bluuebunny/crossref_metadata_2025 huggingface dataset:
Global stability of obligate mutualism in community modules with facultative mutualists
Authors: Takimoto Gaku , Suzuki Kenta
Published: September 2015

Mutualism is a fundamental building block of ecological communities and an important driver of biotic evolution. Classic theory suggests that a pairwise two‐species obligate mutualism is fragile, with a large perturbation potentially driving both mutualist populations into extinction. In nature, however, there are many cases of pairwise obligate mutualism. Such pairwise obligate mutualisms are occasionally associated with additional interactions with facultative mutualists. Here, we use a mathematical model to show that when a two‐species obligate mutualism has a single additional link to a third facultative mutualist, the obligate mutualism can become permanently persistent. In the model, a facultative mutualist interacts with one of two inter‐dependent obligate mutualists, and the facultative mutualist enhances the persistence not only of its directly interacting obligate mutualist, but also that of the other obligate mutualist indirectly, enabling the permanent coexistence of the three mutualist species. The effect of the facultative mutualist is strong; it can allow a three‐species permanent coexistence even when two obligate mutualists by themselves are not sustainable (i.e. not locally stable). These results suggest that facultative mutualists can play a pivotal role for the persistence of obligate mutualisms, and contribute to a better understanding on the mechanisms maintaining more complex mutualistic networks of multiple species.
Selection of soybean mutant lines with altered seed coat colour and their antioxidant activity
Authors: Lee Kyung Jun , Kim Jin‐Baek , Choi Hong‐Il , Ha Bo‐Keun , Kang Si‐Yong , Kim Dong Sub
Published: September 2015

In this study, the flavonoid and isoflavone contents in four checks with seed coat colour altered from yellow to black were determined, and their antioxidant activity was measured. Three anthocyanins (delphinidin‐3‐O‐β‐D‐glucoside, D3G; cyanidin‐3‐O‐β‐D‐glucoside, C3G; and petunidin‐3‐O‐β‐D‐glucoside, Pt3G) were detected in the four checks, while their controls (cvs. ‘Danbaek’ and ‘Daepung’) were not found. Among them, D‐16 derived from cv. ‘Danbaek’ showed the highest anthocyanin contents. The isoflavone contents of all checks showed lower levels compared to their controls. Among six isoflavones, glycitein was only detected in DP‐39. To analyse the radical scavenging activities among the four checks, we conducted DPPH, FRAP and UWLA assays. Significant differences in antioxidant activities were obtainable in the four checks, which contained significant differences in levels of anthocyanins and isoflavones. Based on these results, gamma irradiation may change the isoflavone and anthocyanin contents of soybean. Our four checks selected in this study may be useful for breeding soybean varieties to alter their nutritional values.
Factors Associated with Increased HPV Vaccine Use in Rural‐Frontier U.S. States
Authors: Lai Djin , Ding Qian , Bodson Julia , Warner Echo L. , Kepka Deanna
Published: September 2015

Objective

This study sought to examine sociodemographic factors surrounding human papillomavirus (HPV) vaccine initiation and three‐dose completion rates in the Intermountain West (IW).

Design and Sample

Analysis of the Centers for Disease Control and Prevention's 2012 National Immunization Survey‐Teen dataset was conducted with a survey‐weighted Pearson chi‐square test and multivariable Poisson regression to produce bivariate and multivariate analyses. Participants with daughters aged 13–17 with provider‐verified immunization records were included. Dual‐frame adjusted prevalence ratios (PR) and 95% confidence intervals (CI) were produced with provider‐phase sampling weights.

Measures

Factors included parents' and adolescents' sociodemographic and healthcare usage variables. Outcome measures included adolescents' receipt and completion of the HPV vaccine.

Results

Older parental ages (45 years and above) showed lower prevalence of adolescent HPV vaccine initiation (PR = 0.73, 95% CI = 0.59–0.87, p = .003) and completion (PR = 0.65, 95% CI = 0.44–0.96, p = .031) compared with parents younger than 35. Seventeen‐year‐old adolescents demonstrated highest prevalence of initiating (PR = 1.88, 95% CI = 1.47–2.39, p < .001) and completing (PR = 2.92, 95% CI = 1.97–4.33, p < .001) the vaccination series compared to 13‐year olds. Those who had received meningitis vaccinations had high prevalence of initiating (PR = 1.93, 95% CI = 1.50–2.48, p < .001) and completing the HPV vaccine (PR = 2.52, 95% CI = 1.64–3.86, p < .001).

