bluuebunny/crossref_metadata_2025 huggingface dataset:
Controlling feeding practices and maternal migrant background: an analysis of a multicultural sample
Authors: Somaraki Maria , Eli Karin , Ek Anna , Lindberg Louise , Nyman Jonna , Marcus Claude , Flodmark Carl-Erik , Pietrobelli Angelo , Faith Myles S , Sorjonen Kimmo , Nowicka Paulina
Published: November 2016

Objective

Parental feeding practices shape children’s relationships with food and eating. Feeding is embedded socioculturally in values and attitudes related to food and parenting. However, few studies have examined associations between parental feeding practices and migrant background.

Design

Cross-sectional study. Parental feeding practices (restriction, pressure to eat, monitoring) were assessed using the Child Feeding Questionnaire. Differences were explored in four sub-samples grouped by maternal place of birth: Sweden, Nordic/Western Europe, Eastern/Southern Europe and countries outside Europe. Crude, partly and fully adjusted linear regression models were created. Potential confounding variables included child’s age, gender and weight status, and mother’s age, weight status, education and concern about child weight.

Setting

Malmö and Stockholm, Sweden.

Subjects

Mothers (n1325, representing seventy-three countries; mean age 36·5 years; 28·1 % of non-Swedish background; 30·7 % with overweight/obesity; 62·8 % with university education) of pre-school children (mean age 4·8 years; 50·8 % boys; 18·6 % with overweight/obesity).

Results

Non-Swedish-born mothers, whether European-born or non-European-born, were more likely to use restriction. Swedish-born mothers and Nordic/Western European-born mothers reported lower levels of pressure to eat compared with mothers born in Eastern/Southern Europe and mothers born outside Europe. Differences in monitoring were small. Among the potential confounding variables, child weight status and concern about child weight were highly influential. Concern about child weight accounted for some of the effect of maternal origin on restriction.

Conclusions

Non-European-born mothers were more concerned about children being overweight and more likely to report controlling feeding practices. Future research should examine acculturative and structural factors underlying differences in feeding.
Nano-Localized Thermal Analysis and Mapping of Surface and Sub-Surface Thermal Properties Using Scanning Thermal Microscopy (SThM)
Authors: Pereira Maria J. , Amaral Joao S. , Silva Nuno J. O. , Amaral Vitor S.
Published: November 2016

Determining and acting on thermo-physical properties at the nanoscale is essential for understanding/managing heat distribution in micro/nanostructured materials and miniaturized devices. Adequate thermal nano-characterization techniques are required to address thermal issues compromising device performance. Scanning thermal microscopy (SThM) is a probing and acting technique based on atomic force microscopy using a nano-probe designed to act as a thermometer and resistive heater, achieving high spatial resolution. Enabling direct observation and mapping of thermal properties such as thermal conductivity, SThM is becoming a powerful tool with a critical role in several fields, from material science to device thermal management. We present an overview of the different thermal probes, followed by the contribution of SThM in three currently significant research topics. First, in thermal conductivity contrast studies of graphene monolayers deposited on different substrates, SThM proves itself a reliable technique to clarify the intriguing thermal properties of graphene, which is considered an important contributor to improve the performance of downscaled devices and materials. Second, SThM’s ability to perform sub-surface imaging is highlighted by thermal conductivity contrast analysis of polymeric composites. Finally, an approach to induce and study local structural transitions in ferromagnetic shape memory alloy Ni–Mn–Ga thin films using localized nano-thermal analysis is presented.
Women Matter: The Impact of Gender Empowerment on Abortion Regulation in 16 European Countries between 1960 and 2010
Authors: Budde Emma , Heichel Stephan
Published: November 2016

Abortion is undeniably a gender issue—even if not an exclusive one (e.g., Mazur 2002, 137–153; Warren 2000, 201–223. Due to a woman's physical reproductive capacities and, even more so, the patriarchal allocation of care work, members of the female sex bear by far the larger share of all burdens that come with pregnancy and especially unwanted pregnancy—be they physical, emotional, economic, life-course related, or other (England 2001; Tribe 1992, 106). For the longest time in history and across most societies and cultures, women were denied rights to make autonomous decisions in terms of whether and when to procreate, which is in one core aspect of bodily self-determination (Corrêa 2001; Staggenborg 2001).
Ethnic diversity and conflict
Authors: BLEANEY MICHAEL , DIMICO ARCANGELO
Published: November 2016

We argue that the reason why it has proved hard to determine whether negative effects on economic performance and conflict are more strongly associated with polarized rather than fractionalized societies is because the distinction between polarization and fractionalization is only relevant for societies with ethnic diversity above a certain threshold. In addition, high levels of ethnic fractionalization at a country level are generally associated with regional concentration of minorities, and as a result, many regions may have a very different ethnic composition from the national average, and in particular, they may have much higher levels of ethnic polarization than the national level. Because of the very different ethnic composition of different regions in this situation, conflict is more likely to be confined to a limited geographical area.
Yet more on a stochastic economic model: Part 3B: stochastic bridging for retail prices and wages
Authors: Wilkie A. D. , Şahin Şule
Published: November 2016

This is the second subpart of three in a long paper in which we consider stochastic interpolation for the Wilkie asset model, considering both Brownian bridges and Ornstein–Uhlenbeck (OU) bridges. In Part 3A, we developed certain properties for both these types of stochastic bridge, and we investigate the properties of many of our data series on the same lines. We have several economic or investment series, which all have their own peculiarities. In this paper, we cover only retail prices and wages. The other series are dealt with in Part 3C. We find that, although the annual series for the rate of inflation is generated by an AR(1) model, which is the discrete time equivalent of an OU process, an OU bridge is not suitable. We need to use a Brownian bridge on the logarithm of the Price Index. Further, the standard deviation of the monthly increments in any year is, as we find empirically from the data, a function of the change in the annual value, and further there is correlation between the monthly increments in successive years.
Cancer incidence in young and middle-aged people with schizophrenia: nationwide cohort study in Taiwan, 2000–2010
Authors: Chen L. Y. , Hung Y. N. , Chen Y. Y. , Yang S. Y. , Pan C. H. , Chen C. C. , Kuo C. J.
Published: November 2016

Aims.

