bluuebunny/crossref_metadata_2025 huggingface dataset:
Retro-inverso Urokinase Receptor Antagonists for the Treatment of Metastatic Sarcomas
Authors: Carriero Maria Vincenza , Bifulco Katia , Ingangi Vincenzo , Costantini Susan , Botti Giovanni , Ragone Concetta , Minopoli Michele , Motti Maria Letizia , Rea Domenica , Scognamiglio Giosuè , Botti Gerardo , Arra Claudio , Ciliberto Gennaro , Pessi Antonello
Published: April 2017

The development of metastases is a multistep process that requires the activation of physiological and biochemical processes that govern migration, invasion and entry of metastatic cells into blood vessels. The urokinase receptor (uPAR) promotes cell migration by interacting with the Formyl Peptide Receptors (FPRs). Since both uPAR and FPR1 are involved in tumor progression, the uPAR-FPR1 interaction is an attractive therapeutic target. We previously described peptide antagonists of the uPAR-FPR1 interaction that inhibited cell migration and angiogenesis. To develop enzyme-resistant analogues, we applied here the Retro-Inverso (RI) approach, whereby the topology of the side chains is maintained by inverting the sequence of the peptide and the chirality of all residues. Molecular dynamics suggests that peptide RI-3 adopts the turn structure typical of uPAR-FPR1 antagonists. Accordingly, RI-3 is a nanomolar competitor of N-formyl-Met-Leu-Phe for binding to FPR1 and inhibits migration, invasion, trans-endothelial migration of sarcoma cells and VEGF-triggered endothelial tube formation. When sarcoma cells were subcutaneously injected in nude mice, tumor size, intra-tumoral microvessel density, circulating tumor cells and pulmonary metastases were significantly reduced in animals treated daily with 6 mg/Kg RI-3 as compared to animals treated with vehicle only. Thus, RI-3 represents a promising lead for anti-metastatic drugs.
Estrogen deficiency accelerates lumbar facet joints arthritis
Authors: Chen Hao , Zhu Hai , Zhang Kai , Chen Kangwu , Yang Huilin
Published: April 2017

Dramatic increase in the prevalence of lumbar facet joint (LFJ) arthritis in women around the age of menopause indicates a protective role for estrogen in LFJ arthritis. To date, there is no evidence for this indication and the mechanism of such an effect remains poorly understood. In this study, ovariectomized (OVX) mice were used to mimic the estrogen-deficient status of post-menopausal women. Micro-CT and immunohistochemistry was employed to assess the morphological and molecular changes in ovariectomy-induced LFJ arthritis. The results show that the LFJ subchondral bone mass was significantly decreased in OVX mice, with increased cavities on the interface of the subchondral bone. Severe cartilage degradation was observed in ovariectomy-induced LFJ arthritis. Increased blood vessels and innervations were also found in degenerated LFJ, particularly in the subchondral bone area. 17β-Estradiol treatment efficiently suppressed LFJ subchondral bone turnover, markedly inhibited cartilage degradation, and increased blood vessel and nerve ending growth in degenerated LFJ in OVX mice. Our study reveals that estrogen is a key factor in regulating LFJ metabolism. Severe LFJ degeneration occurs when estrogen is absent in vivo. Collapsed subchondral bone may be the initiation of this process, and estrogen replacement therapy can effectively prevent degeneration of LFJ under estrogen-deficient conditions.
Analysis of biofilm bacterial communities under different shear stresses using size-fractionated sediment
Authors: Fang Hongwei , Chen Yishan , Huang Lei , He Guojian
Published: April 2017

Microorganisms are ubiquitous in aqueous environments and are crucial for biogeochemical processes, but their community structures and functions remain poorly understood. In this paper, a rotating reactor was designed to study the effects of substrata and flow conditions on sediment bacterial communities using 16S rRNA gene sequencing, assaying three groups of size-fractionated sediments and three different levels of applied shear stress. Proteobacteria, Firmicutes, and Bacteroidetes were the dominant phyla of the microbial communities, with more anaerobic bacteria and opportunistic pathogens being detected under static water conditions, while more aerobic bacteria were detected under dynamic water flow conditions. Most of the top 10 genera were present in all the samples; however, there were significant differences in the species abundance. Paludibacter and Comamonadaceae_unclassified were the most abundant genera under static and dynamic conditions, respectively. Under static water conditions, the medium-grained sediment had the highest microbial diversity, followed by the fine and coarse sediments. Under dynamic water flow conditions, a higher flow velocity corresponded to a greater microbial diversity. Overall, there was no significant difference in the community richness or diversity between the static and dynamic water flow conditions. This study is beneficial for further understanding the heterogeneities of microbial communities in natural aquatic ecosystems.
Control of in vivo ictogenesis via endogenous synaptic pathways
Authors: Luna-Munguia Hiram , Starski Phillip , Chen Wu , Gliske Stephen , Stacey William C.
Published: April 2017

The random nature of seizures poses difficult challenges for epilepsy research. There is great need for a reliable method to control the pathway to seizure onset, which would allow investigation of the mechanisms of ictogenesis and optimization of treatments. Our hypothesis is that increased random afferent synaptic activity (i.e. synaptic noise) within the epileptic focus is one endogenous method of ictogenesis. Building upon previous theoretical and in vitro work showing that synaptic noise can induce seizures, we developed a novel in vivo model of ictogenesis. By increasing the excitability of afferent connections to the hippocampus, we control the risk of temporal lobe seizures during a specific time period. The afferent synaptic activity in the hippocampus was modulated by focal microinjections of potassium chloride into the nucleus reuniens, during which the risk of seizure occurrence increased substantially. The induced seizures were qualitatively and quantitatively indistinguishable from spontaneous ones. This model thus allows direct control of the temporal lobe seizure threshold via endogenous pathways, providing a novel tool in which to investigate the mechanisms and biomarkers of ictogenesis, test for seizure threshold, and rapidly tune antiseizure treatments.
Activation of the ileal neuroendocrine tumor cell line P-STS by acetylcholine is amplified by histamine: role of H3R and H4R
Authors: Pfanzagl Beatrix , Mechtcheriakova Diana , Meshcheryakova Anastasia , Aberle Stephan W. , Pfragner Roswitha , Jensen-Jarolim Erika
Published: April 2017