Conclusion

This study highlights parental, adolescent, and health care characteristics related to use of the HPV vaccine. Future research to investigate specific barriers and strategies for addressing HPV vaccination use in the IW is recommended.
The mystery of underground death: cell death in roots during ontogeny and in response to environmental factors
Authors: Bagniewska‐Zadworna A. , Arasimowicz‐Jelonek M.
Published: September 2015

Programmed cell death (PCD) is an essential part of the ontogeny of roots and their tolerance/resistance mechanisms, allowing adaptation and growth under adverse conditions. It occurs not only at the cellular and subcellular level, but also at the levels of tissues, organs and even whole plants. This process involves a wide spectrum of mechanisms, from signalling and the expression of specific genes to the degradation of cellular structures. The major goals of this review were to broaden current knowledge about PCD processes in roots, and to identify mechanisms associated with both developmental and stress‐associated cell death in roots. Vacuolar cell death, when cell contents are removed by a combination of an autophagy‐associated process and the release of hydrolases from a collapsed vacuole, is responsible for programming self‐destruction. Regardless of the conditions and factors inducing PCD, its subcellular events usually include the accumulation of autophagosome‐like structures, and the formation of massive lytic compartments. In some cases these are followed by the nuclear changes of chromatin condensation and DNA fragmentation. Tonoplast disruption and vacuole implosion occur very rapidly, are irreversible and constitute a definitive step toward cell death in roots. Active cell elimination plays an important role in various biological processes in the life history of plants, leading to controlled cellular death during adaptation to changing environmental conditions, and organ remodelling throughout development and senescence.
Direct Democracy and Institutional Trust: Relationships and Differences Across Personality Traits
Authors: Freitag Markus , Ackermann Kathrin
Published: September 2015

Direct democracy plays a prominent role in the explanation of institutional trust. To date, however, empirical findings on the effects of direct democracy remain inconclusive. In this article, we argue that this inconclusiveness can be partly ascribed to the diverse effects direct democracy has on individuals. In other words, direct democracy influences institutional trust, but how and to what degree depends on individuals’ personality traits. Running hierarchical analyses of unique survey data from a random sample of eligible Swiss voters, we document three findings: First, we show that the number of ballot measures is not directly associated with institutional trust. Second, we demonstrate that the Big Five personality traits affect the propensity to trust. Third, some of these traits also alter the relationship between direct democracy and institutional trust, suggesting that certain personality types are more likely to be sensitive to popular votes than others and that not everyone is equally likely to respond to political stimuli, even in highly democratic environments.
Characteristics of nursing studies in diabetes research published over three decades in Sweden, Norway, Denmark and Iceland: a narrative review of the literature
Authors: Iversen Marjolein M. , Graue Marit , Leksell Janeth , Smide Bibbi , Zoffmann Vibeke , Sigurdardottir Arun K.
Published: September 2015

Similarities and differences across borders of Nordic countries constitute a suitable context for investigating and discussing factors related to the development of diabetes nursing research over the last three decades. The present study reviewed the entire body of contemporary diabetes nursing research literature originating in four Nordic countries: Norway, Sweden, Denmark and Iceland. Our aims were (i) to catalogue and characterise trends in research designs and research areas of these studies published over time and (ii) to describe how research involving nurses in Nordic countries has contributed to diabetes research overall. The larger goal of our analyses was to produce a comprehensive picture of this research in order to guide future studies in the field. We conducted a narrative literature review by systematically searching Medline, Medline in process, EMBASE, CINAHL, PsycINFO and Cochrane databases. These searches were limited to studies published between 1979 and 2009 that had an abstract available in English or a Nordic language. Two researchers independently selected studies for analysis, leading to the inclusion of 164 relevant publications for analysis. In summary, Nordic nurse researchers have contributed to the development of new knowledge in self‐management of diabetes in childhood, adolescence and adulthood, and to some extent also in the treatment and care of diabetes foot ulcers. Future research may benefit from (i) larger nurse‐led research programmes organised in networks in order to share knowledge and expertise across national groups and borders, (ii) more multidisciplinary collaborations in order to promote patient‐centred care and (iii) further research directed towards improving the dissemination and implementation of research findings. Using complex intervention designs and a mix of research methods will enrich the research.
Bone Disorders in Chronic Kidney Disease: An Update in Diagnosis and Management
Authors: Babayev Revekka , Nickolas Thomas L.
Published: September 2015

Renal osteodystrophy (ROD) is a bone disorder that occurs in chronic kidney disease (CKD) patients and is associated with 2‐ to 14‐fold increased fracture risk compared to the general population. Risk of fractures is also increased in kidney transplant recipients especially within the first 5 years after transplantation. Fractures in CKD patients are associated with increased morbidity and mortality; thus, proper screening and management of CKD bone complications is critical to improving clinical outcomes. Tetracycline double‐labeled transiliac crest bone biopsy with histomorphometry is the gold standard for the diagnosis and classification of ROD. However, bone biopsy is not practical to obtain in all patients. Thus, there is great interest in noninvasive approaches that can be used in the clinic to assess ROD. Here, we discuss the role of surrogate measures of bone health in CKD patients, such as dual energy X‐ray absorptiometry (DXA) and novel high‐resolution imaging, in conjunction with biochemical biomarkers of bone turnover. Recommended guidelines for diagnosis and management of CKD‐MBD are discussed.
In vitro Assay for Screening of Optimal Targets for Antigen‐Delivery to Murine Dendritic Cells
Authors: Pugholm L. H. , Varming K. , Agger R.
Published: September 2015

