bluuebunny/crossref_metadata_2025 huggingface dataset:
Sustainability by design: automated nanoscale 2,3,4-trisubstituted quinazoline diversity
Authors: Hadian Mojgan , Shaabani Shabnam , Patil Pravin , Shishkina Svitlana V. , Böltz Harry , Dömling Alexander
Published: February 2020

Automated, one step, nanoscale synthesis of 2,3,4-trisubstituted quinazoline derivatives using positive pressure facilitated dispensing to access a very large chemical space exemplified by more than 1000 compounds.
Structure assembly regularities in vapour-deposited gold–fullerene mixture films
Authors: Lavrentiev V. , Motylenko M. , Barchuk M. , Schimpf C. , Lavrentieva I. , Pokorný J. , Röder C. , Vacik J. , Dejneka A. , Rafaja D.
Published: February 2020

Three compositional intervals x (R1, R2 and R3) with different mechanisms of nanostructure self-assembling in the AuxC60 mixture films (0 < x < 30) have been established.
Functional carbon nitride materials for water oxidation: from heteroatom doping to interface engineering
Authors: Zhang Huayang , Tian Wenjie , Duan Xiaoguang , Sun Hongqi , Shen Yonglong , Shao Guosheng , Wang Shaobin
Published: February 2020

Strategies for modifying polymeric carbon nitrides and their intrinsic structure–activity relationships for photo-, electro-, and photoelectro-chemical water oxidation are discussed.
The strain effects in 2D hybrid organic–inorganic perovskite microplates: bandgap, anisotropy and stability
Authors: Wang Shuai , Gong Zibo , Li Guangxuan , Du Zixiao , Ma Jiaqi , Shen Hongzhi , Wang Jiaqi , Li Wancai , Ren Junwen , Wen Xinglin , Li Dehui
Published: February 2020

The applied strain would lead to a redshift of the bandgap, enhanced optical anisotropy and a fast degradation rate, due to the distortion of the octahedra in 2D perovskites.
Correction: Effect of aspect ratios of rutile TiO2 nanorods on overall photocatalytic water splitting performance
Authors: Fu Bing , Wu Zhijiao , Cao Shuang , Guo Kai , Piao Lingyu
Published: February 2020

Correction for ‘Effect of aspect ratios of rutile TiO2 nanorods on overall photocatalytic water splitting performance’ by Bing Fu et al., Nanoscale, 2020, DOI: 10.1039/c9nr10870j.
Dynamic contrast with reversibly photoswitchable fluorescent labels for imaging living cells
Authors: Chouket Raja , Pellissier-Tanon Agnès , Lemarchand Annie , Espagne Agathe , Le Saux Thomas , Jullien Ludovic
Published: February 2020

Interrogating living cells requires sensitive imaging of a large number of components in real time.
MicroRNA-129-5p alleviates spinal cord injury in mice via suppressing the apoptosis and inflammatory response through HMGB1/TLR4/NF-κB pathway
Authors: Wan Guang , An Yongbo , Tao Jingang , Wang Yanli , Zhou Qinglan , Yang Rongli , Liang Qiudong
Published: February 2020

Secondary injury after spinal cord injury (SCI) is one reversible pathological change mainly involving excessive inflammatory response and neuro-apoptosis. Since in recent years, microRNAs (miRNAs) have been proposed as novel regulators of inflammation in different disease conditions. However, the role of miRNAs in the inflammatory response and apoptosis of secondary injury after SCI remains to be fully elucidated. Here, we tried to explore the influence and mechanism of miRNAs on the neuron inflammatory response and apoptosis after SCI. The expression profiles of miRNA were examined using miRNA microarray, and among the candidate miRNAs, miR-129-5p was found to be the most down-regulated miRNA in spinal tissues. Overexpression of miR-129-5p using agomir-miR-129-5p promoted injury mice functional recovery, suppressed the apoptosis and alleviated inflammatory response in spinal tissues. Using LPS-induced BV-2 cell model, we found miR-129-5p was also proved in protecting inflammatory response and cell apoptosis in vitro. High-mobility group protein B1 (HMGB1), a well-known inflammatory mediator, was found to be directly targeted by miR-129-5p and it was associated with the inhibitory effect of miR-129-5p on the activation of toll-like receptor (TLR)-4 (TLR4)/ nuclear factor-κB (NF-κB) pathway in vitro and in vivo. Further experiments revealed that the anti-apoptosis and anti-inflammatory effects of miR-129-5p were reversed by HMGB1 overexpression in BV-2 cells. Collectively, these data revealed that miR-129-5p alleviated SCI in mice via suppressing the apoptosis and inflammatory response through HMGB1//TLR4/NF-κB pathway. Our data suggest that up-regulation of miR-129-5p may be a novel therapeutic target for SCI.
Smart campus: definition, framework, technologies, and services
Authors: Dong Zhao Yang , Zhang Yuchen , Yip Christine , Swift Sharon , Beswick Kim
Published: February 2020