Neuroendocrine tumors may present with pseudoallergic reactions like diarrhea and idiopathic anaphylaxis. Here we present the P-STS human ileal neuroendocrine cell line as a model cell line for these tumors. Neuroendocrine markers and changes in cytoplasmic calcium concentration ([Ca2+]i) in response to several possible activators of 5-hydroxytryptamine (﻿5-HT) release were analyzed. P-STS cells still expressed chromogranin A and synaptophysin after 2 years of culture. Tryptophan hydroxylase 1 mRNA and a low amount of 5-HT were also detected. Acetylcholine (ACh) caused a rise in [Ca2+]i. Somatostatin inhibited, whereas histamine (HA) but not the HA receptor ligand betahistine enhanced activation by ACh. The [Ca2+]iresponse to ACh/HA was inhibited by the HA receptor H3 (H3R) agonist methimepip and by the antidepressant imipramine. Further [Ca2+]iresponse studies indicated the presence of H4Rs and of a functional calcium sensing receptor. High or low affinity IgE receptor protein or mRNA were not detected. Taken together, neuroendocrine markers and response to intestinal neurotransmitters approve the P-STS cell line as a valuable model for enterochromaffin cells. Enhancement of their ACh-induced pro-secretory response by HA, with a role for H3R and H4R, suggests an amplifying role of neuroendocrine cells in allergen-induced diarrhea or anaphylaxis.
Lentinan from shiitake selectively attenuates AIM2 and non-canonical inflammasome activation while inducing pro-inflammatory cytokine production
Authors: Ahn Huijeong , Jeon Eunsaem , Kim Jin-Chul , Kang Seung Goo , Yoon Sung-il , Ko Hyun-Jeong , Kim Pyeung-Hyeun , Lee Geun-Shik
Published: April 2017

Lentinan extracted from shiitake (Lentinula edodes) is a β-glucan that has been reported as an intravenous anti-tumor polysaccharide via enhancement of the host immune system. In this study, we determined the effect of lentinan on inflammasome activation, a multi-protein platform, in myeloid cells. Mouse bone marrow-derived macrophages were treated with lentinan with/without inflammasome triggers, and maturation of interleukin (IL)-1β, IL-18, or caspase-1 was measured as a readout of inflammasome activation. As a result, lentinan selectively inhibited absent in melanoma 2 (AIM2) inflammasome activation. In addition, lentinan up-regulated pro-inflammatory cytokines and induced expression of inflammasome-related genes through toll-like receptor 4 signaling. Furthermore, we assessed the effect of lentinan on mice treated with Listeria monocytogenes or lipopolysaccharide as an AIM2 or non-canonical inflammasome-mediated model. Lentinan attenuated IL-1β secretion resulting from Listeria-mediated AIM2 inflammasome activation and reduced endotoxin lethality via inhibition of non-canonical inflammasome activation. Thus, lentinan is suggested as an anti-AIM2 and anti-non-canonical inflammasome candidate despite its up-regulation of cytokine expression.
Paleochannel and beach-bar palimpsest topography as initial substrate for coralligenous buildups offshore Venice, Italy
Authors: Tosi Luigi , Zecchin Massimo , Franchi Fulvio , Bergamasco Andrea , Da Lio Cristina , Baradello Luca , Mazzoli Claudio , Montagna Paolo , Taviani Marco , Tagliapietra Davide , Carol Eleonora , Franceschini Gianluca , Giovanardi Otello , Donnici Sandra
Published: April 2017

We provide a model for the genesis of Holocene coralligenous buildups occurring in the northwestern Adriatic Sea offshore Venice at 17–24 m depth. High-resolution geophysical surveys and underwater SCUBA diving reconnaissance revealed meandering shaped morphologies underneath bio-concretionned rocky buildups. These morphologies are inferred to have been inherited from Pleistocene fluvial systems reactivated as tidal channels during the post- Last Glacial Maximum transgression, when the study area was a lagoon protected by a sandy barrier. The lithification of the sandy fossil channel-levee systems is estimated to have occurred at ca. 7 cal. ka BP, likely due to the interaction between marine and less saline fluids related to onshore freshwater discharge at sea through a sealed water-table. The carbonate-cemented sandy layers served as nucleus for subsequent coralligenous buildups growth.
Accelerated crystallization of colloidal glass by mechanical oscillation
Authors: Nakamura Nobutomo , Inayama Kyosuke , Okuno Tasuku , Ogi Hirotsugu , Hirao Masahiko
Published: April 2017

Crystallization of a hard-sphere colloidal glass by mechanical oscillation is investigated, and accelerated crystallization is found at a specific frequency. The crystallization frequency increases as attractive force between particles increases, indicating that interparticle interaction affects the crystallization frequency. Time scale of the mechanical oscillation is different from that of the slow relaxation, and notable relationship with the low-frequency mode is not observed. The experimental results are not explained by the previously proposed model for crystallization by oscillatory shear. Conversely, we speculate that activations of the fast relaxation and particle motion in crystal-like clusters are possible causes of the observations.
Risk of death from cardiovascular disease following breast cancer in Southeast Asia: a prospective cohort study
Authors: Gernaat S. A. M. , Ho P. J. , Rijnberg N. , Lee S. C. , Lim S. H. , Yap Y. S. , Grobbee D. E. , Hartman M. , Verkooijen H. M.
Published: April 2017

