bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spin-polarized magneto-electronic properties in buckled monolayer GaAs
Authors: Chung Hsien-Ching , Chiu Chih-Wei , Lin Ming-Fa 
Published: February 2019

AbstractWe develop the generalized tight-binding model to fully explore the magneto-electronic properties of monolayer GaAs, where the buckled structure, multi-orbital chemical bondings, spin-orbit coupling, electric field, and magnetic field are considered simultaneously. The diverse magnetic quantization covers three groups of spin-polarized Landau levels (LLs) near the Fermi level, with the unique initial energies, LL degeneracy, energy spacings, magnetic-field-dependence, and spin splitting. Furthermore, the Landau state probabilities exhibit specific oscillation patterns, being composed of the localization centers, node regularities, and energy-dependent variations of the dominating orbitals. The density of states directly reflects the main features of the LL energy spectra in the form, height, number, and frequency of the spin-split delta-function-like prominent peaks. The electric field leads to the monotonous/nonmonotonous LL energy dispersions, LL crossing behavior, gap modulation, phase transition and enhancement of spin splitting. The complex gap modulations and even semiconductor-semimetal transitions are attributed to the strong competition among the intrinsic interactions, magnetic field, and electric field. Such predicted magneto-electronic properties could be verified by scanning tunneling spectroscopy and are helpful in designing the top-gated and phase-change electronic devices.
Nash Equilibria in the Response Strategy of Correlated Games
Authors: Correia A. D. , Stoof H. T. C. 
Published: February 2019

AbstractIn nature and society, problems that arise when different interests are difficult to reconcile are modeled in game theory. While most applications assume that the players make decisions based only on the payoff matrix, a more detailed modeling is necessary if we also want to consider the influence of correlations on the decisions of the players. We therefore extend here the existing framework of correlated strategies by giving the players the freedom to respond to the instructions of the correlation device by probabilistically following or not following its suggestions. This creates a new type of games that we call “correlated games”. The associated response strategies that can solve these games turn out to have a rich structure of Nash equilibria that goes beyond the correlated equilibrium and pure or mixed-strategy solutions and also gives better payoffs in certain cases. We here determine these Nash equilibria for all possible correlated Snowdrift games and we find these solutions to be describable by Ising models in thermal equilibrium. We believe that our approach paves the way to a study of correlations in games that uncovers the existence of interesting underlying interaction mechanisms, without compromising the independence of the players.
Identification of a Xist silencing domain by Tiling CRISPR
Authors: Wang Yang , Zhong Yang , Zhou Yingyao , Tanaseichuk Olga , Li Zhizhong , Zhao Jing Crystal 
Published: February 2019

AbstractDespite essential roles played by long noncoding RNAs (lncRNAs) in development and disease, methods to determine lncRNA cis-elements are lacking. Here, we developed a screening method named “Tiling CRISPR” to identify lncRNA functional domains. Using this approach, we identified Xist A-Repeats as the silencing domain, an observation in agreement with published work, suggesting Tiling CRISPR feasibility. Mechanistic analysis suggested a novel function for Xist A-repeats in promoting Xist transcription. Overall, our method allows mapping of lncRNA functional domains in an unbiased and potentially high-throughput manner to facilitate the understanding of lncRNA functions.
Recommendation of long-term and systemic management according to the risk factors in rectal NETs patients
Authors: Kojima Motohiro , Chen Yu , Ikeda Koji , Tsukada Yuichiro , Takahashi Daigoro , Kawano Shingo , Amemiya Kota , Ito Masaaki , Ohki Rieko , Ochiai Atsushi 
Published: February 2019

