bluuebunny/crossref_metadata_2025_split huggingface dataset:
An unexpected protein interaction promotes drug resistance in leukemia
Authors: Pitre Aaron , Ge Yubin , Lin Wenwei , Wang Yao , Fukuda Yu , Temirov Jamshid , Phillips Aaron H. , Peters Jennifer L. , Fan Yiping , Ma Jing , Nourse Amanda , Sinha Chandrima , Lin Hai , Kriwacki Richard , Downing James R. , Gruber Tanja A. , Centonze Victoria E. , Naren Anjaparavanda P. , Chen Taosheng , Schuetz John D. 
Published: November 2017

AbstractThe overall survival of patients with acute myeloid leukemia (AML) is poor and identification of new disease-related therapeutic targets remains a major goal for this disease. Here we show that expression of MPP1, a PDZ-domain-containing protein, highly correlated with ABCC4 in AML, is associated with worse overall survival in AML. Murine hematopoietic progenitor cells overexpressing MPP1 acquired the ability to serially replate in methylcellulose culture, a property crucially dependent upon ABCC4. The highly conserved PDZ-binding motif of ABCC4 is required for ABCC4 and MPP1 to form a protein complex, which increased ABCC4 membrane localization and retention, to enhance drug resistance. Specific disruption of this protein complex, either genetically or chemically, removed ABCC4 from the plasma membrane, increased drug sensitivity, and abrogated MPP1-dependent hematopoietic progenitor cell replating in methylcellulose. High-throughput screening identified Antimycin A as a small molecule that disrupted the ABCC4–MPP1 protein complex and reversed drug resistance in AML cell lines and in primary patient AML cells. In all, targeting the ABCC4–MPP1 protein complex can lead to new therapies to improve treatment outcome of AML, a disease where the long-term prognosis is poor.
Comparative genomic analysis of esophageal squamous cell carcinoma between Asian and Caucasian patient populations
Authors: Deng Jiaying , Chen Hu , Zhou Daizhan , Zhang Junhua , Chen Yun , Liu Qi , Ai Dashan , Zhu Hanting , Chu Li , Ren Wenjia , Zhang Xiaofei , Xia Yi , Sun Menghong , Zhang Huiwen , Li Jun , Peng Xinxin , Li Liang , Han Leng , Lin Hui , Cai Xiujun , Xiang Jiaqing , Chen Shufeng , Sun Yihua , Zhang Yawei , Zhang Jie , Chen Haiquan , Zhang Shijian , Zhao Yi , Liu Yun , Liang Han , Zhao Kuaile 
Published: November 2017

AbstractEsophageal squamous cell carcinoma is a major histological type of esophageal cancer, with distinct incidence and survival patterns among races. Although previous studies have characterized somatic mutations in this disease, a rigorous comparison between different patient populations has not been conducted. Here we sequence the samples of 316 Chinese patients, combine them with those from The Cancer Genome Atlas, and perform a comparative analysis between Asian and Caucasian patients. We find that mutated CSMD3 is associated with better prognosis in Asian patients. Applying a robust computational strategy that adjusts for both technical and biological confounding factors, we find that TP53, EP300, and NFE2L2 show higher mutational frequencies in Asian patients. Moreover, NFE2L2 mutations correlate with the allele status of a nearby high-Fst SNP, suggesting their potential interaction. Our study provides insights into the molecular basis underlying the striking racial disparities of this disease, and represents a general computational framework for such a cross-population comparison.
Giant magnetic splitting inducing near-unity valley polarization in van der Waals heterostructures
Authors: Nagler Philipp , Ballottin Mariana V. , Mitioglu Anatolie A. , Mooshammer Fabian , Paradiso Nicola , Strunk Christoph , Huber Rupert , Chernikov Alexey , Christianen Peter C. M. , Schüller Christian , Korn Tobias 
Published: November 2017