For nearly a century, the incidence of cancer in people with schizophrenia was lower than in the general population. In the recent decade, the relationship between cancer and schizophrenia has become obscured. Thus, we investigated the cancer risk among young and middle-aged patients with schizophrenia.

Methods.

Records of newly admitted patients with schizophrenia (n = 32 731) from January 2000 through December 2008 were retrieved from the Psychiatric Inpatient Medical Claims database in Taiwan, and the first psychiatric admission of each patient during the same period was defined as the baseline. We obtained 514 incident cancer cases that were monitored until December 2010. Standardised incidence ratios (SIRs) were calculated to compare the risk of cancer between those with schizophrenia and the general population. Stratified analyses of cancer incidences were performed by gender, site of cancers and duration since baseline (first psychiatric admission).

Results.

The incidence of cancer for all sites was slightly higher than that of the general population for the period (SIR = 1.15 [95% CI 1.06–1.26], p = 0.001). Men had a significantly higher incidence of colorectal cancer (SIR = 1.48 [95% CI 1.06–2.06], p = 0.019). Women had a higher incidence of breast cancer (SIR = 1.47 [95% CI 1.22–1.78], p < 0.001). Intriguingly, the risk for colorectal cancer was more pronounced 5 years after the first psychiatric admission rather than earlier (SIR = 1.94 [1.36–2.75], p < 0.001) and so was the risk for breast cancer (SIR = 1.85 [1.38–2.48], p < 0.001). The cancer incidence was higher in patients with schizophrenia contradicting the belief that schizophrenia was protective of cancers.

Conclusions.

Our analyses suggest that men and women with schizophrenia were more vulnerable to certain types of cancers, which indicates the need for gender-specific cancer screening programs. The fact that risk of colorectal cancer was more pronounced 5 years after the first psychiatric admission could imply the impact of unhealthy lifestyles or the possibility of delayed diagnoses.
An Intervention With Meaning
Authors: Levandowski Brooke A. , Cass Constance M. , Miller Stephanie N. , Kemp Janet E. , Conner Kenneth R.
Published: November 2016

Abstract. Background: The Veterans Health Administration (VHA) health-care system utilizes a multilevel suicide prevention intervention that features the use of standardized safety plans with veterans considered to be at high risk for suicide. Aims: Little is known about clinician perceptions on the value of safety planning with veterans at high risk for suicide. Method: Audio-recorded interviews with 29 VHA behavioral health treatment providers in a southeastern city were transcribed and analyzed using qualitative methodology. Results: Clinical providers consider safety planning feasible, acceptable, and valuable to veterans at high risk for suicide owing to the collaborative and interactive nature of the intervention. Providers identified the types of veterans who easily engaged in safety planning and those who may experience more difficulty with the process. Conclusion: Additional research with VHA providers in other locations and with veteran consumers is needed.
A brief intervention for weight control based on habit-formation theory delivered through primary care: results from a randomised controlled trial
Authors: Beeken R J , Leurent B , Vickerstaff V , Wilson R , Croker H , Morris S , Omar R Z , Nazareth I , Wardle J
Published: November 2016

Background:

Primary care is the 'first port of call' for weight control advice, creating a need for simple, effective interventions that can be delivered without specialist skills. Ten Top Tips (10TT) is a leaflet based on habit-formation theory that could fill this gap. The aim of the current study was to test the hypothesis that 10TT can achieve significantly greater weight loss over 3 months than ‘usual care’.

Methods:

A two-arm, individually randomised, controlled trial in primary care. Adults with obesity were identified from 14 primary care providers across England. Patients were randomised to either 10TT or 'usual care' and followed up at 3, 6, 12, 18 and 24 months. The primary outcome was weight loss at 3 months, assessed by a health professional blinded to group allocation. Difference between arms was assessed using a mixed-effect linear model taking into account the health professionals delivering 10TT, and adjusted for baseline weight. Secondary outcomes included body mass index, waist circumference, the number achieving a 5% weight reduction, clinical markers for potential comorbidities, weight loss over 24 months and basic costs.

Results:

Five-hundred and thirty-seven participants were randomised to 10TT (n=267) or to ‘usual care' (n=270). Data were available for 389 (72%) participants at 3 months and for 312 (58%) at 24 months. Participants receiving 10TT lost significantly more weight over 3 months than those receiving usual care (mean difference =−0.87kg; 95% confidence interval: −1.47 to −0.27; P=0.004). At 24 months, the 10TT group had maintained their weight loss, but the ‘usual care’ group had lost a similar amount. The basic cost of 10TT was low, that is, around £23 ($32) per participant.