Targeting of antigen to dendritic cells (DCs) increase the efficiency of immunization procedures and may facilitate the development of more effective vaccines. Several surface molecules on DCs have shown to be useful for antigen targeting, but many more deserves investigation for their efficacy in this respect. With this end in mind, a simple in vitro assay for screening of optimal targets for antigen‐delivery to murine DCs was established. Splenocytes from mice immunized with rat IgG were targeted in vitro with a panel of different rat monoclonal antibodies (mAbs) directed against surface markers on murine DCs. The resulting T‐cell activation was analysed by determining the number of IFN‐γ and IL‐4 secreting cells by ELISPOT. A positive effect of targeting was evident with several of the mAbs. Thus, mAbs against CD11c, CD36, CD205 and Clec7A all induced IFN‐γ responses that were significantly higher than those induced by non‐targeting control mAbs. Anti‐CD36 also induced IL‐4 responses that were significantly higher than the control. The assay described here allows simultaneous analysis of a large number of potential target structures and facilitates direct comparison between the different targets regarding the strength of the T‐cell responses induced by the targeted DCs. The assay could be useful as a first‐line screening of potential target structures on murine DCs.
CCL20‐CCR6 Cytokine Network Facilitate Treg Activity in Advanced Grades and Metastatic Variants of Hepatocellular Carcinoma
Authors: Li W.‐M. , Liu H.‐R.
Published: September 2015

Tumour immunity regulates tumour restriction to the site of occurrence. Failure of this balance facilitates tumour spread beyond the primary organ of origin. Tregs are known to be recruited in infections, including viral infections like hepatitis B and hepatitis C. Thus, they form a continuum of initial viral infection, an environment of immune suppression by recruitment of Tregs, intrinsic viral‐mediated nuclear transformation and carcinogenesis, and thereafter worsening of progress, including metastasis due to the Tregs suppressing the cell‐mediated destruction of tumour cells. In this study, we obtained advanced grades of hepatocellular carcinoma (HCC) and examined the cytokines that is potentially known to recruit Tregs. We examined the expression of CCL20, the cytokine that recruits Tregs. We isolated Tregs from HCC samples and examined expression of CCR6, the receptor for CCL20 and compared expression in control tissues obtained mainly from subjects with cirrhosis, but no evidence of cancer. The findings of this study indicate that mRNA expression of CCL20 is significantly enhanced, along with expression of mRNA for the cytokines IL17 and IL6. Furthermore, tissue expression of Gamma‐interferon was reduced in HCC. When Tregs were isolated from the liver cancer samples, the expression of CCR6, the only and specific receptor for CCL20, was upregulated in the cancer tissue derived Tregs. Furthermore, STAT3 levels were significantly increased in these tumour‐derived Tregs. This study demonstrates that immune evasion mechanisms are operant in hepatocellular carcinoma through a transcriptional network of CCL20‐IL17‐IL6 cytokines that facilitate immune suppression‐mediated cancer cell elimination and metastasis.
Epstein–Barr virus‐driven B Cell Proliferation with CD4+ T Cell Expansion: A Lymphomatoid Granulomatosis‐like Disease Related to Hyperinterleukin‐10 Secretion of Remarkably Favourable Outcome with Rituximab
Authors: Cervera P. , Guihot A. , Gorochov G. , Lassoued K. , Coppo P.
Published: September 2015

Granulomatous lymphomatosis is an Epstein–Barr virus (EBV)‐driven B cell proliferation associated with an exuberant CD4+ T cell reaction with usually histopathological pictures of angiocentrism. So far, the characteristics of CD4+ T cells in granulomatous lymphomatosis and the mechanism leading to their expansion remain poorly explored. We report a 56‐year‐old female with a past history of cold agglutinin disease, which was successfully treated with 4 weekly infusions of rituximab. She presented one year later with features of granulomatous lymphomatosis that resulted in severe lung and bone marrow infiltration. We provide evidence that CD4+ T cell expansion was oligoclonal, involved anergic cells and did not result from an EBV‐driven stimulation. Rather, it resulted possibly from a high production of interleukin‐10 by immunoblastic EBV‐positive B cells. The outcome was remarkably favourable with rituximab and steroids. Our results suggest that an EBV‐driven B cell proliferation should be investigated in patients presenting with a CD4+ T cells alveolitis or other systemic manifestations resulting from a CD4+ T cell expansion. These features should prompt to introduce an immunosuppressive therapy including steroids and rituximab. Our results deserve further investigations to confirm our pathophysiological hypotheses in CD4+ T cell expansions associated with EBV‐driven B cell proliferations and to assess whether granulomatous lymphomatosis could result from comparable mechanisms.
The Uptake of Extracellular Vesicles is Affected by the Differentiation Status of Myeloid Cells
Authors: Czernek L. , Chworos A. , Duechler M.
Published: September 2015

Intercellular communication includes the exchange of various membrane vesicles including exosomes. Exosomes are intraluminal nanovesicles generated from multivesicular bodies, a late endosomal compartment. Cancer cells release exosomes that influence their proximate and distant environment to facilitate angiogenesis, metastatic dissemination and immune escape. Cancer‐derived vesicles may also trigger an anti‐tumour response by transferring tumour antigens to immune cells. We wanted to investigate whether differentiation and maturation of myeloid cells changes their capacity to take up cancer‐derived extracellular vesicles (EV). We compared the efficiency of vesicle uptake by monocytes, macrophages and dendritic cells. To visualize and quantify the cellular uptake, EV were labelled with two different dyes, carboxyfluoresceine diacetate succinimidyl‐ester (CFSE), or DSSN+, a water soluble distyrylstilbene oligoelectrolyte which preferentially intercalates into the cell membrane. With the help of cytokines, THP‐1 monocytes were differentiated into immature or mature dendritic cells, or macrophages. EV uptake was monitored by flow cytometry and immunofluorescence microscopy. The results show that macrophages and mature dendritic cells acquired stronger fluorescence transferred by EV than monocytes or immature dendritic cells indicating that the differentiation status influences the efficiency of EV uptake.
Feuerbach's theory of object‐relations and its legacy in 20th century post‐Hegelian philosophy
Authors: Deranty Jean‐Philippe
Published: September 2015

