bluuebunny/crossref_metadata_2025_split huggingface dataset:
Anomalous quantum Griffiths singularity in ultrathin crystalline lead films
Authors: Liu Yi , Wang Ziqiao , Shan Pujia , Tang Yue , Liu Chaofei , Chen Cheng , Xing Ying , Wang Qingyan , Liu Haiwen , Lin Xi , Xie X. C. , Wang Jian 
Published: August 2019

AbstractSuperconductor-insulator/metal transition (SIT/SMT) represents a prototype of quantum phase transition, where quantum fluctuation plays a dominant role and dramatically changes the physical properties of low-dimensional superconducting systems. Recent observation of quantum Griffiths singularity (QGS) offers an essential perspective to understand the subtleties of quantum phase transition in two-dimensional superconductors. Here we study the magnetic field induced SMT in ultrathin crystalline Pb films down to ultralow temperatures. The divergent critical exponent is observed when approaching zero temperature quantum critical point, indicating QGS. Distinctively, the anomalous phase boundary of SMT that the onset critical field decreases with decreasing temperatures in low temperature regime distinguishes our observation from previous reports of QGS in various two-dimensional superconductors. We demonstrate that the anomalous phase boundary originates from the superconducting fluctuations in ultrathin Pb films with pronounced spin-orbit interaction. Our findings reveal a novel aspect of QGS of SMT in two-dimensional superconductors with anomalous phase boundary.
Hierarchical graphical model reveals HFR1 bridging circadian rhythm and flower development in Arabidopsis thaliana
Authors: Duren Zhana , Wang Yaling , Wang Jiguang , Zhao Xing-Ming , Lv Le , Li Xiaobo , Liu Jingdong , Zhu Xin-Guang , Chen Luonan , Wang Yong 
Published: August 2019

AbstractsTo study systems-level properties of the cell, it is necessary to go beyond individual regulators and target genes to study the regulatory network among transcription factors (TFs). However, it is difficult to directly dissect the TFs mediated genome-wide gene regulatory network (GRN) by experiment. Here, we proposed a hierarchical graphical model to estimate TF activity from mRNA expression by building TF complexes with protein cofactors and inferring TF’s downstream regulatory network simultaneously. Then we applied our model on flower development and circadian rhythm processes in Arabidopsis thaliana. The computational results show that the sequence specific bHLH family TF HFR1 recruits the chromatin regulator HAC1 to flower development master regulator TF AG and further activates AG’s expression by histone acetylation. Both independent data and experimental results supported this discovery. We also found a flower tissue specific H3K27ac ChIP-seq peak at AG gene body and a HFR1 motif in the center of this H3K27ac peak. Furthermore, we verified that HFR1 physically interacts with HAC1 by yeast two-hybrid experiment. This HFR1–HAC1–AG triplet relationship may imply that flower development and circadian rhythm are bridged by epigenetic regulation and enrich the classical ABC model in flower development. In addition, our TF activity network can serve as a general method to elucidate molecular mechanisms on other complex biological regulatory processes.
Metabolomics reveals a link between homocysteine and lipid metabolism and leukocyte telomere length: the ENGAGE consortium
Authors: van der Spek Ashley , Broer Linda , Draisma Harmen H. M. , Pool René , Albrecht Eva , Beekman Marian , Mangino Massimo , Raag Mait , Nyholt Dale R. , Dharuri Harish K. , Codd Veryan , Amin Najaf , de Geus Eco J. C. , Deelen Joris , Demirkan Ayse , Yet Idil , Fischer Krista , Haller Toomas , Henders Anjali K. , Isaacs Aaron , Medland Sarah E. , Montgomery Grant W. , Mooijaart Simon P. , Strauch Konstantin , Suchiman H. Eka D. , Vaarhorst Anika A. M. , van Heemst Diana , Wang-Sattler Rui , Whitfield John B. , Willemsen Gonneke , Wright Margaret J. , Martin Nicholas G. , Samani Nilesh J. , Metspalu Andres , Eline Slagboom P. , Spector Tim D. , Boomsma Dorret I. , van Duijn Cornelia M. , Gieger Christian 
Published: August 2019

