bluuebunny/crossref_metadata_2025 huggingface dataset:
Antibiotic-induced release of small extracellular vesicles (exosomes) with surface-associated DNA
Authors: Németh Andrea , Orgovan Norbert , Sódar Barbara W , Osteikoetxea Xabier , Pálóczi Krisztina , Szabó-Taylor Katalin É. , Vukman Krisztina V. , Kittel Ágnes , Turiák Lilla , Wiener Zoltán , Tóth Sára , Drahos László , Vékey Károly , Horvath Robert , Buzás Edit I.
Published: August 2017

Recently, biological roles of extracellular vesicles (which include among others exosomes, microvesicles and apoptotic bodies) have attracted substantial attention in various fields of biomedicine. Here we investigated the impact of sustained exposure of cells to the fluoroquinolone antibiotic ciprofloxacin on the released extracellular vesicles. Ciprofloxacin is widely used in humans against bacterial infections as well as in cell cultures against Mycoplasma contamination. However, ciprofloxacin is an inducer of oxidative stress and mitochondrial dysfunction of mammalian cells. Unexpectedly, here we found that ciprofloxacin induced the release of both DNA (mitochondrial and chromosomal sequences) and DNA-binding proteins on the exofacial surfaces of small extracellular vesicles referred to in this paper as exosomes. Furthermore, a label-free optical biosensor analysis revealed DNA-dependent binding of exosomes to fibronectin. DNA release on the surface of exosomes was not affected any further by cellular activation or apoptosis induction. Our results reveal for the first time that prolonged low-dose ciprofloxacin exposure leads to the release of DNA associated with the external surface of exosomes.
Forces and Disease: Electrostatic force differences caused by mutations in kinesin motor domains can distinguish between disease-causing and non-disease-causing mutations
Authors: Li Lin , Jia Zhe , Peng Yunhui , Godar Subash , Getov Ivan , Teng Shaolei , Alper Joshua , Alexov Emil
Published: August 2017

The ability to predict if a given mutation is disease-causing or not has enormous potential to impact human health. Typically, these predictions are made by assessing the effects of mutation on macromolecular stability and amino acid conservation. Here we report a novel feature: the electrostatic component of the force acting between a kinesin motor domain and tubulin. We demonstrate that changes in the electrostatic component of the binding force are able to discriminate between disease-causing and non-disease-causing mutations found in human kinesin motor domains using the receiver operating characteristic (ROC). Because diseases may originate from multiple effects not related to kinesin-microtubule binding, the prediction rate of 0.843 area under the ROC plot due to the change in magnitude of the electrostatic force alone is remarkable. These results reflect the dependence of kinesin’s function on motility along the microtubule, which suggests a precise balance of microtubule binding forces is required.
Fine Structure of Posterior Alpha Rhythm in Human EEG: Frequency Components, Their Cortical Sources, and Temporal Behavior
Authors: Barzegaran Elham , Vildavski Vladimir Y. , Knyazeva Maria G.
Published: August 2017

Heterogeneity of the posterior alpha rhythm (AR) is a widely assumed but rarely tested phenomenon. We decomposed the posterior AR in the cortical source space with a 3-way PARAFAC technique, taking into account the spatial, frequency, and temporal aspects of mid-density EEG. We found a multicomponent AR structure in 90% of a group of 29 healthy adults. The typical resting-state structure consisted of a high-frequency occipito-parietal component of the AR (ARC1) and a low-frequency occipito-temporal component (ARC2), characterized by individual dynamics in time. In a few cases, we found a 3-component structure, with two ARC1s and one ARC2. The AR structures were stable in their frequency and spatial features over weeks to months, thus representing individual EEG alpha phenotypes. Cortical topography, individual stability, and similarity to the primate AR organization link ARC1 to the dorsal visual stream and ARC2 to the ventral one. Understanding how many and what kind of posterior AR components contribute to the EEG is essential for clinical neuroscience as an objective basis for AR segmentation and for interpreting AR dynamics under various conditions, both normal and pathological, which can selectively affect individual components.
Inhibin-A and Decorin Secreted by Human Adult Renal Stem/Progenitor Cells Through the TLR2 Engagement Induce Renal Tubular Cell Regeneration
Authors: Sallustio Fabio , Curci Claudia , Aloisi Alessandra , Toma Chiara Cristina , Marulli Elisabetta , Serino Grazia , Cox Sharon Natasha , De Palma Giuseppe , Stasi Alessandra , Divella Chiara , Rinaldi Rosaria , Schena Francesco Paolo
Published: August 2017

