bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Elusive Nature of APOE ε4 in Mid-adulthood: Understanding the Cognitive Profile
Authors: Lancaster Claire , Tabet Naji , Rusted Jennifer 
Published: January 2017

AbstractObjectives: The apolipoprotein E (APOE) ε4 allele is an established risk factor for dementia, yet this genetic variant is associated with a mixed cognitive profile across the lifespan. This study undertakes both a systematic and meta-analytic review of research investigating APOE-related differences in cognition in mid-adulthood, when detrimental effects of the allele may first be detectable. Methods: Thirty-six papers investigating the behavioral effects of APOE ε4 in mid-adulthood (defined as a mean sample age between 35 and 60 years) were reviewed. In addition, the effect of carrying an ε4 allele on individual cognitive domains was assessed in separate meta-analyses. Results: The average effect size of APOE ε4 status was non-significant across cognitive domains. Further consideration of genotype effects indicates preclinical effects of APOE ε4 may be observable in memory and executive functioning. Conclusions: The cognitive profile of APOE ε4 carriers at mid-age remains elusive. Although there is support for comparable performance by ε4 and non-e4 carriers in the 5th decade, studies administering sensitive cognitive paradigms indicate a more nuanced profile of cognitive differences. Methodological issues in this field preclude strong conclusions, which future research must address, as well as considering the influence of further vulnerability factors on genotype effects. (JINS, 2016, 23, 239–253)
Single-cell transcriptomics of small microbial eukaryotes: limitations and potential
Authors: Liu Zhenfeng , Hu Sarah K , Campbell Victoria , Tatters Avery O , Heidelberg Karla B , Caron David A 
Published: January 2017

Abstract
Single-cell transcriptomics is an emerging research tool that has huge untapped potential in the study of microbial eukaryotes. Its application has been tested in microbial eukaryotes 50 μm or larger, and it generated transcriptomes similar to those obtained from culture-based RNA-seq. However, microbial eukaryotes have a wide range of sizes and can be as small as 1 μm. Single-cell RNA-seq was tested in two smaller protists (8 and 15 μm). Transcript recovery rate was much lower and randomness in observed gene expression levels was much higher in single-cell transcriptomes than those derived from bulk cultures of cells. We found that the reason of such observation is that the smaller organisms had much lower mRNA copy numbers. We discuss the application of single-cell RNA-seq in studying smaller microbial eukaryotes in the context of these limitations.
Cheating fosters species co-existence in well-mixed bacterial communities
Authors: Leinweber Anne , Fredrik Inglis R , Kümmerli Rolf 
Published: January 2017

AbstractExplaining the enormous biodiversity observed in bacterial communities is challenging because ecological theory predicts that competition between species occupying the same niche should lead to the exclusion of less competitive community members. Competitive exclusion should be particularly strong when species compete for a single limiting resource or live in unstructured habitats that offer no refuge for weaker competitors. Here, we describe the ‘cheating effect’, a form of intra-specific competition that can counterbalance between-species competition, thereby fostering biodiversity in unstructured habitats. Using experimental communities consisting of the strong competitor Pseudomonas aeruginosa (PA) and its weaker counterpart Burkholderia cenocepacia (BC), we show that co-existence is impossible when the two species compete for a single limiting resource, iron. However, when introducing a PA cheating mutant, which specifically exploits the iron-scavenging siderophores produced by the PA wild type, we found that biodiversity was preserved under well-mixed conditions where PA cheats could outcompete the PA wild type. Cheating fosters biodiversity in our system because it creates strong intra-specific competition, which equalizes fitness differences between PA and BC. Our study identifies cheating – typically considered a destructive element – as a constructive force in shaping biodiversity.
Rapid control and feedback rates enhance neuroprosthetic control
Authors: Shanechi Maryam M. , Orsborn Amy L. , Moorman Helene G. , Gowda Suraj , Dangi Siddharth , Carmena Jose M. 
Published: January 2017

