bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exfoliation of natural van der Waals heterostructures to a single unit cell thickness
Authors: Velický Matěj , Toth Peter S. , Rakowski Alexander M. , Rooney Aidan P. , Kozikov Aleksey , Woods Colin R. , Mishchenko Artem , Fumagalli Laura , Yin Jun , Zólyomi Viktor , Georgiou Thanasis , Haigh Sarah J. , Novoselov Kostya S. , Dryfe Robert A. W. 
Published: February 2017

AbstractWeak interlayer interactions in van der Waals crystals facilitate their mechanical exfoliation to monolayer and few-layer two-dimensional materials, which often exhibit striking physical phenomena absent in their bulk form. Here we utilize mechanical exfoliation to produce a two-dimensional form of a mineral franckeite and show that the phase segregation of chemical species into discrete layers at the sub-nanometre scale facilitates franckeite’s layered structure and basal cleavage down to a single unit cell thickness. This behaviour is likely to be common in a wider family of complex minerals and could be exploited for a single-step synthesis of van der Waals heterostructures, as an alternative to artificial stacking of individual two-dimensional crystals. We demonstrate p-type electrical conductivity and remarkable electrochemical properties of the exfoliated crystals, showing promise for a range of applications, and use the density functional theory calculations of franckeite’s electronic band structure to rationalize the experimental results.
Induced p53 loss in mouse luminal cells causes clonal expansion and development of mammary tumours
Authors: Tao Luwei , Xiang Dongxi , Xie Ying , Bronson Roderick T. , Li Zhe 
Published: February 2017

AbstractMost breast cancers may have a luminal origin. TP53 is one of the most frequently mutated genes in breast cancers. However, how p53 deficiency contributes to breast tumorigenesis from luminal cells remains elusive. Here we report that induced p53 loss in Krt8+ mammary luminal cells leads to their clonal expansion without directly affecting their luminal identity. All induced mice develop mammary tumours with 9qA1 (Yap1) and/or 6qA2 (Met) amplification(s). These tumours exhibit a mammary stem cell (MaSC)-like expression signature and most closely resemble claudin-low breast cancer. Thus, although p53 does not directly control the luminal fate, its loss facilitates acquisition of MaSC-like properties by luminal cells and predisposes them to development of mammary tumours with loss of luminal identity. Our data also suggest that claudin-low breast cancer can develop from luminal cells, possibly via a basal-like intermediate state, although further study using a different luminal promoter is needed to fully support this conclusion.
Integrative analyses of transcriptome sequencing identify novel functional lncRNAs in esophageal squamous cell carcinoma
Authors: Li C-Q , Huang G-W , Wu Z-Y , Xu Y-J , Li X-C , Xue Y-J , Zhu Y , Zhao J-M , Li M , Zhang J , Wu J-Y , Lei F , Wang Q-Y , Li S , Zheng C-P , Ai B , Tang Z-D , Feng C-C , Liao L-D , Wang S-H , Shen J-H , Liu Y-J , Bai X-F , He J-Z , Cao H-H , Wu B-L , Wang M-R , Lin D-C , Koeffler H P , Wang L-D , Li X , Li E-M , Xu L-Y 
Published: February 2017

AbstractLong non-coding RNAs (lncRNAs) have a critical role in cancer initiation and progression, and thus may mediate oncogenic or tumor suppressing effects, as well as be a new class of cancer therapeutic targets. We performed high-throughput sequencing of RNA (RNA-seq) to investigate the expression level of lncRNAs and protein-coding genes in 30 esophageal samples, comprised of 15 esophageal squamous cell carcinoma (ESCC) samples and their 15 paired non-tumor tissues. We further developed an integrative bioinformatics method, denoted URW-LPE, to identify key functional lncRNAs that regulate expression of downstream protein-coding genes in ESCC. A number of known onco-lncRNA and many putative novel ones were effectively identified by URW-LPE. Importantly, we identified lncRNA625 as a novel regulator of ESCC cell proliferation, invasion and migration. ESCC patients with high lncRNA625 expression had significantly shorter survival time than those with low expression. LncRNA625 also showed specific prognostic value for patients with metastatic ESCC. Finally, we identified E1A-binding protein p300 (EP300) as a downstream executor of lncRNA625-induced transcriptional responses. These findings establish a catalog of novel cancer-associated functional lncRNAs, which will promote our understanding of lncRNA-mediated regulation in this malignancy.
Molecular dynamics simulations reveal ligand-controlled positioning of a peripheral protein complex in membranes
Authors: Ryckbosch Steven M. , Wender Paul A. , Pande Vijay S. 
Published: February 2017