As the high‐end form of a smart education system, the smart campus has received increasing research attention over the world. Owing to the multidisciplinary nature of the smart campus, the existing research is mostly one‐ended on either the state‐or‐the‐art technologies or the innovative education concepts but lacks a deep fusion view on them and omits the smart campus implication on other smart city domains. This study highlights the interdisciplinary view on smart campus. Based on an integral review on the supporting technologies and existing smart campus propositions, a human‐centred learning‐oriented smart campus is envisaged, defined and framed up, primarily aiming at meeting stakeholders’ interests and elevating educational performance in pace of the technology development, as well as discussing the interdisciplinary factors that either promote or constrain the smart campus revolution. The expected contribution throughout this study is to provide a benchmark reference of a smart campus for international educational providers, government, and technological companies providing such services.
Influence of the dissolved hydrogen concentration on the radioactive contamination of the primary loops of DOEL-4 PWR using the OSCAR code
Authors: Gherrab Mehdi , Dacquait Frédéric , You Dominique , Tevissen Etienne , Lecocq Raphaël , Schildermans Kim
Published: February 2020

Corrosion products are generated in the primary circuit during normal operation and are activated in the core. Those activated corrosion products, mainly 58Co and 60Co (coming respectively from the activation of 58Ni and 59Co), are then transported by the primary fluid and deposited on the out-of-flux surfaces (steam generators, primary coolant pipes…). To minimize this radioactive contamination, one needs to understand the behavior of corrosion products by carrying out measurements in PWRs and test loops combined with a reactor contamination assessment code named OSCAR. The aim of this article is to evaluate the influence of the change in the Dissolved Hydrogen (DH) concentration on the contamination of the primary loops of DOEL-4 PWR, a Belgian unit. After the description of the principle of the OSCAR V1.3 code, its use is illustrated with the simulation of DOEL-4. Finally, those calculations are compared to autoclave experiments called DUPLEX with thermodynamic and chemical conditions closed to those observed in PWRs. OSCAR V1.3 calculations show that an increase in the DH concentration results in a decrease in 58Co surface activities. These results are consistent with those from the DUPLEX experiments. Finally, an increase of the DH concentration is then recommended in operating PWRs to reduce the 58Co surface contamination.
Le vieillissement de la peau
Authors: Baspeyras Martine
Published: February 2020

L’auteur donne les éléments à découvrir lors de l’examen clinique et para-clinique qui permettent de diagnostiquer le vieillissement de la peau et de décrire les mécanismes de ce vieillissement.
Particularités du traitement orthodontique du patient de plus de cinquante ans
Authors: Muller Christine , Canal Pierre
Published: February 2020

L’augmentation de l’espérance de vie de notre population et ce dans de bonnes conditions, fait que l’on porte de plus en plus d’attention au sénior et à son bien-être. Les séniors sont de plus en plus nombreux dans nos cabinets d’orthodontie. C’est pourquoi cet article va étudier successivement l’état parodontal, dentaire, général du patient âgé ainsi que sa psychologie, sa motivation et son potentiel de collaboration. Nous envisagerons les demandes de ces patients avant tout esthétiques et fonctionnelles mais visant également à améliorer leur santé bucco-dentaire. Nous définirons la technique la plus appropriée pour traiter ces patients, la moins visible possible et contrôlant précisément le déplacement dentaire. L’abord de ces patients est nécessairement pluridisciplinaire, ce que nous verrons ainsi que le coût préalable de l’ensemble de la remise en état de la cavité buccale. Nous souhaitons grâce à cet article améliorer la prise en charge orthodontique du sénior !
PET/CT Parameters are Useful in Discrimination of Incidental Benign, Premalignant and Malignant Colonic Lesions
Authors: Budak Emine , Yanarateş Ahmet
Published: February 2020

Aim The present study evaluates the role of PET parameters pertaining to incidentally detected foci of colorectal uptake (IFCU) on FDG PET/CT in the differentiation of benign, premalignant and malignant lesions.

Methods This retrospective study included 74 patients. The colonoscopic and histopathological findings were regarded as the reference standards. The results were evaluated on a lesion basis by dividing the lesions into three groups as benign, premalignant and malignant. The maximum standardized uptake value (SUVmax), SUVmean, metabolic tumor volume(MTV) and total lesion glycolysis(TLG) values of the three groups were compared.

Results There were 88 IFCU in a total of 74 patients (27 female, 47 male, mean age 65 years). Of the 88 IFCU, 26 were qualified as benign, 42 as premalignant and 20 as malignant. Malignant + premalignant lesions were found in 62/88 (70.4 %) of the IFCU. The SUVmax of the benign lesions was significantly lower than those of the premalignant and malignant lesions; and SUVmean was lower than that of the malignant lesions. The MTV of the malignant lesions was significantly higher than that of the premalignant and benign lesions; and TLG was higher than that of the premalignant lesions. The optimum cut-off value in differentiating between the malignant and non-malignant lesions was 9.15 for SUVmax, 5.05 for SUVmean, 4.7 for MTV and 30.25 for TLG.