AbstractBrain-machine interfaces (BMI) create novel sensorimotor pathways for action. Much as the sensorimotor apparatus shapes natural motor control, the BMI pathway characteristics may also influence neuroprosthetic control. Here, we explore the influence of control and feedback rates, where control rate indicates how often motor commands are sent from the brain to the prosthetic, and feedback rate indicates how often visual feedback of the prosthetic is provided to the subject. We developed a new BMI that allows arbitrarily fast control and feedback rates, and used it to dissociate the effects of each rate in two monkeys. Increasing the control rate significantly improved control even when feedback rate was unchanged. Increasing the feedback rate further facilitated control. We also show that our high-rate BMI significantly outperformed state-of-the-art methods due to higher control and feedback rates, combined with a different point process mathematical encoding model. Our BMI paradigm can dissect the contribution of different elements in the sensorimotor pathway, providing a unique tool for studying neuroprosthetic control mechanisms.
Discovery of high-performance low-cost n-type Mg3Sb2-based thermoelectric materials with multi-valley conduction bands
Authors: Zhang Jiawei , Song Lirong , Pedersen Steffen Hindborg , Yin Hao , Hung Le Thanh , Iversen Bo Brummerstedt 
Published: January 2017

AbstractWidespread application of thermoelectric devices for waste heat recovery requires low-cost high-performance materials. The currently available n-type thermoelectric materials are limited either by their low efficiencies or by being based on expensive, scarce or toxic elements. Here we report a low-cost n-type material, Te-doped Mg3Sb1.5Bi0.5, that exhibits a very high figure of merit zT ranging from 0.56 to 1.65 at 300−725 K. Using combined theoretical prediction and experimental validation, we show that the high thermoelectric performance originates from the significantly enhanced power factor because of the multi-valley band behaviour dominated by a unique near-edge conduction band with a sixfold valley degeneracy. This makes Te-doped Mg3Sb1.5Bi0.5 a promising candidate for the low- and intermediate-temperature thermoelectric applications.
Radioiodinated Capsids Facilitate In Vivo Non-Invasive Tracking of Adeno-Associated Gene Transfer Vectors
Authors: Kothari P. , De B. P. , He B. , Chen A. , Chiuchiolo M. J. , Kim D. , Nikolopoulou A. , Amor-Coarasa A. , Dyke J. P. , Voss H. U. , Kaminsky S. M. , Foley C. P. , Vallabhajosula S. , Hu B. , DiMagno S. G. , Sondhi D. , Crystal R. G. , Babich J. W. , Ballon D. 
Published: January 2017

AbstractViral vector mediated gene therapy has become commonplace in clinical trials for a wide range of inherited disorders. Successful gene transfer depends on a number of factors, of which tissue tropism is among the most important. To date, definitive mapping of the spatial and temporal distribution of viral vectors in vivo has generally required postmortem examination of tissue. Here we present two methods for radiolabeling adeno-associated virus (AAV), one of the most commonly used viral vectors for gene therapy trials, and demonstrate their potential usefulness in the development of surrogate markers for vector delivery during the first week after administration. Specifically, we labeled adeno-associated virus serotype 10 expressing the coding sequences for the CLN2 gene implicated in late infantile neuronal ceroid lipofuscinosis with iodine-124. Using direct (Iodogen) and indirect (modified Bolton-Hunter) methods, we observed the vector in the murine brain for up to one week using positron emission tomography. Capsid radioiodination of viral vectors enables non-invasive, whole body, in vivo evaluation of spatial and temporal vector distribution that should inform methods for efficacious gene therapy over a broad range of applications.
Scaling of titanium implants entrains inflammation-induced osteolysis
Authors: Eger Michal , Sterer Nir , Liron Tamar , Kohavi David , Gabet Yankel 
Published: January 2017

AbstractWith millions of new dental and orthopedic implants inserted annually, periprosthetic osteolysis becomes a major concern. In dentistry, peri-implantitis management includes cleaning using ultrasonic scaling. We examined whether ultrasonic scaling releases titanium particles and induces inflammation and osteolysis. Titanium discs with machined, sandblasted/acid-etched and sandblasted surfaces were subjected to ultrasonic scaling and we physically and chemically characterized the released particles. These particles induced a severe inflammatory response in macrophages and stimulated osteoclastogenesis. The number of released particles and their chemical composition and nanotopography had a significant effect on the inflammatory response. Sandblasted surfaces released the highest number of particles with the greatest nanoroughness properties. Particles from sandblasted/acid-etched discs induced a milder inflammatory response than those from sandblasted discs but a stronger inflammatory response than those from machined discs. Titanium particles were then embedded in fibrin membranes placed on mouse calvariae for 5 weeks. Using micro-CT, we observed that particles from sandblasted discs induced more osteolysis than those from sandblasted/acid-etched discs. In summary, ultrasonic scaling of titanium implants releases particles in a surface type-dependent manner and may aggravate peri-implantitis. Future studies should assess whether surface roughening affects the extent of released wear particles and aseptic loosening of orthopedic implants.
Deficiency of the eIF4E isoform nCBP limits the cell-to-cell movement of a plant virus encoding triple-gene-block proteins in Arabidopsis thaliana
Authors: Keima Takuya , Hagiwara-Komoda Yuka , Hashimoto Masayoshi , Neriya Yutaro , Koinuma Hiroaki , Iwabuchi Nozomu , Nishida Shuko , Yamaji Yasuyuki , Namba Shigetou 
Published: January 2017