AbstractBryostatin is in clinical trials for Alzheimer’s disease, cancer, and HIV/AIDS eradication. It binds to protein kinase C competitively with diacylglycerol, the endogenous protein kinase C regulator, and plant-derived phorbol esters, but each ligand induces different activities. Determination of the structural origin for these differing activities by X-ray analysis has not succeeded due to difficulties in co-crystallizing protein kinase C with relevant ligands. More importantly, static, crystal-lattice bound complexes do not address the influence of the membrane on the structure and dynamics of membrane-associated proteins. To address this general problem, we performed long-timescale (400–500 µs aggregate) all-atom molecular dynamics simulations of protein kinase C–ligand–membrane complexes and observed that different protein kinase C activators differentially position the complex in the membrane due in part to their differing interactions with waters at the membrane inner leaf. These new findings enable new strategies for the design of simpler, more effective protein kinase C analogs and could also prove relevant to other peripheral protein complexes.
Specific membrane capacitance, cytoplasm conductivity and instantaneous Young’s modulus of single tumour cells
Authors: Wang Ke , Zhao Yang , Chen Deyong , Fan Beiyuan , Lu Yulan , Chen Lianhong , Long Rong , Wang Junbo , Chen Jian 
Published: February 2017

AbstractAs label-free biomarkers, biophysical properties of cells are widely used for cell type classification. However, intrinsic biophysical markers, e.g., specific membrane capacitance (Cspecific membrane), cytoplasm conductivity (σconductivity) and instantaneous Young’s modulus (Einstantaneous) measured for hundreds of single cells were not yet reported. In this study, single cells in suspension (adherent cells treated with trypsin) were aspirated through a microfluidic constriction channel at 25 °C, and the entry processes and impedance profiles were recorded and translated to Cspecific membrane, σconductivity and Einstantaneous. Cspecific membrane, σconductivity and Einstantaneous of five cell types were quantified as 2.10±0.38 μF cm−2, 0.91±0.15 S m−1 and 5.52±0.95 kPa for H460 cells (ncell=437); 2.52±0.54 μF cm−2, 0.83±0.12 S m−1 and 5.54±1.04 kPa for H446 cells (ncell=410); 2.45±0.57 μF cm−2, 0.99±0.18 S m−1 and 5.16±1.68 kPa for A549 cells (ncell=442); 1.86±0.31 μF cm−2, 1.07±0.18 S m−1 and 3.86±0.81 kPa for 95D cells (ncell=415); 2.03±0.35 μF cm−2, 0.99±0.16 S m−1 and 3.49±0.70 kPa for 95C cells (ncell=290). The database of Cspecific membrane, σconductivity and Einstantaneous may serve as a reference for future studies of cellular biophysical properties.
The French Muséum national d’histoire naturelle vascular plant herbarium collection dataset
Authors: Le Bras Gwenaël , Pignal Marc , Jeanson Marc L. , Muller Serge , Aupic Cécile , Carré Benoît , Flament Grégoire , Gaudeul Myriam , Gonçalves Claudia , Invernón Vanessa R. , Jabbour Florian , Lerat Elodie , Lowry Porter P. , Offroy Bérangère , Pimparé Eva Pérez , Poncy Odile , Rouhan Germinal , Haevermans Thomas 
Published: February 2017

AbstractWe provide a quantitative description of the French national herbarium vascular plants collection dataset. Held at the Muséum national d’histoire naturelle, Paris, it currently comprises records for 5,400,000 specimens, representing 90% of the estimated total of specimens. Ninety nine percent of the specimen entries are linked to one or more images and 16% have field-collecting information available. This major botanical collection represents the results of over three centuries of exploration and study. The sources of the collection are global, with a strong representation for France, including overseas territories, and former French colonies. The compilation of this dataset was made possible through numerous national and international projects, the most important of which was linked to the renovation of the herbarium building. The vascular plant collection is actively expanding today, hence the continuous growth exhibited by the dataset, which can be fully accessed through the GBIF portal or the MNHN database portal (available at: https://science.mnhn.fr/institution/mnhn/collection/p/item/search/form). This dataset is a major source of data for systematics, global plants macroecological studies or conservation assessments.
The Mole Mapper Study, mobile phone skin imaging and melanoma risk data collected using ResearchKit
Authors: Webster Dan E. , Suver Christine , Doerr Megan , Mounts Erin , Domenico Lisa , Petrie Tracy , Leachman Sancy A. , Trister Andrew D. , Bot Brian M. 
Published: February 2017