Acute kidney injury (AKI) is a public health problem worldwide. Several therapeutic strategies have been made to accelerate recovery and improve renal survival. Recent studies have shown that human adult renal progenitor cells (ARPCs) participate in kidney repair processes, and may be used as a possible treatment to promote regeneration in acute kidney injury. Here, we show that human tubular ARPCs (tARPCs) protect physically injured or chemically damaged renal proximal tubular epithelial cells (RPTECs) by preventing cisplatin-induced apoptosis and enhancing proliferation of survived cells. tARPCs without toll-like receptor 2 (TLR2) expression or TLR2 blocking completely abrogated this regenerative effect. Only tARPCs, and not glomerular ARPCs, were able to induce tubular cell regeneration process and it occurred only after damage detection. Moreover, we have found that ARPCs secreted inhibin-A and decorin following the RPTEC damage and that these secreted factors were directly involved in cell regeneration process. Polysaccharide synthetic vesicles containing these molecules were constructed and co-cultured with cisplatin damaged RPTECs. These synthetic vesicles were not only incorporated into the cells, but they were also able to induce a substantial increase in cell number and viability. The findings of this study increase the knowledge of renal repair processes and may be the first step in the development of new specific therapeutic strategies for renal repair.
Deregulation of transcription factors controlling intestinal epithelial cell differentiation; a predisposing factor for reduced enteroendocrine cell number in morbidly obese individuals
Authors: Wölnerhanssen Bettina K. , Moran Andrew W. , Burdyga Galina , Meyer-Gerspach Anne Christin , Peterli Ralph , Manz Michael , Thumshirn Miriam , Daly Kristian , Beglinger Christoph , Shirazi-Beechey Soraya P.
Published: August 2017

Morbidly obese patients exhibit impaired secretion of gut hormones that may contribute to the development of obesity. After bariatric surgery there is a dramatic increase in gut hormone release. In this study, gastric and duodenal tissues were endoscopically collected from lean, and morbidly obese subjects before and 3 months after laparoscopic sleeve gastrectomy (LSG). Tissue morphology, abundance of chromogranin A, gut hormones, α-defensin, mucin 2, Na+/glucose co-transporter 1 (SGLT1) and transcription factors, Hes1, HATH1, NeuroD1, and Ngn3, were determined. In obese patients, the total number of enteroendocrine cells (EEC) and EECs containing gut hormones were significantly reduced in the stomach and duodenum, compared to lean, and returned to normality post-LSG. No changes in villus height/crypt depth were observed. A significant increase in mucin 2 and SGLT1 expression was detected in the obese duodenum. Expression levels of transcription factors required for differentiation of absorptive and secretory cell lineages were altered. We propose that in obesity, there is deregulation in differentiation of intestinal epithelial cell lineages that may influence the levels of released gut hormones. Post-LSG cellular differentiation profile is restored. An understanding of molecular mechanisms controlling epithelial cell differentiation in the obese intestine assists in the development of non-invasive therapeutic strategies.
Inhibition of connexin hemichannels alleviates non-alcoholic steatohepatitis in mice
Authors: Willebrords Joost , Cogliati Bruno , Pereira Isabel Veloso Alves , da Silva Tereza Cristina , Crespo Yanguas Sara , Maes Michaël , Govoni Veronica Mollica , Lima Andressa , Felisbino Daniele Aparecida , Decrock Elke , Nogueira Marina Sayuri , de Castro Inar Alves , Leclercq Isabelle , Leybaert Luc , Rodrigues Robim Marcelino , Vinken Mathieu
Published: August 2017

While gap junctions mediate intercellular communication and support liver homeostasis, connexin hemichannels are preferentially opened by pathological stimuli, including inflammation and oxidative stress. The latter are essential features of non-alcoholic steatohepatitis. In this study, it was investigated whether connexin32 and connexin43 hemichannels play a role in non-alcoholic steatohepatitis. Mice were fed a choline-deficient high-fat diet or normal diet for 8 weeks. Thereafter, TAT-Gap24 or TAT-Gap19, specific inhibitors of hemichannels composed of connexin32 and connexin43, respectively, were administered for 2 weeks. Subsequently, histopathological examination was carried out and various indicators of inflammation, liver damage and oxidative stress were tested. In addition, whole transcriptome microarray analysis of liver tissue was performed. Channel specificity of TAT-Gap24 and TAT-Gap19 was examined in vitro by fluorescence recovery after photobleaching analysis and measurement of extracellular release of adenosine triphosphate. TAT-Gap24 and TAT-Gap19 were shown to be hemichannel-specific in cultured primary hepatocytes. Diet-fed animals treated with TAT-Gap24 or TAT-Gap19 displayed decreased amounts of liver lipids and inflammatory markers, and augmented levels of superoxide dismutase, which was supported by the microarray results. These findings show the involvement of connexin32 and connexin43 hemichannels in non-alcoholic steatohepatitis and, simultaneously, suggest a role as potential drug targets in non-alcoholic steatohepatitis.
Optimization of Storage Temperature for Retention of Undifferentiated Cell Character of Cultured Human Epidermal Cell Sheets
Authors: Jackson Catherine J. , Reppe Sjur , Eidet Jon R. , Eide Lars , Tønseth Kim A. , Bergersen Linda H. , Dartt Darlene A. , Griffith May , Utheim Tor P.
Published: August 2017

