bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular and Biological Analysis of Potato virus M (PVM) Isolates from the Czech Republic
Authors: Plchova Helena , Vaculik Petr , Cerovska Noemi , Moravec Tomas , Dedic Petr 
Published: October 2015

AbstractThe sequences of the 3′‐terminal region of four Czech Potato virus M isolates VIRUBRA 4/007, VIRUBRA 4/009, VIRUBRA 4/016 and VIRUBRA 4/035 were determined and compared with sequences of PVM isolates available in GenBank. Among the Czech isolates, VIRUBRA 4/007 and 4/016 as well as VIRUBRA 4/016 and 4/035 showed the highest nucleotide identity (93%). Isolates VIRUBRA 4/007, 4/016 and 4/035 were most similar to the PV0273 isolate from Germany and to the wild isolate from Russia. Interestingly, isolate VIRUBRA 4/009 significantly differed from the other three Czech isolates and was the only European isolate that showed the highest nucleotide identity with American isolates. Moreover, the PVM isolates from the Czech Republic and Germany differed in their host range. Phylogenetic analysis based on ORF5 coding for coat protein showed that the Czech isolates could be classified in two of the three groupings of the phylogenetic tree obtained. This is the first report on molecular and biological analysis of the genome sequences of PVM isolates from the Czech Republic.
Numerical Order Processing in Children: From Reversing the Distance‐Effect to Predicting Arithmetic
Authors: Lyons Ian M. , Ansari Daniel 
Published: October 2015

ABSTRACTRecent work has demonstrated that how we process the relative order—ordinality—of numbers may be key to understanding how we represent numbers symbolically, and has proven to be a robust predictor of more sophisticated math skills in both children and adults. However, it remains unclear whether numerical ordinality is primarily a by‐product of other numerical processes, such as familiarity with overlearned count sequence, or is in fact a fundamental property of symbolic number processing. In a sample of nearly 1,500 children, we show that the reversed distance effect—a hallmark of symbolic ordinal processing—obtains in children as young as first grade, and is larger for less familiar sets of numbers. Furthermore, we show that the children's efficiency in evaluating the simplest ordered sequences (e.g., 2‐3‐4, 6‐7‐8) captures more unique variance in mental arithmetic than any other type of numerical sequence, and that this result cannot be accounted for by counting ability. Indeed, performance on just five such trials captured more unique mental arithmetic variance than any of several other numerical tasks assessed here. In sum, our results are consistent with the notion that ordinality is a fundamental property of how children process numerical symbols, that this property helps underpin more complex math processing, and that it shapes numerical processing even at the earliest stages of elementary education.
Genetic diversity loss in a biodiversity hotspot: ancient DNA quantifies genetic decline and former connectivity in a critically endangered marsupial
Authors: Pacioni Carlo , Hunt Helen , Allentoft Morten E. , Vaughan Timothy G. , Wayne Adrian F. , Baynes Alexander , Haouchar Dalal , Dortch Joe , Bunce Michael 
Published: October 2015

AbstractThe extent of genetic diversity loss and former connectivity between fragmented populations are often unknown factors when studying endangered species. While genetic techniques are commonly applied in extant populations to assess temporal and spatial demographic changes, it is no substitute for directly measuring past diversity using ancient DNA (aDNA). We analysed both mitochondrial DNA (mtDNA) and nuclear microsatellite loci from 64 historical fossil and skin samples of the critically endangered Western Australian woylie (Bettongia penicillata ogilbyi), and compared them with 231 (n = 152 for mtDNA) modern samples. In modern woylie populations 15 mitochondrial control region (CR) haplotypes were identified. Interestingly, mtDNA CR data from only 29 historical samples demonstrated 15 previously unknown haplotypes and detected an extinct divergent clade. Through modelling, we estimated the loss of CR mtDNA diversity to be between 46% and 91% and estimated this to have occurred in the past 2000–4000 years in association with a dramatic population decline. In addition, we obtained near‐complete 11‐loci microsatellite profiles from 21 historical samples. In agreement with the mtDNA data, a number of ‘new’ microsatellite alleles was only detected in the historical populations despite extensive modern sampling, indicating a nuclear genetic diversity loss >20%. Calculations of genetic diversity (heterozygosity and allelic rarefaction) showed that these were significantly higher in the past and that there was a high degree of gene flow across the woylie's historical range. These findings have an immediate impact on how the extant populations are managed and we recommend the implementation of an assisted migration programme to prevent further loss of genetic diversity. Our study demonstrates the value of integrating aDNA data into current‐day conservation strategies.
Speciation with gene flow in whiptail lizards from a Neotropical xeric biome
Authors: Oliveira Eliana F. , Gehara Marcelo , São‐Pedro Vinícius A. , Chen Xin , Myers Edward A. , Burbrink Frank T. , Mesquita Daniel O. , Garda Adrian A. , Colli Guarino R. , Rodrigues Miguel T. , Arias Federico J. , Zaher Hussam , Santos Rodrigo M. L. , Costa Gabriel C. 
Published: October 2015