AbstractOne of the important antiviral genetic strategies used in crop breeding is recessive resistance. Two eukaryotic translation initiation factor 4E family genes, eIF4E and eIFiso4E, are the most common recessive resistance genes whose absence inhibits infection by plant viruses in Potyviridae, Carmovirus, and Cucumovirus. Here, we show that another eIF4E family gene, nCBP, acts as a novel recessive resistance gene in Arabidopsis thaliana toward plant viruses in Alpha- and Betaflexiviridae. We found that infection by Plantago asiatica mosaic virus (PlAMV), a potexvirus, was delayed in ncbp mutants of A. thaliana. Virus replication efficiency did not differ between an ncbp mutant and a wild type plant in single cells, but viral cell-to-cell movement was significantly delayed in the ncbp mutant. Furthermore, the accumulation of triple-gene-block protein 2 (TGB2) and TGB3, the movement proteins of potexviruses, decreased in the ncbp mutant. Inoculation experiments with several viruses showed that the accumulation of viruses encoding TGBs in their genomes decreased in the ncbp mutant. These results indicate that nCBP is a novel member of the eIF4E family recessive resistance genes whose loss impairs viral cell-to-cell movement by inhibiting the efficient accumulation of TGB2 and TGB3.
Study on relationship between pollen exine ornamentation pattern and germplasm evolution in flowering crabapple
Authors: Zhang Wang-Xiang , Zhao Ming-Ming , Fan Jun-Jun , Zhou Ting , Chen Yong-Xia , Cao Fu-Liang 
Published: January 2017

AbstractPollen ornamentation patterns are important in the study of plant genetic evolution and systematic taxonomy. However, they are normally difficult to quantify. Based on observations of pollen exine ornamentation characteristics of 128 flowering crabapple germplasms (44 natural species and 84 varieties), three qualitative variables with binary properties (Xi: regularity of pollen exine ornamentation; Yi: scope of ornamentation arrangement regularity; Zi: ornamentation arrangement patterns) were extracted to establish a binary three-dimensional data matrix (XiYiZi) and the matrix data were converted to decimal data through weight assignment, which facilitated the unification of qualitative analysis and quantitative analysis. The result indicates that from species population to variety population and from parent population to variety population, the exine ornamentation of all three dimensions present the evolutionary trend of regular → irregular, wholly regular → partially regular, and single pattern → multiple patterns. Regarding the evolutionary degree, the regularity of ornamentation was significantly lower in both the variety population and progeny population, with a degree of decrease 0.82–1.27 times that of the regularity range of R-type ornamentation. In addition, the evolutionary degree significantly increased along Xi→ Yi → Zi. The result also has certain reference values for defining the taxonomic status ofMalusspecies.
Membrane translocation of t-SNARE protein syntaxin-4 abrogates ground-state pluripotency in mouse embryonic stem cells
Authors: Hagiwara-Chatani Natsumi , Shirai Kota , Kido Takumi , Horigome Tomoatsu , Yasue Akihiro , Adachi Naoki , Hirai Yohei 
Published: January 2017

