bluuebunny/crossref_metadata_2025 huggingface dataset:
Assessing urban fortunes in six late medieval ports: an archaeological application of assemblage theory
Authors: JERVIS BEN
Published: November 2015

Variations in the fortunes of six late medieval ports in Sussex are considered using data derived from archaeological excavations. Several indicators are used to assess differences in urban fortunes and to critique the concept of urban ‘decline’. The interpretive framework of assemblage theory is then used to examine why the fortunes of these ports varied. The article argues for a turn from discussions of decay and decline towards considerations of changes, continuities and transformations in urban life in late medieval England.
Linolenic acid improves oocyte developmental competence and decreases apoptosis ofin vitro-produced blastocysts in goat
Authors: Veshkini Arash , Khadem Ali Akbar , Mohammadi-Sangcheshmeh Abdollah , Alamouti Ali Asadi , Soleimani Masoud , Gastal Eduardo L.
Published: November 2015

The effects of α-linolenic acid (ALA) on developmental competence of oocytes in goats were evaluated in this study. Initially, the level of ALA in small and large antral follicles was determined to be in a range of 0.018–0.028 mg/ml (64.6–100.6 μM, respectively).In vitromaturation was performed in the presence of various concentrations (10, 50, 100, or 200 μM) of ALA. Cumulus expansion, meiotic maturation, levels of intracellular glutathione (GSH), embryonic cleavage, blastocyst formation following parthenogenetic activation (PA) andin vitrofertilization (IVF), number of total and apoptotic cells in blastocyst, and expression ofBax, Bcl-2, and p53 genes in blastocyst cells were determined. Compared with the control, no improvement was observed in cumulus expansion in ALA-treated groups. At 50 μM concentration, ALA increased meiotic maturation rate but had no effect on GSH level. When oocytes treated with 50 μM ALA were subsequently used for PA or IVF, a higher rate of blastocyst formation was observed, and these embryos had a higher total cell number and a lower apoptotic cell number. Expression analyses of genes in blastocysts revealed lesser transcript abundances forBaxgene, and higher transcript abundances forBcl-2gene in 50 μM ALA group. Expression ofp53gene was also less observed in ALA-treated blastocysts. Our results show that ALA treatment at 50 μM duringin vitromaturation (IVM) had a beneficial effect on maturation of goat oocytes and this, in turn, stimulated embryonic development and regulated apoptotic gene expression.
Vitamin D deficiency prevalence and risk factors among pregnant Chinese women
Authors: Yun Chunfeng , Chen Jing , He Yuna , Mao Deqian , Wang Rui , Zhang Yu , Yang Chun , Piao Jianhua , Yang Xiaoguang
Published: November 2015

Objective

To evaluate vitamin D deficiency prevalence and risk factors among pregnant Chinese women.

Design

A descriptive cross-sectional analysis.

Setting

China National Nutrition and Health Survey (CNNHS) 2010–2013.

Subjects

A total of 1985 healthy pregnant women participated. Possible predictors of vitamin D deficiency were evaluated via multiple logistic regression analyses.

Results

The median serum 25-hydroxyvitamin D level was 15·5 (interquartile range 11·9–20·0, range 3·0–51·5) ng/ml, with 74·9 (95 % CI 73·0, 76·7) % of participants being vitamin D deficient (25-hydroxyvitamin D <20 ng/ml). According to the multivariate logistic regression analyses, vitamin D deficiency was positively correlated with Hui ethnicity (P=0·016), lack of vitamin D supplement use (P=0·021) and low ambient UVB level (P<0·001). In the autumn months, vitamin D deficiency was related to Hui ethnicity (P=0·012) and low ambient UVB level (P<0·001). In the winter months, vitamin D deficiency was correlated with younger age (P=0·050), later gestational age (P=0·035), higher pre-pregnancy BMI (P=0·019), low ambient UVB level (P<0·001) and lack of vitamin D supplement use (P=0·007).

Conclusions

Vitamin D deficiency is prevalent among pregnant Chinese women. Residing in areas with low ambient UVB levels increases the risk of vitamin D deficiency, especially for women experiencing advanced stages of gestation, for younger pregnant women and for women of Hui ethnicity; therefore, vitamin D supplementation and sensible sun exposure should be encouraged, especially in the winter months. Further studies must determine optimal vitamin D intake and sun exposure levels for maintaining sufficient vitamin D levels in pregnant Chinese women.
Seasonality and household diets in Ethiopia
Authors: Hirvonen Kalle , Taffesse Alemayehu Seyoum , Worku Hassen Ibrahim
Published: November 2015

Objective

To revisit seasonality by assessing how household diets vary across agricultural seasons in rural and urban Ethiopia. The role of seasonality on the sources and intake of energy (per capita) and household dietary diversity score (HDDS) was analysed.

Design

The use of nationally representative household-level data collected each month over one year to study the seasonal changes in the sources and intake of energy and HDDS.

Setting

Eleven regions of Ethiopia, including rural and urban settings.

Subjects

Total of 27 835 households were interviewed between July 2010 and July 2011 in all eleven regions of the country. On average each month saw 2300 household interviews, yielding nationally representative data for each calendar month.

