bluuebunny/crossref_metadata_2025_split huggingface dataset:
Controlling a Van Hove singularity and Fermi surface topology at a complex oxide heterostructure interface
Authors: Mori Ryo , Marshall Patrick B. , Ahadi Kaveh , Denlinger Jonathan D. , Stemmer Susanne , Lanzara Alessandra 
Published: December 2019

AbstractThe emergence of saddle-point Van Hove singularities (VHSs) in the density of states, accompanied by a change in Fermi surface topology, Lifshitz transition, constitutes an ideal ground for the emergence of different electronic phenomena, such as superconductivity, pseudo-gap, magnetism, and density waves. However, in most materials the Fermi level, $${E}_{{\rm{F}}}$$

E

F

, is too far from the VHS where the change of electronic topology takes place, making it difficult to reach with standard chemical doping or gating techniques. Here, we demonstrate that this scenario can be realized at the interface between a Mott insulator and a band insulator as a result of quantum confinement and correlation enhancement, and easily tuned by fine control of layer thickness and orbital occupancy. These results provide a tunable pathway for Fermi surface topology and VHS engineering of electronic phases.
CD4+ T cell help creates memory CD8+ T cells with innate and help-independent recall capacities
Authors: Ahrends Tomasz , Busselaar Julia , Severson Tesa M. , Bąbała Nikolina , de Vries Evert , Bovens Astrid , Wessels Lodewyk , van Leeuwen Fred , Borst Jannie 
Published: December 2019

AbstractCD4+ T cell help is required for the generation of CD8+ cytotoxic T lymphocyte (CTL) memory. Here, we use genome-wide analyses to show how CD4+ T cell help delivered during priming promotes memory differentiation of CTLs. Help signals enhance IL-15-dependent maintenance of central memory T (TCM) cells. More importantly, help signals regulate the size and function of the effector memory T (TEM) cell pool. Helped TEM cells produce Granzyme B and IFNγ upon antigen-independent, innate-like recall by IL-12 and IL-18. In addition, helped memory CTLs express the effector program characteristic of helped primary CTLs upon recall with MHC class I-restricted antigens, likely due to epigenetic imprinting and sustained mRNA expression of effector genes. Our data thus indicate that during priming, CD4+ T cell help optimizes CTL memory by creating TEM cells with innate and help-independent antigen-specific recall capacities.
Gut uropathogen abundance is a risk factor for development of bacteriuria and urinary tract infection
Authors: Magruder Matthew , Sholi Adam N. , Gong Catherine , Zhang Lisa , Edusei Emmanuel , Huang Jennifer , Albakry Shady , Satlin Michael J. , Westblade Lars F. , Crawford Carl , Dadhania Darshana M. , Lubetzky Michelle , Taur Ying , Littman Eric , Ling Lilan , Burnham Philip , De Vlaminck Iwijn , Pamer Eric , Suthanthiran Manikkam , Lee John Richard 
Published: December 2019

AbstractThe origin of most bacterial infections in the urinary tract is often presumed to be the gut. Herein, we investigate the relationship between the gut microbiota and future development of bacteriuria and urinary tract infection (UTI). We perform gut microbial profiling using 16S rRNA gene deep sequencing on 510 fecal specimens from 168 kidney transplant recipients and metagenomic sequencing on a subset of fecal specimens and urine supernatant specimens. We report that a 1% relative gut abundance of Escherichia is an independent risk factor for Escherichia bacteriuria and UTI and a 1% relative gut abundance of Enterococcus is an independent risk factor for Enterococcus bacteriuria. Strain analysis establishes a close strain level alignment between species found in the gut and in the urine in the same subjects. Our results support a gut microbiota–UTI axis, suggesting that modulating the gut microbiota may be a potential novel strategy to prevent UTIs.
The Escherichia coli transcriptome mostly consists of independently regulated modules
Authors: Sastry Anand V. , Gao Ye , Szubin Richard , Hefner Ying , Xu Sibei , Kim Donghyuk , Choudhary Kumari Sonal , Yang Laurence , King Zachary A. , Palsson Bernhard O. 
Published: December 2019