AbstractRectal neuroendocrine tumors (NETs) are often found as small lesions, which can be treated by endoscopic resection. However, high risk cases with lymph node (LN) metastasis are indication of radical surgery. Furthermore, rectal NETs are often associated with late recurrences and/or multiple cancer development. Therefore, proper surgical indication and patients’ management are required. We investigated the clinicopathological features of 79 rectal NET cases in order to elucidate risk factors for synchronous LN metastasis, recurrence, and multiple cancers. Recently, we reported that in pancreatic NET patients, a loss of heterozygosity (LOH) in PHLDA3 was associated with poorer prognosis, and that LOH of both PHLDA3 and MEN1 was frequently observed. Therefore, PHLDA3 and MEN1 LOH were also assessed in rectal NET patients for their association with clinicopathological features. Of the 79 patients, LN metastases were found in 12.7%, recurrences in 3.8%, and multiple cancers in 30.4% of the subjects. PHLDA3 and MEN1 LOH were found in 60.0% and 66.7% of the subjects, respectively. Lymphatic invasion and WHO classification 2010 were found to be independent risks for LN metastasis. There were three cases of recurrence, all of which occurred more than 3 years after resection and two of which exhibited LN metastasis. Older age and LOH in PHLDA3 were associated with the presence of multiple cancers. Long-term and systemic management of patients with rectal NETs is therefore recommended in accordance with these risk factors.
A vegetation configuration pattern with a high-efficiency purification ability for TN, TP, AN, AP, and COD based on comprehensive assessment results
Authors: Hou Guirong , Bi Huaxing , Yu Xinxiao , Jia Guodong , Wang Dandan , Zhang Zhenyao , Liu Ziqiang 
Published: February 2019

AbstractTo identify a vegetation configuration pattern with a high-efficiency purification ability for total nitrogen (TN), available nitrogen (AN), total phosphorous (TP), available phosphorous (AP), and chemical oxygen demand (COD) based on comprehensive assessment results, a water discharge experiment was performed in the Luan River in China with the following riparian forests: I, pure broad-leaved; II, mixed broad-leaved; III, mixed coniferous and broad-leaved; IV, mixed coniferous; and V, pure coniferous. From the riparian buffer zone to the river channel, the evaluation showed that pattern I had the highest purification ability at 1 m and 2 m; at a width of 4 m, pattern III had the highest purification ability; at a distance of 7 m, pattern V showed the highest purification ability; at 10 m, pattern IV showed the highest purification ability, pattern II the lowest. It is advisable to give priority to plant coniferous species from 0 m to 4 m from the river bank, while it is advisable to give priority to plant broad-leaved species from 4 m to 10 m from the river bank. We therefore recommend these vegetation configuration patterns in the development and management of runoff purification systems.
Identification and profiling of microRNAs during gonadal development in the giant freshwater prawn Macrobrachium rosenbergii
Authors: Liu Xue , Luo Bi-Yun , Feng Jian-Bin , Zhou Ling-Xia , Ma Ke-Yi , Qiu Gao-Feng 
Published: February 2019

AbstractAs post-transcriptional regulators, microRNAs (miRNAs) play an important role in growth and reproductive processes. So far, there is limited information regarding crustacean miRNAs. To explore the potential role of miRNAs in the gonadal development of the prawn Macrobrachium rosenbergii, we constructed seven small RNA libraries from ovarian and testicular tissues at various stages using somatic tissue as the control. A total of 1,954 known and 129 novel miRNAs were retrieved. By comparing differentially expressed miRNAs (DEMs) between testes and ovaries, forty-one miRNAs were identified with sex-biased expression patterns, including 17 ovary-biased and 24 testis-biased patterns. Furthermore, the putative target genes of the sex-biased miRNAs, such as cyclin L1, mitogen-activated protein kinase 7 (MAPK 7), heat shock protein (HSP), and zinc finger protein, were significantly enriched in many reproduction-related pathways including the Gonadotropin-releasing hormone (GnRH) pathway, glycolysis, gluconeogenesis pathway, ovarian steroidogenesis, estrogen signaling pathway, MAPK pathway, Wnt pathway, and insulin signaling pathway, implicating potential regulatory roles of miRNAs in reproduction. These data aid in the further investigation of the mechanism of gonadal development and reproductive regulation mediated by miRNA in M. rosenbergii.
Biochar reduces the efficiency of nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) mitigating N2O emissions
Authors: Fuertes-Mendizábal T. , Huérfano X. , Vega-Mas I. , Torralbo F. , Menéndez S. , Ippolito J. A. , Kammann C. , Wrage-Mönnig N. , Cayuela M. L. , Borchard N. , Spokas K. , Novak J. , González-Moro M. B. , González-Murua C. , Estavillo J. M. 
Published: February 2019