This paper focuses on the way in which Feuerbach's attempt to develop a naturalistic, realist remodeling of Hegel's relational ontology, which culminated in his own version of “sensualism”, led him to emphasize the vulnerability of the subject and the role of affectivity, thus making object‐dependence a constitutive feature of subjectivity. We find in Feuerbach the first lineaments of a philosophical theory of object‐relations, one that anticipates the well‐known psychological theory of the same name, but one that also offers a broader metaphysical basis in which all types of “essential objects” are shown to matter to subjectivity. This Feuerbachian theory of object‐relations, the paper then argues, foreshadows a number of important developments in 20th century post‐Hegelian philosophy. In it can be found an anticipation of Adorno's later theory of mimesis. Equally, this theory already emphasizes the “libidinal” nature of intentionality, in a way that announces Merleau‐Ponty's ontology of the flesh. Finally, the last section of the article proposes a model with which we might reconstruct the way in which object‐relations and self‐relations can be brought together consistently. In this instance, Feuerbach uses concepts that announce Freud's notion of “primary narcissism”. One contemporary philosopher who has proposed a sophisticated model of subjectivity, in which primary narcissism is shown to complement object‐dependence, is Axel Honneth. The last section argues that Feuerbach's full image of subjective identity as reciprocal scaffolding of self‐ and object‐relations reminds strongly of Honneth's core concept of “positive self‐relation”.
World Culture, Uncoupling, Institutional Logics, and Recoupling: Practices and Self‐Identification as Institutional Microfoundations of Political Violence
Authors: Velitchkova Ana
Published: September 2015

This study proposes a micro‐institutional theory of political violence, according to which citizens' participation in political violence is partially an outcome of tight coupling of persons' practices and self‐identifications with institutional logics opposed to dominant logics associated with world culture, such as the nation‐state and gender equality. The study focuses on two types of institutional carriers through which persons adopt institutional logics: routine practices and self‐identifications associated with three institutional logics: the familial, the ethnic, and the religious logics. Using a 15‐country survey data from early twenty‐first‐century sub‐Saharan Africa, the study finds evidence in support of the theory. Reported participation in political violence is associated with practices and self‐identifications uncoupled from dominant world‐culture logics but tightly coupled with the patriarchal familial logic, with an oppositional ethnic logic, and with a politicized oppositional religious logic.
Naming Regulations and Indigenous Rights in Argentina
Authors: Warren Sarah D.
Published: September 2015

In Argentina, parents must register their children at the Civil Registry to receive a national identification card, choosing their child's name from a list maintained by provincial Civil Registry offices. This process regulates all citizens, but it is particularly onerous for indigenous parents who wish to give their child an indigenous name. In tracing the letter and practice of the law and responses to the law, I argue that the regulation of names is a political process with racial and gender assumptions built into it. These assumptions translate into exclusionary implications for membership in national identity. For indigenous people in Argentina, this is particularly problematic, as they are already largely invisible to the national body. Although indigenous people are challenging aspects of the law they are not challenging the very premise of the law—that the state has the right to control their access to citizenship through a law regulating children's names. Finally, the successes of indigenous parents in using an indigenous name has the unintended consequence of turning indigenous names into cultural commodities, thus diminishing the validity of indigenous political critiques of the law.
The Social Costs of Gender Nonconformity for Transgender Adults: Implications for Discrimination and Health
Authors: Miller Lisa R. , Grollman Eric Anthony
Published: September 2015

Research suggests that transgender people face high levels of discrimination in society, which may contribute to their disproportionate risk for poor health. However, little is known about whether gender nonconformity, as a visible marker of one's stigmatized status as a transgender individual, heightens trans people's experiences with discrimination and, in turn, their health. Using data from the largest survey of transgender adults in the United States, the National Transgender Discrimination Survey (N = 4,115), we examine the associations among gender nonconformity, transphobic discrimination, and health‐harming behaviors (i.e., attempted suicide, drug/alcohol abuse, and smoking). The results suggest that gender nonconforming trans people face more discrimination and, in turn, are more likely to engage in health‐harming behaviors than trans people who are gender conforming. Our findings highlight the important role of gender nonconformity in the social experiences and well‐being of transgender people.
A node‐localized transporter OsZIP3 is responsible for the preferential distribution of Zn to developing tissues in rice
Authors: Sasaki Akimasa , Yamaji Naoki , Mitani‐Ueno Namiki , Kashino Miho , Ma Jian Feng
Published: September 2015