Cultured epidermal cell sheets (CES) containing undifferentiated cells are useful for treating skin burns and have potential for regenerative treatment of other types of epithelial injuries. The undifferentiated phenotype is therefore important for success in both applications. This study aimed to optimize a method for one-week storage of CES for their widespread distribution and use in regenerative medicine. The effect of storage temperatures 4 °C, 8 °C, 12 °C, 16 °C, and 24 °C on CES was evaluated. Analyses included assessment of viability, mitochondrial reactive oxygen species (ROS), membrane damage, mitochondrial DNA (mtDNA) integrity, morphology, phenotype and cytokine secretion into storage buffer. Lowest cell viability was seen at 4 °C. Compared to non-stored cells, ABCG2 expression increased between temperatures 8–16 °C. At 24 °C, reduced ABCG2 expression coincided with increased mitochondrial ROS, as well as increased differentiation, cell death and mtDNA damage. P63, C/EBPδ, CK10 and involucrin fluorescence combined with morphology observations supported retention of undifferentiated cell phenotype at 12 °C, transition to differentiation at 16 °C, and increased differentiation at 24 °C. Several cytokines relevant to healing were upregulated during storage. Importantly, cells stored at 12 °C showed similar viability and undifferentiated phenotype as the non-stored control suggesting that this temperature may be ideal for storage of CES.
Effects of contaminants of emerging concern on Megaselia scalaris (Lowe, Diptera: Phoridae) and its microbial community
Authors: Pennington Marcus J. , Rothman Jason A. , Jones Michael B. , McFrederick Quinn S. , Gan Jay , Trumble John T.
Published: August 2017

Drought, rising temperatures, and expanding human populations are increasing water demands. Many countries are extending potable water supplies by irrigating crops with wastewater. Unfortunately, wastewater contains biologically active, long-lived pharmaceuticals, even after treatment. Run-off from farms and wastewater treatment plant overflows contribute high concentrations of pharmaceuticals to the environment. This study assessed the effects of common pharmaceuticals on a cosmopolitan saprophagous insect, Megaselia scalaris (Diptera: Phoridae). Larvae were reared on artificial diets spiked with contaminants of emerging concern (CECs) at environmentally relevant concentrations. Female flies showed no oviposition preference for treated or untreated diets. Larvae exposed to caffeine in diets showed increased mortality, and larvae fed antibiotics and hormones showed signs of slowed development, especially in females. The normal sex ratio observed in M. scalaris from control diets was affected by exposure to caffeine and pharmaceutical mixture treatments. There was an overall effect of treatment on the flies’ microbial communities; notably, caffeine fed insects displayed higher microbial variability. Eight bacterial families accounted for approximately 95% of the total microbes in diet and insects. Our results suggest that CECs at environmentally relevant concentrations can affect the biology and microbial communities of an insect of ecological and medical importance.
Localized iron accumulation precedes nucleation and growth of magnetite crystals in magnetotactic bacteria
Authors: Werckmann Jacques , Cypriano Jefferson , Lefèvre Christopher T. , Dembelé Kassiogé , Ersen Ovidiu , Bazylinski Dennis A. , Lins Ulysses , Farina Marcos
Published: August 2017