AbstractUnderlying cellular responses is a transcriptional regulatory network (TRN) that modulates gene expression. A useful description of the TRN would decompose the transcriptome into targeted effects of individual transcriptional regulators. Here, we apply unsupervised machine learning to a diverse compendium of over 250 high-qualityEscherichia coliRNA-seq datasets to identify 92 statistically independent signals that modulate the expression of specific gene sets. We show that 61 of these transcriptomic signals represent the effects of currently characterized transcriptional regulators. Condition-specific activation of signals is validated by exposure ofE. colito new environmental conditions. The resulting decomposition of the transcriptome provides: a mechanistic, systems-level, network-based explanation of responses to environmental and genetic perturbations; a guide to gene and regulator function discovery; and a basis for characterizing transcriptomic differences in multiple strains. Taken together, our results show that signal summation describes the composition of a model prokaryotic transcriptome.
The GenomeAsia 100K Project enables genetic discoveries across Asia
Authors:   GenomeAsia100K Consortium, Wall Jeffrey D. , Stawiski Eric W. , Ratan Aakrosh , Kim Hie Lim , Kim Changhoon , Gupta Ravi , Suryamohan Kushal , Gusareva Elena S. , Purbojati Rikky Wenang , Bhangale Tushar , Stepanov Vadim , Kharkov Vladimir , Schröder Markus S. , Ramprasad Vedam , Tom Jennifer , Durinck Steffen , Bei Qixin , Li Jiani , Guillory Joseph , Phalke Sameer , Basu Analabha , Stinson Jeremy , Nair Sandhya , Malaichamy Sivasankar , Biswas Nidhan K. , Chambers John C. , Cheng Keith C. , George Joyner T. , Khor Seik Soon , Kim Jong-Il , Cho Belong , Menon Ramesh , Sattibabu Thiramsetti , Bassi Akshi , Deshmukh Manjari , Verma Anjali , Gopalan Vivek , Shin Jong-Yeon , Pratapneni Mahesh , Santhosh Sam , Tokunaga Katsushi , Md-Zain Badrul M. , Chan Kok Gan , Parani Madasamy , Natarajan Purushothaman , Hauser Michael , Allingham R. Rand , Santiago-Turla Cecilia , Ghosh Arkasubhra , Gadde Santosh Gopi Krishna , Fuchsberger Christian , Forer Lukas , Schoenherr Sebastian , Sudoyo Herawati , Lansing J. Stephen , Friedlaender Jonathan , Koki George , Cox Murray P. , Hammer Michael , Karafet Tatiana , Ang Khai C. , Mehdi Syed Q. , Radha Venkatesan , Mohan Viswanathan , Majumder Partha P. , Seshagiri Somasekar , Seo Jeong-Sun , Schuster Stephan C. , Peterson Andrew S. 
Published: December 2019

AbstractThe underrepresentation of non-Europeans in human genetic studies so far has limited the diversity of individuals in genomic datasets and led to reduced medical relevance for a large proportion of the world’s population. Population-specific reference genome datasets as well as genome-wide association studies in diverse populations are needed to address this issue. Here we describe the pilot phase of the GenomeAsia 100K Project. This includes a whole-genome sequencing reference dataset from 1,739 individuals of 219 population groups and 64 countries across Asia. We catalogue genetic variation, population structure, disease associations and founder effects. We also explore the use of this dataset in imputation, to facilitate genetic studies in populations across Asia and worldwide.
Structural and solvent control over activation parameters for a pair of retro Diels-Alder reactions
Authors: Widstrom Andrea L. , Lear Benjamin J. 
Published: December 2019

AbstractWe report the temperature dependent NMR of two Diels-Alder adducts of furan: one formed with maleic anhydride and the other with N-methylmaleimide. These adducts are the products of so-called ‘click’ reactions, widely valued for providing simple, reliable, and robust reactivity. Under our experimental conditions, these adducts undergo a retro Diels-Alder reaction and we use our temperature dependent NMR to determine the rates of these reactions at multiple temperatures—ultimately providing estimates of the activation parameters for the reversion. We repeat these measurements in three solvents. We find that, in all solvents, the barrier to reversion is larger for the adduct formed with N-methylmaleimide. The barrier to reversion for this adduct is relatively insensitive to changes in solvent while the adduct formed with maleic anhydride responds more strongly to changes in solvent polarity. The differences in reaction barrier and solvent dependence arises because the adduct formed with N-methylmalemide is more stable—leading to a larger barrier to reversion—while the adduct formed with maleic anhydride experiences a larger change in dipole during the reaction—leading to a larger solvent dependence.
Electronic structure and core electron fingerprints of caesium-based multi-alkali antimonides for ultra-bright electron sources
Authors: Cocchi Caterina , Mistry Sonal , Schmeißer Martin , Amador Raymond , Kühn Julius , Kamps Thorsten 
Published: December 2019