AbstractAmong strategies suggested to decrease agricultural soil N2O losses, the use of nitrification inhibitors such as DMPP (3,4-dimethylpyrazole phosphate) has been proposed. However, the efficiency of DMPP might be affected by soil amendments, such as biochar, which has been shown to reduce N2O emissions. This study evaluated the synergic effect of a woody biochar applied with DMPP on soil N2O emissions. A incubation study was conducted with a silt loam soil and a biochar obtained from Pinus taeda at 500 °C. Two biochar rates (0 and 2% (w/w)) and three different nitrogen treatments (unfertilized, fertilized and fertilized + DMPP) were assayed under two contrasting soil water content levels (40% and 80% of water filled pore space (WFPS)) over a 163 day incubation period. Results showed that DMPP reduced N2O emissions by reducing ammonia-oxidizing bacteria (AOB) populations and promoting the last step of denitrification (measured by the ratio nosZI + nosZII/nirS + nirK genes). Biochar mitigated N2O emissions only at 40% WFPS due to a reduction in AOB population. However, when DMPP was applied to the biochar amended soil, a counteracting effect was observed, since the N2O mitigation induced by DMPP was lower than in control soil, demonstrating that this biochar diminishes the efficiency of the DMPP both at low and high soil water contents.
Modular type I polyketide synthase acyl carrier protein domains share a common N-terminally extended fold
Authors: Moretto Luisa , Heylen Rachel , Holroyd Natalie , Vance Steven , Broadhurst R. William 
Published: February 2019

AbstractAcyl carrier protein (ACP) domains act as interaction hubs within modular polyketide synthase (PKS) systems, employing specific protein-protein interactions to present acyl substrates to a series of enzyme active sites. Many domains from the multimodular PKS that generates the toxin mycolactone display an unusually high degree of sequence similarity, implying that the few sites which vary may do so for functional reasons. When domain boundaries based on prior studies were used to prepare two isolated ACP segments from this system for studies of their interaction properties, one fragment adopted the expected tertiary structure, but the other failed to fold, despite sharing a sequence identity of 49%. Secondary structure prediction uncovered a previously undetected helical region (H0) that precedes the canonical helix-bundle ACP topology in both cases. This article reports the NMR solution structures of two N-terminally extended mycolactone mACP constructs, mH0ACPa and mH0ACPb, both of which possess an additional α-helix that behaves like a rigid component of the domain. The interactions of these species with a phosphopantetheinyl transferase and a ketoreductase domain are unaffected by the presence of H0, but a shorter construct that lacks the H0 region is shown to be substantially less thermostable than mH0ACPb. Bioinformatics analysis suggests that the extended H0-ACP motif is present in 98% of type I cis-acyltransferase PKS chain-extension modules. The polypeptide linker that connects an H0-ACP motif to the preceding domain must therefore be ~12 residues shorter than previously thought, imposing strict limits on ACP-mediated substrate delivery within and between PKS modules.
Quantitative assessment of outer retinal folds on enface optical coherence tomography after vitrectomy for rhegmatogenous retinal detachment
Authors: Fukuyama H. , Yagiri H. , Araki T. , Iwami H. , Yoshida Y. , Ishikawa H. , Kimura N. , Kakusho K. , Okadome T. , Gomi F. 
Published: February 2019

