bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

Abstract
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

AbstractAmino 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

AbstractMetal 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

AbstractThe 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

AbstractAlthough 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

AbstractCatalytic 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

AbstractIn 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

AbstractElastic 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

AbstractIn 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

AbstractRealization 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

AbstractHuman 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

AbstractIn 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

AbstractGlobal 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

AbstractThe 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

AbstractThe 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

AbstractAnalysis 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.