AbstractThe development of novel photocathode materials for ultra-bright electron sources demands efficient and cost-effective strategies that provide insight and understanding of the intrinsic material properties given the constraints of growth and operational conditions. To address this question, we propose a viable way to establish correlations between calculated and measured data on core electronic states of Cs-K-Sb materials. To do so, we combine first-principles calculations based on all-electron density-functional theory on the three alkali antimonides Cs3Sb, Cs2KSb, and CsK2Sb with x-ray photoemission spectroscopy (XPS) on Cs-K-Sb photocathode samples. Within the GW approximation of many-body perturbation theory, we obtain quantitative predictions of the band gaps of these materials, which range from 0.57 eV in Cs2KSb to 1.62 eV in CsK2Sb and manifest direct or indirect character depending on the relative potassium content. Our theoretical electronic-structure analysis also reveals that the core states of these systems have binding energies that depend only on the atomic species and their crystallographic sites, with largest shifts of the order of 2 eV and 0.5 eV associated to K 2p and Sb 3d states, respectively. This information can be correlated to the maxima in the XPS survey spectra, where such peaks are clearly visible. In this way, core-level shifts can be used as fingerprints to identify specific compositions of Cs-K-Sb materials and their relation with the measured values of quantum efficiency. Our results represent the first step towards establishing a robust connection between the experimental preparation and characterization of photocathodes, the ab initio prediction of their electronic structure, and the modeling of emission and beam formation processes.
Measurement of Cyanobacterial Bloom Magnitude using Satellite Remote Sensing
Authors: Mishra Sachidananda , Stumpf Richard P. , Schaeffer Blake A. , Werdell P. Jeremy , Loftin Keith A. , Meredith Andrew 
Published: December 2019

AbstractCyanobacterial harmful algal blooms (cyanoHABs) are a serious environmental, water quality and public health issue worldwide because of their ability to form dense biomass and produce toxins. Models and algorithms have been developed to detect and quantify cyanoHABs biomass using remotely sensed data but not for quantifying bloom magnitude, information that would guide water quality management decisions. We propose a method to quantify seasonal and annual cyanoHAB magnitude in lakes and reservoirs. The magnitude is the spatiotemporal mean of weekly or biweekly maximum cyanobacteria biomass for the season or year. CyanoHAB biomass is quantified using a standard reflectance spectral shape-based algorithm that uses data from Medium Resolution Imaging Spectrometer (MERIS). We demonstrate the method to quantify annual and seasonal cyanoHAB magnitude in Florida and Ohio (USA) respectively during 2003–2011 and rank the lakes based on median magnitude over the study period. The new method can be applied to Sentinel-3 Ocean Land Color Imager (OLCI) data for assessment of cyanoHABs and the change over time, even with issues such as variable data acquisition frequency or sensor calibration uncertainties between satellites. CyanoHAB magnitude can support monitoring and management decision-making for recreational and drinking water sources.
Carcinoembryonic antigen cell adhesion molecule 6 (CEACAM6) in Pancreatic Ductal Adenocarcinoma (PDA): An integrative analysis of a novel therapeutic target
Authors: Pandey Ritu , Zhou Muhan , Islam Shariful , Chen Baowei , Barker Natalie K , Langlais Paul , Srivastava Anup , Luo Moulun , Cooke Laurence S. , Weterings Eric , Mahadevan Daruka 
Published: December 2019