Conclusions:

The 10TT leaflet delivered through primary care is effective in the short-term and a low-cost option over the longer term. It is the first habit-based intervention to be used in a health service setting and offers a low-intensity alternative to ‘usual care’.
A systems study reveals concurrent activation of AMPK and mTOR by amino acids
Authors: Dalle Pezze Piero , Ruf Stefanie , Sonntag Annika G. , Langelaar-Makkinje Miriam , Hall Philip , Heberle Alexander M. , Razquin Navas Patricia , van Eunen Karen , Tölle Regine C. , Schwarz Jennifer J. , Wiese Heike , Warscheid Bettina , Deitersen Jana , Stork Björn , Fäßler Erik , Schäuble Sascha , Hahn Udo , Horvatovich Peter , Shanley Daryl P. , Thedieck Kathrin
Published: November 2016

Amino acids (aa) are not only building blocks for proteins, but also signalling molecules, with the mammalian target of rapamycin complex 1 (mTORC1) acting as a key mediator. However, little is known about whether aa, independently of mTORC1, activate other kinases of the mTOR signalling network. To delineate aa-stimulated mTOR network dynamics, we here combine a computational–experimental approach with text mining-enhanced quantitative proteomics. We report that AMP-activated protein kinase (AMPK), phosphatidylinositide 3-kinase (PI3K) and mTOR complex 2 (mTORC2) are acutely activated by aa-readdition in an mTORC1-independent manner. AMPK activation by aa is mediated by Ca2+/calmodulin-dependent protein kinase kinase β (CaMKKβ). In response, AMPK impinges on the autophagy regulators Unc-51-like kinase-1 (ULK1) and c-Jun. AMPK is widely recognized as an mTORC1 antagonist that is activated by starvation. We find that aa acutely activate AMPK concurrently with mTOR. We show that AMPK under aa sufficiency acts to sustain autophagy. This may be required to maintain protein homoeostasis and deliver metabolite intermediates for biosynthetic processes.
The influence of large cations on the electrochemical properties of tunnel-structured metal oxides
Authors: Yuan Yifei , Zhan Chun , He Kun , Chen Hungru , Yao Wentao , Sharifi-Asl Soroosh , Song Boao , Yang Zhenzhen , Nie Anmin , Luo Xiangyi , Wang Hao , Wood Stephen M. , Amine Khalil , Islam M. Saiful , Lu Jun , Shahbazian-Yassar Reza
Published: November 2016

Metal oxides with a tunnelled structure are attractive as charge storage materials for rechargeable batteries and supercapacitors, since the tunnels enable fast reversible insertion/extraction of charge carriers (for example, lithium ions). Common synthesis methods can introduce large cations such as potassium, barium and ammonium ions into the tunnels, but how these cations affect charge storage performance is not fully understood. Here, we report the role of tunnel cations in governing the electrochemical properties of electrode materials by focusing on potassium ions in α-MnO2. We show that the presence of cations inside 2 × 2 tunnels of manganese dioxide increases the electronic conductivity, and improves lithium ion diffusivity. In addition, transmission electron microscopy analysis indicates that the tunnels remain intact whether cations are present in the tunnels or not. Our systematic study shows that cation addition to α-MnO2 has a strong beneficial effect on the electrochemical performance of this material.
Mid-infrared ultra-high-Q resonators based on fluoride crystalline materials
Authors: Lecaplain C. , Javerzac-Galy C. , Gorodetsky M. L. , Kippenberg T. J.
Published: November 2016

The unavailability of highly transparent materials in the mid-infrared has been the main limitation in the development of ultra-sensitive molecular sensors or cavity-based spectroscopy applications. Whispering gallery mode microresonators have attained ultra-high-quality (Q) factor resonances in the near-infrared and visible. Here we report ultra-high Q factors in the mid-infrared using polished alkaline earth metal fluoride crystals. Using an uncoated chalcogenide tapered fibre as a high-ideality coupler in the mid-infrared, we study via cavity ringdown technique the losses of BaF2, CaF2, MgF2 and SrF2 microresonators. We show that MgF2 is limited by multiphonon absorption by studying the temperature dependence of the Q factor. In contrast, in SrF2 and BaF2 the lower multiphonon absorption leads to ultra-high Q factors at 4.5 μm. These values correspond to an optical finesse of "Equation missing", the highest value achieved for any type of mid-infrared resonator to date.
Direct identification of clinically relevant neoepitopes presented on native human melanoma tissue by mass spectrometry
Authors: Bassani-Sternberg Michal , Bräunlein Eva , Klar Richard , Engleitner Thomas , Sinitcyn Pavel , Audehm Stefan , Straub Melanie , Weber Julia , Slotta-Huspenina Julia , Specht Katja , Martignoni Marc E. , Werner Angelika , Hein Rüdiger , H. Busch Dirk , Peschel Christian , Rad Roland , Cox Jürgen , Mann Matthias , Krackhardt Angela M.
Published: November 2016

