyrus (13.9%; F(1,20)=5.374, P=0.031) volumes were found in cases with schizophrenia and ‘high inflammation’ status relative to schizophrenia cases with ‘low inflammation’ status in the prefrontal cortex. The expression of inflammatory mRNAs in the orbitofrontal cortex was significantly correlated with those in dorsolateral prefrontal cortex (all r>0.417, all P<0.022), except for IL-8. Moreover, average daily and lifetime antipsychotic intake negatively correlated with cortical grey matter and superior frontal gyrus volumes (all r<−0.362, all P<0.05). The results suggest that the reduction in cortical grey matter volume in people with schizophrenia is exaggerated in those who have high expression of inflammatory cytokines. Further, antipsychotic medication intake does not appear to ameliorate the reduction in brain volume.
Molecular genetic aetiology of general cognitive function is enriched in evolutionarily conserved regions
Authors: Hill W D , Davies G , Harris S E , Hagenaars S P ,   The neuroCHARGE Cognitive Working group, Davies Gail , Deary Ian J , Debette Stephanie , Verbaas Carla I , Bressler Jan , Schuur Maaike , Smith Albert V , Bis Joshua C , Bennett David A , Ikram M Arfan , Launer Lenore J , Fitzpatrick Annette L , Seshadri Sudha , van Duijn Cornelia M , Mosley Jr Thomas H , Liewald D C , Penke L , Gale C R , Deary I J 
Published: December 2016

AbstractDifferences in general cognitive function have been shown to be partly heritable and to show genetic correlations with several psychiatric and physical disease states. However, to date, few single-nucleotide polymorphisms (SNPs) have demonstrated genome-wide significance, hampering efforts aimed at determining which genetic variants are most important for cognitive function and which regions drive the genetic associations between cognitive function and disease states. Here, we combine multiple large genome-wide association study (GWAS) data sets, from the CHARGE cognitive consortium (n=53 949) and UK Biobank (n=36 035), to partition the genome into 52 functional annotations and an additional 10 annotations describing tissue-specific histone marks. Using stratified linkage disequilibrium score regression we show that, in two measures of cognitive function, SNPs associated with cognitive function cluster in regions of the genome that are under evolutionary negative selective pressure. These conserved regions contained ~2.6% of the SNPs from each GWAS but accounted for ~40% of the SNP-based heritability. The results suggest that the search for causal variants associated with cognitive function, and those variants that exert a pleiotropic effect between cognitive function and health, will be facilitated by examining these enriched regions.
Brain structure and intragenic DNA methylation are correlated, and predict executive dysfunction in fragile X premutation females
Authors: Shelton A L , Cornish K M , Kolbe S , Clough M , Slater H R , Li X , Kraan C M , Bui Q M , Godler D E , Fielding J 
Published: December 2016

AbstractDNA methylation of the Fragile X mental retardation 1 (FMR1) exon 1/intron 1 boundary has been associated with executive dysfunction in female carriers of a FMR1 premutation (PM: 55–199 CGG repeats), whereas neuroanatomical changes have been associated with executive dysfunction in PM males. To our knowledge, this study for the first time examined the inter-relationships between executive function, neuroanatomical structure and molecular measures (DNA methylation and FMR1 mRNA levels in blood) in PM and control (<44 CGG repeats) females. In the PM group, FMR1 intron 1 methylation was positively associated with executive function and cortical thickness in middle and superior frontal gyri, and left inferior parietal gyrus. By contrast, in the control group, FMR1 intron 1 methylation was negatively associated with cortical thickness of the left middle frontal gyrus and superior frontal gyri. No significant associations were revealed for either group between FMR1 mRNA and neuroanatomical structure or executive function. In the PM group, the lack of any significant association between FMR1 mRNA levels and phenotypic measures found in this study suggests that either FMR1 expression is not well conserved between tissues, or that FMR1 intron 1 methylation is linked to neuroanatomical and cognitive phenotype in PM females via a different mechanism.
False Belief Performance of Children Adopted Internationally
Authors: Hwa-Froelich Deborah A. , Matsuo Hisako , Jacobs Kristal 
Published: December 2016

Purpose
The purpose of this study was to explore relationships among adoption, individual, and family variables on false belief performance of children adopted internationally (CAI).

Method
Using a quasiexperimental design, thirty-five 4-year-old children adopted from Asian and Eastern European countries before age 2 years were compared with a U.S. group of 33 nonadopted 4-year-old children on a standardized English-language measure, 3 false belief tasks, and a go/no-go inhibition measure.