Breast cancer incidence and survival is high in Southeast Asia. As such, many women diagnosed with breast cancer are at risk of dying of other causes. Given the increased risk of cardiotoxicity induced by breast cancer treatments, it is important to identify patients at high risk of cardiovascular disease (CVD) mortality. The aim of this study was to investigate if this risk varies by age and ethnicity. Patient details were obtained from 5,868 Chinese, Malay, and Indian women diagnosed with in situ or non-metastasized invasive breast cancer at the National University Hospital of Singapore and KK Women’s and Children’s Hospital in Singapore. Death causes were obtained from the National Registry of Births and Deaths. Flexible parametric survival models estimated CVD mortality rates and hazard ratios. During a median follow-up of six years, 1,010 deaths occurred of which 6.8% were due to CVD. CVD mortality rates of older women peaked within the first year following diagnosis and increased over time since diagnosis. Indian had more than double the risk of CVD mortality than Chinese, independent of age at diagnosis and stage. Taking ethnicity and age into account may promote CVD risk stratification and management in (Southeast Asian) women with breast cancer.
Gravimetric sensors operating at 1.1 GHz based on inclined c-axis ZnO grown on textured Al electrodes
Authors: Rughoobur Girish , DeMiguel-Ramos Mario , Escolano José-Miguel , Iborra Enrique , Flewitt Andrew John
Published: April 2017

Shear mode solidly mounted resonators (SMRs) are fabricated using an inclined c-axis ZnO grown on a rough Al electrode. The roughness of the Al surface is controlled by changing the substrate temperature during the deposition process to promote the growth of inclined ZnO microcrystals. The optimum substrate temperature to obtain homogeneously inclined c-axis grains in ZnO films is achieved by depositing Al at 100 °C with a surface roughness ~9.2 nm, which caused an inclination angle of ~25° of the ZnO c-axis with respect to the surface normal. Shear mode devices with quality-factors at resonance, Qr and effective electromechanical coupling factors, $${{\boldsymbol{k}}}_{{\bf{eff}}}^{{\bf{2}}}$$

k

eff

2

, as high as 180 and 3.4% are respectively measured. Mass sensitivities, Sm of (4.9 ± 0.1) kHz · cm2/ng and temperature coefficient of frequency (TCF) of ~−67 ppm/K are obtained using this shear mode. The performance of the devices as viscosity sensors and biosensors is demonstrated by determining the frequency shifts of water-ethanol mixtures and detection of Rabbit immunoglobin G (IgG) whole molecule (H&L) respectively.
Improved Analytical Sensitivity of Lateral Flow Assay using Sponge for HBV Nucleic Acid Detection
Authors: Tang Ruihua , Yang Hui , Gong Yan , Liu Zhi , Li XiuJun , Wen Ting , Qu ZhiGuo , Zhang Sufeng , Mei Qibing , Xu Feng
Published: April 2017

Hepatitis B virus (HBV) infection is a serious public health problem, which can be transmitted through various routes (e.g., blood donation) and cause hepatitis, liver cirrhosis and liver cancer. Hence, it is necessary to do diagnostic screening for high-risk HBV patients in these transmission routes. Nowadays, protein-based technologies have been used for HBV testing, which however involve the issues of large sample volume, antibody instability and poor specificity. Nucleic acid hybridization-based lateral flow assay (LFA) holds great potential to address these limitations due to its low-cost, rapid, and simple features, but the poor analytical sensitivity of LFA restricts its application. In this study, we developed a low-cost, simple and easy-to-use method to improve analytical sensitivity by integrating sponge shunt into LFA to decrease the fluid flow rate. The thickness, length and hydrophobicity of the sponge shunt were sequentially optimized, and achieved 10-fold signal enhancement in nucleic acid testing of HBV as compared to the unmodified LFA. The enhancement was further confirmed by using HBV clinical samples, where we achieved the detection limit of 103 copies/ml as compared to 104 copies/ml in unmodified LFA. The improved LFA holds great potential for diseases diagnostics, food safety control and environment monitoring at point-of-care.
Forest cover mapping in post-Soviet Central Asia using multi-resolution remote sensing imagery
Authors: Yin He , Khamzina Asia , Pflugmacher Dirk , Martius Christopher
Published: April 2017

Despite rapid advances and large-scale initiatives in forest mapping, reliable cross-border information about the status of forest resources in Central Asian countries is lacking. We produced consistent Central Asia forest cover (CAFC) maps based on a cost-efficient approach using multi-resolution satellite imagery from Landsat and MODIS during 2009–2011. The spectral-temporal metrics derived from 2009–2011 Landsat imagery (overall accuracy of 0.83) was used to predict sub-pixel forest cover on the MODIS scale for 2010. Accuracy assessment confirmed the validity of MODIS-based forest cover map with a normalized root-mean-square error of 0.63. A general paucity of forest resources in post-Soviet Central Asia was indicated, with 1.24% of the region covered by forest. In comparison to the CAFC map, a regional map derived from MODIS Vegetation Continuous Fields tended to underestimate forest cover, while the Global Forest Change product matched well. The Global Forest Resources Assessments, based on individual country reports, overestimated forest cover by 1.5 to 147 times, particularly in the more arid countries of Turkmenistan and Uzbekistan. Multi-resolution imagery contributes to regionalized assessment of forest cover in the world’s drylands while developed CAFC maps (available at https://data.zef.de/) aim to facilitate decisions on biodiversity conservation and reforestation programs in Central Asia.
Omnidirectional zero-field ferromagnetic resonance driven by rotatable anisotropy in FeNi/FeMn bilayers without exchange bias
Authors: Wang Wenfeng , Chai Guozhi , Xue Desheng
Published: April 2017