Although mutations may represent attractive targets for immunotherapy, direct identification of mutated peptide ligands isolated from human leucocyte antigens (HLA) on the surface of native tumour tissue has so far not been successful. Using advanced mass spectrometry (MS) analysis, we survey the melanoma-associated immunopeptidome to a depth of 95,500 patient-presented peptides. We thereby discover a large spectrum of attractive target antigen candidates including cancer testis antigens and phosphopeptides. Most importantly, we identify peptide ligands presented on native tumour tissue samples harbouring somatic mutations. Four of eleven mutated ligands prove to be immunogenic by neoantigen-specific T-cell responses. Moreover, tumour-reactive T cells with specificity for selected neoantigens identified by MS are detected in the patient’s tumour and peripheral blood. We conclude that direct identification of mutated peptide ligands from primary tumour material by MS is possible and yields true neoepitopes with high relevance for immunotherapeutic strategies in cancer.
Bisguanidinium dinuclear oxodiperoxomolybdosulfate ion pair-catalyzed enantioselective sulfoxidation
Authors: Zong Lili , Wang Chao , Moeljadi Adhitya Mangala Putra , Ye Xinyi , Ganguly Rakesh , Li Yongxin , Hirao Hajime , Tan Choon-Hong
Published: November 2016

Catalytic use of peroxomolybdate for asymmetric transformations has attracted increasing attention due to its catalytic properties and application in catalysis. Herein, we report chiral bisguanidinium dinuclear oxodiperoxomolybdosulfate [BG]2+[(μ-SO4)Mo2O2(μ-O2)2(O2)2]2−ion pair, as a catalyst for enantioselective sulfoxidation using aqueous H2O2as the terminal oxidant. The ion pair catalyst is isolatable, stable and useful for the oxidation of a range of dialkyl sulfides. The practical utility was illustrated using a gram-scale synthesis of armodafinil, a commercial drug, with the catalyst generatedin situfrom 0.25 mol% of bisguanidinium and 2.5 mol% of Na2MoO4·2H2O. Structural characterization of this ion pair catalyst has been successfully achieved using single-crystal X-ray crystallography.
A radial map of multi-whisker correlation selectivity in the rat barrel cortex
Authors: Estebanez Luc , Bertherat Julien , Shulz Daniel E. , Bourdieu Laurent , Léger Jean- François
Published: November 2016

In the barrel cortex, several features of single-whisker stimuli are organized in functional maps. The barrel cortex also encodes spatio-temporal correlation patterns of multi-whisker inputs, but so far the cortical mapping of neurons tuned to such input statistics is unknown. Here we report that layer 2/3 of the rat barrel cortex contains an additional functional map based on neuronal tuning to correlated versus uncorrelated multi-whisker stimuli: neuron responses to uncorrelated multi-whisker stimulation are strongest above barrel centres, whereas neuron responses to correlated and anti-correlated multi-whisker stimulation peak above the barrel–septal borders, forming rings of multi-whisker synchrony-preferring cells.
Polarization bandgaps and fluid-like elasticity in fully solid elastic metamaterials
Authors: Ma Guancong , Fu Caixing , Wang Guanghao , del Hougne Philipp , Christensen Johan , Lai Yun , Sheng Ping
Published: November 2016

Elastic waves exhibit rich polarization characteristics absent in acoustic and electromagnetic waves. By designing a solid elastic metamaterial based on three-dimensional anisotropic locally resonant units, here we experimentally demonstrate polarization bandgaps together with exotic properties such as ‘fluid-like’ elasticity. We construct elastic rods with unusual vibrational properties, which we denote as ‘meta-rods’. By measuring the vibrational responses under flexural, longitudinal and torsional excitations, we find that each vibration mode can be selectively suppressed. In particular, we observe in a finite frequency regime that all flexural vibrations are forbidden, whereas longitudinal vibration is allowed—a unique property of fluids. In another case, the torsional vibration can be suppressed significantly. The experimental results are well interpreted by band structure analysis, as well as effective media with indefinite mass density and negative moment of inertia. Our work opens an approach to efficiently separate and control elastic waves of different polarizations in fully solid structures.
T-cell stimuli independently sum to regulate an inherited clonal division fate
Authors: Marchingo J. M. , Prevedello G. , Kan A. , Heinzel S. , Hodgkin P. D. , Duffy K. R.
Published: November 2016

In the presence of antigen and costimulation, T cells undergo a characteristic response of expansion, cessation and contraction. Previous studies have revealed that population-level reproducibility is a consequence of multiple clones exhibiting considerable disparity in burst size, highlighting the requirement for single-cell information in understanding T-cell fate regulation. Here we show that individual T-cell clones resulting from controlled stimulation in vitro are strongly lineage imprinted with highly correlated expansion fates. Progeny from clonal families cease dividing in the same or adjacent generations, with inter-clonal variation producing burst-size diversity. The effects of costimulatory signals on individual clones sum together with stochastic independence; therefore, the net effect across multiple clones produces consistent, but heterogeneous population responses. These data demonstrate that substantial clonal heterogeneity arises through differences in experience of clonal progenitors, either through stochastic antigen interaction or by differences in initial receptor sensitivities.
Quantum memory with strong and controllable Rydberg-level interactions
Authors: Li Lin , Kuzmich A
Published: November 2016

Realization of distributed quantum systems requires fast generation and long-term storage of quantum states. Ground atomic states enable memories with storage times in the range of a minute, however their relatively weak interactions do not allow fast creation of non-classical collective states. Rydberg atomic systems feature fast preparation of singly excited collective states and their efficient mapping into light, but storage times in these approaches have not yet exceeded a few microseconds. Here we demonstrate a system that combines fast quantum state generation and long-term storage. An initially prepared coherent state of an atomic memory is transformed into a non-classical collective atomic state by Rydberg-level interactions in less than a microsecond. By sheltering the quantum state in the ground atomic levels, the storage time is increased by almost two orders of magnitude. This advance opens a door to a number of quantum protocols for scalable generation and distribution of entanglement.
The genome of Onchocerca volvulus, agent of river blindness
Authors: Cotton James A. , Bennuru Sasisekhar , Grote Alexandra , Harsha Bhavana , Tracey Alan , Beech Robin , Doyle Stephen R. , Dunn Matthew , Hotopp Julie C. Dunning , Holroyd Nancy , Kikuchi Taisei , Lambert Olivia , Mhashilkar Amruta , Mutowo Prudence , Nursimulu Nirvana , Ribeiro Jose M. C. , Rogers Matthew B. , Stanley Eleanor , Swapna Lakshmipuram S. , Tsai Isheng J. , Unnasch Thomas R. , Voronin Denis , Parkinson John , Nutman Thomas B. , Ghedin Elodie , Berriman Matthew , Lustigman Sara
Published: November 2016