Developing tissues such as meristem with low transpiration require high Zn levels for their active growth, but the molecular mechanisms underlying the preferential distribution to these tissues are poorly understood. We found that a member of the ZIP (ZRT, IRT‐like protein), OsZIP3, showed high expression in the nodes of rice (Oryza sativa). Immunostaining revealed that OsZIP3 was localized at the xylem intervening parenchyma cells and xylem transfer cells of the enlarged vascular bundle in both basal and upper nodes. Neither OsZIP3 gene expression nor encoded protein was affected by either deficiency or toxic levels of Zn. Knockdown of OsZIP3 resulted in significantly reduced Zn levels in the shoot basal region containing the shoot meristem and elongating zone, but increased Zn levels in the transpiration flow. A short‐term experiment with the 67Zn stable isotope showed that more Zn was distributed to the lower leaves, but less to the shoot elongating zone and nodes in the knockdown lines compared with the wild‐type rice at both the vegetative and reproductive growth stages. Taken together, OsZIP3 located in the node is responsible for unloading Zn from the xylem of enlarged vascular bundles, which is the first step for preferential distribution of Zn to the developing tissues in rice.
Cytogenetic mapping with centromeric bacterial artificial chromosomes contigs shows that this recombination‐poor region comprises more than half of barley chromosome 3H
Authors: Aliyeva‐Schnorr Lala , Beier Sebastian , Karafiátová Miroslava , Schmutzer Thomas , Scholz Uwe , Doležel Jaroslav , Stein Nils , Houben Andreas
Published: September 2015

Genetic maps are based on the frequency of recombination and often show different positions of molecular markers in comparison to physical maps, particularly in the centromere that is generally poor in meiotic recombinations. To decipher the position and order of DNA sequences genetically mapped to the centromere of barley (Hordeum vulgare) chromosome 3H, fluorescence in situ hybridization with mitotic metaphase and meiotic pachytene chromosomes was performed with 70 genomic single‐copy probes derived from 65 fingerprinted bacterial artificial chromosomes (BAC) contigs genetically assigned to this recombination cold spot. The total physical distribution of the centromeric 5.5 cM bin of 3H comprises 58% of the mitotic metaphase chromosome length. Mitotic and meiotic chromatin of this recombination‐poor region is preferentially marked by a heterochromatin‐typical histone mark (H3K9me2), while recombination enriched subterminal chromosome regions are enriched in euchromatin‐typical histone marks (H3K4me2, H3K4me3, H3K27me3) suggesting that the meiotic recombination rate could be influenced by the chromatin landscape.
Identification and genome organization of saponin pathway genes from a wild crucifer, and their use for transient production of saponins in Nicotiana benthamiana
Authors: Khakimov Bekzod , Kuzina Vera , Erthmann Pernille Ø. , Fukushima Ery Odette , Augustin Jörg M. , Olsen Carl Erik , Scholtalbers Jelle , Volpin Hanne , Andersen Sven Bode , Hauser Thure P. , Muranaka Toshiya , Bak Søren
Published: September 2015

The ability to evolve novel metabolites has been instrumental for the defence of plants against antagonists. A few species in the Barbarea genus are the only crucifers known to produce saponins, some of which make plants resistant to specialist herbivores, like Plutella xylostella, the diamondback moth. Genetic mapping in Barbarea vulgaris revealed that genes for saponin biosynthesis are not clustered but are located in different linkage groups. Using co‐location with quantitative trait loci (QTLs) for resistance, transcriptome and genome sequences, we identified two 2,3‐oxidosqualene cyclases that form the major triterpenoid backbones. LUP2 mainly produces lupeol, and is preferentially expressed in insect‐susceptible B. vulgaris plants, whereas LUP5 produces β‐amyrin and α‐amyrin, and is preferentially expressed in resistant plants; β‐amyrin is the backbone for the resistance‐conferring saponins in Barbarea. Two loci for cytochromes P450, predicted to add functional groups to the saponin backbone, were identified: CYP72As co‐localized with insect resistance, whereas CYP716As did not. When B. vulgaris sapogenin biosynthesis genes were transiently expressed by CPMV‐HT technology in Nicotiana benthamiana, high levels of hydroxylated and carboxylated triterpenoid structures accumulated, including oleanolic acid, which is a precursor of the major resistance‐conferring saponins. When the B. vulgaris gene for sapogenin 3‐O‐glucosylation was co‐expressed, the insect deterrent 3‐O‐oleanolic acid monoglucoside accumulated, as well as triterpene structures with up to six hexoses, demonstrating that N. benthamiana further decorates the monoglucosides. We argue that saponin biosynthesis in the Barbarea genus evolved by a neofunctionalized glucosyl transferase, whereas the difference between resistant and susceptible B. vulgaris chemotypes evolved by different expression of oxidosqualene cyclases (OSCs).
Genomic limitations to RNA sequencing expression profiling
Authors: Hirsch Cory D. , Springer Nathan M. , Hirsch Candice N.
Published: September 2015