AbstractTwo main hypotheses have been proposed to explain the diversification of the Caatinga biota. The riverine barrier hypothesis (RBH) claims that the São Francisco River (SFR) is a major biogeographic barrier to gene flow. The Pleistocene climatic fluctuation hypothesis (PCH) states that gene flow, geographic genetic structure and demographic signatures on endemic Caatinga taxa were influenced by Quaternary climate fluctuation cycles. Herein, we analyse genetic diversity and structure, phylogeographic history, and diversification of a widespread Caatinga lizard (Cnemidophorus ocellifer) based on large geographical sampling for multiple loci to test the predictions derived from the RBH and PCH. We inferred two well‐delimited lineages (Northeast and Southwest) that have diverged along the Cerrado–Caatinga border during the Mid‐Late Miocene (6–14 Ma) despite the presence of gene flow. We reject both major hypotheses proposed to explain diversification in the Caatinga. Surprisingly, our results revealed a striking complex diversification pattern where the Northeast lineage originated as a founder effect from a few individuals located along the edge of the Southwest lineage that eventually expanded throughout the Caatinga. The Southwest lineage is more diverse, older and associated with the Cerrado–Caatinga boundaries. Finally, we suggest that C. ocellifer from the Caatinga is composed of two distinct species. Our data support speciation in the presence of gene flow and highlight the role of environmental gradients in the diversification process.
Phylogeographic breaks within Asian butternuts indicate the existence of a phytogeographic divide in East Asia
Authors: Bai Wei‐Ning , Wang Wen‐Ting , Zhang Da‐Yong 
Published: October 2015

SummaryEast Asia has been hypothesized to be subdivided into two distinct northern and southern areas, separated by a band of dry climate that was far more severe in the early Tertiary but still exists today. However, this biogeographic hypothesis has rarely been tested using a molecular phylogeographic approach.We genotyped 70 populations throughout the distributional range of Asian butternuts (JuglanssectionCardiocaryon) using eight chloroplast DNA regions, one single‐copy nuclear gene, and 17 nuclear microsatellite loci, supplemented with paleodistribution modeling of the major genetic clades.The genetic data consistently identified two clades, one northern, comprisingJuglans mandshuricaandJuglans ailantifolia, and one southern, comprisingJuglans cathayensis. The two clades diverged through climate‐induced vicariance of an ancestral northern range during the mid‐Miocene and remained mostly separate thereafter, with geographical isolation of the Japanese Islands and refugial isolation or secondary contacts in the late Pleistocene producing further subdivision within the northern clade. But beyond all that, we also discovered a role of environmental adaptation in maintaining and/or reinforcing the north–south divergence.Asian butternuts offer a strong case for the existence of a biogeographic divide between the northern and southern parts of East Asia during the Neogene and into the Pleistocene.
Exploring Drivers of Innovative Technology Adoption Intention: The Case of Plug‐In Vehicles
Authors: Siddiki Saba , Dumortier Jerome , Curley Cali , Graham John D. , Carley Sanya , Krause Rachel M. 
Published: October 2015

AbstractHow individuals respond to innovative technologies depends on how motivated they are by an array of internal and external factors and the informational and cost barriers they face. To better understand technology adoption decision making we (i) assess changes in intent to purchase plug‐in vehicles in response to reductions in their price and (ii) identify motivators that incline new car buyers toward plug‐ins under status quo and reduced vehicle cost scenarios. We find that individuals already inclined toward alternative vehicles have a higher interest in plug‐ins under a reduced‐cost scenario than individuals who favor conventional vehicles. We also find that individuals who shift their vehicle preference from conventional gasoline to plug‐in vehicles are motivated by material factors and fears relating to the innovative technology, whereas those shifting preferences between less to more innovative technologies are likely to be motivated by a mix of material and nonmaterial factors.
Contextual Factors Influencing Collaboration Levels and Outcomes in National Forest Stewardship Contracting
Authors: Mattor Katherine M. , Cheng Antony S. 
Published: October 2015