AbstractWe aimed to investigate the possible causes of metamorphopsia for rhegmatogenous retinal detachment (RRD) based on findings of enface optical coherence tomography (OCT). The study was a retrospective, consecutive case series of 33 eyes with macula-off RRD. Metamorphopsia was measured by M-CHARTS and enface OCT images covering a macular area of 6 × 6 mm square obtained at 1, 3, and 6 months postoperatively. Within the outer retinal slabs of enface OCT, multiple lines that looked like folds were delineated in all eyes at month 1, and we succeeded in extracting images of folds by subtracting retinal vessels. We calculated their density by an image-processing technique. The mean M-CHARTS scores were 0.62 ± 0.47 at month 1 and 0.30 ± 0.29 at month 6 (P < 0.001). The fold density was 8.3 ± 4.2 at month 1 and 6.1 ± 3.1 at month 6 (P = 0.0044). The M-CHARTS scores at 6 months were significantly associated with the fold density at 1 month (r = 0.515, P = 0.002). In conclusion, enface OCT visualized the outer retinal folds in eyes that had undergone successful RRD surgery, and a larger number of folds was related to the remaining metamorphopsia.
Cell Identity Codes: Understanding Cell Identity from Gene Expression Profiles using Deep Neural Networks
Authors: Abdolhosseini Farzad , Azarkhalili Behrooz , Maazallahi Abbas , Kamal Aryan , Motahari Seyed Abolfazl , Sharifi-Zarchi Ali , Chitsaz Hamidreza 
Published: February 2019

AbstractUnderstanding cell identity is an important task in many biomedical areas. Expression patterns of specific marker genes have been used to characterize some limited cell types, but exclusive markers are not available for many cell types. A second approach is to use machine learning to discriminate cell types based on the whole gene expression profiles (GEPs). The accuracies of simple classification algorithms such as linear discriminators or support vector machines are limited due to the complexity of biological systems. We used deep neural networks to analyze 1040 GEPs from 16 different human tissues and cell types. After comparing different architectures, we identified a specific structure of deep autoencoders that can encode a GEP into a vector of 30 numeric values, which we call the cell identity code (CIC). The original GEP can be reproduced from the CIC with an accuracy comparable to technical replicates of the same experiment. Although we use an unsupervised approach to train the autoencoder, we show different values of the CIC are connected to different biological aspects of the cell, such as different pathways or biological processes. This network can use CIC to reproduce the GEP of the cell types it has never seen during the training. It also can resist some noise in the measurement of the GEP. Furthermore, we introduce classifier autoencoder, an architecture that can accurately identify cell type based on the GEP or the CIC.
Spatial dynamics of a zoonotic orthohantavirus disease through heterogenous data on rodents, rodent infections, and human disease
Authors: Vanwambeke Sophie O. , Zeimes Caroline B. , Drewes Stephan , Ulrich Rainer G. , Reil Daniela , Jacob Jens 
Published: February 2019

AbstractZoonotic diseases are challenging to study from the ecological point of view as, broadly speaking, datasets tend to be either detailed on a small spatial extent, or coarse on a large spatial extent. Also, there are many ways to assess zoonotic disease transmission systems, from pathogens to hosts to humans. We explore the complementarity of datasets considering the pathogen in its host, the host and human cases in the context ofPuumala orthohantavirusinfection in Germany. We selected relevant environmental predictors using a conceptual framework based on resource-based habitats. This framework assesses the functions, and associated environmental resources of the pathogen and associated host. A resource-based habitat framework supports variable selection and result interpretation. Multiplying ‘keyholes’ to view a zoonotic disease transmission system is valuable, but requires a strong conceptual framework to select and interpret environmental explanatory variables. This study highlights the usefulness of a structured, ecology-based approach to study drivers of zoonotic diseases at the level of virus, host, and human - not only for PUUV but also for other zoonotic pathogens. Our results show that human disease cases are best explained by a combination of variables related to zoonotic pathogen circulation and human exposure.
The effect of age-related hearing loss and listening effort on resting state connectivity
Authors: Rosemann Stephanie , Thiel Christiane M. 
Published: February 2019