AbstractSensor-embedded phones are an emerging facilitator for participant-driven research studies. Skin cancer research is particularly amenable to this approach, as phone cameras enable self-examination and documentation of mole abnormalities that may signal a progression towards melanoma. Aggregation and open sharing of this participant-collected data can be foundational for research and the development of early cancer detection tools. Here we describe data from Mole Mapper, an iPhone-based observational study built using the Apple ResearchKit framework. The Mole Mapper app was designed to collect participant-provided images and measurements of moles, together with demographic and behavioral information relating to melanoma risk. The study cohort includes 2,069 participants who contributed 1,920 demographic surveys, 3,274 mole measurements, and 2,422 curated mole images. Survey data recapitulates associations between melanoma and known demographic risks, with red hair as the most significant factor in this cohort. Participant-provided mole measurements indicate an average mole size of 3.95 mm. These data have been made available to engage researchers in a collaborative, multidisciplinary effort to better understand and prevent melanoma.
Patterned transparent electrode with a continuous distribution of silver nanowires produced by an etching-free patterning method
Authors: Shin Kwonwoo , Park Ji Sun , Han Jong Hun , Choi Yunsu , Chung Dae Sung , Kim Se Hyun 
Published: February 2017

AbstractThe outstanding electrical, optical, and mechanical properties of silver nanowire transparent electrodes are attractive for use in many optoelectronic devices, and the recent developments related to these electrodes have led to their commercialization. To more fully utilize the advantages of this technology, developing new process technologies in addition to performance improvements is important. In this report, we propose a novel ultra-simple patterning technology to generate a silver nanowire transparent layer and a unique patterned structure with continuously distributed silver nanowires without any etched areas. The patterning is conducted by exposure to ultraviolet light and rinsing. The exposed and unexposed regions of the resulting layer have dramatically different electrical conductivities, which produces an electrical pathway without using any etching or lift-off processes. The unique patterned structure produced by this etching-free method creates hardly any optical difference between the two regions and results in excellent visibility of the patterned transparent electrode layer.
Ecological risk assessment on heavy metals in soils: Use of soil diffuse reflectance mid-infrared Fourier-transform spectroscopy
Authors: Wang Cheng , Li Wei , Guo Mingxing , Ji Junfeng 
Published: February 2017

AbstractThe bioavailability of heavy metals in soil is controlled by their concentrations and soil properties. Diffuse reflectance mid-infrared Fourier-transform spectroscopy (DRIFTS) is capable of detecting specific organic and inorganic bonds in metal complexes and minerals and therefore, has been employed to predict soil composition and heavy metal contents. The present study explored the potential of DRIFTS for estimating soil heavy metal bioavailability. Soil and corresponding wheat grain samples from the Yangtze River Delta region were analyzed by DRIFTS and chemical methods. Statistical regression analyses were conducted to correlate the soil spectral information to the concentrations of Cd, Cr, Cu, Zn, Pb, Ni, Hg and Fe in wheat grains. The principal components in the spectra influencing soil heavy metal bioavailability were identified and used in prediction model construction. The established soil DRIFTS-based prediction models were applied to estimate the heavy metal concentrations in wheat grains in the mid-Yangtze River Delta area. The predicted heavy metal concentrations of wheat grain were highly consistent with the measured levels by chemical analysis, showing a significant correlation (r2 > 0.72) with acceptable root mean square error RMSE. In conclusion, DRIFTS is a promising technique for assessing the bioavailability of soil heavy metals and related ecological risk.
Paenibacillus polymyxa NSY50 suppresses Fusarium wilt in cucumbers by regulating the rhizospheric microbial community
Authors: Shi Lu , Du Nanshan , Shu Sheng , Sun Jin , Li Shuzhan , Guo Shirong 
Published: February 2017