AbstractThe number of policies promoting collaborative processes in national forest management has increased considerably over the past decade but do mandates alone increase the levels of collaboration in national forest management? Collaborative governance literature identifies the importance of the situational context for the emergence and performance of collaboration but does not identify the role of specific attributes and processes. This article presents a comparative case‐study analysis of factors influencing levels of collaboration in USDA Forest Service stewardship contracting processes. Incorporating concepts from the collaborative governance literature and Institutional Analysis and Development framework we found policy and administrative guidance alone will not increase the use of collaborative processes associated with stewardship contracts. A combination of existing agency‐community planning efforts, leadership, and agency support were essential for collaboration to materialize. Top‐down policy direction meant to increase the use of collaboration to achieve natural resource management objectives must incorporate opportunities to establish these conditions.
When Whites' Attempts to Be Multicultural Backfire in Intergroup Interactions
Authors: Zou Linda , Cheryan Sapna 
Published: October 2015

AbstractWhites' attempts to enact multicultural ideals in intergroup interactions can sometimes have negative interpersonal consequences. This paper reviews the instances when Whites' efforts to acknowledge, appreciate, and learn about racial and ethnic differences can make people of color's group identity uncomfortably salient (minority spotlight effect), make people of color feel that certain attributes are being imposed onto their group identity (positive stereotyping), or make people of color feel precluded from another group identity (identity denial). Each of these situations introduces a hurtful discrepancy between how people of color are seen by others and how they wish to be seen. Suggestions for how to “do” multiculturalism in ways that avoid creating this discrepancy are discussed.
Implicit Affect Primes Effort: Basic Processes, Moderators, and Boundary Conditions
Authors: Gendolla Guido H.E. 
Published: October 2015

AbstractThis article informs about the implicit‐affect‐primes‐effort (IAPE) model – a theory on the impact of implicit affect on resource mobilization – and research testing this account. Beside basic influences of implicitly processed affective stimuli on behavior, this article highlights moderators and boundary conditions of this process. The IAPE model posits that affect primes implicitly activate mental representations of affective states containing information about performance ease and difficulty. This influences subjective task demand during performance, which determines effort. A series of experiments assessing implicit affect's impact on effort‐related cardiovascular response in cognitive tasks revealed replicated support for the IAPE model. Moreover, objective task difficulty and incentive moderated the effect of implicit affect on effort, and especially controlled processing of affect primes and activated concepts turned out to be boundary conditions.
Evidence that the Entamoeba histolytica Mitochondrial Carrier Family Links Mitosomal and Cytosolic Pathways through Exchange of 3′-Phosphoadenosine 5′-Phosphosulfate and ATP
Authors: Mi-ichi Fumika , Nozawa Akira , Yoshida Hiroki , Tozawa Yuzuru , Nozaki Tomoyoshi 
Published: October 2015

ABSTRACT

Entamoeba histolytica
, a microaerophilic protozoan parasite, possesses mitosomes. Mitosomes are mitochondrion-related organelles that have largely lost typical mitochondrial functions, such as those involved in the tricarboxylic acid cycle and oxidative phosphorylation. The biological roles of
Entamoeba
mitosomes have been a long-standing enigma. We previously demonstrated that sulfate activation, which is not generally compartmentalized to mitochondria, is a major function of
E. histolytica
mitosomes. Sulfate activation cooperates with cytosolic enzymes, i.e., sulfotransferases (SULTs), for the synthesis of sulfolipids, one of which is cholesteryl sulfate. Notably, cholesteryl sulfate plays an important role in encystation, an essential process in the
Entamoeba
life cycle. These findings identified a biological role for
Entamoeba
mitosomes; however, they simultaneously raised a new issue concerning how the reactions of the pathway, separated by the mitosomal membranes, cooperate. Here, we demonstrated that the
E. histolytica
mitochondrial carrier family (EhMCF) has the capacity to exchange 3′-phosphoadenosine 5′-phosphosulfate (PAPS) with ATP. We also confirmed the cytosolic localization of all the
E. histolytica
SULTs, suggesting that in
Entamoeba
, PAPS, which is produced through mitosomal sulfate activation, is translocated to the cytosol and becomes a substrate for SULTs. In contrast, ATP, which is produced through cytosolic pathways, is translocated into the mitosomes and is a necessary substrate for sulfate activation. Taking our findings collectively, we suggest that EhMCF functions as a PAPS/ATP antiporter and plays a crucial role in linking the mitosomal sulfate activation pathway to cytosolic SULTs for the production of sulfolipids.
Evolution of the highly networked deubiquitinating enzymes USP4, USP15, and USP11
Authors: Vlasschaert Caitlyn , Xia Xuhua , Coulombe Josée , Gray Douglas A. 
Published: October 2015