Many magnetotactic bacteria (MTB) biomineralize magnetite crystals that nucleate and grow inside intracellular membranous vesicles that originate from invaginations of the cytoplasmic membrane. The crystals together with their surrounding membranes are referred to magnetosomes. Magnetosome magnetite crystals nucleate and grow using iron transported inside the vesicle by specific proteins. Here we address the question: can iron transported inside MTB for the production of magnetite crystals be spatially mapped using electron microscopy? Cultured and uncultured MTB from brackish and freshwater lagoons were studied using analytical transmission electron microscopy in an attempt to answer this question. Scanning transmission electron microscopy was used at sub-nanometric resolution to determine the distribution of elements by implementing high sensitivity energy dispersive X-ray (EDS) mapping and electron energy loss spectroscopy (EELS). EDS mapping showed that magnetosomes are enmeshed in a magnetosomal matrix in which iron accumulates close to the magnetosome forming a continuous layer visually appearing as a corona. EELS, obtained at high spatial resolution, confirmed that iron was present close to and inside the lipid bilayer magnetosome membrane. This study provides important clues to magnetite formation in MTB through the discovery of a mechanism where iron ions accumulate prior to magnetite biomineralization.
Artificial hagfish protein fibers with ultra-high and tunable stiffness
Authors: Fu Jing , Guerette Paul A. , Pavesi Andrea , Horbelt Nils , Lim Chwee Teck , Harrington Matthew J. , Miserez Ali
Published: August 2017

Recombinant hagfish slime proteins are self-assembled into coiled-coil filaments, drawn from a solution, and phase-transformed into elongated β-sheets with high stiffness.
Hollow AuxAg/Au core/shell nanospheres as efficient catalysts for electrooxidation of liquid fuels
Authors: Xu Hui , Wang Jin , Yan Bo , Zhang Ke , Li Shumin , Wang Caiqin , Shiraishi Yukihide , Du Yukou , Yang Ping
Published: August 2017

Facilely control the crystal structures of the nanocrystals can effectively endow them with both of enhanced activity and stability for the electrooxidation of liquid fuels.
Microbial consortium OEM1 cultivation for higher lignocellulose degradation and chlorophenol removal
Authors: Liang Jiajin , Lin Yunqin , Li Tian , Mo Fanyong
Published: August 2017

Herein, microbial consortium OEM1 that could simultaneously decompose lignocellulose and chlorophenols was screened from spent mushroom substrates.
Pyridine-based functionalized graphene oxides as a new class of corrosion inhibitors for mild steel: an experimental and DFT approach
Authors: Gupta Rajeev Kumar , Malviya Manisha , Verma Chandrabhan , Gupta Neeraj K. , Quraishi M. A.
Published: August 2017

Two functionalized graphene oxides, diazo pyridine functionalized graphene oxide and diamino pyridine functionalized graphene oxide, were synthesised and evaluated as corrosion inhibitors on mild steel in 1 M hydrochloric acid.
The combination of glass dust and glass fiber as fluxing agents for ceramifiable silicone rubber composites
Authors: Lou Feipeng , Cheng Lihong , Li Qiuying , Wei Ting , Guan Xinyuan , Guo Weihong
Published: August 2017

A novel ceramifying silicone rubber composite filled with mica powder, glass dust and glass fiber was prepared for high-temperature applications.
Spin transport properties and spin logic gates in manganese phthalocyanine-based molecular combinational circuits
Authors: Zhao Wenkai , Zou Dongqing , Yang Chuan-Lu , Sun Zhaopeng
Published: August 2017

Spintronic devices are very important for futuristic information technology.
A design strategy of bipolar host materials for more than 30 times extended lifetime in phosphorescent organic light-emitting diodes using benzocarbazole and quinazoline
Authors: Kim Sung Moo , Yun Ju Hui , Han Si Hyun , Lee Jun Yeob
Published: August 2017

Stable host materials based on benzocarbazole and quinazoline were synthesized to establish a design strategy of bipolar hosts for elongated lifetime in orange phosphorescent organic light-emitting diodes (PHOLEDs).
Toxicological effects of patulin mycotoxin on the mammalian system: an overview
Authors: Pal Saurabh , Singh Neha , Ansari Kausar Mahmood
Published: August 2017

The mycotoxin PAT (4-hydroxy-4H-furo[3,2c]pyran-2[6H]-one) is a secondary metabolic product of molds such as Penicillium, Aspergillus, and Byssochlamys species. PAT is a common contaminant of fruit and vegetable based products, most notably apples. Despite PAT's original discovery as an antibiotic, it has come under heavy scrutiny for its potential to impart negative health effects. Studies investigating these health effects have proved its toxic potential. PAT occurrence in the food commodities poses a serious threat and necessitates novel and cost-effective mitigation methods to remove it from food products. It also creates a demand to improve handling and food processing techniques. With this being the case, several studies have been devoted to understanding the key biological and chemical attributes of PAT. While past research has elucidated a great deal, PAT contamination continues to be a challenge for the food industry. Here, we review its influence within the mammalian system, including its regulation, incidences of experimental evidence of PAT toxicity, its interaction with intracellular components, and the effects of PAT induced systemic toxicity on vital organs. Finally, key areas where future PAT research should focus to best control the PAT contamination problem within the food industry have been addressed.
MicroRNA-211/BDNF axis regulates LPS-induced proliferation of normal human astrocyte through PI3K/AKT pathway
Authors: Zhang Kexiang , Wu Song , Li Zhiyue , Zhou Jiahui
Published: August 2017