In this work, the zero- field GHz frequency permeability spectra and the rotatable anisotropy of FeMn/FeNi bilayers are investigated. Omnidirectional zero-field ferromagnetic resonance (FMR) driven by rotatable anisotropy can be achieved in the FeMn/FeNi bilayers without exchange bias. Instead of uniaxial anisotropy and exchange bias field, it is the rotatable anisotropy field that dominates in the unbiased bilayer, due to the absence of the exchange bias. The quantitative analysis of exchange bias field, uniaxial anisotropy and rotatable anisotropy is discussed by comparing the dynamical and static magnetic properties of FeNi single layer, biased and unbiased FeMn/FeNi bilayers.
Correction: Corrigendum: One Step Quantum Key Distribution Based on EPR Entanglement
Authors: Li Jian , Li Na , Li Lei-Lei , Wang Tao
Published: April 2017

Scientific Reports 6: Article number: 28767; published online: 30 June 2016; updated: 25 April 2017 In the Article, we did not take into account the entanglement swapping that can be caused by eavesdropping efforts. Due to entanglement swapping, in Group 2 of Table 3 and Group 3 of Table 4, the initial states will never lead to a measurement outcome by Eve and .
Correction: Corrigendum: Patient-specific hepatocyte-like cells derived from induced pluripotent stem cells model pazopanib-mediated hepatotoxicity
Authors: Choudhury Yukti , Toh Yi Chin , Xing Jiangwa , Qu Yinghua , Poh Jonathan , Li Huan , Tan Hui Shan , Kanesvaran Ravindran , Yu Hanry , Tan Min-Han
Published: April 2017

Scientific Reports 7: Article number: 41238; published online: 25 January 2017; updated: 25 April 2017 The original version of this Article contained an error in the spelling of the author Huan Li, which was incorrectly given as Li Huan. The Author Contributions Statement, Study concept and design: Y.
LPS independent activation of the pro-inflammatory receptor Trem1 by C/EBPε in granulocytes
Authors: Suh Hyung C. , Benoukraf Touati , Shyamsunder Pavithra , Yin Tong , Cao Qi , Said Jonathan , Lee Stephen , Lim Ricky , Yang Henry , Salotti Jacqueline , Johnson Peter F. , Madan Vikas , Koeffler H. Phillip
Published: April 2017

C/EBPε is a critical transcriptional factor for granulocyte differentiation and function. Individuals with germline mutations of C/EBPε fail to develop normal granulocytes and suffer from repeated infections. In order to gain a global view of the transcriptional machinery regulated by C/EBPε, we performed whole-genome ChIP-Seq using mouse bone marrow cells. To complement the C/EBPε DNA binding analyses, RNA-Sequencing was done in parallel using sorted mature and immature granulocytes from WT and C/EBPε KO bone marrow. This approach led to the identification of several direct targets of C/EBPε, which are potential effectors of its role in granulocytic differentiation and function. Interestingly, Trem1, a gene critical to granulocyte function, was identified as a direct C/EBPε target gene. Trem1 expression overlaps very closely with expression signature of C/EBPε during hematopoietic development. Luciferase reporter and EMSA assays revealed that C/EBPε binds to the regulatory elements of Trem1 and regulates its expression during granulocytic differentiation. In addition, we provide evidence that inflammatory stimuli (LPS) can also control the expression of Trem1 independent of C/EBPε. Overall, this study provides comprehensive profiling of the transcriptional network controlled by C/EBPε during granulopoiesis and identifies Trem1 as one of its downstream effectors involved in eliciting an immune response.
The peripheral blood proteome signature of idiopathic pulmonary fibrosis is distinct from normal and is associated with novel immunological processes
Authors: O’Dwyer David N. , Norman Katy C. , Xia Meng , Huang Yong , Gurczynski Stephen J. , Ashley Shanna L. , White Eric S. , Flaherty Kevin R. , Martinez Fernando J. , Murray Susan , Noth Imre , Arnold Kelly B. , Moore Bethany B.
Published: April 2017

Idiopathic pulmonary fibrosis (IPF) is a progressive and fatal interstitial pneumonia. The disease pathophysiology is poorly understood and the etiology remains unclear. Recent advances have generated new therapies and improved knowledge of the natural history of IPF. These gains have been brokered by advances in technology and improved insight into the role of various genes in mediating disease, but gene expression and protein levels do not always correlate. Thus, in this paper we apply a novel large scale high throughput aptamer approach to identify more than 1100 proteins in the peripheral blood of well-characterized IPF patients and normal volunteers. We use systems biology approaches to identify a unique IPF proteome signature and give insight into biological processes driving IPF. We found IPF plasma to be altered and enriched for proteins involved in defense response, wound healing and protein phosphorylation when compared to normal human plasma. Analysis also revealed a minimal protein signature that differentiated IPF patients from normal controls, which may allow for accurate diagnosis of IPF based on easily-accessible peripheral blood. This report introduces large scale unbiased protein discovery analysis to IPF and describes distinct biological processes that further inform disease biology.
Insecticide-induced leg loss does not eliminate biting and reproduction in Anopheles gambiae mosquitoes
Authors: Isaacs Alison T. , Lynd Amy , Donnelly Martin J.
Published: April 2017