AbstractAge-related hearing loss is associated with a decrease in hearing abilities for high frequencies. This increases not only the difficulty to understand speech but also the experienced listening effort. Task based neuroimaging studies in normal-hearing and hearing-impaired participants show an increased frontal activation during effortful speech perception in the hearing-impaired. Whether the increased effort in everyday listening in hearing-impaired even impacts functional brain connectivity at rest is unknown. Nineteen normal-hearing and nineteen hearing-impaired participants with mild to moderate hearing loss participated in the study. Hearing abilities, listening effort and resting state functional connectivity were assessed. Our results indicate no differences in functional connectivity between hearing-impaired and normal-hearing participants. Increased listening effort, however, was related to significantly decreased functional connectivity between the dorsal attention network and the precuneus and superior parietal lobule as well as between the auditory and the inferior frontal cortex. We conclude that already mild to moderate age-related hearing loss can impact resting state functional connectivity. It is however not the hearing loss itself but the individually perceived listening effort that relates to functional connectivity changes.
Biogeographical patterns in the structural blue of male Polyommatus icarus butterflies
Authors: Kertész Krisztián , Piszter Gábor , Bálint Zsolt , Biró László P. 
Published: February 2019

AbstractColor is a widely used communication channel in the living world for a variety of functions ranging from sexual communication to warning colors. A particularly rich spectrum of colors appears on the wings of many butterflies. The males of lycaenid butterflies often exhibit a conspicuous blue coloration generated by photonic nanoarchitectures on their dorsal wing surfaces. Using UV-VIS spectroscopy, we investigated the spatio-temporal variations of this coloration forPolyommatus icarusbutterflies, considering an interval of more than 100 years and a geographical range spanning Europe (west) and Asia (east). The blue coloration in Hungary is very stable both within a year (three broods typical in Hungary) and within the period of 100 years (more than 300 generations). East-west geographic variation was investigated among 314 maleP. icarusbutterflies. In agreement with earlier genetic and morphometric studies, it was found that the western males are not divided in distinct lineages. Clear differences in coloration were found between the eastern and western groups, with a transition in the region of Turkey. These differences are tentatively attributed to bottleneck effects during past glaciations.
Optimization of the co-digestion of sewage sludge, maize straw and cow manure: microbial responses and effect of fractional organic characteristics
Authors: Wei Liangliang , Qin Kena , Ding Jing , Xue Mao , Yang Chaoyong , Jiang Junqiu , Zhao Qingliang 
Published: February 2019

AbstractThe aim of this study was to evaluate the efficiency and optimization of co-digestion using sewage sludge (SS), maize straw (MS) and cow manure (CM) as feeds, and the effects of the mixing ratio and C/N ratio of the substrates were analyzed in detail. Among the three substrates tested, CM/MS exhibited better digestion than CM/SS and SS/MS in terms of all measures, including total daily biogas and net methane volume production, due to the hydrophilic characteristics and high level of biodegradability of CM, as well as its higher C/N ratio. The average biogas production was 613.8 mL/g VS for the co-digestion of CM/MS at a feed concentration of 15 g VS/L and using a 1:1 mixing ratio (C/N ratio of 28.3). The co-digestion of SS/CM/MS performed better than the individual digestion of the components because of the balanced C/N ratios and supply of carbon. The optimum conditions for maximizing methane potential were an SS:CM:MS ratio of 30:35:35 and a bulk VS concentration of 15.0 g VS/L, which led to a maximum methane production of 8047.31 mL (C/N ratio of 12.7). The high-throughput sequencing analysis showed clear differences in microbial communities during the entire co-digestion process.