Conclusion PET parameters can guide the differentiation of benign, premalignant and malignant lesions with IFCU. Besides, patients with IFCU should undergo further evaluation due to high probability of premalignant and malignant lesions.
Relativistic dynamics for a particle carrying a non-Abelian charge in a non-Abelian background electromagnetic field
Authors: Dossa Finagnon A. , Avossevou Gabriel Y. H.
Published: February 2020

We study the relativistic dynamics of a particle carrying a non-Abelian charge in the presence of a non-Abelian background electromagnetic field. To this end, we extract the non-Abelian Dirac Hamiltonian from a system describing the interaction between the Yang–Mills field and a spin-1/2 field. The dynamics of a particle with non-Abelian charge is quantized directly by analogy with its quantum theory. By choosing a suitable non-Abelian gauge field, we investigate the spectrum in two-dimensional space, paying particular attention to the role of the total angular momentum. Relativistic Landau levels are obtained explicitly by means of an analytical method. The wave functions of the system are obtained in terms of the generalized Laguerre polynomials. Interesting features of such models are discussed through the spectrum.
Correlation between phase composition and exchange bias in CoFe/MnN and MnN/CoFe polycrystalline films
Authors: Chang H. W. , Chien Y. H. , Yuan F. T. , Lai Y. R. , Wang C. R. , Horng Lance , Chang W. C.
Published: February 2020

Magnetic properties and phase composition of both MnN/CoFe (MnN at top of bilayer) and CoFe/MnN films (MnN at bottom of bilayer) bilayers through annealing at various temperatures (Ta = 300-450 °C) and then cooling to room temperature under the application of an external magnetic field of 1.5 kOe are compared. The exchange bias field (HE), the magnitude of magnetic hysteresis loop shift, of the studied films is highly related to phase composition of antiferromagnetic (AF) layer. The increase of HE with increasing Ta in the range of 300-375 °C possibly results from the improvement of magnetocrystalline anisotropy of AF related to the promoted crystallinity and stress relaxation of tetragonal face-centered θ-MnN phase. The reduction of HE at higher Ta is due to the decreased volume fraction or disappearance of θ-MnN phase and the formation of impurity phases, such as Mn4N and Mn. The induction of impurity phases is possibly related to the diffusion of part of N out of MnN phase at higher Ta. Higher HE for CoFe/MnN than MnN/CoFe at Ta = 300-375 °C might be attributed to larger amount and higher degree of stress relaxation for θ-MnN phase. For CoFe/MnN film annealed at 375 °C, the highest HE = 562 Oe is attained, and the corresponding interfacial exchange energy of 0.47 mJ/m2 in this study is comparable to that reported by Meinert et al. [Phys. Rev. B 92, 144408 (2015)].
Cathodoluminescence study of electric field induced migration of defects in single crystal m-plane ZnO
Authors: Manyam Jedsada , Ton-That Cuong , Phillips Matthew R.
Published: February 2020

Internal electric fields can have a significant effect on the behavior of charged defects, dopants, and impurities in operating electronic devices that can adversely impact on their long-term performance and reliability. In this paper, we investigate the redistribution of charged centers in single crystal m-plane ZnO under the action of a DC electric field at 873 K using in-plane and in-depth spatially resolved cathodoluminescence (CL) spectroscopy. The CL intensities of the ultra-violet near band edge (NBE) emission at 3.28 eV and green luminescence (GL) at 2.39 eV were observed to both uniformly increase on the anode side of the electrode gap. Conversely, toward the cathode, the NBE and GL steadily decrease and increase, respectively. The GL quenched after hydrogen donor doping, confirming that the emission is related to acceptor-like centers. Based on the electro-migration and hydrogen doping results, the GL is attributed to radiative recombination involving ZniandVZn pairs. The intensity of an orange luminescence centered at 2.01 eV was unaffected by the electric field and is assigned to substitutional Li acceptors.
The art of laser ablation in aeroengine: The crown jewel of modern industry
Authors: Zhou Rui , Zhang Zi , Hong Minghui
Published: February 2020

In this perspective, laser interaction with materials and its applications in precision engineering are mainly introduced for the manufacturing, as well as maintenance, repair, and overhaul (MRO) of aeroengines. In precision engineering, the laser ablation tool has also been more applicable considering its great advantages in microprocessing and nanofabrication. It is interesting to explore the specific process and characteristics of laser ablation, which play an important role in advanced manufacturing. Due to the complicated production procedures of an aeroengine, it is important to explore the physics behind laser interaction with aerospace and aeronautical metallic materials in order to properly utilize the unique characteristics of lasers, such as high monochromaticity, high brightness, high directivity, and high coherence. Meanwhile, it is beneficial to study the dynamic process of interactions and its mechanisms in laser applications, such as laser cleaning, texturing, and shock peening. There exist both photo-chemical and photo-thermal processes when lasers and materials interact. Several typical cases are introduced, which have great potential and high impact applications in the manufacturing and MRO industry of aeroengines. Based on laser ablation in specific industries, the building-up of MRO support system for aeroengines could be provided by a dynamic mechanism between the pioneering research results and industrial demand, leading to the fast development of advanced high-end manufacturing equipment.
A deep neural network based hierarchical multi-label classification method
Authors: Feng Shou , Zhao Chunhui , Fu Ping
Published: February 2020