The field of genomics has grown rapidly with the advent of massively parallel sequencing technologies, allowing for novel biological insights with regards to genomic, transcriptomic, and epigenomic variation. One widely utilized application of high‐throughput sequencing is transcriptional profiling using RNA sequencing (RNAseq). Understanding the limitations of a technology is critical for accurate biological interpretations, and clear interpretation of RNAseq data can be difficult in species with complex genomes. To understand the limitations of accurate profiling of expression levels we simulated RNAseq reads from annotated gene models in several plant species including Arabidopsis, brachypodium, maize, potato, rice, soybean, and tomato. The simulated reads were aligned using various parameters such as unique versus multiple read alignments. This allowed the identification of genes recalcitrant to RNAseq analyses by having over‐ and/or under‐estimated expression levels. In maize, over 25% of genes deviated by more than 20% from the expected count values, suggesting the need for cautious interpretation of RNAseq data for certain genes. The reasons identified for deviation from expected expression varied between species due to differences in genome structure including, but not limited to, genes encoding short transcripts, overlapping gene models, and gene family size. Utilizing existing empirical datasets we demonstrate the potential for biological misinterpretation resulting from inclusion of ‘flagged genes’ in analyses. While RNAseq is a powerful tool for understanding biology, there are limitations to this technology that need to be understood in order to improve our biological interpretations.
Distinct Trafficking of Cell Surface and Endosomal TIM‐1 to the Immune Synapse
Authors: Echbarthi Meriem , Zonca Manuela , Mellwig Rachel , Schwab Yannick , Kaplan Gerardo , DeKruyff Rosemarie H. , Roda‐Navarro Pedro , Casasnovas Jose M.
Published: September 2015

The T‐cell/transmembrane, mucin and immunoglobulin domain protein 1 (TIM‐1) is a phosphatidlyserine (PtdSer) receptor and a T‐cell costimulatory molecule linked to the development of atopic diseases. TIM‐1 locates preferentially in intracellular compartments. Here we show that in human and mouse lymphoid cells, TIM‐1 localizes in different types of endosomes and that its domain structure is important for protein sorting to intracellular vesicles. The BALB/c mouse TIM‐1 protein, which has a longer mucin domain, is sorted more efficiently to endosomes than the shorter C57BL/6 variant. High affinity ligands such as PtdSer increase the amount of cell surface TIM‐1; the protein also polarizes toward cell contacts with apoptotic cells. The large pool of intracellular TIM‐1 translocates to the immune synapse (IS) with the CD3‐TCR (T‐cell receptor) complex and colocalizes to the central supramolecular activation cluster (cSMAC). In contrast, cell surface TIM‐1 does not traffic to the IS, but is located away from it. The bipolar TIM‐1 sorting observed during IS formation is determined by differences in its subcellular location, and might modulate antigen‐driven immune responses.
An inventory of concerns behind blood safety policies in five Western countries
Authors: Kramer Koen , Verweij Marcel F. , Zaaijer Hans L.
Published: September 2015

BACKGROUND

The availability of costly safety measures against transfusion‐transmissible infections forces Western countries to confront difficult ethical questions. How to decide about implementing such measures? When are such decisions justified? As a preliminary to addressing these questions, we assessed which concerns shape actual donor blood safety policymaking in five Western countries.

STUDY DESIGN AND METHODS

Our qualitative study involved determining which issues had been discussed in advisory committee meetings and capturing these issues in general categories. Appropriate documents were identified in collaboration with local decision‐making experts in Canada, Germany, the Netherlands, the United States, and the United Kingdom. The introduction of hepatitis B virus nucleic acid testing and selected measures against variant Creutzfeldt‐Jakob disease, West Nile virus, and Q‐fever were chosen as cases representing decision‐making on safety measures with high costs and low or uncertain added safety.

RESULTS

A broad inventory of concerns was established, including: 1) nine categories of advantages and disadvantages of candidate safety policies; 2) six kinds of difficulties in assessing risks and forecasting the effects of safety policies; 3) 13 decision‐making principles; and 4) six kinds of practical barriers hampering the translation of candidate policies into decisions.

CONCLUSION

Blood safety policymaking involves a wide variety of competing concerns, and approaches to reconcile these considerations are themselves contested. Developing a systematic decision‐making approach requires ethical reflection on, among others, reasonable costs of safety and the value of transparency in public policy.
Fat removal during cell salvage: an optimized program for a discontinuous autotransfusion device
Authors: Seyfried Timo F. , Gruber Michael , Breu Anita , Aumeier Christoph , Zech Nina , Hansen Ernil
Published: September 2015

BACKGROUND

Fat in wound blood observed in orthopedic or cardiac surgery might pose a risk for fat embolism during blood salvage. Fat removal was optimized in the washing process.

STUDY DESIGN AND METHODS

In an experimental study blood from fresh donations was adjusted to a hematocrit (Hct) of 25% and an admixture of 1.25% human tissue fat. This blood was processed with the cell salvage device XTRA in a modified program mode. Volumetric quantification of fat was performed after centrifugation of blood samples in Pasteur pipettes. From the volumes, the Hct levels and the concentrations of fat and other variables elimination rates and RBC recovery were calculated.