Results

For rural households, the mean daily per capita energy intake was 10 288 kJ (2459 kcal) in February (post-harvest period) and lower in the lean season: 9703 kJ (2319 kcal) in June (P<0·05) and 9552 kJ (2283 kcal) in July (P<0·001). HDDS for rural households was highest in February (6·73) and lowest in June (5·98; P<0·001) but high again in July (6·57). Urban energy intake was also lower in the lean season but HDDS varied less by season. Considerable seasonal variation was also found in energy sources in rural areas, less so in urban areas.

Conclusions

Household diets in Ethiopia remain subjected to significant seasonal stress. HDDS and food security measured using energy intake do not always agree. Preferably, HDDS and energy intake data should be used together to assess food security.
Trends in food and beverage television brand appearances viewed by children and adolescents from 2009 to 2014 in the USA
Authors: Elsey James WB , Harris Jennifer L
Published: November 2015

Objective

Public health experts raise concerns about marketing unhealthy products to young people through television (TV) product placements. Coca-Cola brand appearances (product placements) reached a substantial child and adolescent audience in 2008, but additional brands now sponsor popular programming. We aimed to quantify child and adolescent exposure to food and beverage appearances since 2008.

Design

In 2015, we purchased Nielsen data on occurrences and child/adolescent exposure to food, beverage and restaurant brand appearances on US prime-time TV from 2009 to 2014, and analysed appearances by product category, company, brand and year. We compared exposure to appearances with exposure to traditional commercials for top brands.

Setting

Nationally representative panel of approximately 20 000 TV-viewing households.

Subjects

Children (2–11 years) and adolescents (12–17 years).

Results

Exposure to food and beverage brand appearances peaked in 2012 and declined through 2014. Whereas full-calorie soda brands dominated before 2012, other sugary drink and quick-serve restaurant brands contributed over one-third of appearances viewed by children in 2013 and 2014. Nine hundred and fifty-four companies had brand appearances from 2009 to 2014, but just four were responsible for over half of exposures: The Coca-Cola Company, Dr Pepper Snapple Group, PepsiCo and Starbucks. Approximately half were viewed on reality TV programmes and one sitcom. Each year from 2009 to 2013, brand appearance exposure exceeded traditional advertising exposure for at least one brand.

Conclusions

Despite recent reductions in brand appearances viewed by young people, some unhealthy branded products continue to be marketed via this method. We suggest policy options to reduce child and adolescent exposure to such appearances.
Anatomy, Histochemistry, and Antifungal Activity of Anacardium humile (Anacardiaceae) Leaf
Authors: Royo Vanessa de A. , Mercadante-Simões Maria Olívia , Ribeiro Leonardo M. , Oliveira Dario A. de , Aguiar Marcela Magda R. , Costa Ellenhise R. , Ferreira Perácio Rafael B.
Published: November 2015

Leaves of Anacardium humile are used in Brazilian traditional medicine for the treatment of intestinal disturbances and skin lesions. This study aimed to define leaf diagnostic structural characters, to propose a new method of phytochemical analysis of secretions, prospect flavonoids and alkaloids, and to evaluate their inhibitory activity on Candida albicans. Common anatomical, phytochemical, and microbiological methods were used. Leaves of Anacardium occidentale were used as a reference for the structural analyses. The main structural characters were closed vascular system, absence of ducts at the medulla, bilateral mesophyll, absence of bundle sheath extension, and secretory idioblasts at the xylem. The ducts present schizogenous origin, and secreting activity is restricted to the initial phases of leaf blade expansion. The proposed new phytochemical method is practical and inexpensive and has potential for wide application. The abundance of tannins and flavonoids is related to medicinal use. A single peak in high-performance liquid chromatography indicated the presence of a pure substance not previously reported. The extract had a strong inhibitory effect on C. albicans. The obtained results confirm the potential of A. humile for the prospection of new bioactive compounds.
Creating a ‘reverse’ integrated primary and mental healthcare clinic for those with serious mental illness
Authors: Maragakis Alexandros , Siddharthan Ragavan , RachBeisel Jill , Snipes Cassandra
Published: November 2015

Individuals with serious mental illness (SMI) are more likely to experience preventable medical health issues, such as diabetes, hyperlipidemia, obesity, and cardiovascular disease, than the general population. To further compound this issue, these individuals are less likely to seek preventative medical care. These factors result in higher usage of expensive emergency care, lower quality of care, and lower life expectancy. This manuscript presents literature that examines the health disparities this population experiences, and barriers to accessing primary care. Through the identification of these barriers, we recommend that the field of family medicine work in collaboration with the field of mental health to implement ‘reverse’ integrated care (RIC) systems, and provide primary care services in the mental health settings. By embedding primary care practitioners in mental health settings, where individuals with SMI are more likely to present for treatment, this population may receive treatment for somatic care by experts. This not only would improve the quality of care received by patients, but would also remove the burden of managing complex somatic care from providers trained in mental health. The rationale for this RIC system, as well as training and policy reforms, are discussed.
Assessing Affective and Deliberative Decision-Making: Adaptation of the Columbia Card Task to Brazilian Portuguese
Authors: Kluwe-Schiavon Bruno , Sanvicente-Vieira Breno , Viola Thiago W. , Veiga Eduardo , Bortolotto Vanessa , Grassi-Oliveira Rodrigo
Published: November 2015