AbstractTelomere shortening has been associated with multiple age-related diseases such as cardiovascular disease, diabetes, and dementia. However, the biological mechanisms responsible for these associations remain largely unknown. In order to gain insight into the metabolic processes driving the association of leukocyte telomere length (LTL) with age-related diseases, we investigated the association between LTL and serum metabolite levels in 7,853 individuals from seven independent cohorts. LTL was determined by quantitative polymerase chain reaction and the levels of 131 serum metabolites were measured with mass spectrometry in biological samples from the same blood draw. With partial correlation analysis, we identified six metabolites that were significantly associated with LTL after adjustment for multiple testing: lysophosphatidylcholine acyl C17:0 (lysoPC a C17:0, p-value = 7.1 × 10−6), methionine (p-value = 9.2 × 10−5), tyrosine (p-value = 2.1 × 10−4), phosphatidylcholine diacyl C32:1 (PC aa C32:1, p-value = 2.4 × 10−4), hydroxypropionylcarnitine (C3-OH, p-value = 2.6 × 10−4), and phosphatidylcholine acyl-alkyl C38:4 (PC ae C38:4, p-value = 9.0 × 10−4). Pathway analysis showed that the three phosphatidylcholines and methionine are involved in homocysteine metabolism and we found supporting evidence for an association of lipid metabolism with LTL. In conclusion, we found longer LTL associated with higher levels of lysoPC a C17:0 and PC ae C38:4, and with lower levels of methionine, tyrosine, PC aa C32:1, and C3-OH. These metabolites have been implicated in inflammation, oxidative stress, homocysteine metabolism, and in cardiovascular disease and diabetes, two major drivers of morbidity and mortality.
Analysis of circulating cell-free DNA identifies KRAS copy number gain and mutation as a novel prognostic marker in Pancreatic cancer
Authors: Mohan Sumitra , Ayub Mahmood , Rothwell Dominic G. , Gulati Sakshi , Kilerci Bedirhan , Hollebecque Antoine , Sun Leong Hui , Smith Nigel K. , Sahoo Sudhakar , Descamps Tine , Zhou Cong , Hubner Richard A. , McNamara Mairéad G. , Lamarca Angela , Valle Juan W. , Dive Caroline , Brady Ged 
Published: August 2019

AbstractSerial biopsy of pancreatic ductal adenocarcinoma (PDAC), to chart tumour evolution presents a significant challenge. We examined the utility of circulating free DNA (cfDNA) as a minimally invasive approach across a cohort of 55 treatment-naïve patients with PDAC; 31 with metastatic and 24 with locally advanced disease. Somatic mutations in cfDNA were detected using next generation sequencing in 15/24 (62.5%) and 27/31 (87%) of patients with locally advanced and metastatic disease, respectively. Copy number changes were detected in cfDNA of 10 patients of whom 7 exhibited gain of chromosome 12p harbouring KRAS as well as a canonical KRAS codon 12 mutation. In multivariable Cox Regression analysis, we show for the first time that patients with KRAS copy number gain and KRAS mutation have significantly worse outcomes, suggesting that this may be linked to PDAC progression. The simple cfDNA assay we describe will enable determination of the presence of KRAS copy number gain and KRAS mutations in larger studies and clinical trials.
Pretreatment-Integration for Milk Protein Removal and Device-Facilitated Immunochromatographic Assay for 17 Items
Authors: Qie Zhiwei , Huang Ziwei , Gao Zichen , Meng Wu , Zhu Yanhui , Xiao Rui , Wang Shengqi 
Published: August 2019

AbstractAccurate and comprehensive immunochromatographic assay (ICA) data are urgently required in the daily supervision of plants, schools, testing institutions, and law-enforcing departments. Through pretreatment-integration and device-facilitated operation, a quantitative ICA with high sensitivity and throughput was realized on the basis of a commercialized semi-quantitative ICA strip. Three pretreatment methods, namely, acid base, heavy metal salt, and organic solvent methods, have less than three steps. The pretreatment was established for protein removal. A total of 17 pretreated ICA items in milk were considered for the identification of the most suitable pretreatment method. The items are composed of six items pretreated by the acid-base method, six by the heavy salt method, and five by the organic solvent method. Then, the ICA results with pretreatment were compared with those without pretreatment. After pretreatment, the signal intensity increased by 39%, the detection limit decreased to 12%, the half maximal inhibitory concentration decreased to 18%, and the detection range increased fourfold. A device with mixing and centrifugation functions was designed for the pretreatment-related operations. A pre-incubation sampling device was used to facilitate incubation in batch and high-throughput detection. An ICA reader was used. The detection throughput reached 8 samples per batch or 32 samples per hour. The designed devices were printed through 3D printing and rapid prototyping.
Guideline-conform statin use reduces overall mortality in patients with compensated liver disease
Authors: Unger Lukas W. , Forstner Bernadette , Schneglberger Stephan , Muckenhuber Moritz , Eigenbauer Ernst , Bauer David , Scheiner Bernhard , Mandorfer Mattias , Trauner Michael , Reiberger Thomas 
Published: August 2019