AbstractMonolayers of semiconducting transition metal dichalcogenides exhibit intriguing fundamental physics of strongly coupled spin and valley degrees of freedom for charge carriers. While the possibility of exploiting these properties for information processing stimulated concerted research activities towards the concept of valleytronics, maintaining control over spin–valley polarization proved challenging in individual monolayers. A promising alternative route explores type II band alignment in artificial van der Waals heterostructures. The resulting formation of interlayer excitons combines the advantages of long carrier lifetimes and spin–valley locking. Here, we demonstrate artificial design of a two-dimensional heterostructure enabling intervalley transitions that are not accessible in monolayer systems. The resulting giant effective g factor of −15 for interlayer excitons induces near-unity valley polarization via valley-selective energetic splitting in high magnetic fields, even after nonselective excitation. Our results highlight the potential to deterministically engineer novel valley properties in van der Waals heterostructures using crystallographic alignment.
In situ detection of the protein corona in complex environments
Authors: Carril Monica , Padro Daniel , del Pino Pablo , Carrillo-Carrion Carolina , Gallego Marta , Parak Wolfgang J. 
Published: November 2017

AbstractColloidal nanoparticles (NPs) are a versatile potential platform for in vivo nanomedicine. Inside blood circulation, NPs may undergo drastic changes, such as by formation of a protein corona. The in vivo corona cannot be completely emulated by the corona formed in blood. Thus, in situ detection in complex media, and ultimately in vivo, is required. Here we present a methodology for determining protein corona formation in complex media. NPs are labeled with 19F and their diffusion coefficient measured using 19F diffusion-ordered nuclear magnetic resonance (NMR) spectroscopy. 19F diffusion NMR measurements of hydrodynamic radii allow for in situ characterization of NPs in complex environments by quantification of protein adsorption to the surface of NPs, as determined by increase in hydrodynamic radius. The methodology is not optics based, and thus can be used in turbid environments, as in the presence of cells.
Transcriptional profiling provides new insights into the role of nitric oxide in enhancing Ganoderma oregonense resistance to heat stress
Authors: Chen Cheng , Li Qiang , Wang Qiangfeng , Lu Daihua , Zhang Hong , Wang Jian , Fu Rongtao 
Published: November 2017

AbstractGanoderma is well known for its use in traditional Chinese medicine and is widely cultivated in China, Korea, and Japan. Increased temperatures associated with global warming are negatively influencing the growth and development of Ganoderma. Nitric oxide is reported to play an important role in alleviating fungal heat stress (HS). However, the transcriptional profiling of Ganoderma oregonense in response to HS, as well as the transcriptional response regulated by NO to cope with HS has not been reported. We used RNA-Seq technology to generate large-scale transcriptome data from G. oregonense mycelia subjected to HS (32 °C) and exposed to concentrations of exogenous NO. The results showed that heat shock proteins (HSPs), “probable stress-induced proteins”, and unigenes involved in “D-amino-acid oxidase activity” and “oxidoreductase activity” were significantly up-regulated in G. oregonense subjected to HS (P < 0.05). The significantly up-regulated HSPs, “monooxygenases”, “alcohol dehydrogenase”, and “FAD/NAD(P)-binding domain-containing proteins” (P < 0.05) regulated by exogenous NO may play important roles in the enhanced HS tolerance of G. oregonense. These results provide insights into the transcriptional response of G. oregonense to HS and the mechanism by which NO enhances the HS tolerance of fungi at the gene expression level.
Systematic characterization of the effect of Ag@TiO2 nanoparticles on the performance of plasmonic dye-sensitized solar cells
Authors: Nbelayim Pascal , Kawamura Go , Kian Tan Wai , Muto Hiroyuki , Matsuda Atsunori 
Published: November 2017

AbstractThe use of plasmonic nanoparticles (NPs) in dye-sensitized solar cells (DSSCs) in an effort to enhance their power conversion efficiencies (PCEs) increases light absorbance of the cells but also affect their electron dynamics. This has contributed to the failure of plasmonic NPs to make the expected high impact of PCE enhancement. Herein, we investigated the wide range effects of plasmonic NPs on the performance of DSSCs, using extended characterization and a systematic approach. We prepared DSSCs using Ag@TiO2 NPs-doped TiO2 photoanodes. Using a wide range doping concentration, we obtained panchromatic enhancement effect with two optimal doping concentrations (0.1 and 1 wt. %).They enhanced PCE via mainly: a) optimal band alignment for efficient charge injection; and b) a balance of the negative and positive effects of plasmonic NPs on cell performance parameters (open circuit voltage, fill factor, charge transfer resistance against recombination, electron life time and charge collection efficiency); respectively. The PCE of the pristine sample increased from 4.66 to 4.88 and 5.00% via these 2 routes, respectively. The major cause of not obtaining very high PCE was charge recombination from high charge density. Thus, these observations might serve as invaluable guidance for the preparation of highly efficient plasmonic DSSCs.
Deposition of topological silicene, germanene and stanene on graphene-covered SiC substrates
Authors: Matusalem Filipe , Koda Daniel S. , Bechstedt Friedhelm , Marques Marcelo , Teles Lara K. 
Published: November 2017