The ability to predict reward and punishment is essential for decision-making and the ability to learn about an ever-changing environment. Therefore, efforts have been made in understanding the mechanisms underlying decision-making, especially regarding how affective and deliberative processes interact with risk behavior. Objective: To adapt to Brazilian Portuguese the Columbia Card Task (CCT) and investigate affective and deliberative processes involved in decision-making. Methods: This study had two main phases: (1) a transcultural adaptation and (2) a pilot study. Results: The feedback manipulation among the three conditions of CCT had an effect on the risk-taking level (p< .005,ES= .201). In addition, the feedback manipulation among the three conditions of CCT had an effect on the information use at both the individual and group levels. Further, a linear regression suggested that the use of information, indicated by the advantageous level of the scenarios, predict the number of cards chosenR2= .029,p< .001, accounting for 17% of the variance. Conclusions: The Brazilian CCT performs well and is a versatile method for the assessment of affective and deliberative decision-making under risk according to different feedback manipulation scenarios. This study goes further, comparing electrodermal activity during hot and warm conditions and addressing an advantageous level index analysis to asses deliberative processing.
Spanish Version of the Avoidance-Endurance Questionnaire: Factor Structure and Psychometric Properties
Authors: Ruiz-Párraga Gema T. , López-Martínez Alicia E. , Rusu Adina C. , Hasenbring Monika I.
Published: November 2015

To analyze the factorial structure and psychometric properties of the Spanish adaptation of the AEQ, and to validate it by reporting relevant pain-related variables, which were not investigated in the original study. One hundred and fifty Spanish patients diagnosed with chronic back and neck pain were referred by physicians from different pain clinics in Spain; all the patients filled out the questionnaires at their clinic. A series of principal components analyses (PCA) was performed to develop the Spanish version of the AEQ. Reliability and validity were also calculated. The PCAs revealed five fear-avoidance scales (Kaiser-Meyer-Olkin measures were between .60 and .88, and Bartlett’s tests were significant, p < .01): the Depression scale (DS), Anxiety scale (AS), Catastrophizing scale (CS), Helplessness/hopelessness scale (HHS), and Avoidance of Social and Physical Activities scale (ASPAS), and three endurance-related responses scales: Pain Persistence Behaviour and Distraction scale (PPDS), Ignoring Pain scale (IPS), and Humor scale (HS). All the scales showed high internal consistency (α > .73) and suitable validity (p < .05). New results associated with pain-related cognitive/affective and behavioural responses are discussed. This instrument will probably help clinicians to identify Spanish patients at a high risk of chronicity and to develop treatments tailored to the different profiles in order to improve secondary and tertiary prevention in back and neck pain.
The 15-item Systemic Clinical Outcome and Routine Evaluation (SCORE-15) Scale: Portuguese Validation Studies
Authors: Vilaça Margarida , de Sousa Bruno , Stratton Peter , Relvas Ana Paula
Published: November 2015

This study reports on the validity of the 15-item Portuguese version of the Systemic Clinical Outcome Routine Evaluation (SCORE-15; Vilaça, Silva, & Relvas, 2014), a brief and comprehensive measure of family functioning. Previous studies with SCORE-15 show that this version replicates the three-factor solution found for the original English version: Family strengths, Family communication and Family difficulties. In addition to reviewing previous studies, this article analyses the discriminant, convergent and predictive validity of the Portuguese SCORE-15. To do so, the SCORE-15 was administered to family members attending systemic family or couple’s therapy at the start of the first and fourth sessions and also to a group of non-clinical individuals. Overall, data are reported from 618 participants, including 136 from families attending systemic therapy and 482 community family members. Comparisons of community and clinical samples (discriminant validity) showed statistically significant differences for the total scale and subscales (p < .001), with the community participants presenting healthier family functioning than the clinical ones. Analyses using SCORE-15 and the Quality of Life – adult version, another family measure applied simultaneously (convergent validity), indicate that both scales are significantly (p < .01) and moderately (r = –.47) correlated. Mean score analysis of SCORE-15’s therapeutic sensitivity to change (predictive validity) showed that only the Family communication subscale was sensitive to statistically significant improvement (p < .05) from session 1 to session 4, whereas the SCORE-15’s reliability change index points to its ability to detect clinical improvements (RCI = 14%).
Fray Angélico Chávez and the Colonial Southwest: Historiography and Rematerialization
Authors: McCracken Ellen
Published: November 2015

In the summer of 1924, townspeople recount, 14-year-old Manuel Chávez built models of colonial New Mexico mission churches in the dirt outside Our Lady of Guadalupe Church in the village of Peña Blanca. He was staying with the Franciscan friars after expressing his desire to enter the seminary, where he would become the first native New Mexico Hispano to be ordained a Franciscan priest in the centuries since the Spanish colonization. Still a boy, but one who was about to embark on a life-changing path, the small missions he playfully constructed in the dirt and staunchly protected foretold the strategy of rematerialization that would characterize his future: he would become a pioneering Franciscan historian who organized and interpreted the vast collection of Catholic Church documents from the colonial period in New Mexico through the twentieth century. The author of two dozen books and over 600 shorter works, Fray Angélico Chávez (1910–1996) was a visual artist, literary figure, historian, genealogist, translator, and church restorer—one of New Mexico's foremost twentieth-century intellectuals.
Introduction: Brazilian Candomblé: Scholarship at the Crossroads of Africa and New World
Authors: Sweet James
Published: November 2015