AbstractEmbryonic stem (ES) and induced pluripotent stem (iPS) cells are attractive tools for regenerative medicine therapies. However, aberrant cell populations that display flattened morphology and lose ground-state pluripotency often appear spontaneously, unless glycogen synthase kinase 3β (GSK3β) and mitogen-activated protein kinase kinase (MEK1/2) are inactivated. Here, we show that membrane translocation of the t-SNARE protein syntaxin-4 possibly is involved in this phenomenon. We found that mouse ES cells cultured without GSK3β/MEK1/2 inhibitors (2i) spontaneously extrude syntaxin-4 at the cell surface and that artificial expression of cell surface syntaxin-4 induces appreciable morphological changes and mesodermal differentiation through dephosphorylation of Akt. Transcriptome analyses revealed several candidate elements responsible for this, specifically, an E-to P-cadherin switch and a marked downregulation of Zscan4 proteins, which are DNA-binding proteins essential for ES cell pluripotency. Embryonic carcinoma cell lines F9 and P19CL6, which maintain undifferentiated states independently of Zscan4 proteins, exhibited similar cellular behaviors upon stimulation with cell surface syntaxin-4. The functional ablation of E-cadherin and overexpression of P-cadherin reproduced syntaxin-4-induced cell morphology, demonstrating that the E- to P-cadherin switch executes morphological signals from cell surface syntaxin-4. Thus, spontaneous membrane translocation of syntaxin-4 emerged as a critical element for maintenance of the stem-cell niche.
IFN type I and II induce BAFF secretion from human decidual stromal cells
Authors: Lundell Anna-Carin , Nordström Inger , Andersson Kerstin , Lundqvist Christina , Telemo Esbjörn , Nava Silvia , Kaipe Helen , Rudin Anna 
Published: January 2017

AbstractB cell activating factor (BAFF) is a critical cytokine for maturation of immature B cells. In murine lymph nodes, BAFF is mainly produced by podoplanin-expressing stromal cells. We have previously shown that circulating BAFF levels are maximal at birth, and that farmers’ children exhibit higher BAFF levels in cord blood than non-farmers’ children. Here, we sought to investigate whether maternal-derived decidual stromal cells from placenta secrete BAFF and examine what factors could stimulate this production. We found that podoplanin is expressed in decidua basalis and in the underlying villous tissue as well as on isolated maternal-derived decidual stromal cells. Decidual stromal cells produced BAFF when stimulated with IFN-γ and IFN-α, and NK cells and NK-T-like cells competent of IFN-γ production were isolated from the decidua. Finally, B cells at different maturational stages are present in decidua and all expressed BAFF-R, while stromal cells did not. These findings suggest that decidual stromal cells are a cellular source of BAFF for B cells present in decidua during pregnancy.
A derivatization-enhanced detection strategy in mass spectrometry: analysis of 4-hydroxybenzoates and their metabolites after keratinocytes are exposed to UV radiation
Authors: Lee Yi-Hsuan , Lin Ying-Chi , Feng Chia-Hsien , Tseng Wei-Lung , Lu Chi-Yu 
Published: January 2017

Abstract4-Hydroxybenzoate is a phenolic derivative of alkyl benzoates and is a widely used preservative in cosmetic and pharmaceutical products. The presence of 4-hydroxybenzoates in the human body may result from the use of pharmaceutical and personal care products. These compounds are also known to exhibit estrogenic and genotoxic activities. The potential adverse effects of these compounds include endocrine disruption, oxidative and DNA damage, contact dermatitis, and allergic reactions. This study used two mass spectrometry methods that are applicable when using a derivatization-enhanced detection strategy (DEDS) to screen 4-hydroxybenzoates and their metabolites. Chemical derivatization was used to enhance the detection of these compounds. To evaluate the metabolic process triggered by UV radiation, human keratinocyte HaCaT cells treated with these 4-hydroxybenzoates were further exposed to UVA, UVB and UVC radiation. Metabolites transformed by human keratinocytes in the chemical derivatization procedure were identified by a nano ultra-performance liquid chromatographic system (nanoUPLC) coupled with LTQ Orbitrap. The experiments confirmed the feasibility of this method for identifying 4-hydroxybenzoate metabolites and for high-throughput screening of 4-hydroxybenzoate in commercial products (50 samples) by the DEDS.
Exit point in the strong field ionization process
Authors: Ivanov I. A. , Nam Chang Hee , Kim Kyung Taec 
Published: January 2017

AbstractWe analyze the process of strong field ionization using the Bohmian approach. This allows retention of the concept of electron trajectories. We consider the tunnelling regime of ionization. We show that, in this regime, the coordinate distribution for the ionized electron has peaks near the points in space that can be interpreted as exit points. The interval of time during which ionization occurs is marked by a quick broadening of the coordinate distribution. The concept of the exit point in the tunneling regime, which has long been assumed for the description of strong field ionization, is justified by our analysis.
Phosphoproteomic comparison of Pik3ca and Pten signalling identifies the nucleotidase NT5C as a novel AKT substrate
Authors: Moniz Larissa S. , Surinova Silvia , Ghazaly Essam , Velasco Lorena Gonzalez , Haider Syed , Rodríguez-Prados Juan Carlos , Berenjeno Inma M. , Chelala Claude , Vanhaesebroeck Bart 
Published: January 2017