AbstractStatins reduce cardiovascular risk. However, “real-life” data on statin use in patients with chronic liver disease and its impact on overall and liver-related survival are limited. Therefore, we assessed 1265 CLD patients stratified as advanced (ACLD) or non-advanced (non-ACLD) stage. Statin indication was evaluated according to the 2013 ACC/AHA guidelines and survival-status was verified by national death registry data. Overall, 122 (9.6%) patients had an indication for statin therapy but did not receive statins, 178 (14.1%) patients were on statins and 965 (76.3%) patients had no indication for statins. Statin underutilization was 34.2% in non-ACLD and 48.2% in ACLD patients. In non-ACLD patients, survival was worse without a statin despite indication as compared to patients on statin or without indication (log-rank p = 0.018). In ACLD patients, statin use did not significantly impact on survival (log-rank p = 0.264). Multivariate cox regression analysis confirmed improved overall survival in patients with statin as compared to patients with indication but no statin (HR 0.225; 95%CI 0.053–0.959; p = 0.044) and a trend towards reduced liver-related mortality (HR 0.088; 95%CI 0.006–1.200; p = 0.068). This was not observed in ACLD patients. In conclusion, guideline-confirm statin use is often withhold from patients with liver disease and this underutilization is associated with impaired survival in non-ACLD patients.
Preparation of MnOx Supported LiOH Activated Soybean Oil Sludge Catalyst and Its Analysis in Denitration Mechanism of Selective Catalytic Oxidation (SCO)
Authors: Lei Zhang , Min Luo , Tingting Kong , Lei Zhang , Huibin He , Yang Jia , Chao Yang , Yan Wu , Mengting Li 
Published: August 2019

AbstractTreatment with selective catalytic oxidation (SCO) is an effective technology applied recently for conversion of nitrogen oxides pollution control. In order to solve the problems of high cost and difficulties in practical application of SCO catalyst, it was put forward using the solid waste sludge from soybean oil plant as catalyst carrier to prepare denitration catalyst. The sludge was treated by alkaline activation and then MnOx-based sludge was prepared by impregnation. Finally, MnOx-based sludge was calcined in the muffle furnace. The effects of activation and calcination conditions on catalyst activity were investigated. Fourier transform infrared (FTIR), X-ray photoelectron spectroscopy (XPS), X-ray diffraction (XRD) and scanning electron microscopy (SEM) were used to characterize the activity of the sludge based denitration catalyst, and the structure and activity of the sludge based denitration catalyst were furtherly confirmed. According to the achieved results, (1) after activated by LiOH with a mass concentration of 15% for 4 hours, the surface of the sludge catalyst has more alkali functional groups, making the denitration of sludge catalyst the best; (2) the MnOx-based catalyst calcined in the muffle furnace with calcination temperature of 450 °C for 4 hours has obvious denitration efficiency.
The large repertoire of conifer NLR resistance genes includes drought responsive and highly diversified RNLs
Authors: Van Ghelder Cyril , Parent Geneviève J. , Rigault Philippe , Prunier Julien , Giguère Isabelle , Caron Sébastien , Stival Sena Juliana , Deslauriers Annie , Bousquet Jean , Esmenjaud Daniel , MacKay John 
Published: August 2019

AbstractThe NLRs or NBS-LRRs (nucleotide-binding, leucine-rich-repeat) form the largest resistance gene family in plants, with lineage-specific contingents of TNL, CNL and RNL subfamilies and a central role in resilience to stress. The origin, evolution and distribution of NLR sequences has been unclear owing in part to the variable size and diversity of the RNL subfamily and a lack of data in Gymnosperms. We developed, searched and annotated transcriptomes assemblies of seven conifers and identified a resource of 3816 expressed NLR sequences. Our analyses encompassed sequences data spanning the major groups of land plants and determinations of NLR transcripts levels in response to drought in white spruce. We showed that conifers have among the most diverse and numerous RNLs in tested land plants. We report an evolutionary swap in the formation of RNLs, which emerged from the fusion of an RPW8 domain to a NB-ARC domain of CNL. We uncovered a quantitative relationship between RNLs and TNLs across all land plants investigated, with an average ratio of 1:10. The conifer RNL repertoire harbours four distinct groups, with two that differ from Angiosperms, one of which contained several upregulated sequences in response to drought while the majority of responsive NLRs are downregulated.
Stress-induced phospho-ubiquitin formation causes parkin degradation
Authors: Kovalchuke Lyudmila , Mosharov Eugene V. , Levy Oren A. , Greene Lloyd A. 
Published: August 2019