With the accumulation of data generated by biological experimental instruments, using hierarchical multi-label classification (HMC) methods to process these data for gene function prediction has become very important. As the structure of the widely used Gene Ontology (GO) annotation is the directed acyclic graph (DAG), GO based gene function prediction can be changed to the HMC problem for the DAG of GO. Due to HMC, algorithms for tree ontology are not applicable to DAG, and the accuracy of these algorithms is low. Therefore, existing algorithms cannot satisfy the requirements of gene function prediction. To solve this problem, this paper proposes a DAG hierarchical multi-label classification algorithm, C2AE-DAGLabel algorithm. The C2AE-DAGLabel algorithm uses the Canonical Correlated AutoEncoder (C2AE) model as the classifier and designs a DAGLabel algorithm to solve the DAG hierarchical constraint problem. The DAGLabel algorithm can improve the classification accuracy by ensuring that the classification results meet the requirements of the hierarchical constraint. In the experiment, human gene data annotated with GO are used to evaluate the performance of the proposed algorithm. The experimental results show that compared with other state-of-the-art algorithms, the C2AE-DAGLabel algorithm has the best performance in solving the hierarchical multi-label classification problem for DAG.
A maximum extreme-value distribution model for switching conductance of oxide-RRAM in memory applications
Authors: Wu Ernest , Ando Takashi , Kim Youngseok , Muralidhar Ramachandran , Cartier Eduard , Jamison Paul , Wang Miaomiao , Narayanan Vijay
Published: February 2020

In this work, we report an extensive experimental investigation of the important statistical properties of resistive random access memory (RRAM) switching conductance. We demonstrate the Gumbel statistics, a maximum extreme-value distribution for switching-filament conductance, as opposed to the minimum extreme-value distribution such as Weibull model. We apply a Poisson random statistical distribution for the spatial generation of percolation filaments to link the RRAM conductance measurements with device areas. As a result, we can derive two important relations: area scaling properties of percentiles and scale-factors. We show the validity of this maximum extreme-value distribution model by rigorously examining the vertical percentile-scaling characteristics of experimental data. The independently extracted shape-factor from the area-dependence of scale-factors captures the merged conductance distributions in good agreement with the experimental conductance data. It is revealed that larger variability associated with RRAM conductance measurements is directly linked to the maximum-valued statistical characteristics of this model. We also demonstrate that RRAM conductance, rather than resistance, is a fundamental statistical variable.
Series expansion for normal stress differences in large-amplitude oscillatory shear flow from Oldroyd 8-constant framework
Authors: Poungthong P. , Giacomin A. J. , Kolitawong C.
Published: February 2020

The Oldroyd 8-constant framework for continuum constitutive theory contains a rich diversity of popular special cases for polymeric liquids. In this paper, we focus on the normal stress difference responses to large-amplitude oscillatory shear (LAOS) flow. The nonlinearity of the polymeric liquids, triggered by LAOS, causes these responses at even multiples of the test frequency. We call responses at a frequency higher than twice the test frequency higher harmonics. The normal stress difference responses for the Oldroyd 8-constant framework has recently yielded to the exact analytical solution. However, in its closed form, Bessel functions appear 24 times, each within summations to infinity. In this paper, to simplify the exact solution, we expand it in a Taylor series. We truncate the series after its 17th power of the shear rate amplitude. Our main result reduces to the well-known expression for the special cases of the corotational Jeffreys and corotational Maxwell fluids. Whereas these special cases yielded to the Goddard integral expansion (GIE), the more general Oldroyd 8-constant framework does not. We use Ewoldt grids to show our main result to be highly accurate for the corotational Jeffreys and corotational Maxwell fluids. For these two special cases, our solutions agree closely with the exact solutions as long as Wi/De<3310. We compare our main result, for the special case of the Johnson–Segalman fluid, with measurements on dissolved polyisobutylene in the isobutylene oligomer. For this, we use the Spriggs relations to generalize our main result to multimode, which then agrees closely with the measurements.
Seasonality and trends in human- and lightning-caused wildfires ≥ 2 ha in Canada, 1959–2018
Authors: Coogan Sean C. P. , Cai Xinli , Jain Piyush , Flannigan Mike D.
Published: February 2020

We examined the seasonal distribution of lightning- and human-caused wildfires ≥ 2ha in Canada for two time periods: 1959–2018 and 1981–2018. Furthermore, we investigated trends in seasonality, number of fires per year and number of days with fire starts per year for human- and lightning-caused fires. Nationally, lightning fires peaked from June to August, whereas human fires peaked during May. There was, however, notable variation in the seasonal distributions of human- and lightning-caused fires between ecozones. Likewise, trends in season start and end dates varied among ecozones and time series, with trends generally being stronger for human-caused fires. Trends in the number of fires from 1959 to 2018 suggested significant increases in the number of lightning-caused fires and days with lightning ignitions across almost all ecozones, while from 1981 to 2018 there was a significantly decreasing trend in the number of human-caused fires and days with human ignitions in almost all ecozones. The highest densities of human-caused fires occurred in the Montane Cordillera and Atlantic Maritime, while the highest density of lightning-caused fires occurred in the Boreal Shield West. The Montane Cordillera and Taiga Shield West showed significant increases in the number of lightning fires and days with lightning ignitions across both time series.
A cnidarian parasite of salmon (Myxozoa:
Henneguya
) lacks a mitochondrial genome
Authors: Yahalomi Dayana , Atkinson Stephen D. , Neuhof Moran , Chang E. Sally , Philippe Hervé , Cartwright Paulyn , Bartholomew Jerri L. , Huchon Dorothée
Published: February 2020