AbstractTo identify novel effectors and processes regulated by PI3K pathway activation, we performed an unbiased phosphoproteomic screen comparing two common events of PI3K deregulation in cancer: oncogenic Pik3ca mutation (Pik3caH1047R) and deletion of Pten. Using mouse embryonic fibroblast (MEF) models that generate inducible, low-level pathway activation as observed in cancer, we quantified 7566 unique phosphopeptides from 3279 proteins. A number of proteins were found to be differentially-regulated by Pik3caH1047R and Pten loss, suggesting unique roles for these two events in processes such as vesicular trafficking, DNA damage repair and RNA splicing. We also identified novel PI3K effectors that were commonly-regulated, including putative AKT substrates. Validation of one of these hits, confirmed NT5C (5′,3′-Nucleotidase, Cytosolic) as a novel AKT substrate, with an unexpected role in actin cytoskeleton regulation via an interaction with the ARP2/3 complex. This study has produced a comprehensive data resource and identified a new link between PI3K pathway activation and actin regulation.
Pyruvic oxime dioxygenase from heterotrophic nitrifier Alcaligenes faecalis is a nonheme Fe(II)-dependent enzyme homologous to class II aldolase
Authors: Tsujino Shuhei , Uematsu Chisato , Dohra Hideo , Fujiwara Taketomo 
Published: January 2017

AbstractPyruvic oxime dioxygenase (POD), a key enzyme in heterotrophic nitrification, was purified from Alcaligenes faecalis, and the molecular and catalytic characteristics were reexamined. POD was purified as the homotetramer of the subunit whose molecular weight was 30,000. The deduced amino acid sequence of POD was homologous with a class II aldolase that has been regarded as the Zn(II)-dependent enzyme catalyzing aldol reactions. The recombinant protein showed weak POD activity, and was activated by reconstitution with Fe(II). Affinity and catalytic constants were estimated at 470 μM and 4.69 sec−1, respectively. The POD was inactivated by EDTA to remove bound divalent metal cations. A reconstitution experiment demonstrated that Fe(II), not Zn(II), is essential for POD activity and that Mn(II) could partially fulfill the function of Fe(II). A mutant POD with replacement of His183, corresponding to one of three Zn(II)-binding ligands in the class II aldolase, by Asn was purified as a homotetrameric protein but showed no catalytic activities. Those results suggest that the POD is homologous to class II aldolase having non-heme Fe(II) as a catalytic center instead of Zn(II). A possible mechanism of the POD reaction is discussed on the basis of that of a known Fe(II)-dependent dioxygenase.
Rapidly discriminate commercial medicinal Pulsatilla chinensis (Bge.) Regel from its adulterants using ITS2 barcoding and specific PCR-RFLP assay
Authors: Shi Yuhua , Zhao Mingming , Yao Hui , Yang Pei , Xin Tianyi , Li Bin , Sun Wei , Chen Shilin 
Published: January 2017

AbstractPulsatillae radix is a conventional traditional Chinese medicine (TCM) with common name Baitouweng, and has notable effects on inflammation and dysentery. Pulsatilla chinensis (Bge.) Regel is the only source plant of Baitouweng recorded in Chinese Pharmacopoeia, but its adulteration often occurs in the market that possibly affects medicinal efficacy and safety. We have established an internal transcribed spacer 2 (ITS2) barcode library based on 105 plant samples from 12 Pulsatilla species and 10 common adulterants. Results indicate that ITS2 barcoding can accurately distinguish Pulsatilla species from their adulterants. Pulsatilla chinensis can be discriminated from 11 congeneric species by two stable single nucleotide polymorphisms (SNPs) in the ITS2 region. Additionally, a quick specific PCR-RFLP identification assay based on the ITS2 barcode was developed. Using specific primers ITS2/PR1 combined with restriction enzyme Bgl I, Pu. chinensis can rapidly be differentiated from other species via simple and low-cost test procedures. Furthermore, 30 commercial Baitouweng products were tested and only two products were derived from authentic Pu. chinensis. Thus, these two molecular approaches provide practical tools for quick identification of commercial Baitouweng products and can help ensure the safe use of this TCM product.