The following pages present an important scholarly exchange on a central sociocultural issue in Latin American history. First, we present J. Lorand Matory's review of Luis Nicolau Parés's 2013 book The Formation of Candomblé: Vodun History and Ritual in Brazil. Second, we present Parés's response to the review.
In-Depth Review: The Formation of Candomblé: Vodun History and Ritual in Brazil, by Luis Nicolau Parés
Authors: Matory J. Lorand
Published: November 2015

The Atlantic slave trade extracted kidnapped populations from the entirety of the western African coast between what are now Senegal and Angola, as well as parts of the east African coast in what is now Mozambique. Western slave traders and buyers regularly classified their human merchandise in terms of the African region, coastal town, or commercial fortress from which they had embarked, or in terms of an ethnic group that presumably derived from that place. With such presumptions, ethnic groupings such as Congo, Angola, Carabalí, Ibo, Nagô, Lucumí, Mina, Arará, Koromantee, and so forth were called “nations.”
Closing Thoughts
Authors: Sweet James
Published: November 2015

As someone who assigns both Matory and Parés in my graduate courses, I find myself asking what is at stake in this debate. If we take Matory at face value, Parés is an unreformed “Herskovitsian” who searches for linear connections between vodun religion in West Africa and the Jeje Candomblé in Bahia. According to Matory, Parés's emphasis on primordial Africa is based on a quest “to avenge the honor of the Jeje nation.” But avenge it from what? Against whom? As both authors make clear, Nagô Candomblé houses transcended Jeje houses in power and prestige, starting in the late nineteenth century. Matory acknowledges the continuing influence of Jeje, especially through the dialogic exchanges of Jeje elites who traveled back and forth between Africa and Brazil in the 1890s. However, he firmly rejects Parés’ claim that memory of earlier Jeje structures shaped Candomblé as it evolved in the twentieth century.
A Multifactorial Conceptualization of Impulsivity
Authors: Knezevic-Budisin Bojana , Pedden Vanessa , White Andrew , Miller Carlin J. , Hoaken Peter N. S.
Published: November 2015

Abstract. Despite the multiple phenotypic presentations of impulsivity, the underlying factor structure of the construct has yet to be settled. The aim of this study, with two multimethod, multisource datasets, was to further explore the multifactorial nature of impulsivity and propose a measure-selection approach. Unlike previous studies that relied on a single type of statistical analysis, the current study explored the relations between personality and behavioral measures of impulsivity utilizing exploratory factor analysis (EFA) and principal component analysis (PCA). Participants comprised two samples of young adults (n(study 1) = 175 and n(study 2) = 118) from separate communities in southwestern Ontario, Canada. Various facets of impulsivity were assessed including adult ADHD symptoms, planning and organizational skills, executive dysfunction, impulsive personality traits (i.e., sensation-seeking), risk-taking behavior, disinhibition, cognitive flexibility, and delay discounting. Both statistical analyses yielded two-factor models. The Dysexecutive Control factor reflected a tendency to act without thinking or planning, and difficulty focusing for a sustained period of time. The Reward-Seeking factor reflected a general need for excitement, and a preference for novel situations despite adverse consequences. For the purposes of standardized assessment of cognitive, emotional, and behavioral manifestations of impulsivity, trans-theoretical measure selection for research and clinical purposes is discussed.
FGFR1 inhibition in lung squamous cell carcinoma: questions and controversies
Authors: Weeden CE , Solomon B , Asselin-Labat M-L
Published: November 2015

Although the incidence of lung cancer has decreased due to the reduction of tobacco use, lung cancer remains the leading cause of cancer-related death. Lung squamous cell carcinoma represents 30% of lung cancers and only recently have possible drug-targetable mutations been identified in this disease, including fibroblast growth factor receptor 1 (FGFR1) gene amplification and genetic alterations in the phosphoinositide-3 kinase pathway. These discoveries have generated a great interest in the clinic and the initiation of clinical trials using FGFR tyrosine kinase inhibitors to treat FGFR-altered lung cancers. However, preliminary results from these studies have shown that not all patients respond to therapy. Here we review current unresolved questions on the selection of patients for their recruitment in FGFR tyrosine kinase inhibitor trials, how FGFR inhibitors could be combined with other targeted therapies or immunotherapies to improve patient outcome, and how the current preclinical models can help address these questions.
CYP epoxygenase metabolites of docosahexaenoic acid protect HL-1 cardiac cells against LPS-induced cytotoxicity through SIRT1
Authors: Samokhvalov V , Jamieson K L , Vriend J , Quan S , Seubert J M
Published: November 2015