Results
The adopted group differed significantly from the U.S. nonadopted group in expressive language and false belief performance. For the adopted group, inhibition measures were significantly correlated with core language scores. Core language scores and number of older siblings predicted false belief performance.

Conclusions
Similar to children who are not adopted, language competence and living with older siblings positively influenced social understanding in CAI. Because CAI experience interrupted language acquisition and live with fewer older siblings, they are at risk of having weaker language competence and social understanding in their adopted language. When working with CAI, practitioners should assess social communication, language competence, and inhibition skills. They should assist adoptive families in providing socially mentored opportunities for their children to observe and interact with older children.
Self‐adjusting sensing circuit without speed penalty for reliable STT‐MRAM
Authors: Ryu J.‐W. , Kwon K.‐W. 
Published: December 2016

A self‐adjusting sensing circuit spin‐torque transfer magnetic random access memory (STT‐MRAM) is proposed. STT‐MRAM is considered to be the most promising candidate among the new emerging memories. However, read performance has emerged as a new bottleneck, because of its low tunnelling magneto‐resistance ratio (TMR) and low read current. The proposed self‐adjusting sensing circuit shows an improved sensing margin, overcoming the weaknesses of the STT‐MRAM. The proposed circuit using Verilog‐A model, a 65 nm complementary metal–oxide–semiconductor process also evaluated, and Monte Carlo analysis. The results of analysis show that the proposed circuit ensures a certain sensing margin, which is more than 200 mV in TMR 150% and about 50 mV in TMR 100%.
What do postdocs need to succeed? A survey of current standing and future directions for Australian researchers
Authors: Hardy Margaret C. , Carter Adrian , Bowden Nikola 
Published: December 2016

AbstractWhen discussing the postdoctoral period in a researcher’s life, a lack of career progression often boils down to “is it you, or is it me?” Is it a reduction in the quality of candidates, or the fact that there are now too many candidates for a rapidly shrinking pool of jobs? Australia provides an ideal case study, as a large and decentralized country with a government mandate to build the STEMM (Science, Technology, Engineering, Mathematics and Medicine) workforce. The goal of the present study was 1) to provide a baseline for postdoctoral experiences and career aspirations in Australia, and 2) to identify gaps in postdoctoral training. When undertaking a capacity building programme it is important to know where efforts should be focused. To better understand the demographic and career progression of Australia’s current cohort of postdoctoral researchers, a national survey was undertaken from 2014–2015. More than 280 postdoctoral researchers from government, industry and academic institutions responded. Our results indicate that although postdoctoral researchers work more than the legal maximum of a 38-hour a week (on average) and have a long-term plan to stay in research, there is significant concern over the long-term viability of research careers due to job insecurity and a shortage of funding.
Evaluation of the quality of science, technology and innovation advice available to lawmakers in Nigeria
Authors: Sanni Maruf , Oluwatope Omolayo , Adeyeye Adedamola , Egbetokun Abiodun 
Published: December 2016

AbstractAccess to quality science, technology and innovation (STI) information by lawmakers, as one of the key determinants of the effectiveness of policies in sub-Saharan Africa, has generated much debate. The main objective of this article therefore is to examine the sources of, and access to, STI information available to lawmakers in Nigeria. We also investigate factors associated with the use of STI information from experts and other sources in the policymaking process in Nigeria. Data were collected from lawmakers in both the state and national assemblies across Nigeria. Those selected from the states are those with an active S&T structure, such as a fully fledged Ministry dedicated to S&T. The sample was drawn from legislators in S&T committees and other cognate ministries. Our findings reveal that most lawmakers do not use evidence-based STI information on a regular basis. We also note that the use of expert opinion is one of the main sources of STI information, while academic journals and public opinions are some of the least utilized sources. Some of the major factors that affect the use of information from experts are the law makers’ level of education, number of years spent in the committee and duration of period as members of a committee. We recommend regular capacity-building programmes for legislators and their scientific advisers and personal assistants. This article is published as part of a collection on scientific advice to governments.
Palmitoylation regulates glutamate receptor distributions in postsynaptic densities through control of PSD95 conformation and orientation
Authors: Jeyifous Okunola , Lin Eric I. , Chen Xiaobing , Antinone Sarah E. , Mastro Ryan , Drisdel Renaldo , Reese Thomas S. , Green William N. 
Published: December 2016