Abstract
Background
USP4, USP15 and USP11 are paralogous deubiquitinating enzymes as evidenced by structural organization and sequence similarity. Based on known interactions and substrates it would appear that they have partially redundant roles in pathways vital to cell proliferation, development and innate immunity, and elevated expression of all three has been reported in various human malignancies. The nature and order of duplication events that gave rise to these extant genes has not been determined, nor has their functional redundancy been established experimentally at the organismal level.

Methods
We have employed phylogenetic and syntenic reconstruction methods to determine the chronology of the duplication events that generated the three paralogs and have performed genetic crosses to evaluate redundancy in mice.

Results
Our analyses indicate that USP4 and USP15 arose from whole genome duplication prior to the emergence of jawed vertebrates. Despite having lower sequence identity USP11 was generated later in vertebrate evolution by small-scale duplication of the USP4-encoding region. While USP11 was subsequently lost in many vertebrate species, all available genomes retain a functional copy of either USP4 or USP15, and through genetic crosses of mice with inactivating mutations we have confirmed that viability is contingent on a functional copy of USP4 or USP15. Loss of ubiquitin-exchange regulation, constitutive skipping of the seventh exon and neural-specific expression patterns are derived states of USP11. Post-translational modification sites differ between USP4, USP15 and USP11 throughout evolution.

Conclusions
In isolation sequence alignments can generate erroneous USP gene phylogenies. Through a combination of methodologies the gene duplication events that gave rise to USP4, USP15, and USP11 have been established. Although it operates in the same molecular pathways as the other USPs, the rapid divergence of the more recently generated USP11 enzyme precludes its functional interchangeability with USP4 and USP15. Given their multiplicity of substrates the emergence (and in some cases subsequent loss) of these USP paralogs would be expected to alter the dynamics of the networks in which they are embedded.
Cardiac Bmi1
+ cells contribute to myocardial renewal in the murine adult heart
Authors: Valiente-Alandi Iñigo , Albo-Castellanos Carmen , Herrero Diego , Arza Elvira , Garcia-Gomez Maria , Segovia José C. , Capecchi Mario , Bernad Antonio 
Published: October 2015

Abstract
Introduction
The mammalian adult heart maintains a continuous, low cardiomyocyte turnover rate throughout life. Although many cardiac stem cell populations have been studied, the natural source for homeostatic repair has not yet been defined. The Polycomb protein BMI1 is the most representative marker of mouse adult stem cell systems. We have evaluated the relevance and role of cardiac Bmi1
+
cells in cardiac physiological homeostasis.

Methods
Bmi1CreER/+;Rosa26YFP/+ (Bmi1-YFP) mice were used for lineage tracing strategy. After tamoxifen (TM) induction, yellow fluorescent protein (YFP) is expressed under the control of Rosa26 regulatory sequences in Bmi1
+
cells. These cells and their progeny were tracked by FACS, immunofluorescence and RT-qPCR techniques from 5 days to 1 year.

Results
FACS analysis of non-cardiomyocyte compartment from TM-induced Bmi1-YFP mice showed a Bmi1+-expressing cardiac progenitor cell (Bmi1-CPC: B-CPC) population, SCA-1 antigen-positive (95.9 ± 0.4 %) that expresses some stemness-associated genes. B-CPC were also able to differentiate in vitro to the three main cardiac lineages. Pulse-chase analysis showed that B-CPC remained quite stable for extended periods (up to 1 year), which suggests that this Bmi1+ population contains cardiac progenitors with substantial self-maintenance potential. Specific immunostaining of Bmi1-YFP hearts serial sections 5 days post-TM induction indicated broad distribution of B-CPC, which were detected in variably sized clusters, although no YFP+ cardiomyocytes (CM) were detected at this time. Between 2 to 12 months after TM induction, YFP+ CM were clearly identified (3 ± 0.6 % to 6.7 ± 1.3 %) by immunohistochemistry of serial sections and by flow cytometry of total freshly isolated CM. B-CPC also contributed to endothelial and smooth muscle (SM) lineages in vivo.