Spinal cord injury (SCI) makes a major contribution to disability and deaths worldwide. Reactive astrogliosis, a typical feature after SCI, which undergoes varying molecular and morphological changes, is ubiquitous but poorly understood. Reactive astrogliosis contributes to glial scar formation that impedes axonal regeneration. Brain-derived neurotrophic factor (BDNF), a well-established neurotrophic factor, exerts neuroprotective and growth-promoting effects on a variety of neuronal populations after injury. In the present study, by using LPS-induced in vitro injury model of astroglial cultures, we observed a high expression of interleukin (IL)-6, IL-1β, and BDNF in LPS-stimulated normal human astrocytes (NHAs). BDNF significantly promoted NHA proliferation. Further, online tools were employed to screen the candidate miRNAs which might directly target BDNF to inhibit its expression. Amongst the candidate miRNAs, miR-211 expression was down-regulated by LPS stimulation in a dose-dependent manner. Through direct targetting, miR-211 inhibited BDNF expression. Ectopic miR-211 expression significantly suppressed NHA proliferation, as well as LPS-induced activation of PI3K/Akt pathway. In contrast, inhibition of miR-211 expression significantly promoted NHA proliferation and LPS-induced activation of PI3K/Akt pathway. Taken together, miR-211/BDNF axis regulates LPS-induced NHA proliferation through PI3K/AKT pathway; miR-211/BDNF might serve as a promising target in the strategy against reactive astrocyte proliferation after SCI.
Visible-Light-Induced Trifluoromethylation of Highly Functionalized Arenes and Heteroarenes in Continuous Flow
Authors: Alcazar Jesus , Noёl Timothy , Abdiaj Irini , Bottecchia Cecilia
Published: August 2017

We report a continuous-flow protocol for the trifluoromethylation of arenes, heteroarenes, and benzofused heterocycles. This photoredox methodology relies on the use of solid sodium trifluoromethanesulfinate (CF3SO2Na) as the trifluoromethylating agent and the iridium complex [Ir{dF(CF3)ppy}2](dtbpy)]PF6 as the photoredox catalyst. A diverse set of highly functionalized heterocycles proved compatible with the methodology, and moderate to good yields were obtained within 30 minutes of residence time.
Positionierungskissen in der ATP-G
Authors: Bartels Friedhilde , Eckardt Claudia
Published: August 2017

Basismaterial Positionierungskissen Was dem Arzt die Medikamente und Instrumente, sind für Pflegende, den Patienten oder Bewohner das
Material zur passenden Positionierung. Der Patient soll in seinen Ressourcen unterstützt werden. Die Entwicklung geht hin zu neuen
Materialien.
Genome-scale regression analysis reveals a linear relationship for promoters and enhancers after combinatorial drug treatment
Authors: Rapakoulia Trisevgeni , Gao Xin , Huang Yi , de Hoon Michiel , Okada-Hatakeyama Mariko , Suzuki Harukazu , Arner Erik
Published: August 2017

Motivation

Drug combination therapy for treatment of cancers and other multifactorial diseases has the potential of increasing the therapeutic effect, while reducing the likelihood of drug resistance. In order to reduce time and cost spent in comprehensive screens, methods are needed which can model additive effects of possible drug combinations.

Results

We here show that the transcriptional response to combinatorial drug treatment at promoters, as measured by single molecule CAGE technology, is accurately described by a linear combination of the responses of the individual drugs at a genome wide scale. We also find that the same linear relationship holds for transcription at enhancer elements. We conclude that the described approach is promising for eliciting the transcriptional response to multidrug treatment at promoters and enhancers in an unbiased genome wide way, which may minimize the need for exhaustive combinatorial screens.

Availability and implementation

The CAGE sequence data used in this study is available in the DDBJ Sequence Read Archive (http://trace.ddbj.nig.ac.jp/index_e.html), accession number DRP001113.

Supplementary information

Supplementary data are available at Bioinformatics online.
MIRMMR: binary classification of microsatellite instability using methylation and mutations
Authors: Foltz Steven M , Liang Wen-Wei , Xie Mingchao , Ding Li
Published: August 2017

MIRMMR predicts microsatellite instability status in cancer samples using methylation and mutation information, in contrast to existing methods that rely on observed microsatellites. Additionally, MIRMMR highlights those genetic alterations contributing to microsatellite instability.