Bacterial LPS is an environmental toxin capable of promoting various cardiac complications. Current evidence suggests that LPS-induced myocardial dysfunction emerges as a consequence of compromised quality of cardiac mitochondria. Docosahexaenoic acid (DHA, 22:6n3) is an n-3 polyunsaturated fatty acid (PUFA), which produces a broad spectrum of intrinsic physiological effects including regulation of cell survival and death mechanisms. Although, numerous studies revealed fundamentally beneficial effects of DHA on cardiovascular system, it remains unknown whether these effects were produced by DHA or one of its possibly more potent metabolites. Emerging evidence indicates that cytochrome P450 (CYP) epoxygenase metabolites of DHA, epoxydocosapentaenoic acids (EDPs), produce more potent biological activity compared to its precursor DHA. In this study, we investigated whether DHA and its metabolite 19,20-EDP could protect HL-1 cardiac cells against LPS-induced cytotoxicity. We provide evidence that exogenously added or DHA-derived EDPs promote mitochondrial biogenesis and function in HL-1 cardiac cells. Our results illustrate the CYP epoxygenase metabolite of DHA, 19,20-EDP, confers extensive protection to HL-1 cardiac cells against LPS-induced cytotoxicity via activation of SIRT1.
p53 Configures the G2/M arrest response of nucleostemin-deficient cells
Authors: Huang G , Meng L , Tsai RYL
Published: November 2015

Nucleostemin (NS) protects the genome from replication-induced DNA damage and has an indispensable role in maintaining the continuous proliferation of both p53-wild-type and mutant cells. Yet, some outcomes of NS-deficient cells appear to be shaped by their p53 status, which stimulates conflicting claims on the role of p53 in executing the NS function. This disparity was conveniently attributed to the usual suspect of cell-type variations. To provide a definitive resolution, we investigated the interplay between NS and p53 in two pairs of isogenic cells, that is, genetically modified mouse embryonic fibroblast (MEF) cells and HCT116 human colon cancer cells. In MEF cells, p53 deletion further compromises rather than rescues the proliferative potential of NS-depleted cells without changing their G2/M arrest fate before prophase entry. The detrimental effect of p53 loss in NS-depleted MEF cells correlates with a dramatic increase of polyploid giant cells (PGCs) (up to 24%), which indicates aberrant mitosis. To determine how p53 shapes the response of cells to NS depletion at the molecular level, we showed that p53 turns on the expression of reprimo and MDM2 in NS-deficient MEF cells. In absence of p53, NS-deficient MEF cells exhibit increased levels of phosphorylated cdc2 (Y15) protein and cyclin B1. In cancer (HCT116) cells, NS loss leads to G2/M arrest under both p53wt and p53ko conditions and increases phosphorylated cdc2 more in p53ko than in p53wt cells, as it does in MEF cells. Unlike its effect in MEF cells, NS depletion decreases tumor growth and increases the expression of reprimo and cyclin B1 in a p53-independent manner in HCT116 cells. Our data indicate that the p53 status of NS-deficient cells orchestrates how they respond to G2/M arrest in a normal versus cancer cell distinct fashion.
Novel RNA- and FMRP-binding protein TRF2-S regulates axonal mRNA transport and presynaptic plasticity
Authors: Zhang Peisu , Abdelmohsen Kotb , Liu Yong , Tominaga-Yamanaka Kumiko , Yoon Je-Hyun , Ioannis Grammatikakis , Martindale Jennifer L. , Zhang Yongqing , Becker Kevin G. , Yang In Hong , Gorospe Myriam , Mattson Mark P.
Published: November 2015

Despite considerable evidence that RNA-binding proteins (RBPs) regulate mRNA transport and local translation in dendrites, roles for axonal RBPs are poorly understood. Here we demonstrate that a non-telomeric isoform of telomere repeat-binding factor 2 (TRF2-S) is a novel RBP that regulates axonal plasticity. TRF2-S interacts directly with target mRNAs to facilitate their axonal delivery. The process is antagonized by fragile X mental retardation protein (FMRP). Distinct from the current RNA-binding model of FMRP, we show that FMRP occupies the GAR domain of TRF2-S protein to block the assembly of TRF2-S–mRNA complexes. Overexpressing TRF2-S and silencing FMRP promotes mRNA entry to axons and enhances axonal outgrowth and neurotransmitter release from presynaptic terminals. Our findings suggest a pivotal role for TRF2-S in an axonal mRNA localization pathway that enhances axon outgrowth and neurotransmitter release.
Single-cell analysis and stochastic modelling unveil large cell-to-cell variability in influenza A virus infection
Authors: Heldt Frank S. , Kupke Sascha Y. , Dorl Sebastian , Reichl Udo , Frensing Timo
Published: November 2015

Biochemical reactions are subject to stochastic fluctuations that can give rise to cell-to-cell variability. Yet, how this variability affects viral infections, which themselves involve noisy reactions, remains largely elusive. Here we present single-cell experiments and stochastic simulations that reveal a large heterogeneity between influenza A virus (IAV)-infected cells. In particular, experimental data show that progeny virus titres range from 1 to 970 plaque-forming units and intracellular viral RNA (vRNA) levels span three orders of magnitude. Moreover, the segmentation of IAV genomes seems to increase the susceptibility of their replication to noise, since the level of different genome segments can vary substantially within a cell. In addition, simulations suggest that the abortion of virus entry and random degradation of vRNAs can result in a large fraction of non-productive cells after single-hit infection. These results challenge current beliefs that cell population measurements and deterministic simulations are an accurate representation of viral infections.
Imaging thermal conductivity with nanoscale resolution using a scanning spin probe
Authors: Laraoui Abdelghani , Aycock-Rizzo Halley , Gao Yang , Lu Xi , Riedo Elisa , Meriles Carlos A.
Published: November 2015