Significance
Synaptic AMPA-type and NMDA-type glutamate receptors (AMPARs and NMDARs) have different dynamic characteristics critical for synaptic plasticity. We find that the posttranslational modification, palmitoylation, changes the conformation of postsynaptic density protein 95 (PSD95), a major synaptic scaffold, promoting interactions with AMPARs and NMDARs. In synapses, we measured the conformation and orientation of palmitoylated PSD95 relative to the scaffold, synapse-associated protein 97 (SAP97), and found that changing PSD95 palmitoylation altered PSD95 and AMPAR levels, but not NMDAR levels. We conclude that palmitoylation regulates PSD95 conformation and retention of AMPAR and NMDARs at synapses. Differences in PSD95 palmitoylation appear to occur when AMPARs and NMDARs are in separate synaptic domains, likely contributing to differences in AMPAR and NMDAR dynamics in synapses.
Enhanced inflammatory cell profiles in schistosomiasis‐induced pulmonary vascular remodeling
Authors: Ali Zahara , Kosanovic Djuro , Kolosionek Ewa , Schermuly Ralph T. , Graham Brian B. , Mathie Alistair , Butrous Ghazwan 
Published: December 2016

Schistosomiasis (bilharzia) is a neglected parasitic disease caused by trematode flatworms of the genus Schistosoma which affects over 240 million people worldwide. It is characterized by the formation of inflammatory granulomas around deposited parasite eggs. Recent studies have revealed that immune and inflammatory responses play a crucial role in pathogenesis of schistosomiasis. The aim of this paper is to systematically evaluate the number and distribution of inflammatory cells in S. mansoni‐infected mice at different doses and time points. Immunohistochemistry was performed on lung and liver tissue sections from Schistosoma‐infected mice and uninfected healthy controls. Positively stained cells in whole‐lung/liver tissue sections, surrounding the eggs, and in the different compartments of the tissues, were counted. We found a significant increase in the number of mast cells (toluidine blue+), CD3+ cells, CD14+ cells, CD68+ cells, and CD15+ cells in Schistosoma‐infected tissues compared with untreated healthy controls (P ≤ 0.05 for all). Our findings revealed altered and enhanced immune cell infiltration in schistosomiasis. We suggest that these cells may contribute to the pathophysiology of Schistosoma resulting in pulmonary vascular remodeling.
Radiation feedback in dusty clouds
Authors: Ishiki Shohei , Okamoto Takashi 
Published: December 2016

Abstract
We have investigated the impact of photoionization and radiation pressure on a dusty star-forming cloud using one-dimensional radiation hydrodynamic simulations, which include absorption and re-emission of photons by dust. We find that, in a cloud of mass 105 M⊙ and radius 17 pc, the effect of radiation pressure is negligible when star formation efficiency is 2 per cent. The importance of radiation pressure increases with increasing star formation efficiency or an increasing dust-to-gas mass ratio. The net effect of radiation feedback, however, becomes smaller with the increasing dust-to-gas mass ratio, since the absorption of ultraviolet photons by dust grains suppresses photoionization and hence photoheating.
The Relationship Between Early Haloperidol Response and Associated Extrapyramidal Side Effects
Authors: Rasmussen Sean A. , Rosebush Patricia I. , Mazurek Michael F. 
Published: December 2016

Abstract

Background
Early response to antipsychotic medication within 2 weeks of initiating treatment can predict psychiatric outcomes. However, it is unclear whether early response is also predictive of extrapyramidal side effects (EPSs) associated with antipsychotic medications.

Methods
In this study, we investigated 136 consecutive antipsychotic-naive, first-episode psychosis patients naturalistically treated with haloperidol. Patients were assessed at baseline and weekly after treatment initiation using the Brief Psychiatric Rating Scale, Hamilton Depression Rating Scale, and Hamilton Anxiety Rating Scale. Dystonia, parkinsonism, akathisia, and dyskinesia were also assessed weekly using standardized rating scales. Regression analyses were used to determine whether early response at week 2 of treatment predicted the incidence of EPS at any point during hospitalization. A secondary analysis was conducted to determine whether early response continued to predict EPS in patients who experienced no EPS within the first 2 weeks of treatment.

Results
The analyses demonstrated that greater Brief Psychiatric Rating Scale percent improvement at week 2 predicted a decreased risk of EPSs (P = 0.004), even in patients who did not show any EPSs within the first 2 weeks of treatment (P = 0.005). For specific EPS, early response predicted decreased incidences of parkinsonism (P = 0.028) and dyskinesia (P = 0.025), but not akathisia or dystonia. Hamilton Depression Rating Scale and Hamilton Anxiety Rating Scale improvement at week 2 did not predict EPSs. In addition, EPSs were not predicted by the maximum antipsychotic dose received during hospitalization.

Conclusions
These results indicate that early antipsychotic response is valuable not only for predicting psychiatric outcomes, but also for predicting the risk of EPSs.