Human onchocerciasis is a serious neglected tropical disease caused by the filarial nematode Onchocerca volvulus that can lead to blindness and chronic disability. Control of the disease relies largely on mass administration of a single drug, and the development of new drugs and vaccines depends on a better knowledge of parasite biology. Here, we describe the chromosomes of O. volvulus and its Wolbachia endosymbiont. We provide the highest-quality sequence assembly for any parasitic nematode to date, giving a glimpse into the evolution of filarial parasite chromosomes and proteomes. This resource was used to investigate gene families with key functions that could be potentially exploited as targets for future drugs. Using metabolic reconstruction of the nematode and its endosymbiont, we identified enzymes that are likely to be essential for O. volvulus viability. In addition, we have generated a list of proteins that could be targeted by Federal-Drug-Agency-approved but repurposed drugs, providing starting points for anti-onchocerciasis drug development.
A microarray whole-genome gene expression dataset in a rat model of inflammatory corneal angiogenesis
Authors: Mukwaya Anthony , Lindvall Jessica M. , Xeroudaki Maria , Peebo Beatrice , Ali Zaheer , Lennikov Anton , Jensen Lasse Dahl Ejby , Lagali Neil
Published: November 2016

In angiogenesis with concurrent inflammation, many pathways are activated, some linked to VEGF and others largely VEGF-independent. Pathways involving inflammatory mediators, chemokines, and micro-RNAs may play important roles in maintaining a pro-angiogenic environment or mediating angiogenic regression. Here, we describe a gene expression dataset to facilitate exploration of pro-angiogenic, pro-inflammatory, and remodelling/normalization-associated genes during both an active capillary sprouting phase, and in the restoration of an avascular phenotype. The dataset was generated by microarray analysis of the whole transcriptome in a rat model of suture-induced inflammatory corneal neovascularisation. Regions of active capillary sprout growth or regression in the cornea were harvested and total RNA extracted from four biological replicates per group. High quality RNA was obtained for gene expression analysis using microarrays. Fold change of selected genes was validated by qPCR, and protein expression was evaluated by immunohistochemistry. We provide a gene expression dataset that may be re-used to investigate corneal neovascularisation, and may also have implications in other contexts of inflammation-mediated angiogenesis.
A global gas flaring black carbon emission rate dataset from 1994 to 2012
Authors: Huang Kan , Fu Joshua S.
Published: November 2016

Global flaring of associated petroleum gas is a potential emission source of particulate matters (PM) and could be notable in some specific regions that are in urgent need of mitigation. PM emitted from gas flaring is mainly in the form of black carbon (BC), which is a strong short-lived climate forcer. However, BC from gas flaring has been neglected in most global/regional emission inventories and is rarely considered in climate modeling. Here we present a global gas flaring BC emission rate dataset for the period 1994–2012 in a machine-readable format. We develop a region-dependent gas flaring BC emission factor database based on the chemical compositions of associated petroleum gas at various oil fields. Gas flaring BC emission rates are estimated using this emission factor database and flaring volumes retrieved from satellite imagery. Evaluation using a chemical transport model suggests that consideration of gas flaring emissions can improve model performance. This dataset will benefit and inform a broad range of research topics, e.g., carbon budget, air quality/climate modeling, and environmental/human exposure.
Systematic chemical-genetic and chemical-chemical interaction datasets for prediction of compound synergism
Authors: Wildenhain Jan , Spitzer Michaela , Dolma Sonam , Jarvik Nick , White Rachel , Roy Marcia , Griffiths Emma , Bellows David S. , Wright Gerard D. , Tyers Mike
Published: November 2016

The network structure of biological systems suggests that effective therapeutic intervention may require combinations of agents that act synergistically. However, a dearth of systematic chemical combination datasets have limited the development of predictive algorithms for chemical synergism. Here, we report two large datasets of linked chemical-genetic and chemical-chemical interactions in the budding yeast Saccharomyces cerevisiae. We screened 5,518 unique compounds against 242 diverse yeast gene deletion strains to generate an extended chemical-genetic matrix (CGM) of 492,126 chemical-gene interaction measurements. This CGM dataset contained 1,434 genotype-specific inhibitors, termed cryptagens. We selected 128 structurally diverse cryptagens and tested all pairwise combinations to generate a benchmark dataset of 8,128 pairwise chemical-chemical interaction tests for synergy prediction, termed the cryptagen matrix (CM). An accompanying database resource called ChemGRID was developed to enable analysis, visualisation and downloads of all data. The CGM and CM datasets will facilitate the benchmarking of computational approaches for synergy prediction, as well as chemical structure-activity relationship models for anti-fungal drug discovery.
Endotoxin free hyaluronan and hyaluronan fragments do not stimulate TNF-α, interleukin-12 or upregulate co-stimulatory molecules in dendritic cells or macrophages
Authors: Dong Yifei , Arif Arif , Olsson Mia , Cali Valbona , Hardman Blair , Dosanjh Manisha , Lauer Mark , Midura Ronald J. , Hascall Vincent C. , Brown Kelly L. , Johnson Pauline
Published: November 2016