The ability to probe nanoscale heat flow in a material is often limited by lack of spatial resolution. Here, we use a diamond-nanocrystal-hosted nitrogen-vacancy centre attached to the apex of a silicon thermal tip as a local temperature sensor. We apply an electrical current to heat up the tip and rely on the nitrogen vacancy to monitor the thermal changes the tip experiences as it is brought into contact with surfaces of varying thermal conductivity. By combining atomic force and confocal microscopy, we image phantom microstructures with nanoscale resolution, and attain excellent agreement between the thermal conductivity and topographic maps. The small mass and high thermal conductivity of the diamond host make the time response of our technique short, which we demonstrate by monitoring the tip temperature upon application of a heat pulse. Our approach promises multiple applications, from the investigation of phonon dynamics in nanostructures to the characterization of heterogeneous phase transitions and chemical reactions in various solid-state systems.
Uncertain behaviours of integrated circuits improve computational performance
Authors: Yoshimura Chihiro , Yamaoka Masanao , Hayashi Masato , Okuyama Takuya , Aoki Hidetaka , Kawarabayashi Ken-ichi , Mizuno Hiroyuki
Published: November 2015

Improvements to the performance of conventional computers have mainly been achieved through semiconductor scaling; however, scaling is reaching its limitations. Natural phenomena, such as quantum superposition and stochastic resonance, have been introduced into new computing paradigms to improve performance beyond these limitations. Here, we explain that the uncertain behaviours of devices due to semiconductor scaling can improve the performance of computers. We prototyped an integrated circuit by performing a ground-state search of the Ising model. The bit errors of memory cell devices holding the current state of search occur probabilistically by inserting fluctuations into dynamic device characteristics, which will be actualised in the future to the chip. As a result, we observed more improvements in solution accuracy than that without fluctuations. Although the uncertain behaviours of devices had been intended to be eliminated in conventional devices, we demonstrate that uncertain behaviours has become the key to improving computational performance.
Quantum Process Tomography of an Optically-Controlled Kerr Non-linearity
Authors: Kupchak Connor , Rind Samuel , Jordaan Bertus , Figueroa Eden
Published: November 2015

Any optical quantum information processing machine would be comprised of fully-characterized constituent devices for both single state manipulations and tasks involving the interaction between multiple quantum optical states. Ideally for the latter, would be an apparatus capable of deterministic optical phase shifts that operate on input quantum states with the action mediated solely by auxiliary signal fields. Here we present the complete experimental characterization of a system designed for optically controlled phase shifts acting on single-photon level probe coherent states. Our setup is based on a warm vapor of rubidium atoms under the conditions of electromagnetically induced transparency with its dispersion properties modified through the use of an optically triggered N-type Kerr non-linearity. We fully characterize the performance of our device by sending in a set of input probe states and measuring the corresponding output via time-domain homodyne tomography and subsequently performing the technique of coherent state quantum process tomography. This method provides us with the precise knowledge of how our optical phase shift will modify any arbitrary input quantum state engineered in the mode of the reconstruction.
Discovery of Novel Plant Interaction Determinants from the Genomes of 163 Root Nodule Bacteria
Authors: Seshadri Rekha , Reeve Wayne G. , Ardley Julie K. , Tennessen Kristin , Woyke Tanja , Kyrpides Nikos C. , Ivanova Natalia N.
Published: November 2015

Root nodule bacteria (RNB) or “rhizobia” are a type of plant growth promoting bacteria, typified by their ability to fix nitrogen for their plant host, fixing nearly 65% of the nitrogen currently utilized in sustainable agricultural production of legume crops and pastures. In this study, we sequenced the genomes of 110 RNB from diverse hosts and biogeographical regions and undertook a global exploration of all available RNB genera with the aim of identifying novel genetic determinants of symbiotic association and plant growth promotion. Specifically, we performed a subtractive comparative analysis with non-RNB genomes, employed relevant transcriptomic data and leveraged phylogenetic distribution patterns and sequence signatures based on known precepts of symbiotic- and host-microbe interactions. A total of 184 protein families were delineated, including known factors for nodulation and nitrogen fixation and candidates with previously unexplored functions, for which a role in host-interaction, -regulation, biocontrol and more, could be posited. These analyses expand our knowledge of the RNB purview and provide novel targets for strain improvement in the ultimate quest to enhance plant productivity and agricultural sustainability.
Control of Separation and Diameter of Ag Nanorods through Self-organized Seeds
Authors: Elliott Paul R. , Stagon Stephen P. , Huang Hanchen
Published: November 2015

This paper proposes a mechanism of controlling the diameter and separation of metallic nanorods from physical vapor deposition through self-organized seeds and experimentally demonstrates the feasibility using Ag as the prototype metal, In as the seed and Si the substrate. Being non-wetting on Si substrates, deposited In atoms self-organize into islands. Subsequently deposited Ag atoms attach to In islands, rather than to Si substrates, due to preferential bonding and geometrical shadowing. The experimental results show that self-organized In seeds of 5 nm nominal thickness give rise to the best separation and the smallest diameter of Ag nanorods.
Atomic force microscopy measurements of bacterial adhesion and biofilm formation onto clay-sized particles
Authors: Huang Qiaoyun , Wu Huayong , Cai Peng , Fein Jeremy B. , Chen Wenli
Published: November 2015