AbstractGrowth of X-enes, such as silicene, germanene and stanene, requires passivated substrates to ensure the survival of their exotic properties. Using first-principles methods, we study as-grown graphene on polar SiC surfaces as suitable substrates. Trilayer combinations with coincidence lattices with large hexagonal unit cells allow for strain-free group-IV monolayers. In contrast to the Si-terminated SiC surface, van der Waals-bonded honeycomb X-ene/graphene bilayers on top of the C-terminated SiC substrate are stable. Folded band structures show Dirac cones of the overlayers with small gaps of about 0.1 eV in between. The topological invariants of the peeled-off X-ene/graphene bilayers indicate the presence of topological character and the existence of a quantum spin Hall phase.
Variations in nutrient and trace element composition of rice in an organic rice-frog coculture system
Authors: Sha Zhimin , Chu Qingnan , Zhao Zheng , Yue Yubo , Lu Linfang , Yuan Jing , Cao Linkui 
Published: November 2017

AbstractIntroducing frogs into paddy fields can control pests and diseases, and organic farming can improve soil fertility and rice growth. The aim of this 2-year field study was compare the yield and elemental composition of rice between an organic farming system including frogs (ORF) and a conventional rice culture system (CR). The grain yields were almost the same in the ORF system and the CR system. The ORF significantly increased the contents of phosphorus (P), ion (Fe), zinc (Zn), molybdenum (Mo) and selenium (Se) in rice grain at one or both years. However, the ORF system decreased the calcium (Ca) content in grice grains, and increased the concentration of cadmium, which is potentially toxic. A principal components analysis showed the main impacts of ORF agro-ecosystem on the rice grain ionome was to increase the concentration of P and trace metal(loid)s. The results showed that the ORF system is an ecologically, friendly strategy to avoid excessive use of chemical fertilizers, herbicides and pesticides without decreasing yields, and to improve the nutritional status of rice by increasing the micronutrient contents. The potential risks of increasing Cd contents in rice grain should be addressed if this cultivation pattern is used in the long term.
How gluttonous cell aggregates clear substrates coated with microparticles
Authors: Beaune Grégory , Lam Andy Y. W. , Dufour Sylvie , Winnik Françoise M. , Brochard-Wyart Françoise 
Published: November 2017

AbstractWe study the spreading of cell aggregates deposited on adhesive substrates decorated with microparticles (MPs). A cell monolayer expands around the aggregate. The cells on the periphery of the monolayer take up the MPs, clearing the substrate as they progress and forming an aureole of cells filled with MPs. We study the dynamics of spreading and determine the width of the aureole and the level of MP internalization in cells as a function of MP size, composition, and density. From the radius and width of the aureole, we quantify the volume fraction of MPs within the cell, which leads to an easy, fast, and inexpensive measurement of the cell – particle internalization.
Observation of dielectric universalities in albumin, cytochrome C and Shewanella oneidensis MR-1 extracellular matrix
Authors: Motovilov K. A. , Savinov M. , Zhukova E. S. , Pronin A. A. , Gagkaeva Z. V. , Grinenko V. , Sidoruk K. V. , Voeikova T. A. , Barzilovich P. Yu. , Grebenko A. K. , Lisovskii S. V. , Torgashev V. I. , Bednyakov P. , Pokorný J. , Dressel M. , Gorshunov B. P. 
Published: November 2017

AbstractThe electrodynamics of metals is well understood within the Drude conductivity model; properties of insulators and semiconductors are governed by a gap in the electronic states. But there is a great variety of disordered materials that do not fall in these categories and still respond to external field in an amazingly uniform manner. At radiofrequencies delocalized charges yield a frequency-independent conductivity σ1(ν) whose magnitude exponentially decreases while cooling. With increasing frequency, dispersionless conductivity starts to reveal a power-law dependence σ1(ν)∝ν
s
with s < 1 caused by hopping charge carriers. At low temperatures, such Universal Dielectric Response can cross over to another universal regime with nearly constant loss ε″∝σ1/ν = const. The powerful research potential based on such universalities is widely used in condensed matter physics. Here we study the broad-band (1–1012 Hz) dielectric response of Shewanella oneidensis MR-1 extracellular matrix, cytochrome C and serum albumin. Applying concepts of condensed matter physics, we identify transport mechanisms and a number of energy, time, frequency, spatial and temperature scales in these biological objects, which can provide us with deeper insight into the protein dynamics.
Cat-D: a targeted sequencing method for the simultaneous detection of small DNA mutations and large DNA deletions with flexible boundaries
Authors: Hong Ru , Chandola Udita , Zhang Li-Feng 
Published: November 2017