AbstractWe investigated biomarker CEACAM6, a highly abundant cell surface adhesion receptor that modulates the extracellular matrix (ECM) in pancreatic ductal adenocarcinoma (PDA). The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) RNA-Seq data from PDA patients were analyzed for CEACAM6 expression and evaluated for overall survival, association, enrichment and correlations. A CRISPR/Cas9 Knockout (KO) of CEACAM6 in PDA cell line for quantitative proteomics, mitochondrial bioenergetics and tumor growth in mice were conducted. We found CEACAM6 is over-expressed in primary and metastatic basal and classical PDA subtypes. Highest levels are in classical activated stroma subtype. CEACAM6 over-expression is universally a poor prognostic marker in KRAS mutant and wild type PDA. High CEACAM6 expression is associated with low cytolytic T-cell activity in both basal and classical PDA subtypes and correlates with low levels of T-REG markers. In HPAF-II cells knockout of CEACAM6 alters ECM-cell adhesion, catabolism, immune environment, transmembrane transport and autophagy. CEACAM6 loss increases mitochondrial basal and maximal respiratory capacity. HPAF-II CEACAM6−/− cells are growth suppressed by >65% vs. wild type in mice bearing tumors. CEACAM6, a key regulator affects several hallmarks of PDA including the fibrotic reaction, immune regulation, energy metabolism and is a novel therapeutic target in PDA.
The mixed quantum Rabi model
Authors: Duan Liwei , Xie You-Fei , Chen Qing-Hu 
Published: December 2019

AbstractThe analytical exact solutions to the mixed quantum Rabi model (QRM) including both one- and two-photon terms are found by using Bogoliubov operators. Transcendental functions in terms of 4 × 4 determinants responsible for the exact solutions are derived. These so-called G-functions with pole structures can be reduced to the previous ones in the unmixed QRMs. The zeros of G-functions reproduce completely the regular spectra. The exceptional eigenvalues can also be obtained by another transcendental function. From the pole structure, we can derive two energy limits when the two-photon coupling strength tends to the collapse point. All energy levels only collapse to the lower one, which diverges negatively. The level crossings in the unmixed QRMs are relaxed to avoided crossings in the present mixed QRM due to absence of parity symmetry. In the weak two-photon coupling regime, the mixed QRM is equivalent to an one-photon QRM with an effective positive bias, suppressed photon frequency and enhanced one-photon coupling, which may pave a highly efficient and economic way to access the deep-strong one-photon coupling regime.
Investigating Emotion in Malay, Australian and Iranian Individuals with and without Depression
Authors: Jobson Laura , Mirabolfathi Vida , Moshirpanahi Shiva , Parhoon Hadi , Gillard Julia , Mukhtar Firdaus , Moradi Ali Reza , Mohan Sindhu Nair 
Published: December 2019

AbstractThis study investigated the influence of culture and depression on (1) emotion priming reactions, (2) the recall of subjective experience of emotion, and (3) emotion meaning. Members of individualistic culture (Australia, n = 42) and collectivistic culture (Iran, n = 32, Malaysia, n = 74) with and without depression completed a biological motion task, subjective experience questionnaire and emotion meaning questionnaire. Those with depression, regardless of cultural group, provided significantly fewer correct responses on the biological motion task than the control group. Second, the collectivistic control groups reported greater social engaging emotion than the Australian control group. However, the three depressed groups did not differ culturally. The Australian depressed group reported significantly greater interpersonally engaging emotion than the Australian control group. Third, the collectivistic groups reported significantly greater social worth, belief changes and sharing of emotion than the individualistic group. Depression did not influence these cultural effects. Instead we found that those with depression, when compared to controls, considered emotions as subjective phenomena, that were qualifying for relationships with others, and associated with greater agency appraisals. The applicability of the biocultural framework of emotion in depression was considered.
Adipose-derived stromal/stem cells improve epidermal homeostasis
Authors: Moriyama Mariko , Sahara Shunya , Zaiki Kaori , Ueno Ayumi , Nakaoji Koichi , Hamada Kazuhiko , Ozawa Toshiyuki , Tsuruta Daisuke , Hayakawa Takao , Moriyama Hiroyuki 
Published: December 2019