RESULTS

Pretests showed wash volume, wash flow, and process interruptions affecting fat elimination. With the new optimized fat elimination program Pfat removal rate of fat increased to 98.5 ± 0.9% for the 225‐mL bowl. The product had a mean Hct of 48.7 ± 1.2% and a RBC recovery rate of 93.5 ± 2.3%. The program conserved the high elimination rates for albumin, heparin, potassium, and free plasma hemoglobin (98.8, 99.3, 95.3, and 94.9%, respectively). Similar high fat removal was also observed with bowls of smaller size, namely, 98.1% for the 175‐mL bowl and 98.2% for the 125‐ and the 55‐mL bowls. With test blood of Hct 10% a mean fat elimination of 99.6 ± 01% was observed.

CONCLUSIONS

A special program modification Pfat involving extra washing and RBC concentration steps significantly improves fat removal by the Latham bowl–based autotransfusion device XTRA, thus yielding results equivalent to the continuous cell salvage system.
Determinants of International Student Migration
Authors: Abbott Andrew , Silles Mary
Published: September 2015

This paper considers what factors determine the migration of overseas students, when students cross borders for higher education. We utilise a gravity model for international student mobility and derive estimates for a sample of 18 countries of destination and 38 countries of origin over the period 2005–11. Our results confirm that geographical distance and the presence of a common language are powerful in explaining bilateral student flows. Our most interesting finding is that time zone differences have a statistically significant and economically large effect in determining international student flows.
Phylogenetic relationships within Aglaopheniidae (Cnidaria, Hydrozoa) reveal unexpected generic diversity
Authors: Postaire Bautisse , Magalon Helene , Bourmaud Chloe A.‐F. , Gravier‐Bonnet Nicole , Bruggemann J. Henrich
Published: September 2015

Morphology can be misleading in the representation of phylogenetic relationships, especially in simple organisms like cnidarians and particularly in hydrozoans. These suspension feeders are widely distributed in many marine ecosystems, and the family Aglaopheniidae Marktanner‐Turneretscher, 1890 is among the most diverse and visible, especially on tropical coral reefs. The taxonomy of this family is based on morphological characters with emphasis on reproductive structures for the identification of genera. This study is the most comprehensive molecular phylogeny of the Aglaopheniidae to date, including six genera and 38 species, of which 13 were investigated for the first time and sampled on tropical coral reefs throughout the Indo‐Pacific region. For newly sampled individuals, we sequenced the 16S rRNA, the nuclear locus comprising the complete ITS1‐5.8S rRNA gene‐ITS2 and the first intron of the calmodulin nuclear gene. Phylogenetic analyses of the data revealed and confirmed a general polyphyly, or doubtful monophyly, of all sampled genera in tropical regions based on both the mitochondrial and nuclear markers. Our results revealed that several morphological characters used today are unsuited to resolve phylogenetic relationships between species and genera, as well as the high phyletic diversity within this family. Future revision of the classification of this family will require extensive geographic sampling and the use of an integrative approach.
Uncertainty Quantification of the RELAP5 Interfacial Friction Model in the Rod Bundle Geometry
Authors: Kinoshita Ikuo , Torige Toshihide , Yamada Minoru
Published: September 2015

Interfacial friction in the core affects the two-phase mixture level and the distribution of the dispersed gas phase during a small-break loss-of-coolant accident (LOCA). The RELAP5/MOD3.2 code uses the drift flux model to describe the interfacial friction force in vertical dispersed flow, and the Chexal–Lellouche drift flux correlation is used for the rod bundle geometry. In the present study, the RELAP5 model uncertainty was quantified for the bubbly–slug interfacial friction model in the rod bundle geometry by conducting numerical analyses of void profile tests in the Thermal Hydraulic Test Facility (THTF) of the Oak Ridge National Laboratory (ORNL). The model uncertainty parameter was defined as a multiplier for the interfacial friction coefficient. Numerical analyses were performed by adjusting the multiplier so that the predicted void fractions agreed with the measured test data. The resultant distribution of the multipliers represented the interfacial friction model uncertainty.
Feasibility of Fiber-Deposition Control by Secondary Electric Fields in Near-Field Electrospinning
Authors: Martinez-Prieto Nicolas , Abecassis Maxwell , Xu Jiachen , Guo Ping , Cao Jian , Ehmann Kornel F.
Published: September 2015

Product miniaturization has become a trending technology in a broad range of industries and its development is being pushed by the requirements for complexity and resolution of micromanufactured products. However, there still exists a gap in the manufacturing spectrum for complex three-dimensional (3D) structure generation capabilities with micron and submicron resolution. This paper extends the near-field electrospinning (NFES) process and develops a direct-writing (DW) technology for microfiber deposition with micrometer resolution. The proposed method presented uses an auxiliary electrode to generate an electric field perpendicular to the fiber flight path. This tunable electric field grants the user real-time control of the fiber flight path, increasing the resolution of the deposited structure. The use of an auxiliary electrode ring for fiber manipulation is proposed to further improve control over the deposition process.
Measurement and Characterization of the Initial Geometric Imperfections in High Strength U-ing, O-ing and Expanding Manufactured Steel Pipes
Authors: Kainat Muntaseer , Roger Cheng J. J. , Martens Michael , Adeeb Samer
Published: September 2015