AbstractWe developed a targeted DNA sequencing method that is capable of detecting a comprehensive panel of DNA mutations including small DNA mutations and large DNA deletions with unknown/flexible boundaries. The method directly identifies the large DNA deletions (Cat-D) without relying on sequencing coverage to make the genotype calls. We performed the method to simultaneously detect 10 small DNA mutations in β-thalassemia and 2 large genomic deletions in α-thalassemia from 10 genomic DNA samples. Cat-D was performed on 8 genomic DNA samples in duplicate. The 18 Cat-D samples were combined in one sequencing run. In total, 216 genotype calls were made, and 215 of the genotype calls were accurate. No false negative genotype calls were made. One false positive genotype call was made on one target mutation in one experimental duplicate from a genomic DNA sample. In summary, Cat-D can be developed into a robust, high-throughput and cost-effective method suitable for population-based carrier screens.
Structure of FlgK reveals the divergence of the bacterial Hook-Filament Junction of Campylobacter
Authors: Bulieris Paula V. , Shaikh Nausad H. , Freddolino Peter L. , Samatey Fadel A. 
Published: November 2017

AbstractEvolution of a nano-machine consisting of multiple parts, each with a specific function, is a complex process. A change in one part should eventually result in changes in other parts, if the overall function is to be conserved. In bacterial flagella, the filament and the hook have distinct functions and their respective proteins, FliC and FlgE, have different three-dimensional structures. The filament functions as a helical propeller and the hook as a flexible universal joint. Two proteins, FlgK and FlgL, assure a smooth connectivity between the hook and the filament. Here we show that, in Campylobacter, the 3D structure of FlgK differs from that of its orthologs in Salmonella and Burkholderia, whose structures have previously been solved. Docking the model of the FlgK junction onto the structure of the Campylobacter hook provides some clues about its divergence. These data suggest how evolutionary pressure to adapt to structural constraints, due to the structure of Campylobacter hook, causes divergence of one element of a supra-molecular complex in order to maintain the function of the entire flagellar assembly.
Enforced GFI1 expression impedes human and murine leukemic cell growth
Authors: Hönes Judith M. , Thivakaran Aniththa , Botezatu Lacramioara , Patnana Pradeep , Castro Symone Vitoriano da Conceição , Al-Matary Yahya S. , Schütte Judith , Fischer Karen B. I. , Vassen Lothar , Görgens André , Dührsen Ulrich , Giebel Bernd , Khandanpour Cyrus 
Published: November 2017

AbstractThe differentiation of haematopoietic cells is regulated by a plethora of so-called transcription factors (TFs). Mutations in genes encoding TFs or graded reduction in their expression levels can induce the development of various malignant diseases such as acute myeloid leukaemia (AML). Growth Factor Independence 1 (GFI1) is a transcriptional repressor with key roles in haematopoiesis, including regulating self-renewal of haematopoietic stem cells (HSCs) as well as myeloid and lymphoid differentiation. Analysis of AML patients and different AML mouse models with reducedGFI1gene expression levels revealed a direct link between low GFI1 protein level and accelerated AML development and inferior prognosis. Here, we report that upregulated expression ofGFI1in several widely used leukemic cell lines inhibits their growth and decreases the ability to generate coloniesin vitro. Similarly, elevated expression ofGFI1impedes thein vitroexpansion of murine pre-leukemic cells. Using a humanized AML model, we demonstrate that upregulation ofGFI1expression leads to myeloid differentiation morphologically and immunophenotypically, increased level of apoptosis and reduction in number of cKit+cells. These results suggest that increasing GFI1 level in leukemic cells with lowGFI1expression level could be a therapeutic approach.
Splenic glucocorticoid resistance following psychosocial stress requires physical injury
Authors: Foertsch Sandra , Füchsl Andrea M. , Faller Sandra D. , Hölzer Hannah , Langgartner Dominik , Messmann Joanna , Strauß Gudrun , Reber Stefan O. 
Published: November 2017