AbstractMutations in the E3 ubiquitin ligase parkin are the most common known cause of autosomal recessive Parkinson’s disease (PD), and parkin depletion may play a role in sporadic PD. Here, we sought to elucidate the mechanisms by which stress decreases parkin protein levels using cultured neuronal cells and the PD-relevant stressor, L-DOPA. We find that L-DOPA causes parkin loss through both oxidative stress-independent and oxidative stress-dependent pathways. Characterization of the latter reveals that it requires both the kinase PINK1 and parkin’s interaction with phosphorylated ubiquitin (phospho-Ub) and is mediated by proteasomal degradation. Surprisingly, autoubiquitination and mitophagy do not appear to be required for such loss. In response to stress induced by hydrogen peroxide or CCCP, parkin degradation also requires its association with phospho-Ub, indicating that this mechanism is broadly generalizable. As oxidative stress, metabolic dysfunction and phospho-Ub levels are all elevated in PD, we suggest that these changes may contribute to a loss of parkin expression.
Reproducibility via coordinated standardization: a multi-center study in a Shank2 genetic rat model for Autism Spectrum Disorders
Authors: Arroyo-Araujo María , Graf Radka , Maco Martine , van Dam Elsbeth , Schenker Esther , Drinkenburg Wilhelmus , Koopmans Bastijn , de Boer Sietse F. , Cullum-Doyle Michaela , Noldus Lucas P. J. J. , Loos Maarten , van Dommelen Wil , Spooren Will , Biemans Barbara , Buhl Derek L. , Kas Martien J. 
Published: August 2019

AbstractInconsistent findings between laboratories are hampering scientific progress and are of increasing public concern. Differences in laboratory environment is a known factor contributing to poor reproducibility of findings between research sites, and well-controlled multisite efforts are an important next step to identify the relevant factors needed to reduce variation in study outcome between laboratories. Through harmonization of apparatus, test protocol, and aligned and non-aligned environmental variables, the present study shows that behavioral pharmacological responses in Shank2 knockout (KO) rats, a model of synaptic dysfunction relevant to autism spectrum disorders, were highly replicable across three research centers. All three sites reliably observed a hyperactive and repetitive behavioral phenotype in KO rats compared to their wild-type littermates as well as a dose-dependent phenotype attenuation following acute injections of a selective mGluR1 antagonist. These results show that reproducibility in preclinical studies can be obtained and emphasizes the need for high quality and rigorous methodologies in scientific research. Considering the observed external validity, the present study also suggests mGluR1 as potential target for the treatment of autism spectrum disorders.
Hydrogels formed by anammox extracellular polymeric substances: structural and mechanical insights
Authors: Lotti Tommaso , Carretti Emiliano , Berti Debora , Montis Costanza , Del Buffa Stefano , Lubello Claudio , Feng Cuijie , Malpei Francesca 
Published: August 2019

AbstractThe recovery of biopolymers from the waste sludge produced in wastewater treatments and their application in other industrial sectors, would substantially increase the environmental and economical sustainability of the process, promoting the development of a circular economy. In this study, extracellular polymeric substances (EPS) extracted from anammox granular waste sludge, were investigated and characterized. Rheological and differential scanning calorimetry measurements on EPS aqueous dispersions indicate the formation of an extended 3-D network above a threshold concentration, with a clear dependence of the mechanical and water retention properties on EPS content. The structural characterization, performed with transmission electron microscopy and small angle X-ray scattering, reveals the presence of functional amyloids as putative structural units, observed for the first time in an EPS-based hydrogel. As a proof of concept of the applicative potential, we explored the water and grease resistance provided to paper by an EPS coating. These results shed light on the structural details of EPS-based hydrogels, and pave the way for the possible use of EPS-based materials as a cheap, eco-friendly alternative to commonly adopted paper coatings, in line with a circular economy pattern for wastewater treatment.
Interplay of strain and intermixing effects on direct-bandgap optical transition in strained Ge-on-Si under thermal annealing
Authors: Lee Chulwon , Yoo Yang-Seok , Ki Bugeun , Jang Min-Ho , Lim Seung-Hyuk , Song Hyun Gyu , Cho Jong-Hoi , Oh Jungwoo , Cho Yong-Hoon 
Published: August 2019