The geometric imperfections in high strength U-ing, O-ing and expanding (UOE) manufactured pipes are investigated in this paper using a high-resolution 3D surface scanner, and a reverse engineering and inspection software. The geometric analyses show that the initial imperfection patterns in the UOE manufactured pipes are not at all random, although the magnitudes of imperfections may vary across specimens. These patterns of outside radii and pipe wall thickness imperfections consistently appear along the length of the specimens regardless of their D/t ratios and manufacturer. The sources of these imperfections can potentially be traced back to the UOE manufacturing process.
Improved One-Dimensional Models for Rapid Emptying and Filling of Pipelines
Authors: Tijsseling Arris S. , Hou Qingzhi , Bozkuş Zafer , Laanearu Janek
Published: September 2015

Improved one-dimensional (1D) models—compared to previous work by the authors—are proposed which are able to predict the velocity, length, and position of the liquid column in the rapid emptying and filling of a pipeline. The models include driving pressure and gravity, skin friction and local drag, and holdup at the tail and gas intrusion at the front of the liquid column. Analytical and numerical results are validated against each other, and against experimental data from a large-scale laboratory setup.
Characterization of small microfluidic valves for studies of mechanical properties of bacteria
Authors: Yang Da , Greer Clayton M. , Jones Branndon P. , Jennings Anna D. , Retterer Scott T. , Männik Jaan
Published: September 2015

Lab-on-a-chip platforms present many new opportunities to study bacterial cells and cellular assemblies. Here, a new platform is described that allows application of uniaxial stress to individual bacterial cells while observing the cell and its subcellular assemblies using a high resolution optical microscope. The microfluidic chip consists of arrays of miniature pressure actuated valves. By placing a bacterium under one of such valves and partially closing the valve by externally applied pressure, the cell can be deformed. Although large pressure actuated valves used in integrated fluidic circuits have been extensively studied previously, here those microfluidic valves are downsized and flow channels with rectangular cross-sections are used to maintain the bacteria in contact with cell culture medium during the experiments. The closure of these valves has not been characterized before. First, these valves are modeled using finite element analysis, and then the modeling results are compared to the actual closing profiles of the valves, which is determined from absorption measurements. The measurements and modeling show with good agreement that the deflection of valves is a linear function of externally applied pressure and the deflection scales proportionally to the width of the flow channel. In addition to characterizing the valve, the report also demonstrates at a proof-of-principle level that the device can be used to deform a bacterial cell at considerable magnitude. The largest deformations are found in 5 μm wide channels where the bacterial width and length increase by 1.6 and 1.25 times, respectively. Narrower and broader channels are less optimal for these studies. The platform presents a promising approach to probe, in a quantitative and systematic way, the mechanical properties of not only bacterial cells but possibly also yeast and other single-celled organisms.
A brite idea for noncoding variants
Authors: Suzuki Masako
Published: September 2015

Epigenomic and genomic analyses combined with genome-editing reveal the mechanism of the obesity-associated
FTO
noncoding variant.
Development of a Pefloxacin Disk Diffusion Method for Detection of Fluoroquinolone-Resistant Salmonella enterica
Authors: Skov Robert , Matuschek Erika , Sjölund-Karlsson Maria , Åhman Jenny , Petersen Andreas , Stegger Marc , Torpdahl Mia , Kahlmeter Gunnar
Published: September 2015

Fluoroquinolones (FQs) are among the drugs of choice for treatment of
Salmonella
infections. However, fluoroquinolone resistance is increasing in
Salmonella
due to chromosomal mutations in the quinolone resistance-determining regions (QRDRs) of the topoisomerase genes
gyrA
,
gyrB
,
parC
, and
parE
and/or plasmid-mediated quinolone resistance (PMQR) mechanisms including
qnr
variants,
aac
(
6
′)-
Ib-cr
,
qepA
, and
oqxAB
. Some of these mutations cause only subtle increases in the MIC, i.e., MICs ranging from 0.12 to 0.25 mg/liter for ciprofloxacin (just above the wild-type MIC of ≤0.06 mg/liter). These isolates are difficult to detect with standard ciprofloxacin disk diffusion, and plasmid-mediated resistance, such as
qnr
, is often not detected by the nalidixic acid screen test. We evaluated 16 quinolone/fluoroquinolone disks for their ability to detect low-level-resistant
Salmonella enterica
isolates that are not serotype Typhi. A total of 153
Salmonella
isolates characterized for the presence (
n
= 104) or absence (
n
= 49) of
gyrA
and/or
parC
topoisomerase mutations,
qnrA
,
qnrB
,
qnrD
,
qnrS
,
aac
(
6
′)-
Ib-cr
, or
qepA
genes were investigated. All isolates were MIC tested by broth microdilution against ciprofloxacin, levofloxacin, and ofloxacin and by disk diffusion using EUCAST or CLSI methodology. MIC determination correctly categorized all isolates as either wild-type isolates (MIC of ≤0.06 mg/liter and absence of resistance genes) or non-wild-type isolates (MIC of >0.06 mg/liter and presence of a resistance gene). Disk diffusion using these antibiotics and nalidixic acid failed to detect some low-level-resistant isolates, whereas the 5-μg pefloxacin disk correctly identified all resistant isolates. However, pefloxacin will not detect isolates having
aac
(
6
′)-
Ib-cr
as the only resistance determinant. The pefloxacin disk assay was approved and implemented by EUCAST (in 2014) and CLSI (in 2015).