Availability and implementation

Source code is freely available at https://github.com/ding-lab/MIRMMR under the MIT license, implemented in R and supported on Unix/OS X operating systems.

Supplementary information

Supplementary data are available at Bioinformatics online.
Improving protein fold recognition by extracting fold-specific features from predicted residue–residue contacts
Authors: Zhu Jianwei , Zhang Haicang , Li Shuai Cheng , Wang Chao , Kong Lupeng , Sun Shiwei , Zheng Wei-Mou , Bu Dongbo
Published: August 2017

Motivation

Accurate recognition of protein fold types is a key step for template-based prediction of protein structures. The existing approaches to fold recognition mainly exploit the features derived from alignments of query protein against templates. These approaches have been shown to be successful for fold recognition at family level, but usually failed at superfamily/fold levels. To overcome this limitation, one of the key points is to explore more structurally informative features of proteins. Although residue–residue contacts carry abundant structural information, how to thoroughly exploit these information for fold recognition still remains a challenge.

Results

In this study, we present an approach (called DeepFR) to improve fold recognition at superfamily/fold levels. The basic idea of our approach is to extract fold-specific features from predicted residue–residue contacts of proteins using deep convolutional neural network (DCNN) technique. Based on these fold-specific features, we calculated similarity between query protein and templates, and then assigned query protein with fold type of the most similar template. DCNN has showed excellent performance in image feature extraction and image recognition; the rational underlying the application of DCNN for fold recognition is that contact likelihood maps are essentially analogy to images, as they both display compositional hierarchy. Experimental results on the LINDAHL dataset suggest that even using the extracted fold-specific features alone, our approach achieved success rate comparable to the state-of-the-art approaches. When further combining these features with traditional alignment-related features, the success rate of our approach increased to 92.3%, 82.5% and 78.8% at family, superfamily and fold levels, respectively, which is about 18% higher than the state-of-the-art approach at fold level, 6% higher at superfamily level and 1% higher at family level. An independent assessment on SCOP_TEST dataset showed consistent performance improvement, indicating robustness of our approach. Furthermore, bi-clustering results of the extracted features are compatible with fold hierarchy of proteins, implying that these features are fold-specific. Together, these results suggest that the features extracted from predicted contacts are orthogonal to alignment-related features, and the combination of them could greatly facilitate fold recognition at superfamily/fold levels and template-based prediction of protein structures.

Availability and implementation

Source code of DeepFR is freely available through https://github.com/zhujianwei31415/deepfr, and a web server is available through http://protein.ict.ac.cn/deepfr.

Supplementary information

Supplementary data are available at Bioinformatics online.
Multi-Vortex States in Mesoscopic Superconductors
Authors: Kokubo N. , Okayasu S. , Kadowaki K.
Published: August 2017

This article investigates multi-vortex states in mesoscopic amorphous superconductors with different geometries by means of scanning SQUID microscopy. It first describes the setup of the scanning SQUID microscope used in magnetic imaging of superconducting vortices before discussing the physical properties of amorphous superconducting thin films. It then presents the results of experiments showing the formation of multi-vortex states in mesoscopic dots of weak pinning, amorphous MoGe thin films, along with the formation of vortex polygons and concentric vortex rings in mesoscopic disks. It also considers the concept of multiple vortex shells and its applicability to vortex patterns observed in mesoscopic circle and square dots. The article highlights some of the key features of mesoscopic superconducting dots, including commensurability effect, multiple shell structures, repeated packing sequences, inclusion structural hierarchy, and pinning effect.
Mesoscopic Effects in Superconductor–Ferromagnet Hybrids
Authors: Karapetrov G. , Moore S.A. , Iavarone M.
Published: August 2017

This article examines the occurrence of mesoscopic effects in superconductor-ferromagnet hybrids. It begins with an overview of theories underpinning superconducting/ferromagnetic (S/F) hybrid structures, focusing on their vortex nucleation conditions and vortex behavior as well as the localized nucleation of superconductivity in an ideal S/F system. It then presents experimental measurements of the localized superconducting state in the cases of domain wall and reverse domain superconductivity, along with the vortex state in planar S/F hybrids. In particular, it considers nucleation thresholds for superconducting vortices and equilibrium vortex configurations. Finally, it discusses the results of local scanning probe measurements of the novel mesoscopic effects that emerge in magnetically coupled S/F hybrid structures in the absence of proximity effects.
The problem of a “general” theory in mathematics
Authors: Rabouin David
Published: August 2017