AbstractMice exposed to chronic subordinate colony housing (CSC) stress show glucocorticoid (GC) resistance of in vitro lipopolysaccharide (LPS)-stimulated splenocytes, increased anxiety and colitis. Similar effects were reported in wounded mice exposed to social disruption (SDR). Here we show that CSC exposure induced GC resistance in isolated and in vitro LPS-stimulated, but not unstimulated, splenocytes, and these effects were absent when CD11b+ splenocytes were depleted. Moreover, re-active coping behaviour during CSC correlated with the attacks and bites received by the resident, which in turn highly correlated with the dimension of splenic GC resistance, as with basal and LPS-induced in vitro splenocyte viability. Importantly, social stress promoted spleen cell activation, independent of bite wounds or CD11b+/CD11b− cell phenotype, whereas GC resistance was dependent on both bite wounds and the presence of CD11b+ cells. Together, our findings indicate that the mechanisms underlying splenic immune activation and GC resistance following social stress in male mice are paradigm independent and, to a large extent, dependent on wounding, which, in turn, is associated with a re-active coping style.
Nitrogen-related intermediate band in P-rich GaNxPyAs1−x−y alloys
Authors: Zelazna K. , Gladysiewicz M. , Polak M. P. , Almosni S. , Létoublon A. , Cornet C. , Durand O. , Walukiewicz W. , Kudrawiec R. 
Published: November 2017

AbstractThe electronic band structure of phosphorus-rich GaNxPyAs1−x−y alloys (x ~ 0.025 and y ≥ 0.6) is studied experimentally using optical absorption, photomodulated transmission, contactless electroreflectance, and photoluminescence. It is shown that incorporation of a few percent of N atoms has a drastic effect on the electronic structure of the alloys. The change of the electronic band structure is very well described by the band anticrossing (BAC) model in which localized nitrogen states interact with the extended states of the conduction band of GaAsP host. The BAC interaction results in the formation of a narrow intermediate band (E− band in BAC model) with the minimum at the Γ point of the Brillouin zone resulting in a change of the nature of the fundamental band gap from indirect to direct. The splitting of the conduction band by the BAC interaction is further confirmed by a direct observation of the optical transitions to the E+ band using contactless electroreflectance spectroscopy.
Drosophila muscles regulate the immune response against wasp infection via carbohydrate metabolism
Authors: Yang Hairu , Hultmark Dan 
Published: November 2017

AbstractWe recently found that JAK/STAT signaling in skeletal muscles is important for the immune response of Drosophila larvae against wasp infection, but it was not clear how muscles could affect the immune response. Here we show that insulin signaling is required in muscles, but not in fat body or hemocytes, during larval development for an efficient encapsulation response and for the formation of lamellocytes. This effect requires TOR signaling. We show that muscle tissue affects the immune response by acting as a master regulator of carbohydrate metabolism in the infected animal, via JAK/STAT and insulin signaling in the muscles, and that there is indirect positive feedback between JAK/STAT and insulin signaling in the muscles. Specifically, stimulation of JAK/STAT signaling in the muscles can rescue the deficient immune response when insulin signaling is suppressed. Our results shed new light on the interaction between metabolism, immunity, and tissue communication.
Correlations and forecast of death tolls in the Syrian conflict
Authors: Fujita Kazuki , Shinomoto Shigeru , Rocha Luis E. C. 
Published: November 2017

AbstractThe Syrian armed conflict has been ongoing since 2011 and has already caused thousands of deaths. The analysis of death tolls helps to understand the dynamics of the conflict and to better allocate resources and aid to the affected areas. In this article, we use information on the daily number of deaths to study temporal and spatial correlations in the data, and exploit this information to forecast events of deaths. We found that the number of violent deaths per day in Syria varies more widely than that in England in which non-violent deaths dominate. We have identified strong positive auto-correlations in Syrian cities and non-trivial cross-correlations across some of them. The results indicate synchronization in the number of deaths at different times and locations, suggesting respectively that local attacks are followed by more attacks at subsequent days and that coordinated attacks may also take place across different locations. Thus the analysis of high temporal resolution data across multiple cities makes it possible to infer attack strategies, warn potential occurrence of future events, and hopefully avoid further deaths.