AbstractPaenibacillus polymyxa (P. polymyxa) NSY50, isolated from vinegar residue substrate, suppresses the growth of Fusarium oxysporum in the cucumber rhizosphere and protects the host plant from pathogen invasion. The aim of the present study was to evaluate the effects of NSY50 application on cucumber growth, soil properties and composition of the rhizospheric soil microbial community after exposure to Fusarium oxysporum. Bacterial and fungal communities were investigated by Illumina sequencing of the 16S rRNA gene and the internal transcribed spacer (ITS) regions (ITS1 and ITS2). The results showed that NSY50 effectively reduced the incidence of Fusarium wilt (56.4%) by altering the soil physico-chemical properties (e.g., pH, Cmic, Rmic, total N and Corg) and enzyme activities, especially of urease and β-glucosidase, which were significantly increased by 2.25- and 2.64-fold, respectively, relative to the pathogen treatment condition. More specifically, NSY50 application reduced the abundance of Fusarium and promoted potentially beneficial groups, including the Bacillus, Actinobacteria, Streptomyces, Actinospica, Catenulispora and Pseudomonas genera. Thus, our results suggest that NSY50 application can improve soil properties, shift the microbial community by increasing beneficial strains and decreasing pathogen colonization in the cucumber rhizosphere, and reduce the occurrence of cucumber Fusarium wilt, thereby promoting cucumber growth.
Pitfalls of invasive blood pressure monitoring using the caudal ventral artery in rats
Authors: Ohta Hiroki , Ohki Takao , Kanaoka Yuji , Koizumi Makoto , Okano Hirotaka J. 
Published: February 2017

AbstractDuring rodent experiments, the caudal ventral artery (CVA) is useful for blood pressure (BP) measurement. However, CVA measurements may not reflect the true BP. This study was performed to verify the site-specific accuracy of invasive arterial BP monitoring during surgery in rats. Invasive arterial BP was simultaneously measured in rats via the CVA and the common carotid artery (CCA). The BP values were analysed while the rats were subjected to cooling of the head or tail. Additionally, the rats underwent digital subtraction angiography and histological examination of these arteries. The pressure difference was more significant in the tail cooling group than in the head cooling group. Digital subtraction angiography revealed that angiospasms occurred more frequently in the CVA than in the CCA upon cooling. This phenomenon was supported by histological analysis, which showed that the tunica media area was significantly larger in the CVA than in the CCA. CVA pressure is susceptible to environmental changes and may not accurately reflect the true BP without a strictly controlled laboratory environment. Therefore, understanding the pitfalls of this method is necessary to avoid cooling of the tail during BP measurement.
Snapshot linear-Stokes imaging spectropolarimeter using division-of-focal-plane polarimetry and integral field spectroscopy
Authors: Mu Tingkui , Pacheco Shaun , Chen Zeyu , Zhang Chunmin , Liang Rongguang 
Published: February 2017

AbstractIn this paper, the design and experimental demonstration of a snapshot linear-Stokes imaging spectropolarimeter (SLSIS) is presented. The SLSIS, which is based on division-of-focal-plane polarimetry with four parallel linear polarization channels and integral field spectroscopy with numerous slit dispersive paths, has no moving parts and provides video-rate Stokes-vector hyperspectral datacubes. It does not need any scanning in the spectral, spatial or polarization dimension and offers significant advantages of rapid reconstruction without heavy computation during post-processing. The principle and the experimental setup of the SLSIS are described in detail. The image registration, Stokes spectral reconstruction and calibration procedures are included, and the system is validated using measurements of tungsten light and a static scene. The SLSIS’s snapshot ability to resolve polarization spectral signatures is demonstrated using measurements of a dynamic scene.
Polarisers in the focal domain: Theoretical model and experimental validation
Authors: Martínez-Herrero Rosario , Maluenda David , Juvells Ignasi , Carnicer Artur 
Published: February 2017

AbstractPolarisers are one of the most widely used devices in optical set-ups. They are commonly used with paraxial beams that propagate in the normal direction of the polariser plane. Nevertheless, the conventional projection character of these devices may change when the beam impinges a polariser with a certain angle of incidence. This effect is more noticeable if polarisers are used in optical systems with a high numerical aperture, because multiple angles of incidence have to be taken into account. Moreover, the non-transverse character of highly focused beams makes the problem more complex and strictly speaking, the Malus’ law does not apply. In this paper we develop a theoretical framework to explain how ideal polarisers affect the behavior of highly focused fields. In this model, the polarisers are considered as birefringent plates, and the vector behaviour of focused fields is described using the plane-wave angular spectrum approach. Experiments involving focused fields were conducted to verify the theoretical model and a satisfactory agreement between theoretical and experimental results was found.
Reference genes for quantitative real-time PCR analysis in symbiont Entomomyces delphacidicola of Nilaparvata lugens (Stål)
Authors: Wan Pin-Jun , Tang Yao-Hua , Yuan San-Yue , He Jia-Chun , Wang Wei-Xia , Lai Feng-Xiang , Fu Qiang 
Published: February 2017