The extracellular matrix glycosaminoglycan, hyaluronan, has been described as a regulator of tissue inflammation, with hyaluronan fragments reported to stimulate innate immune cells. High molecular mass hyaluronan is normally present in tissues, but upon inflammation lower molecular mass fragments are generated. It is unclear if these hyaluronan fragments induce an inflammatory response or are a consequence of inflammation. In this study, mouse bone marrow derived macrophages and dendritic cells (DCs) were stimulated with various sizes of hyaluronan from different sources, fragmented hyaluronan, hyaluronidases and heavy chain modified-hyaluronan (HA-HC). Key pro-inflammatory molecules, tumour necrosis factor alpha, interleukin-1 beta, interleukin-12, CCL3, and the co-stimulatory molecules, CD40 and CD86 were measured. Only human umbilical cord hyaluronan, bovine testes and Streptomyces hyaluronlyticus hyaluronidase stimulated macrophages and DCs, however, these reagents were found to be contaminated with endotoxin, which was not fully removed by polymyxin B treatment. In contrast, pharmaceutical grade hyaluronan and hyaluronan fragments failed to stimulate in vitro-derived or ex vivo macrophages and DCs, and did not induce leukocyte recruitment after intratracheal instillation into mouse lungs. Hence, endotoxin-free pharmaceutical grade hyaluronan does not stimulate macrophages and DCs in our inflammatory models. These results emphasize the importance of ensuring hyaluronan preparations are endotoxin free.
Classification of Tandem Mass Spectra for Identification of N- and O-linked Glycopeptides
Authors: Toghi Eshghi Shadi , Yang Weiming , Hu Yingwei , Shah Punit , Sun Shisheng , Li Xingde , Zhang Hui
Published: November 2016

Analysis of intact glycopeptides by mass spectrometry is essential to determining the microheterogeneity of protein glycosylation. Higher-energy collisional dissociation (HCD) fragmentation of glycopeptides generates mono- or disaccharide ions called oxonium ions that carry information about the structure of the fragmented glycans. Here, we investigated the link between glycan structures and the intensity of oxonium ions in the spectra of glycopeptides and utilized this information to improve the identification of glycopeptides in biological samples. Tandem spectra of glycopeptides from fetuin, glycophorin A, ovalbumin and gp120 tryptic digests were used to build a spectral database of N- and O-linked glycopeptides. Logistic regression was applied to this database to develop model to distinguish between the spectra of N- and O-linked glycopeptides. Remarkably, the developed model was found to reliably distinguish between the N- and O-linked glycopeptides using the spectral features of the oxonium ions using verification spectral set. Finally, the performance of the developed predictive model was evaluated in HILIC enriched glycopeptides extracted from human serum. The results showed that pre-classification of tandem spectra based on their glycosylation type improved the identification of N-linked glycopeptides. The developed model facilitates interpretation of tandem mass spectrometry data for assignment of glycopeptides.
Realisation of magnetically and atomically abrupt half-metal/semiconductor interface: Co2FeSi0.5Al0.5/Ge(111)
Authors: Nedelkoski Zlatko , Kuerbanjiang Balati , Glover Stephanie E. , Sanchez Ana M. , Kepaptsoglou Demie , Ghasemi Arsham , Burrows Christopher W. , Yamada Shinya , Hamaya Kohei , Ramasse Quentin M. , Hasnip Philip J. , Hase Thomas , Bell Gavin R. , Hirohata Atsufumi , Lazarov Vlado K.
Published: November 2016

Halfmetal-semiconductor interfaces are crucial for hybrid spintronic devices. Atomically sharp interfaces with high spin polarisation are required for efficient spin injection. In this work we show that thin film of half-metallic full Heusler alloy Co2FeSi0.5Al0.5 with uniform thickness and B2 ordering can form structurally abrupt interface with Ge(111). Atomic resolution energy dispersive X-ray spectroscopy reveals that there is a small outdiffusion of Ge into specific atomic planes of the Co2FeSi0.5Al0.5 film, limited to a very narrow "Equation missing"1 nm interface region. First-principles calculations show that this selective outdiffusion along the Fe-Si/Al atomic planes does not change the magnetic moment of the film up to the very interface. Polarized neutron reflectivity, x-ray reflectivity and aberration-corrected electron microscopy confirm that this interface is both magnetically and structurally abrupt. Finally, using first-principles calculations we show that this experimentally realised interface structure, terminated by Co-Ge bonds, preserves the high spin polarization at the Co2FeSi0.5Al0.5/Ge interface, hence can be used as a model to study spin injection from half-metals into semiconductors.
Optical computing for optical coherence tomography
Authors: Zhang Xiao , Huo Tiancheng , Wang Chengming , Liao Wenchao , Chen Tianyuan , Ai Shengnan , Zhang Wenxin , Hsieh Jui-Cheng , Xue Ping
Published: November 2016