Recent successes in malaria control have been largely attributable to the deployment of insecticide-based vector control tools such as bed nets and indoor residual spraying. Pyrethroid-treated bed nets are acutely neurotoxic to mosquitoes, inducing symptoms such as loss of coordination, paralysis, and violent spasms. One result of pyrethroid exposure often seen in laboratory tests is mosquito leg loss, a condition that has thus far been assumed to equate to mortality, as females are not expected to blood feed. However, whilst limb loss is unlikely to be adaptive, females with missing limbs may play a role in the propagation of both their species and pathogens. To test the hypothesis that leg loss inhibits mosquitoes from biting and reproducing, mosquitoes with one, two, or six legs were evaluated for their success in feeding upon a human. These experiments demonstrated that insecticide-induced leg loss had no significant effect upon blood feeding or egg laying success. We conclude that studies of pyrethroid efficacy should not discount mosquitoes that survive insecticide exposure with fewer than six legs, as they may still be capable of biting humans, reproducing, and contributing to malaria transmission.
Live cell imaging of mitochondria following targeted irradiation in situ reveals rapid and highly localized loss of membrane potential
Authors: Walsh Dietrich W. M. , Siebenwirth Christian , Greubel Christoph , Ilicic Katarina , Reindl Judith , Girst Stefanie , Muggiolu Giovanna , Simon Marina , Barberet Philippe , Seznec Hervé , Zischka Hans , Multhoff Gabriele , Schmid Thomas E. , Dollinger Guenther
Published: April 2017

The reliance of all cell types on the mitochondrial function for survival makes mitochondria an interesting target when trying to understand their role in the cellular response to ionizing radiation. By harnessing highly focused carbon ions and protons using microbeams, we have performed in situ live cell imaging of the targeted irradiation of individual mitochondria stained with Tetramethyl rhodamine ethyl ester (TMRE), a cationic fluorophore which accumulates electrophoretically in polarized mitochondria. Targeted irradiation with both carbon ions and protons down to beam spots of <1 μm induced a near instant loss of mitochondrial TMRE fluorescence signal in the targeted area. The loss of TMRE after targeted irradiation represents a radiation induced change in mitochondrial membrane potential. This is the first time such mitochondrial responses have been documented in situ after targeted microbeam irradiation. The methods developed and the results obtained have the ability to shed new light on not just mitochondria’s response to radiation but to further elucidate a putative mechanism of radiation induced depolarization and mitochondrial response.
Performance of machine-learning scoring functions in structure-based virtual screening
Authors: Wójcikowski Maciej , Ballester Pedro J. , Siedlecki Pawel
Published: April 2017

Classical scoring functions have reached a plateau in their performance in virtual screening and binding affinity prediction. Recently, machine-learning scoring functions trained on protein-ligand complexes have shown great promise in small tailored studies. They have also raised controversy, specifically concerning model overfitting and applicability to novel targets. Here we provide a new ready-to-use scoring function (RF-Score-VS) trained on 15 426 active and 893 897 inactive molecules docked to a set of 102 targets. We use the full DUD-E data sets along with three docking tools, five classical and three machine-learning scoring functions for model building and performance assessment. Our results show RF-Score-VS can substantially improve virtual screening performance: RF-Score-VS top 1% provides 55.6% hit rate, whereas that of Vina only 16.2% (for smaller percent the difference is even more encouraging: RF-Score-VS top 0.1% achieves 88.6% hit rate for 27.5% using Vina). In addition, RF-Score-VS provides much better prediction of measured binding affinity than Vina (Pearson correlation of 0.56 and −0.18, respectively). Lastly, we test RF-Score-VS on an independent test set from the DEKOIS benchmark and observed comparable results. We provide full data sets to facilitate further research in this area (http://github.com/oddt/rfscorevs) as well as ready-to-use RF-Score-VS (http://github.com/oddt/rfscorevs_binary).
Quantitative diagnosis of breast tumors by morphometric classification of microenvironmental myoepithelial cells using a machine learning approach
Authors: Yamamoto Yoichiro , Saito Akira , Tateishi Ayako , Shimojo Hisashi , Kanno Hiroyuki , Tsuchiya Shinichi , Ito Ken-ichi , Cosatto Eric , Graf Hans Peter , Moraleda Rodrigo R. , Eils Roland , Grabe Niels
Published: April 2017

Machine learning systems have recently received increased attention for their broad applications in several fields. In this study, we show for the first time that histological types of breast tumors can be classified using subtle morphological differences of microenvironmental myoepithelial cell nuclei without any direct information about neoplastic tumor cells. We quantitatively measured 11661 nuclei on the four histological types: normal cases, usual ductal hyperplasia and low/high grade ductal carcinoma in situ (DCIS). Using a machine learning system, we succeeded in classifying the four histological types with 90.9% accuracy. Electron microscopy observations suggested that the activity of typical myoepithelial cells in DCIS was lowered. Through these observations as well as meta-analytic database analyses, we developed a paracrine cross-talk-based biological mechanism of DCIS progressing to invasive cancer. Our observations support novel approaches in clinical computational diagnostics as well as in therapy development against progression.
Klf5 Mediates Odontoblastic Differentiation through Regulating Dentin-Specific Extracellular Matrix Gene Expression during Mouse Tooth Development
Authors: Chen Zhuo , Zhang Qi , Wang Han , Li Wentong , Wang Feng , Wan Chunyan , Deng Shuli , Chen Hui , Yin Yixin , Li Xiaoyan , Xie Zhijian , Chen Shuo
Published: April 2017

Klf5, a member of the Krüppel-like transcription factor family, has essential roles during embryonic development, cell proliferation, differentiation, migration and apoptosis. This study was to define molecular mechanism of Klf5 during the odontoblastic differentiation. The expression of Klf5, odontoblast-differentiation markers, Dspp and Dmp1 was co-localized in odontoblastic cells at different stages of mouse tooth development and mouse dental papilla mesenchymal cells. Klf5 was able to promote odontoblastic differentiation and enhance mineral formation of mouse dental papilla mesenchymal cells. Furthermore, overexpression of Klf5 could up-regulate Dspp and Dmp1 gene expressions in mouse dental papilla mesenchymal cells. In silico analysis identified that several putative Klf5 binding sites in the promoter and first intron of Dmp1 and Dspp genes that are homologous across species lines. Electrophoretic mobility shift assay and chromatin immunoprecipitation analysis indicated that Klf5 bound to these motifs in vitro and in intact cells. The responsible regions of Dmp1 gene were located in the promoter region while effect of Klf5 on Dspp activity was in the first intron of Dspp gene. Our results identify Klf5 as an activator of Dmp1 and Dspp gene transcriptions by different mechanisms and demonstrate that Klf5 plays a pivotal role in odontoblast differentiation.
Depletion of adult neurogenesis using the chemotherapy drug temozolomide in mice induces behavioural and biological changes relevant to depression
Authors: Egeland M , Guinaudie C , Du Preez A , Musaelyan K , Zunszain P A , Fernandes C , Pariante C M , Thuret S
Published: April 2017