Conclusions
High Bmi1 expression identifies a non-cardiomyocyte resident cardiac population (B-CPC) that contributes to the main lineages of the heart in vitro and in vivo.
The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)
Authors: Huntemann Marcel , Ivanova Natalia N. , Mavromatis Konstantinos , Tripp H. James , Paez-Espino David , Palaniappan Krishnaveni , Szeto Ernest , Pillay Manoj , Chen I-Min A. , Pati Amrita , Nielsen Torben , Markowitz Victor M. , Kyrpides Nikos C. 
Published: October 2015

AbstractThe DOE-JGI Microbial Genome Annotation Pipeline performs structural and functional annotation of microbial genomes that are further included into the Integrated Microbial Genome comparative analysis system. MGAP is applied to assembled nucleotide sequence datasets that are provided via the IMG submission site. Dataset submission for annotation first requires project and associated metadata description in GOLD. The MGAP sequence data processing consists of feature prediction including identification of protein-coding genes, non-coding RNAs and regulatory RNA features, as well as CRISPR elements. Structural annotation is followed by assignment of protein product names and functions.
Encapsulation of pancreatic islet with HMGB1 fragment for attenuating inflammation
Authors: Jo Eun Hee , Hwang Yong Hwa , Lee Dong Yun 
Published: October 2015

Abstract

Background
Pancreatic islet encapsulation is one way to address the disadvantages of islet transplantation. Not only does encapsulation involve bidirectional diffusion of nutrients, oxygen, and glucose, but also it protects the graft from the recipient’s immune reaction. The high mobility group box 1 (HMGB1), one of higher expression proteins in islet, can be secreted from transplanted islets and induce the inflammation. Therefore, the regulation of HMGB1-mediated inflammation is very important for successful islet transplantation. In this study, we used the HMGB1 A box, an antagonist of HMGB1 receptor in the immune cells, in the encapsulation of isolated islets as a new strategy.

Result
For co-encapsulation of HMGB1 A box protein with islets, we evaluated the distribution of alginate bead diameter. The average diameter of empty alginate bead was similar to that of alginate bead with islets. When different concentrations of HMGB1 A box protein was co-encapsulated with islets, it did not affect the viability and insulin secretion function of the islets. When the alginate beads with islets plus HMGB1 A box protein were cultured with macrophage, the amount of TNF-α secreted from the macrophages was significantly attenuated when compared to cultivation of unencapsulated islets or encapsulated islets. When the alginate beads with islets plus HMGB1 A box protein were intraperitoneally xenotransplanted into the diabetic mice, the survival rate of the islets was strongly improved with 2-fold.

Conclusion
Collectively, these results suggested that the encapsulation of HMGB1 A box protein might offer a protective effect in islet transplantation.
Preparation and investigation of hydrolyzed polyacrylonitrile as a preliminary biomedical hydrogel
Authors: Park Ji Hoon , Tai Guo Zhe , Lee Bo Keun , Park Seung Hun , Jang Ja Yong , Lee Jung Soo , Kim Jae Ho , Park Kwideok , Jang Ju Woong , Kim Moon Suk 
Published: October 2015

Abstract

Background

Hydrolyzed polyacrylonitrile (HPAN) ha
s
attracted much attention as a hydrogel for a broad range of biomedical applications
.
Therefore, in this study, we prepared HPAN derivatives with controllable compositions by the radical polymerization of acrylonitrile (AN), methacrylic acid (MAA) and
N
-isopropylacrylamide (NIPAM) monomers.

Results
The prepared poly(AN-co-MAA-co-NIPAM) copolymers had different ratios of AN, MAA, and NIPAM and molecular weights ranging from 2000 to 50,000. The copolymers were prepared as films to examine their properties. The prepared copolymer films showed different solubilities, contact angles, and swelling ratios. The properties of the copolymer films were affected by the hydrophobic PAN segments and the hydrophilic PMAA or PNIPAM segments.

Conclusion
Thus, we conclude that introducing PMAA and PNIPAM segments with different ratios and lengths into PAN segments could represent a method of controlling the hydrogel properties of copolymers.