Although aerobic respiration is a hallmark of eukaryotes, a few unicellular lineages, growing in hypoxic environments, have secondarily lost this ability. In the absence of oxygen, the mitochondria of these organisms have lost all or parts of their genomes and evolved into mitochondria-related organelles (MROs). There has been debate regarding the presence of MROs in animals. Using deep sequencing approaches, we discovered that a member of the Cnidaria, the myxozoan
Henneguya salminicola,
has no mitochondrial genome, and thus has lost the ability to perform aerobic cellular respiration. This indicates that these core eukaryotic features are not ubiquitous among animals. Our analyses suggest that
H. salminicola
lost not only its mitochondrial genome but also nearly all nuclear genes involved in transcription and replication of the mitochondrial genome. In contrast, we identified many genes that encode proteins involved in other mitochondrial pathways and determined that genes involved in aerobic respiration or mitochondrial DNA replication were either absent or present only as pseudogenes. As a control, we used the same sequencing and annotation methods to show that a closely related myxozoan,
Myxobolus squamalis
, has a mitochondrial genome. The molecular results are supported by fluorescence micrographs, which show the presence of mitochondrial DNA in
M. squamalis
, but not in
H. salminicola.
Our discovery confirms that adaptation to an anaerobic environment is not unique to single-celled eukaryotes, but has also evolved in a multicellular, parasitic animal. Hence,
H. salminicola
provides an opportunity for understanding the evolutionary transition from an aerobic to an exclusive anaerobic metabolism.
Chronic virus infection drives CD8 T cell-mediated thymic destruction and impaired negative selection
Authors: Elsaesser Heidi J. , Mohtashami Mahmood , Osokine Ivan , Snell Laura M. , Cunningham Cameron R. , Boukhaled Giselle M. , McGavern Dorian B. , Zúñiga-Pflücker Juan Carlos , Brooks David G.
Published: February 2020

Significance

There is an intense interest in immune reconstitution and immunotherapy to control and cure chronic infections. Yet, how the fundamental processes that are required to generate new T cells are affected by chronic viruses and how these permutations affect therapeutic reconstitution or underlie adverse disease sequelae are not well understood. We demonstrate that type I interferon signaling directly programs peripheral effector T cells to destroy thymic structure and function, leading to a catastrophic organ depletion. Moderate thymic reconstitution associated with immune exhaustion ultimately occurs, but continued ramifications in the efficacy of hematopoietic stem cell therapy to generate new antiviral T cells and to prevent escape of self-reactive T cells remain long term.
STAT3 signaling in myeloid cells promotes pathogenic myelin-specific T cell differentiation and autoimmune demyelination
Authors: Lu Hsueh Chung , Kim Sunja , Steelman Andrew J. , Tracy Kevin , Zhou Beiyan , Michaud Danielle , Hillhouse Andrew E. , Konganti Kranti , Li Jianrong
Published: February 2020

Multiple sclerosis (MS) is an autoimmune inflammatory demyelinating disease of the central nervous system. Dysregulation of STAT3, a transcription factor pivotal to various cellular processes including Th17 cell differentiation, has been implicated in MS. Here, we report that STAT3 is activated in infiltrating monocytic cells near active MS lesions and that activation of STAT3 in myeloid cells is essential for leukocyte infiltration, neuroinflammation, and demyelination in experimental autoimmune encephalomyelitis (EAE). Genetic disruption ofStat3in peripheral myeloid lineage cells abrogated EAE, which was associated with decreased antigen-specific T helper cell responses. Myeloid cells from immunizedStat3mutant mice exhibited impaired antigen-presenting functions and were ineffective in driving encephalitogenic T cell differentiation. Single-cell transcriptome analyses of myeloid lineage cells from preclinical wild-type and mutant mice revealed that loss of myeloid STAT3 signaling disrupted antigen-dependent cross-activation of myeloid cells and T helper cells. This study identifies a previously unrecognized requisite for myeloid cell STAT3 in the activation of myelin-reactive T cells and suggests myeloid STAT3 as a potential therapeutic target for autoimmune demyelinating disease.
Alterations in chromatin at antigen receptor loci define lineage progression during B lymphopoiesis
Authors: Lion Mattia , Muhire Brejnev , Namiki Yuka , Tolstorukov Michael Y. , Oettinger Marjorie A.
Published: February 2020