Bacterial adhesion onto mineral surfaces and subsequent biofilm formation play key roles in aggregate stability, mineral weathering and the fate of contaminants in soils. However, the mechanisms of bacteria-mineral interactions are not fully understood. Atomic force microscopy (AFM) was used to determine the adhesion forces between bacteria and goethite in water and to gain insight into the nanoscale surface morphology of the bacteria-mineral aggregates and biofilms formed on clay-sized minerals. This study yields direct evidence of a range of different association mechanisms between bacteria and minerals. All strains studied adhered predominantly to the edge surfaces of kaolinite rather than to the basal surfaces. Bacteria rarely formed aggregates with montmorillonite, but were more tightly adsorbed onto goethite surfaces. This study reports the first measured interaction force between bacteria and a clay surface and the approach curves exhibited jump-in events with attractive forces of 97 ± 34 pN between E. coli and goethite. Bond strengthening between them occurred within 4 s to the maximum adhesion forces and energies of −3.0 ± 0.4 nN and −330 ± 43 aJ (10−18 J), respectively. Under the conditions studied, bacteria tended to form more extensive biofilms on minerals under low rather than high nutrient conditions.
Additional Arctic observations improve weather and sea-ice forecasts for the Northern Sea Route
Authors: Inoue Jun , Yamazaki Akira , Ono Jun , Dethloff Klaus , Maturilli Marion , Neuber Roland , Edwards Patti , Yamaguchi Hajime
Published: November 2015

During ice-free periods, the Northern Sea Route (NSR) could be an attractive shipping route. The decline in Arctic sea-ice extent, however, could be associated with an increase in the frequency of the causes of severe weather phenomena and high wind-driven waves and the advection of sea ice could make ship navigation along the NSR difficult. Accurate forecasts of weather and sea ice are desirable for safe navigation, but large uncertainties exist in current forecasts, partly owing to the sparse observational network over the Arctic Ocean. Here, we show that the incorporation of additional Arctic observations improves the initial analysis and enhances the skill of weather and sea-ice forecasts, the application of which has socioeconomic benefits. Comparison of 63-member ensemble atmospheric forecasts, using different initial data sets, revealed that additional Arctic radiosonde observations were useful for predicting a persistent strong wind event. The sea-ice forecast, initialised by the wind fields that included the effects of the observations, skilfully predicted rapid wind-driven sea-ice advection along the NSR.
The role of cognitive effort in subjective reward devaluation and risky decision-making
Authors: Apps Matthew A J , Grima Laura L , Manohar Sanjay , Husain Masud
Published: November 2015

Motivation is underpinned by cost-benefit valuations where costs—such as physical effort or outcome risk—are subjectively weighed against available rewards. However, in many environments risks pertain not to the variance of outcomes, but to variance in the possible levels of effort required to obtain rewards (effort risks). Moreover, motivation is often guided by the extent to which cognitive—not physical—effort devalues rewards (effort discounting). Yet, very little is known about the mechanisms that underpin the influence of cognitive effort risks or discounting on motivation. We used two cost-benefit decision-making tasks to probe subjective sensitivity to cognitive effort (number of shifts of spatial attention) and to effort risks. Our results show that shifts of spatial attention when monitoring rapidly presented visual stimuli are perceived as effortful and devalue rewards. Additionally, most people are risk-averse, preferring safe, known amounts of effort over risky offers. However, there was no correlation between their effort and risk sensitivity. We show for the first time that people are averse to variance in the possible amount of cognitive effort to be exerted. These results suggest that cognitive effort sensitivity and risk sensitivity are underpinned by distinct psychological and neurobiological mechanisms.
Mycobacterial infection induces a specific human innate immune response
Authors: Blischak John D. , Tailleux Ludovic , Mitrano Amy , Barreiro Luis B. , Gilad Yoav
Published: November 2015

The innate immune system provides the first response to infection and is now recognized to be partially pathogen-specific.Mycobacterium tuberculosis(MTB) is able to subvert the innate immune response and survive inside macrophages. Curiously, only 5–10% of otherwise healthy individuals infected with MTB develop active tuberculosis (TB). We do not yet understand the genetic basis underlying this individual-specific susceptibility. Moreover, we still do not know which properties of the innate immune response are specific to MTB infection. To identify immune responses that are specific to MTB, we infected macrophages with eight different bacteria, including different MTB strains and related mycobacteria and studied their transcriptional response. We identified a novel subset of genes whose regulation was affected specifically by infection with mycobacteria. This subset includes genes involved in phagosome maturation, superoxide production, response to vitamin D, macrophage chemotaxis and sialic acid synthesis. We suggest that genetic variants that affect the function or regulation of these genes should be considered candidate loci for explaining TB susceptibility.
Chiral resolution of spin angular momentum in linearly polarized and unpolarized light
Authors: Hernández R. J. , Mazzulla A. , Provenzano C. , Pagliusi P. , Cipparrone G.
Published: November 2015