Numerous studies have examined links between postnatal neurogenesis and depression using a range of experimental methods to deplete neurogenesis. The antimitotic drug temozolomide (TMZ) has previously been used successfully as an experimental tool in animals to deplete adult neurogenesis and is used regularly on human patients as a standard chemotherapy for brain cancer. In this study, we wanted to evaluate whether TMZ as a model for chemotherapy treatment could affect parameters related to depression in an animal model. Prevalence rates of depression in patients is thought to be highly underdiagnosed, with some studies reporting rates as high as 90%. Results from this study in mice, treated with a regimen of TMZ similar to humans, exhibited behavioural and biochemical changes that have relevance to the development of depression. In particular, behavioural results demonstrated robust deficits in processing novelty and a significant increase in the corticosterone response. Quantification of neurogenesis using a novel sectioning method, which clearly evaluates dorsal and ventral neurogenesis separately, showed a significant correlation between the level of ventral neurogenesis and the corticosterone response. Depression is a complex disorder with discoveries regarding its neurobiology and how it relates to behaviour being only in their infancy. The findings presented in this study demonstrate that chemotherapy-induced decreases in neurogenesis results in previously unreported behavioural and biochemical consequences. These results, we argue, are indicative of a biological mechanism, which may contribute to the development of depression in patients being treated with chemotherapy and is separate from the mental distress resulting from a cancer diagnosis.
A missense polymorphism in the putative pheromone receptor gene VN1R1 is associated with sociosexual behavior
Authors: Henningsson S , Hovey D , Vass K , Walum H , Sandnabba K , Santtila P , Jern P , Westberg L
Published: April 2017

Pheromones regulate social and reproductive behavior in most mammalian species. These effects are mediated by the vomeronasal and main olfactory systems. Effects of putative pheromones on human neuroendocrine activity, brain activity and attractiveness ratings suggest that humans may communicate via similar chemosignaling. Here we studied two samples of younger and older individuals, respectively, with respect to one nonsynonymous polymorphism in the gene encoding the human vomeronasal type-1 receptor 1, VN1R1, and one nonsynonymous polymorphism in the gene encoding the olfactory receptor OR7D4. Participants in both samples had self-reported their sociosexual behavior using the sociosexual orientation inventory, including questions regarding lifetime number of one-night stands, number of partners last year and expected number of partners the coming 5 years. In women, there was a significant association between the VN1R1 polymorphism and sociosexual behavior in both samples, driven specifically by the question regarding one-night stands. Our results support the hypothesis that human social interaction is modulated by communication via chemosignaling.
Application of hollow porous molecularly imprinted polymers using K2Ti4O9 coupled with SPE-HPLC for the determination of celecoxib in human urine samples: optimization by central composite design (CCD)
Authors: Ansari S.
Published: April 2017

Trace determination of celecoxib by hollow porous molecularly imprinted polymer and solid-phase extraction (HPMIP-SPE) coupled with high-performance liquid chromatography with UV detection (HPLC/UV).
Thermal behaviour of LixMeO2(Me = Co or Ni + Mn + Co) cathode materials
Authors: Gotcu Petronela , Pfleging Wilhelm , Smyrek Peter , Seifert Hans J.
Published: April 2017

Thermal behaviour and thermophysical properties of two typical cathodes for lithium-ion batteries were studied in dependence of temperature and lithiation degree.
Rational molecular design enhancing the photonic performance of red-emitting perylene bisimide dyes
Authors: Avellanal-Zaballa E. , Durán-Sampedro G. , Prieto-Castañeda A. , Agarrabeitia A. R. , García-Moreno I. , López-Arbeloa I. , Bañuelos J. , Ortiz M. J.
Published: April 2017

Perylene red decorated by suitable energy donors as an efficient photoactive medium for tunable and red-emitting energy transfer dye lasers.
Novel high-efficiency visible-light responsive Ag4(GeO4) photocatalyst
Authors: Zhu Xianglin , Wang Peng , Li Mengmeng , Zhang Qianqian , Rozhkova Elena A. , Qin Xiaoyan , Zhang Xiaoyang , Dai Ying , Wang Zeyan , Huang Baibiao
Published: April 2017

The existence of an internal electric field promotes the separation of generated carriers and enhances the photocatalytic activity of polar materials.
Mangiferin functionalized radioactive gold nanoparticles (MGF-198AuNPs) in prostate tumor therapy: green nanotechnology for production, in vivo tumor retention and evaluation of therapeutic efficacy
Authors: Al-Yasiri A. Y. , Khoobchandani M. , Cutler C. S. , Watkinson L. , Carmack T. , Smith C. J. , Kuchuk M. , Loyalka S. K. , Lugão A. B. , Katti K. V.
Published: April 2017

We report here production of MGF-198AuNPs and its application for prostate tumor therapy.
Sample-in-waveguide geometry for TXRF sensitivity improvement
Authors: Panchuk Vitaly , Goydenko Alexander , Grebenyuk Andrey , Irkaev Sobir , Legin Andrey , Kirsanov Dmitry , Semenov Valentin
Published: April 2017