Developing lymphocytes diversify their antigen receptor (AgR) loci by variable (diversity) joining (V[D]J) recombination. Here, using the micrococcal nuclease (MNase)-based chromatin accessibility (MACC) assay with low-cell count input, we profile both small-scale (kilobase) and large-scale (megabase) changes in chromatin accessibility and nucleosome occupancy in primary cells during lymphoid development, tracking the changes as different AgR loci become primed for recombination. The three distinct chromatin structures identified in this work define unique features of immunoglobulin H (IgH), Igκ, and T cell receptor-α (TCRα) loci during B lymphopoiesis. In particular, we find locus-specific temporal changes in accessibility both across megabase-long AgR loci and locally at the recombination signal sequences (RSSs). These changes seem to be regulated independently and can occur prior to lineage commitment. Large-scale changes in chromatin accessibility occur without significant change in nucleosome density and represent key features of AgR loci not previously described. We further identify local dynamic repositioning of individual RSS-associated nucleosomes at IgH and Igκ loci while they become primed for recombination during B cell commitment. These changes in chromatin at AgR loci are regulated in a locus-, lineage-, and stage-specific manner during B lymphopoiesis, serving either to facilitate or to impose a barrier to V(D)J recombination. We suggest that local and global changes in chromatin openness in concert with nucleosome occupancy and placement of histone modifications facilitate the temporal order of AgR recombination. Our data have implications for the organizing principles that govern assembly of these large loci as well as for mechanisms that might contribute to aberrant V(D)J recombination and the development of lymphoid tumors.
Designing heterotropically activated allosteric conformational switches using supercharging
Authors: Schnatz Peter J. , Brisendine Joseph M. , Laing Craig C. , Everson Bernard H. , French Cooper A. , Molinaro Paul M. , Koder Ronald L.
Published: February 2020

Significance

We present a general method to imbue proteins with heterotropic allostery by using surface protein supercharging to impart intrinsic disorder to the protein fold, allowing for functional activation by low concentrations of multivalent ions, including Mg(II), Ca(II), and spermine. We have designed two different proteins which exhibit this property and present a protocol which anyone can employ to impart this property to their protein of interest. This method promises to enable future synthetic biology projects which utilize natural fluxes of these ions to directly actuate function at significantly faster rates than that of genetic activation. Such multivalent ionic activation of disordered proteins may be a mechanism utilized by Nature which has yet to be appreciated.
The habenular G-protein–coupled receptor 151 regulates synaptic plasticity and nicotine intake
Authors: Antolin-Fontes Beatriz , Li Kun , Ables Jessica L. , Riad Michael H. , Görlich Andreas , Williams Maya , Wang Cuidong , Lipford Sylvia M. , Dao Maria , Liu Jianxi , Molina Henrik , Heintz Nathaniel , Kenny Paul J. , Ibañez-Tallon Ines
Published: February 2020

The habenula, an ancient small brain area in the epithalamus, densely expresses nicotinic acetylcholine receptors and is critical for nicotine intake and aversion. As such, identification of strategies to manipulate habenular activity may yield approaches to treat nicotine addiction. Here we show that GPR151, an orphan G-protein–coupled receptor (GPCR) highly enriched in the habenula of humans and rodents, is expressed at presynaptic membranes and synaptic vesicles and associates with synaptic components controlling vesicle release and ion transport. Deletion of
Gpr151
inhibits evoked neurotransmission but enhances spontaneous miniature synaptic currents and eliminates short-term plasticity induced by nicotine. We find that GPR151 couples to the G-alpha inhibitory protein Gα
o1
to reduce cyclic adenosine monophosphate (cAMP) levels in mice and in GPR151-expressing cell lines that are amenable to ligand screens.
Gpr151–
knockout (KO) mice show diminished behavioral responses to nicotine and self-administer greater quantities of the drug, phenotypes rescued by viral reexpression of
Gpr151
in the habenula. These data identify GPR151 as a critical modulator of habenular function that controls nicotine addiction vulnerability.
Division of labor and growth during electrical cooperation in multicellular cable bacteria
Authors: Geerlings Nicole M. J. , Karman Cheryl , Trashin Stanislav , As Karel S. , Kienhuis Michiel V. M. , Hidalgo-Martinez Silvia , Vasquez-Cardenas Diana , Boschker Henricus T. S. , De Wael Karolien , Middelburg Jack J. , Polerecky Lubos , Meysman Filip J. R.
Published: February 2020

Significance

Cable bacteria form centimeter-long, multicellular filaments whose energy metabolism involves cooperation among cells that separately perform oxidation of the electron donor and reduction of the electron acceptor. This cooperative division of labor is facilitated via long-range electrical currents that run from cell to cell along a network of conductive fibers. Here we show that biomass synthesis shows a surprising asymmetry along the filament: only the cells oxidizing the electron donor conserve energy for growth, while the other cells reduce electron acceptors without biosynthesis. Our study hence provides insights into the physiology of an unconventional chemolithotroph, which forms a multicellular electrically connected system with unique functional differentiation, integration, and coordination.
Bottlebrush polymers in the melt and polyelectrolytes in solution share common structural features
Authors: Sarapas Joel M. , Martin Tyler B. , Chremos Alexandros , Douglas Jack F. , Beers Kathryn L.
Published: February 2020

Significance

Bottlebrush polymer materials show great transdisciplinary promise, from tissue engineering to photonics. Homopolymers exhibit exceptionally low moduli while block brushes segregate into micrometer-sized domains. Both effects are attributed to the unique packing of brush polymers, a phenomenon that is difficult to measure without careful experimental design. Through precision synthesis and deuterium labeling, we studied a library of brush polymers in the melt using neutron scattering to quantitatively assess backbone packing. We show that bottlebrush polymers pack similarly to semidilute polyelectrolyte solutions, and that decreasing grafting density is analogous to increasing salt concentration in polyelectrolytes. These findings suggest hidden similarity in these different materials, one driven through sterics and the other through electrostatic repulsion.
Radiative absorption enhancements by black carbon controlled by particle-to-particle heterogeneity in composition
Authors: Fierce Laura , Onasch Timothy B. , Cappa Christopher D. , Mazzoleni Claudio , China Swarup , Bhandari Janarjan , Davidovits Paul , Fischer D. Al , Helgestad Taylor , Lambe Andrew T. , Sedlacek Arthur J. , Smith Geoffrey D. , Wolff Lindsay
Published: February 2020