Linearly polarized (LP) and unpolarized (UP) light are racemic entities since they can be described as superposition of opposite circularly polarized (CP) components of equal amplitude. As a consequence they do not carry spin angular momentum. Chiral resolution of a racemate, i.e. separation of their chiral components, is usually performed via asymmetric interaction with a chiral entity. In this paper we provide an experimental evidence of the chiral resolution of linearly polarized and unpolarized Gaussian beams through the transfer of spin angular momentum to chiral microparticles. Due to the interplay between linear and angular momentum exchange, basic manipulation tasks, as trapping, spinning or orbiting of micro-objects, can be performed by light with zero helicity. The results might broaden the perspectives for development of miniaturized and cost-effective devices.
Spatially-resolved intracellular sensing of hydrogen peroxide in living cells
Authors: Warren Emilie A. K. , Netterfield Tatiana S. , Sarkar Saheli , Kemp Melissa L. , Payne Christine K.
Published: November 2015

Understanding intracellular redox chemistry requires new tools for the site-specific visualization of intracellular oxidation. We have developed a spatially-resolved intracellular sensor of hydrogen peroxide, HyPer-Tau, for time-resolved imaging in live cells. This sensor consists of a hydrogen peroxide-sensing protein tethered to microtubules. We demonstrate the use of the HyPer-Tau sensor for three applications; dose-dependent response of human cells to exogenous hydrogen peroxide, a model immune response of mouse macrophages to stimulation by bacterial toxin and a spatially-resolved response to localized delivery of hydrogen peroxide. These results demonstrate that HyPer-Tau can be used as an effective tool for tracking changes in spatially localized intracellular hydrogen peroxide and for future applications in redox signaling.
Disposable optics for microscopy diagnostics
Authors: Vilmi Pauliina , Varjo Sami , Sliz Rafal , Hannuksela Jari , Fabritius Tapio
Published: November 2015

The point-of-care testing (POCT) is having increasing role on modern health care systems due to a possibility to perform tests for patients conveniently and immediately. POCT includes lot of disposable devices because of the environment they are often used. For a disposable system to be reasonably utilized, it needs to be high in quality but low in price. Optics based POCT systems are interesting approach to be developed and here we describe a low-cost fabrication process for microlens arrays for microscopy. Lens arrays having average lens diameter of 222 μm with 300 μm lens pitch were fabricated. The lenses were characterized to have standard deviation of 0.06 μm in height and 4.61 μm in diameter. The resolution limit of 3.9μm is demonstrated with real images and the images were compared with ones made with glass and polycarbonate lens arrays. The image quality is at the same level than with the glass lenses and the manufacturing costs are very low, thus making them suitable for POCT applications.
BRAFV600E mutation is highly prevalent in thyroid carcinomas in the young population in Fukushima: a different oncogenic profile from Chernobyl
Authors: Mitsutake Norisato , Fukushima Toshihiko , Matsuse Michiko , Rogounovitch Tatiana , Saenko Vladimir , Uchino Shinya , Ito Masahiro , Suzuki Keiji , Suzuki Shinichi , Yamashita Shunichi
Published: November 2015

After the accident at the Fukushima Daiichi Nuclear Power Plant, the thyroid ultrasound screening program for children aged 0–18 at the time of the accident was started from October 2011. The prevalence of thyroid carcinomas in that population has appeared to be very high (84 cases per 296,253). To clarify the pathogenesis, we investigated the presence of driver mutations in these tumours. 61 classic papillary thyroid carcinomas (PTCs), two follicular variant PTCs, four cribriform-morular variant PTCs and one poorly-differentiated thyroid carcinoma were analysed. We detected BRAFV600E in 43 cases (63.2%), RET/PTC1 in six (8.8%), RET/PTC3 in one (1.5%) and ETV6/NTRK3 in four (5.9%). Among classic and follicular variant PTCs, BRAFV600E was significantly associated with the smaller size. The genetic pattern was completely different from post-Chernobyl PTCs, suggesting non-radiogenic etiology of these cancers. This is the first study demonstrating the oncogene profile in the thyroid cancers discovered by large mass screening, which probably reflects genetic status of all sporadic and latent tumours in the young Japanese population. It is assumed that BRAFV600E may not confer growth advantage on paediatric PTCs and many of these cases grow slowly, suggesting that additional factors may be important for tumour progression in paediatric PTCs.
A Description for Rock Joint Roughness Based on Terrestrial Laser Scanner and Image Analysis
Authors: Ge Yunfeng , Tang Huiming , Eldin M. A. M Ez , Chen Pengyu , Wang Liangqing , Wang Jinge
Published: November 2015

Shear behavior of rock mass greatly depends upon the rock joint roughness which is generally characterized by anisotropy, scale effect and interval effect. A new index enabling to capture all the three features, namely brightness area percentage (BAP), is presented to express the roughness based on synthetic illumination of a digital terrain model derived from terrestrial laser scanner (TLS). Since only tiny planes facing opposite to shear direction make contribution to resistance during shear failure, therefore these planes are recognized through the image processing technique by taking advantage of the fact that they appear brighter than other ones under the same light source. Comparison with existing roughness indexes and two case studies were illustrated to test the performance of BAP description. The results reveal that the rock joint roughness estimated by the presented description has a good match with existing roughness methods and displays a wider applicability.