A very simple procedure based on a planar waveguide technique is suggested in this study to improve the sensitivity of the TXRF method.
GeneSPIDER – gene regulatory network inference benchmarking with controlled network and data properties
Authors: Tjärnberg Andreas , Morgan Daniel C. , Studham Matthew , Nordling Torbjörn E. M. , Sonnhammer Erik L. L.
Published: April 2017

A key question in network inference, that has not been properly answered, is what accuracy can be expected for a given biological dataset and inference method.
Characterization of the structure, dynamics and allosteric pathways of human NPP1 in its free form and substrate-bound complex from molecular modeling
Authors: Barbeau Xavier , Mathieu Patrick , Paquin Jean-François , Lagüe Patrick
Published: April 2017

Here we report 3D structure modeling and extensive molecular dynamics simulations of NPP1 complemented with a dynamical network analysis.
Synthesis of double-shell hollow magnetic Au-loaded ellipsoids as highly active and recoverable nanoreactors
Authors: Fang Jiasheng , Zhang Yiwei , Zhou Yuming , Zhao Shuo , Zhang Chao , Huang Mengqiu , Gao Yan , Yang Chenghan
Published: April 2017

A schematic for the synthesis of double-shell magnetic Au-loaded ellipsoids (Fe@MO2–Au@H–SiO2) and the reaction mechanism for the catalytic reduction of 4-NP.
Reconfigurable optical manipulation by phase change material waveguides
Authors: Zhang Tianhang , Mei Shengtao , Wang Qian , Liu Hong , Lim Chwee Teck , Teng Jinghua
Published: April 2017

We proposed a multifunctional optical manipulation platform enabling pushing/pulling and trapping based on phase change material waveguides.
Atomic scale observation of a defect-mediated first-order phase transition in VO2(A)
Authors: Jiang Chao , Chen Lu , Ji Shidong , Liu Jun , Zhang Zhengfei , Jin Ping , Wang Yong , Zhang Ze
Published: April 2017

A defect-mediated phase transition in VO2.
Efficient chiral 1H NMR analysis of indoloquinazoline alkaloids phaitanthrin A, cephalanthrin-A and their analogues with a chiral phosphoric acid
Authors: Liu Chong-Xing , Zheng Longzhangdi , Zhu Linjing , Xiao Hong-Ping , Li Xinhua , Jiang Jun
Published: April 2017

A chiral phosphoric acid promoted enantioselective NMR recognition and determination of indoloquinazoline alkaloids phaitanthrin A, cephalanthrin-A and their analogues was described, which conveniently reveals their optical purities with high accuracy.
Atomic scale investigation of enhanced ferroelectricity in (Ba,Ca)TiO3
Authors: Zhu Xiao Na , Chen Xing , Tian He , Chen Xiang Ming
Published: April 2017

The displacement of Ti atoms (arrows) is greatly enhanced in Ba0.75Ca0.25TiO3 due to Ca-substitution for Ba.
Facile synthesis of mesoporous graphene platelets with in situ nitrogen and sulfur doping for lithium–sulfur batteries
Authors: Yuan Xiqing , Liu Bingchuan , Hou Huijie , Zeinu Kemal , He Yuhang , Yang Xiaorong , Xue Weijun , He Xiulin , Huang Long , Zhu Xiaolei , Wu Longsheng , Hu Jingping , Yang Jiakuan , Xie Jia
Published: April 2017

The interaction between lithium polysulfides and doped heteroatoms could prevent the loss of soluble polysulfides in the cathode and mitigate the shuttle effect in lithium–sulfur batteries.
Facile rapid synthesis of a nanocrystalline Cu2Te multi-phase transition material and its thermoelectric performance
Authors: Qiu Yuchong , Ye Jinwen , Liu Ying , Yang Xiaojiao
Published: April 2017

A highly efficient facile method was used to synthesize Cu2Te via spark plasma sintering (SPS) of high-energy ball-milled elemental powders, followed by annealing, which dramatically reduced the whole process time.
Design of efficient mono-aminosilane precursors for atomic layer deposition of SiO2 thin films
Authors: Huang Liang , Han Bo , Fan Maohong , Cheng Hansong
Published: April 2017

The suitability of six mono(alkylamino)silane precursors for growing SiO2 films via ALD is assessed with DFT calculations.
Amorphous porphyrin glasses exhibit near-infrared excimer luminescence
Authors: Morisue Mitsuhiko , Ueno Ikuya , Nakanishi Takayuki , Matsui Takafumi , Sasaki Sono , Shimizu Masaki , Matsui Jun , Hasegawa Yasuchika
Published: April 2017

The amorphous nature of a series of zinc–porphyrins bearing two 3,4,5-tri((S)-3,7-dimethyloctyloxy)phenyl groups at the meso-positions, named “porphyrin glass”, were tolerant of π-conjugation engineering in ethynylene-linked dimers.
An octupolar bis(porphyrinato) terbium(iii) complex with the highest off-resonant hyperpolarizability
Authors: Sun Junshan , Han Yinfeng
Published: April 2017

A novel bis(porphyrinato) terbium double-decker complex HTb(DADAPor)2 with the octupolar molecular exhibits the large off-resonant first hyperpolarizability.
A sulfate radical based ferrous–peroxydisulfate oxidative system for indomethacin degradation in aqueous solutions
Authors: Li Ruobai , Kong Jing , Liu Haijin , Chen Ping , Liu Guoguang , Li Fuhua , Lv Wenying
Published: April 2017

The degradation of indomethacin (IM) by ferrous ion-activated potassium peroxydisulfate (Fe2+/PDS) was investigated.
Thermal bending coupled with volume change in liquid crystal gels
Authors: Doi Haruka , Urayama Kenji
Published: April 2017

Thermal bending of liquid crystal elastomers in swollen and neat states differs significantly in the total variation of curvature and the temperature range where the curvature varies.
Porous 3D polymers for high pressure methane storage and carbon dioxide capture
Authors: Bracco Silvia , Piga Daniele , Bassanetti Irene , Perego Jacopo , Comotti Angiolina , Sozzani Piero
Published: April 2017