Black carbon (BC) absorbs solar radiation, leading to a strong but uncertain warming effect on climate. A key challenge in modeling and quantifying BC’s radiative effect on climate is predicting enhancements in light absorption that result from internal mixing between BC and other aerosol components. Modeling and laboratory studies show that BC, when mixed with other aerosol components, absorbs more strongly than pure, uncoated BC; however, some ambient observations suggest more variable and weaker absorption enhancement. We show that the lower-than-expected enhancements in ambient measurements result from a combination of two factors. First, the often used spherical, concentric core-shell approximation generally overestimates the absorption by BC. Second, and more importantly, inadequate consideration of heterogeneity in particle-to-particle composition engenders substantial overestimation in absorption by the total particle population, with greater heterogeneity associated with larger model–measurement differences. We show that accounting for these two effects—variability in per-particle composition and deviations from the core-shell approximation—reconciles absorption enhancement predictions with laboratory and field observations and resolves the apparent discrepancy. Furthermore, our consistent model framework provides a path forward for improving predictions of BC’s radiative effect on climate.
The Supra Tutor
Authors: Lima Edna F.
Published: February 2020

Pronunciation is critical for English oral language proficiency because of its immediate role in language
judgments. However, effective and targeted English pronunciation instruction is scarce. Given the need for pronunciation
instruction and the undeniable impact of suprasegmentals on intelligibility and on comprehensibility, the Supra Tutor, a
four-module online pronunciation tutor focusing on suprasegmentals, was developed. This mixed methods study assessed the impact of
the Supra Tutor on the comprehensibility of international teaching assistants (ITAs). Participants were evaluated for
comprehensibility before and after training. The study also examined ITAs’ perceptions of the Supra Tutor in terms of usefulness,
engagement, and overall quality. Findings indicated that the Supra Tutor can provide effective pronunciation instruction and
engage learners to successfully complete the training. Research and pedagogical implications of the Supra Tutor and its
contribution to pronunciation instruction are discussed.
Errors and Interaction
Authors: Trasmundi Sarah Bro
Published: February 2020

Trasmundi combines her background as a cognitive ethnographer with theory of radical embodied cognition and interaction to investigate how healthcare practitioners manage cognitive events in patient treatment and diagnosing that often lead to human errors. This interdisciplinary focus emphasises how professional action underlines various forms of cognitive and social life that involves language, tools, organisational procedures, shared expertise, cultural values and social rules. The book investigates such phenomena which previously have fallen into the gaps between established disciplines of interaction analysis and psychology. In arguing that the multi-scalar constraints of professional action are still underexplored in a naturalistic setting of emergency medicine, Trasmundi uses tools such as multimodal interaction analysis and cognitive event analysis to investigate the cultural and distributed nature of cognition. The book provides the reader with a new take on this heavily investigated topic, both theoretically and methodologically by describing how medical culture affects real-time interaction and how culture itself is shaped by the exact same dynamics.
Deep neural network for x-ray photoelectron spectroscopy data analysis
Authors: Drera G , Kropf C M , Sangaletti L
Published: February 2020

In this work, we characterize the performance of a deep convolutional neural network designed to detect and quantify chemical elements in experimental x-ray photoelectron spectroscopy data. Given the lack of a reliable database in literature, in order to train the neural network we computed a large (<100 k) dataset of synthetic spectra, based on randomly generated materials covered with a layer of adventitious carbon. The trained net performs as well as standard methods on a test set of ≈500 well characterized experimental x-ray photoelectron spectra. Fine details about the net layout, the choice of the loss function and the quality assessment strategies are presented and discussed. Given the synthetic nature of the training set, this approach could be applied to the automatization of any photoelectron spectroscopy system, without the need of experimental reference spectra and with a low computational effort.
Age and the Construction of Gendered and Raced Citizenship in the United States
Authors: Field Corinne T. , Syrett Nicholas L.
Published: February 2020

Focusing on the United States, Field and Syrett argue that the supposed universality of chronological age masks the processes through which legislators and government officials relied upon age to reinforce inequalities rooted in coverture and chattel slavery. Two case studies reveal how bureaucratic and legislative age requirements functioned in tandem to deny equal citizenship to women and formerly enslaved people. During the Civil War, Congress passed legislation to grant age-based Civil War pensions for minor children that appeared neutral in law but came to be administered in ways that denied equal benefits to the families of black Civil War soldiers on the grounds that they lacked adequate proof of age. State governments, meanwhile, continued to pass laws that differentiated between men and women in the realm of legal majority, using chronological age as a means to shore up gender inequality even as women gained new rights and opportunities. Recent conflicts over voter identification laws and age determination for child migrants reveal that chronological age remains a contested category through which government officials can deny equal treatment under the law by defining the criteria for what counts as adequate proof of age. Cracks in the modern regime of government-issued birth certificates reveal that age remains what it has always been: not a neutral fact, but a vector of power through which government officials and ordinary people construct and contest the boundaries of citizenship.
After the Catastrophe: A Reading of Manna’s Nakba and Survival
Authors: Saʾdi Ahmad H.
Published: February 2020