AbstractNilaparvata lugens (Stål) (Hemiptera: Delphacidae) is a major rice pest that harbors an endosymbiont ascomycete fungus, Entomomyces delphacidicola str. NLU (also known as yeast-like symbiont, YLS). Driving by demand of novel population management tactics (e.g. RNAi), the importance of YLS has been studied and revealed, which greatly boosts the interest of molecular level studies related to YLS. The current study focuses on reference genes for RT-qPCR studies related to YLS. Eight previously unreported YLS genes were cloned, and their expressions were evaluated for N. lugens samples of different developmental stages and sexes, and under different nutritional conditions and temperatures. Expression stabilities were analyzed by BestKeeper, geNorm, NormFinder, ΔCt method and RefFinder. Furthermore, the selected reference genes for RT-qPCR of YLS genes were validated using targeted YLS genes that respond to different nutritional conditions (amino acid deprivation) and RNAi. The results suggest that ylsRPS15p/ylsACT are the most suitable reference genes for temporal gene expression profiling, while ylsTUB/ylsACT and ylsRPS15e/ylsGADPH are the most suitable reference gene choices for evaluating nutrition and temperature effects. Validation studies demonstrated the advantage of using endogenous YLS reference genes for YLS studies.
β-Thalassemia Patients Revealed a Significant Change of Untargeted Metabolites in Comparison to Healthy Individuals
Authors: Musharraf Syed Ghulam , Iqbal Ayesha , Ansari Saqib Hussain , Parveen Sadia , Khan Ishtiaq Ahmad , Siddiqui Amna Jabbar 
Published: February 2017

Abstractβ-Thalassemia is one of the most prevalent forms of congenital blood disorders characterized by reduced hemoglobin levels with severe complications, affecting all dimensions of life. The mechanisms underlying the phenotypic heterogeneity of β-thalassemia are still poorly understood. We aimed to work over metabolite biomarkers to improve mechanistic understanding of phenotypic heterogeneity and hence better management of disorder at different levels. Untargeted serum metabolites were analyzed after protein precipitation and SPE (solid phase extraction) from 100 β-thalassemia patients and 61 healthy controls using GC-MS. 40 metabolites were identified having a significance difference between these two groups at probability of 0.05 and fold change >1.5. Out of these 40 metabolites, 17 were up-regulated while 23 were down-regulated. PCA and PLS-DA model was also created that revealed a fine separation with a sensitivity of 70% and specificity of 100% on external validation of samples. Metabolic pathway analysis revealed alteration in multiple pathways including glycolysis, pyruvate, propanoate, glycerophospholipid, galactose, fatty acid, starch and sucrose metabolism along with fatty acid elongation in mitochondria, glycerolipid, glyoxylate and dicarboxylate metabolism pointing towards the shift of metabolism in β-thalassemia patients in comparison to healthy individuals.
Beat-to-Beat Blood Pressure and Two-dimensional (axial and radial) Motion of the Carotid Artery Wall: Physiological Evaluation of Arterial Stiffness
Authors: Xu Chenchu , Xiong Huahua , Gao Zhifan , Liu Xin , Zhang Heye , Zhang Yanping , Du Xiuquan , Wu Wanqing , Liu Guotao , Li Shuo 
Published: February 2017

AbstractThe physiological relationship between local arterial displacement and blood pressure (BP) plays an integral role in assess- ment of the mechanical properties of arteries. In this study, we used more advanced methods to obtain reliable continuous BP and the displacement of the common carotid artery (CCA) simultaneously. We propose a novel evaluation method for arterial stiffness that relies on determining the physiological relationship between the axial and radial displacements of the CCA wall and beat-to-beat BP. Patients (total of 138) were divided into groups according to the following three criteria: essential hyper- tension (EH) and normotension, male and female, elderly and younger. The Pearson correlation test and canonical correlation analysis showed that the CCA indices were significantly correlated with BP indices (r = 0:787;p < 0:05). The slope of the CCA displacement/pressure curve showed a progressive reduction with increasing age and EH disease occurrence (EH: 0.496 vs. normotension: 0.822;age <= 60:0.585 vs.age > 60:0.783). Our method provides an explicit reference value and relationship for the manner in which the CCA wall responds to changes in BP. Short-term and continuous BP were significantly correlated with CCA displacement and exhibited a close inverse relationship with each subject’s BP and EH, age, and systolic blood pressure.