This article examines the so-called problem of generality in Euclid’s Elements. More specifically, it asks whether there is a ‘more general’ point of view from which magnitudes and numbers might be treated without distinction, and if so, whether Euclid violated the Aristotelian prescription by treating general features (typically the operative core of “proportions”) in specific cases in Book V (for magnitudes) and in Book VII (for numbers). The article first considers the general context of the problem of generality, taking into account the object domains in Euclidean mathematics, and some of the modern strategies proposed to solve it. These strategies rely on historical reconstructions and often make use of evidence taken from Aristotle, but tend to have a purely utilitarian relationship to such evidence. The article also discusses Aristotle’s conception of scientific knowledge, the problem of the katholou, and his view of generality in mathematics.
Functionalization of single-walled carbon nanotubes: Chemistry and characterization
Authors: Graupner R. , Hauke F.
Published: August 2017

This article examines the chemical functionalization and structural alteration of single-walled carbon nanotubes (SWCNTs). It describes the covalent functionalization of the SWCNT framework that is the covalent attachment of functional entities onto the CNT scaffold. In particular, it considers the chemical modification and reactivity of SWCNTs in the context of the reactivity of graphite and fullerenes. It also discusses the defect and sidewall functionalization of SWCNTs, along with various techniques used in the characterization ofSWCNTs upon functionalization, namely: thermogravimetric analysis, spectroscopic techniques such as UV-Vis-NIR spectroscopy and Raman spectroscopy, and microscopic techniques like transmission electron microscopy, atomic force microscopy and scanning tunnelling microscopy.
Disorder-induced electron localization in molecular-based materials
Authors: Stafström Sven , Unge Mikael
Published: August 2017

This article examines disorder-induced electron localization in molecular-based materials, using DNA and pentacene molecular crystals as examples. In DNA, the disorder is intrinsic and strong, resulting in very short localization lengths. The pentacene crystal, on the other hand, is intrinsically homogeneous and the disorder is extrinsic and weak, which makes a metal–insulator transition (MIT) possible. After providing an overview of carbon-based materials for electronic applications, the article explains the methodology for calculating the localization properties of a DNA double strand and a pentacene molecular crystal, namely Hamiltonian, transfer matrix, and finite-size scaling. It also discusses the results, which show a substantial increase in the localization length of the electronic state with correlated disorder as compared to the case of uncorrelated disorder.
Atomistic spin-dynamics
Authors: Stamenova M. , Sanvito S.
Published: August 2017

This article reviews recent advances towards the development of a truly atomistic time-dependent theory for spin-dynamics. The focus is on the s-d tight-binding model [where conduction electrons (s) are exchange-coupled to a number of classical spins (d)], including electrostatic corrections at the Hartree level, as the underlying electronic structure theory. In particular, the article considers one-dimensional (1D) magnetic atomic wires and their electronic structure, described by means of the s-d model. The discussion begins with an overview of the model spin Hamiltonian, followed by molecular-dynamics simulations of spin-wave dispersion in a s-d monoatomic chain and spin impurities in a non-magnetic chain. The current-induced motion in a magnetic domain wall (DW) is also explored, along with how an electric current can affect the magnetization landscape of a magnetic nano-object. The article concludes with an assessment of spin-motive force, and especially whether a driven magnetization dynamics can generate an electrical signal.
Selective self-assembly of semi-metal straight and branched nanorods on inert substrates
Authors: Wang X.-S. , Kushvaha S.S. , Chu X. , Zhang H. , Yan Z. , Xiao W.
Published: August 2017

This article discusses the selective self-assembly of semi-metal straight and branched nanorods on inert substrates. In particular, it describes antimony (Sb) nanorods and bismuth (Bi) nanobelts on inert substrates by physical vapor deposition in vacuum without using any catalyst and nanoscale template. After describing the experimental and drift correction procedures, the article reviews previous studies of semi-metal growth on inert substrates. It then measures the surface morphology and atomic structures of self-assembled Sb nanorods and Bi nanobelts using an in-situ scanning tunnelling microscope (STM) in ultrahigh vacuum (UHV). Based on these STM data, a mechanism for the self-assembly of straight and branched semi-metal nanorods is proposed.
Nanoscale Ge1−xMnxTe ferromagnetic semiconductors
Authors: Bi J.F. , Teo K.L.
Published: August 2017