AbstractWound healing is regulated by complex interactions between the keratinocytes and other cell types including fibroblasts. Recently, adipose-derived mesenchymal stromal/stem cells (ASCs) have been reported to influence wound healing positively via paracrine involvement. However, their roles in keratinocytes are still obscure. Therefore, investigation of the precise effects of ASCs on keratinocytes in an in vitro culture system is required. Our recent data indicate that the epidermal equivalents became thicker on a collagen vitrigel membrane co-cultured with human ASCs (hASCs). Co-culturing the human primary epidermal keratinocytes (HPEK) with hASCs on a collagen vitrigel membrane enhanced their abilities for cell proliferation and adhesion to the membrane but suppressed their differentiation suggesting that hASCs could maintain the undifferentiated status of HPEK. Contrarily, the effects of co-culture using polyethylene terephthalate or polycarbonate membranes for HPEK were completely opposite. These differences may depend on the protein permeability and/or structure of the membrane. Taken together, our data demonstrate that hASCs could be used as a substitute for fibroblasts in skin wound repair, aesthetic medicine, or tissue engineering. It is also important to note that a co-culture system using the collagen vitrigel membrane allows better understanding of the interactions between the keratinocytes and ASCs.
A study of dynamic adsorption of propylene and ethylene emitted from the process of coal self-heating
Authors: Wojtacha-Rychter Karolina , Smoliński Adam 
Published: December 2019

AbstractThe gaseous products emitted in the self-heating process constitute one of the parameters suggested for detecting coal spontaneous combustion in underground mining. The objective of the study is to investigate the changes of ethylene and propylene content in a gaseous mixture which flowed through a fixed bed column filled with bituminous coal of different grain size. The mixtures of fire gases were obtained from laboratory simulated heating of coal at the temperatures of 373 K, 423 K, 473 K and 523 K. Hydrocarbons of various initial concentrations were introduced to the adsorption column at the constant flow rate of 2∙10−7 m3/s. The experimental findings show that decreasing the adsorbent granulation and gases concentration causes an extended breakthrough and coal bed saturation times. In all the tests, the saturation time was gained faster for ethylene than for propylene. Thus, the content of tested hydrocarbons, which are some of the indicators for assessing the degree of the coal self-heating process, in mine air may change in time as a result of the adsorption phenomenon. It occurs particularly at the early stage of the self-heating process and in places where coal dust has been left.
Microbiome differences in disease-resistant vs. susceptible Acropora corals subjected to disease challenge assays
Authors: Rosales Stephanie M. , Miller Margaret W. , Williams Dana E. , Traylor-Knowles Nikki , Young Benjamin , Serrano Xaymara M. 
Published: December 2019

AbstractIn recent decades coral gardening has become increasingly popular to restore degraded reef ecosystems. However, the growth and survivorship of nursery-reared outplanted corals are highly variable. Scientists are trying to identify genotypes that show signs of disease resistance and leverage these genotypes in restoring more resilient populations. In a previous study, a field disease grafting assay was conducted on nursery-reared Acropora cervicornis and Acropora palmata to quantify relative disease susceptibility. In this study, we further evaluate this field assay by investigating putative disease-causing agents and the microbiome of corals with disease-resistant phenotypes. We conducted 16S rRNA gene high-throughput sequencing on A. cervicornis and A. palmata that were grafted (inoculated) with a diseased A. cervicornis fragment. We found that independent of health state, A. cervicornis and A. palmata had distinct alpha and beta diversity patterns from one another and distinct dominant bacteria. In addition, despite different microbiome patterns between both inoculated coral species, the genus Sphingomonadaceae was significantly found in both diseased coral species. Additionally, a core bacteria member from the order Myxococcales was found at relatively higher abundances in corals with lower rates of disease development following grafting. In all, we identified Sphingomonadaceae as a putative coral pathogen and a bacterium from the order Myxococcales associated with corals that showed disease resistant phenotypes.
Speed of structured light pulses in free space
Authors: Petrov N. I. 
Published: December 2019

AbstractA plane monochromatic wave propagates in vacuum at the velocity c. However, wave packets limited in space and time are used to transmit energy and information. Here it has been shown based on the wave approach that the on-axis part of the pulsed beams propagates in free space at a variable speed, exhibiting both subluminal and superluminal behaviours in the region close to the source, and their velocity approaches the value of c with distance. Although the pulse can travel over small distances faster than the speed of light in vacuum, the average on-axis velocity, which is estimated by the arrival time of the pulse at distances z ≫ ld (ld is the Rayleigh diffraction range) and z > cτ (τ is the pulse width) is less than c. The total pulsed beam propagates at a constant subluminal velocity over the whole distance. The mutual influence of the spatial distribution of radiation and the temporal shape of the pulse during nonparaxial propagation in vacuum is studied. It is found that the decrease in the width of the incident beam and the increase in the central wavelength of the pulse lead to a decrease in the propagation velocity of the wave packet.