AbstractThe influence of thermal annealing on the properties of germanium grown on silicon (Ge-on-Si) has been investigated. Depth dependencies of strain and photoluminescence (PL) were compared for as-grown and annealed Ge-on-Si samples to investigate how intermixing affects the optical properties of Ge-on-Si. The tensile strain on thermally annealed Ge-on-Si increases at the deeper region, while the PL wavelength becomes shorter. This unexpected blue-shift is attributed to Si interdiffusion at the interface, which is confirmed by energy dispersive X-ray spectroscopy and micro-Raman experiments. Not only Γ- and L-valley emissions but also Δ2-valley related emission could be found from the PL spectra, showing a possibility of carrier escape from Γ valley. Temperature-dependent PL analysis reveals that the thermal activation energy of Γ-valley emission increases at the proximity of the Ge/Si interface. By comparing the PL peak energies and their activation energies, both SiGe intermixing and shallow defect levels are found to be responsible for the activation energy increase and consequent efficiency reduction at the Ge/Si interface. These results provide an in-depth understanding of the influence of strain and Si intermixing on the direct-bandgap optical transition in thermally annealed Ge-on-Si.
Binarized Neural Network with Silicon Nanosheet Synaptic Transistors for Supervised Pattern Classification
Authors: Kim Sungho , Choi Bongsik , Yoon Jinsu , Lee Yongwoo , Kim Hee-Dong , Kang Min-Ho , Choi Sung-Jin 
Published: August 2019

AbstractIn the biological neural network, the learning process is achieved through massively parallel synaptic connections between neurons that can be adjusted in an analog manner. Recent developments in emerging synaptic devices and their networks can emulate the functionality of a biological neural network, which will be the fundamental building block for a neuromorphic computing architecture. However, on-chip implementation of a large-scale artificial neural network is still very challenging due to unreliable analog weight modulation in current synaptic device technology. Here, we demonstrate a binarized neural network (BNN) based on a gate-all-around silicon nanosheet synaptic transistor, where reliable digital-type weight modulation can contribute to improve the sustainability of the entire network. BNN is applied to three proof-of-concept examples: (1) handwritten digit classification (MNIST dataset), (2) face image classification (Yale dataset), and (3) experimental 3 × 3 binary pattern classifications using an integrated synaptic transistor network (total 9 × 9 × 2   162 cells) through a supervised online training procedure. The results consolidate the feasibility of binarized neural networks and pave the way toward building a reliable and large-scale artificial neural network by using more advanced conventional digital device technologies.
Low infiltration of tumor-associated macrophages in high c-Myb-expressing breast tumors
Authors: Volodko Nataliya , Gutor Taras , Petronchak Orest , Huley Roman , Dúcka Monika , Šmarda Jan , Borsig Lubor , Beneš Petr , Knopfová Lucia 
Published: August 2019

AbstractTumor-associated macrophages (TAMs) are prominent components of tumor stroma that promotes tumorigenesis. Many soluble factors participate in the deleterious cross-talk between TAMs and transformed cells; however mechanisms how tumors orchestrate their production remain relatively unexplored. c-Myb is a transcription factor recently described as a negative regulator of a specific immune signature involved in breast cancer (BC) metastasis. Here we studied whether c-Myb expression is associated with an increased presence of TAMs in human breast tumors. Tumors with high frequency of c-Myb-positive cells have lower density of CD68-positive macrophages. The negative association is reflected by inverse correlation between MYB and CD68/CD163 markers at the mRNA levels in evaluated cohorts of BC patients from public databases, which was found also within the molecular subtypes. In addition, we identified potential MYB-regulated TAMs recruiting factors that in combination with MYB and CD163 provided a valuable clinical multigene predictor for BC relapse. We propose that identified transcription program running in tumor cells with high MYB expression and preventing macrophage accumulation may open new venues towards TAMs targeting and BC therapy.