We propose an all-optical Fourier transformation system for real-time massive data processing in high speed optical coherence tomography (OCT). In the so-called optical computing OCT, fast Fourier transformation (FFT) of A-scan signal is optically processed in real time before being detected by photoelectric detector. Therefore, the processing time for interpolation and FFT in traditional Fourier domain OCT can be dramatically eliminated. A processing rate of 10 mega-A-scans/second was experimentally achieved, which is, to our knowledge, the highest speed for OCT imaging. Due to its fiber based all-optical configuration, this optical computing OCT system is ideal for ultrahigh speed volumetric OCT imaging in clinical application.
Demonstration of reconfigurable joint orbital angular momentum mode and space switching
Authors: Liu Jun , Wang Jian
Published: November 2016

We propose and demonstrate space-selective switch functions employing orbital angular momentum (OAM) modes in the space domain for switching network. One is the switching among different OAM modes having different spatial phase structures, called OAM mode switching. The other is the switching among different space locations, called space switching. The switching operation mechanism relies on linear optics. Reconfigurable 4 × 4 OAM mode switching, space switching, and joint OAM mode and space switching fabric using a single spatial light modulator (SLM) are all demonstrated in the experiment. In addition, the presented OAM-incorporated space-selective switch might be further extended to N × N joint OAM mode and space switching with fast response, scalability, cascading ability and compability to facilitate robust switching applications.
Main Effects of Diagnoses, Brain Regions, and their Interaction Effects for Cerebral Metabolites in Bipolar and Unipolar Depressive Disorders
Authors: Tan Hai-Zhu , Li Hui , Liu Chen-Feng , Guan Ji-Tian , Guo Xiao-Bo , Wen Can-Hong , Ou Shao-Min , Zhang Yin-Nan , Zhang Jie , Xu Chong-Tao , Shen Zhi-Wei , Wu Ren-Hua , Wang Xue-Qin
Published: November 2016

Previous studies suggested patients with bipolar depressive disorder (BDd) or unipolar depressive disorder (UDd) have cerebral metabolites abnormalities. These abnormalities may stem from multiple sub-regions of gray matter in brain regions. Thirteen BDd patients, 20 UDd patients and 20 healthy controls (HC) were enrolled to investigate these abnormalities. Absolute concentrations of 5 cerebral metabolites (glutamate-glutamine (Glx), N-acetylaspartate (NAA), choline (Cho), myo-inositol (mI), creatine (Cr), parietal cortex (PC)) were measured from 4 subregions (the medial frontal cortex (mPFC), anterior cingulate cortex (ACC), posterior cingulate cortex (PCC), and parietal cortex (PC)) of gray matter. Main and interaction effects of cerebral metabolites across subregions of gray matter were evaluated. For example, the Glx was significantly higher in BDd compared with UDd, and so on. As the interaction analyses showed, some interaction effects existed. The concentrations of BDds’ Glx, Cho, Cr in the ACC and HCs’ mI and Cr in the PC were higher than that of other interaction effects. In addition, the concentrations of BDds’ Glx and Cr in the PC and HCs’ mI in the ACC were statistically significant lower than that of other interaction effects. These findings point to region-related abnormalities of cerebral metabolites across subjects with BDd and UDd.
Homocysteine and Its Relationship to Asymptomatic Carotid Stenosis in a Chinese Community Population
Authors: Jia Jiaokun , Wang Anxin , Wang Jing , Wu Jianwei , Yan Xiujuan , Zhou Yong , Chen Shengyun , Zhao Xingquan
Published: November 2016

Little is known about the association between homocysteine (Hcy) and asymptomatic CAS in the healthy population. The purpose of this study was to investigate the relationship between Hcy levels and asymptomatic CAS in a Chinese community population. The current study included 5393 participants who were age of 40 years or older, and free of stroke, transient ischemic attack, and coronary artery disease. Demographic and clinical variables were investigated, and the presence of CAS was assessed by Color Doppler Ultrasound. A multivariate logistic regression was used to examine the association between Hcy levels and asymptomatic CAS. 361 (6.69%) participants were diagnosed with asymptomatic CAS, who had higher Hcy levels compared with those without (p-value for trend = 0.0001). After adjusting other possible risk factors, Hcy > 19.3μmol/L was considered as an independent indicator of asymptomatic CAS (OR 1.53, 95%CI 1.05–2.23; p-value for trend = 0.0265), but with a difference between participants with diabetes and without [OR (95%CI): 2.89(1.02–8.22) vs. 1.42(0.95–2.12); P interaction < 0.05]. In this large-population, community-based study, Hcy is an independent indicator of asymptomatic CAS, especially in patients with diabetes.
Importance of the C-terminal histidine residues of Helicobacter pylori GroES for Toll-like receptor 4 binding and interleukin-8 cytokine production
Authors: Lee Haur , Su Yu-Lin , Huang Bo-Shih , Hsieh Feng-Tse , Chang Ya-Hui , Tzeng Shiou-Ru , Hsu Chun-Hua , Huang Po-Tsang , Lou Kuo-Long , Wang Yeng-Tseng , Chow Lu-Ping
Published: November 2016