Porous 3D polymers, fabricated using multidentate monomers, efficiently adsorb CO2 and CH4 up to 180 bar.
Construction of light-harvesting system for enhanced catalytic performance of Pd nanoframes toward Suzuki coupling reaction
Authors: Yang Lini , Zhan Qi , Wang Zhenni , Chen Qiang , Tong Jing , Fang Dawei , Xia Lixin , Jin Mingshang
Published: April 2017

Au octahedra have been encapsulated into Pd nanoframes to further enhance the catalytic activity of Pd nanoframes toward Suzuki coupling reactions.
(D)n–σ–(A)m type partially conjugated block copolymer and its performance in single-component polymer solar cells
Authors: Lee Dae Hee , Lee Ji Hyung , Kim Hyung Jong , Choi Suna , Park Gi Eun , Cho Min Ju , Choi Dong Hoon
Published: April 2017

We synthesized two types of novel poly(3-alkylthiophene)-free (D)n-b-(A)m conjugated block copolymers: PTQI-block-PNDISs.
A novel architecture of dandelion-like Mo2C/TiO2 heterojunction photocatalysts towards high-performance photocatalytic hydrogen production from water splitting
Authors: Yue Xinzheng , Yi Shasha , Wang Runwei , Zhang Zongtao , Qiu Shilun
Published: April 2017

The well-designed Mo2C/TiO2 hierarchical configuration exhibits extremely high photocatalytic H2 production activity from water splitting.
An injectable ionic hydrogel inducing high temperature hyperthermia for microwave tumor ablation
Authors: Wang Jingyun , Wang Dan , Yan Hao , Tao Lei , Wei Yen , Li Yongsan , Wang Xing , Zhao Wei , Zhang Yu , Zhao Lingyun , Sun Xiaodan
Published: April 2017

Microwave tumor ablation is of clinical significance and has been considered as a promising cancer minimally invasive therapy.
Injectable self-healing hydrogels formed via thiol/disulfide exchange of thiol functionalized F127 and dithiolane modified PEG
Authors: Yu Hansen , Wang Yanan , Yang Haiyang , Peng Kang , Zhang Xingyuan
Published: April 2017

An injectable thermo-responsive hydrogel with excellent mechanical properties which can self-heal under mildly acidic to basic conditions was prepared.
A flexible, ultra-sensitive chemical sensor with 3D biomimetic templating for diabetes-related acetone detection
Authors: Wang Lili , Jackman Joshua A. , Park Jae Hyeon , Tan Ee-Lin , Cho Nam-Joon
Published: April 2017

A flexible, ultra-sensitive chemical sensor with 3D biomimetic templating is reported for molecular detection of volatile organic compounds.
To probe the performance of perovskite memory devices: defects property and hysteresis
Authors: Xu Ziqi , Liu Zonghao , Huang Yuan , Zheng Guanhaojie , Chen Qi , Zhou Huanping
Published: April 2017

A hybrid perovskite memory device with a decent set voltage has been successfully demonstrated, and the performance was correlated to the defect density and hysteresis-index of different perovskite films.
Ligand mediated excited state carrier relaxation dynamics of Cd1−xZnxSe1−ySy NCs derived from bile salts
Authors: Chatterjee Sayantan , Maitra Uday
Published: April 2017

Bile acid derived cadmium and zinc precursors were utilized for an efficient and single step synthesis of Cd1−xZnxSe1−ySy NCs. Different capping ligand induced carrier relaxation dynamics of the NCs using time resolved spectroscopy was also studied.
Precisely controllable fabrication of Er3+-doped glass ceramic fibers: novel mid-infrared fiber laser materials
Authors: Kang Shiliang , Fang Zaijin , Huang Xiongjian , Chen Zhi , Yang Dandan , Xiao Xiudi , Qiu Jianrong , Dong Guoping
Published: April 2017

We demonstrated remarkably enhanced 2.7 μm emission in glass-ceramic (GC) fibers containing NaYF4:Er3+ nanocrystals with 980 nm excitation for the first time.
Target recognition based on phase noise of received signal
Authors: Nouri M. , Mivehchy M. , Sabahi M.F.
Published: April 2017

By using the effects of non‐ideal oscillators, a technique is proposed to discriminate targets in continuous wave (CW) tracking radar. This method is based on the fact that each oscillator has an individual effect on the phase noise that helps to recognise real targets from the simulated ones. A simulated fake target, made through complex circuits, e.g. a digital RF memory, has a different phase noise from a real backscatter. Therefore, the transmitted and received signals are different in phase noise levels and patterns. To evaluate the performance of the proposed technique, the probability of detection (PD) is shown in different signal‐to‐noise ratios, ranges, and signal‐to‐jammer ratios based on an experimental setup.
Improved ITU‐R model for digital terrestrial television propagation path loss prediction
Authors: Pérez García N.A. , Pinto A.D. , Torres J.M. , Rengel J.E. , Rujano L.M. , Robles Camargo N. , Donoso Y.
Published: April 2017

The use of a suitable propagation model for coverage prediction is key during the planning and dimensioning process of a digital terrestrial television (DTT) system. This study optimises one of the most detailed models for this purpose, i.e. Recommendation ITU‐R.P.1812‐4, with the aim of improving its accuracy in propagation path loss prediction for DTT systems in outdoor environments of Caracas city, Venezuela. For model adjustment, it is used the bioinspired technique particle swarm optimisation (PSO) and received signal level measurements performed in DTT systems in Caracas city under fixed reception conditions. The results, quantitatively analysed by RMS error and grey relation grade and mean absolute percentage error, shows a significant increase of the accuracy of optimised model in comparison with the original version and even with others propagation models.