Adel Manna’s Nakba and Survival: The Story of the Palestinians Who Remained in Haifa and the Galilee, 1948–1956 appeared in Arabic and Hebrew 2016–2017. Manna’s book gives voice to the experience of the first generation of Palestinians living within the State of Israel. Here, four scholars of Palestinian and Israeli history review Nakba and Survival and weigh its importance for reckoning with the entangled history of the creation of Israel and the related dispossession of Palestinians during and after 1948.
Contextualizing Past Tenses in L2: Combined Effects and Interactions in the Present Perfect versus Simple Past Alternation
Authors: Deshors Sandra C
Published: February 2020

This multifactorial corpus-based exploration of past tenses focuses specifically on the present perfect (PP) versus simple past (SP) alternation in intermediate-to-advanced learner English produced by French and German native speakers. While existing work on past tenses in L2 has traditionally focused on the role of lexical aspect in the acquisition and uses of these past tenses, the current study focuses on the linguistic context of use of these tenses and identifies the linguistic features whose co-occurrence and combined effects cause native speakers and learners to differ in their uses of past tenses. Methodologically, the study uses a random forests approach including a surrogate logistic regression model and interactions between contextual linguistic features. Overall, the multifactorial results suggest that not all linguistic contexts facilitate native-like uses of the PP and SP equally as some contexts more than others are susceptible to cross-linguistic interference.
Sexual size dimorphism and sexual selection in artiodactyls
Authors: Cassini Marcelo H
Published: February 2020

Sexual size dimorphism is biased toward males in most mammalian species. The most common explanation is precopulatory intramale sexual selection. Large males win fights and mate more frequently. In artiodactyls, previous tests of this hypothesis consisted of interspecific correlations of sexual dimorphism with group size as a surrogate for the intensity of sexual selection (Is). However, group size is not a proper measure of sexual selection for several reasons as is largely recognized in other mammalian taxa. I conducted an interspecific test on the role of sexual selection in the evolution of sexual dimorphism using the variance in genetic paternity as a proxy for the Is. I reviewed the literature and found 17 studies that allowed estimating Is= V/(W2), where V and W are the variance and mean number of offspring per male, respectively. A phylogenetic generalized least squares analysis indicated that dimorphism (Wm/Wf) showed a significant positive regression with the intensity of sexual selection but not group size (multiple r2= 0.40; F3,17= 12.78, P = 0.002). This result suggests that sexual selection may have played a role in the evolution of sexual size dimorphism in Artiodactyla. An alternative hypothesis based on natural selection is discussed.
Ensemble learning for classifying single-cell data and projection across reference atlases
Authors: Wang Lin , Catalan Francisca , Shamardani Karin , Babikir Husam , Diaz Aaron
Published: February 2020

Single-cell data are being generated at an accelerating pace. How best to project data across single-cell atlases is an open problem. We developed a boosted learner that overcomes the greatest challenge with status quo classifiers: low sensitivity, especially when dealing with rare cell types. By comparing novel and published data from distinct scRNA-seq modalities that were acquired from the same tissues, we show that this approach preserves cell-type labels when mapping across diverse platforms.

Availability and implementation

https://github.com/diazlab/ELSA

Contact

aaron.diaz@ucsf.edu

Supplementary information

Supplementary data are available at Bioinformatics online.
DNA4mC-LIP: a linear integration method to identify N4-methylcytosine site in multiple species
Authors: Tang Qiang , Kang Juanjuan , Yuan Jiaqing , Tang Hua , Li Xianhai , Lin Hao , Huang Jian , Chen Wei
Published: February 2020

Motivation

DNA N4-methylcytosine (4mC) is a crucial epigenetic modification. However, the knowledge about its biological functions is limited. Effective and accurate identification of 4mC sites will be helpful to reveal its biological functions and mechanisms. Since experimental methods are cost and ineffective, a number of machine learning-based approaches have been proposed to detect 4mC sites. Although these methods yielded acceptable accuracy, there is still room for the improvement of the prediction performance and the stability of existing methods in practical applications.

Results

In this work, we first systematically assessed the existing methods based on an independent dataset. And then, we proposed DNA4mC-LIP, a linear integration method by combining existing predictors to identify 4mC sites in multiple species. The results obtained from independent dataset demonstrated that DNA4mC-LIP outperformed existing methods for identifying 4mC sites. To facilitate the scientific community, a web server for DNA4mC-LIP was developed. We anticipated that DNA4mC-LIP could serve as a powerful computational technique for identifying 4mC sites and facilitate the interpretation of 4mC mechanism.

Availability and implementation

http://i.uestc.edu.cn/DNA4mC-LIP/.

Contact

hlin@uestc.edu.cn or hj@uestc.edu.cn or chenweiimu@gmail.com

Supplementary information

Supplementary data are available at Bioinformatics online.