Helicobacter pylori infection is associated with the development of gastric and duodenal ulcers as well as gastric cancer. GroES of H. pylori (HpGroES) was previously identified as a gastric cancer-associated virulence factor. Our group showed that HpGroES induces interleukin-8 (IL-8) cytokine release via a Toll-like receptor 4 (TLR4)-dependent mechanism and domain B of the protein is crucial for interactions with TLR4. In the present study, we investigated the importance of the histidine residues in domain B. To this end, a series of point mutants were expressed in Escherichia coli, and the corresponding proteins purified. Interestingly, H96, H104 and H115 were not essential, whereas H100, H102, H108, H113 and H118 were crucial for IL-8 production and TLR4 interactions in KATO-III cells. These residues were involved in nickel binding. Four of five residues, H102, H108, H113 and H118 induced certain conformation changes in extended domain B structure, which is essential for interactions with TLR4 and consequent IL-8 production. We conclude that interactions of nickel ions with histidine residues in domain B help to maintain the conformation of the C-terminal region to conserve the integrity of the HpGroES structure and modulate IL-8 release.
In-situ growth of MnO2 crystals under nanopore-constraint in carbon nanofibers and their electrochemical performance
Authors: Le TrungHieu , Yang Ying , Yu Liu , Huang Zheng-hong , Kang Feiyu
Published: November 2016

Growing MnO2 nanocrystals in the bulk of porous carbon nanofibers is conducted in a KMnO4 aqueous solution aimed to enhance the electrochemical performance of MnO2. The rate of redox reaction between KMnO4 and carbon was controlled by the concentration of KMnO4 in a neutral solution. The MnO2 nanoparticles grow along with (211) crystal faces when the redox reaction happens on the surface of fibers under 1D constraint, while the nanoparticles grow along with (200) crystal faces when the redox reaction happens in the bulk of fibers under 3D constraint. The composite, where MnO2 nanoparticles are formed in the bulk under a constraint, yields an electrode material for supercapacitors showing good electron transport, rapid ion penetration, fast and reversible Faradaic reaction, and excellent rate performance. The capacitance of the composite electrode could be 1282 F g−1 under a current density of 0.2 A g−1 in 1 M Na2SO4 electrolyte. A symmetric supercapacitor delivers energy density of 36 Wh kg−1 with power density of 39 W kg−1, and can maintain 7.5 Wh kg−1 at 10.3 kW kg−1. It exhibits an excellent electrochemical cycling stability with 101% initial capacitance and 95% columbic efficiency even after 1000 cycles of charge/discharge.
The ERF transcription factor family in cassava: genome-wide characterization and expression analyses against drought stress
Authors: Fan Wei , Hai Meirong , Guo Yunling , Ding Zehong , Tie Weiwei , Ding Xupo , Yan Yan , Wei Yunxie , Liu Yang , Wu Chunlai , Shi Haitao , Li Kaimian , Hu Wei
Published: November 2016

Cassava (Manihot esculenta) shows strong tolerance to drought stress; however, the mechanisms underlying this tolerance are poorly understood. Ethylene response factor (ERF) family genes play a crucial role in plants responding to abiotic stress. Currently, less information is known regarding the ERF family in cassava. Herein, 147 ERF genes were characterized from cassava based on the complete genome data, which was further supported by phylogenetic relationship, gene structure, and conserved motif analyses. Transcriptome analysis suggested that most of the MeERF genes have similar expression profiles between W14 and Arg7 during organ development. Comparative expression profiles revealed that the function of MeERFs in drought tolerance may be differentiated in roots and leaves of different genotypes. W14 maintained strong tolerance by activating more MeERF genes in roots compared to Arg7 and SC124, whereas Arg7 and SC124 maintained drought tolerance by inducing more MeERF genes in leaves relative to W14. Expression analyses of the selected MeERF genes showed that most of them are significantly upregulated by osmotic and salt stresses, whereas slightly induced by cold stress. Taken together, this study identified candidate MeERF genes for genetic improvement of abiotic stress tolerance and provided new insights into ERF-mediated cassava tolerance to drought stress.
Delivery Room Quality Improvement Project Improved Compliance with Best Practices for a Community NICU
Authors: Sauer Charles W. , Boutin Mallory A. , Fatayerji Aayah N. , Proudfoot James A. , Fatayerji Nabil I. , Golembeski David J.
Published: November 2016

A Quality Improvement bundle was implemented with the goal of standardizing the multidisciplinary approach to delivery room management. We used a Pre-Post Quality Improvement initiative with the following aims: (1) Placement of a functioning pulse oximeter by two minutes after birth, (2) Delayed intubation, (3) Normothermia on Neonatal Intensive Care Unit Admission, (4) Use of a pre-brief, debrief, and delivery room checklist. Data was collected for 548 infants, which represents every admission to the Palomar Rady Children’s Hospital Neonatal Intensive Care Unit during the 35 month study period from January 1, 2010 to November 30, 2012. The intervention began on May 1, 2011. The objective of increasing the frequency of each goal was met. A significant decrease in rates of retinopathy of prematurity in our post-intervention group was found. Odds ratio 0.00 (0.000, 0.696) p = 0.008. However, this was not confirmed in the multivariable analysis so should be interpreted with caution. This quality improvement project had a positive effect on newborn resuscitation at Palomar Medical Center.
Highly Efficient Spin-Current Operation in a Cu Nano-Ring
Authors: Murphy Benedict A. , Vick Andrew J. , Samiepour Marjan , Hirohata Atsufumi
Published: November 2016

An all-metal lateral spin-valve structure has been fabricated with a medial Copper nano-ring to split the diffusive spin-current path. We have demonstrated significant modulation of the non-local signal by the application of a magnetic field gradient across the nano-ring, which is up to 30% more efficient than the conventional Hanle configuration at room temperature. This was achieved by passing a dc current through a current-carrying bar to provide a locally induced Ampère field. We have shown that in this manner a lateral spin-valve gains an additional functionality in the form of three-terminal gate operation for future spintronic logic.