This article discusses the structure characterizations, magnetic and transport behaviors of the nanoscale ferromagnetic semiconductors Ge1-xMnxTe grown by molecular beam epitaxy with various manganese compositions x ranging from 0.14 to 0.98. After providing an overview of the growth procedure and characterization, the article analyzes the structures of the Ge1-xMnxTe system using X-ray diffraction and high-resolution transmission electron microscopy. It then considers the optical, magnetic and transport properties of the semiconductors and shows that the crystal quality is degraded and the proportion of amorphous phase increases with increasing Mn composition. Nanoclusters and nanoscale grains can be observed when x > 0.24, which greatly affect their magnetic and electronic properties. The magnetic anisotropy is weakened due to different orientations of the clusters embedded in the GeTe host. An anomalous Hall effect is also observed in the samples, which can be attributed to extrinsic skew scattering.
Harmonic detection of resonance methods for micro- and nanocantilevers: Theory and selected applications
Authors: Taylor J.D. , Elliott B. , Dickel D. , Keskar G. , Gaillard J. , Skove M.J. , Rao A.M.
Published: August 2017

This article examines the harmonic detection of resonance (HDR) methods for micro- and nanocantilevers, with particular emphasis on theory and selected applications. Micro- and nanocantilevers have the potential to revolutionize physical, chemical, and biological sensing. Microcantilevers in particular are easily integrated into standard high-volume silicon manufacturing processes, making them relatively inexpensive and mass-producible. This article begins with an overview of basic transduction mechanisms applicable to micro- and nanocantilever-based systems. It then considers several detection schemes for measuring the static and/or dynamic response of micro- and nanocantilevers. It goes on to discuss electrostatic actuation and capacitive detection, how HDR works, and the differences between the mechanical and electrical responses of an electrostatically actuated microcantilever. Finally, it presents a number of applications for micro- and nanocantilevers, along with detection results for cantilevered multiwall carbon nanotubes.
Career Progression Expectations and Aspirations of Female Police Officers in England and Wales
Authors: Boag-Munroe Fran
Published: August 2017

The Peelian principle that ‘the police are the public, and the public are the police’ remains a central tenet of the ‘policing by consent’ model of policing. However, the police in England and Wales are currently not gender-representative, most notably at the highest ranks. Using a sample of 21,490 officers in England and Wales between the ranks of Constable and Chief Inspector we addressed two questions to help better understand female officers’ career progression: the extent to which female officers saw hierarchical rank progression, first as realistic and second as desirable. Compared with male officers, and controlling for covariates, female constables were less likely to expect or desire progression to higher ranks, in particular Superintending and Chief Officer ranks. Gender differences in both expectation and aspiration regarding hierarchical rank progression were more limited amongst supervisory ranks. The implications of these findings for achieving a gender-representative police service are discussed.
Initial boundary-value problem for the spherically symmetric Einstein equations with fluids with tangential pressure
Authors: Brito Irene , Mena Filipe C.
Published: August 2017

We prove that, for a given spherically symmetric fluid distribution with tangential pressure on an initial space-like hypersurface with a time-like boundary, there exists a unique, local in time solution to the Einstein equations in a neighbourhood of the boundary. As an application, we consider a particular elastic fluid interior matched to a vacuum exterior.
A tale of two nested elastic rings
Authors: Napoli G. , Goriely A.
Published: August 2017

Elastic rods in contact provide a rich paradigm for understanding shape and deformation in interacting elastic bodies. Here, we consider the problem of determining the static solutions of two nested elastic rings in the plane. If the inner ring is longer than the outer ring, it will buckle creating a space between the two rings. This deformation can be further influenced by either adhesion between the rings or if pressure is applied externally or internally. We obtain an exact solution of this problem when both rings are assumed inextensible and unshearable. Through a variational formulation of the problem, we identify the boundary conditions at the contact point and use the Kirchhoff analogy to give exact solutions of the problems in terms of elliptic functions. The role of both adhesion and pressure is explored.
Exotic species enhance response diversity to land-use change but modify functional composition
Authors: Stavert Jamie R. , Pattemore David E. , Gaskett Anne C. , Beggs Jacqueline R. , Bartomeus Ignasi
Published: August 2017

Two main mechanisms may buffer ecosystem functions despite biodiversity loss. First, multiple species could share similar ecological roles, thus providing functional redundancy. Second, species may respond differently to environmental change (response diversity). However, ecosystem function would be best protected when functionally redundant species also show response diversity. This linkage has not been studied directly, so we investigated whether native and exotic pollinator species with similar traits (functional redundancy) differed in abundance (response diversity) across an agricultural intensification gradient. Exotic pollinator species contributed most positive responses, which partially stabilized overall abundance of the pollinator community. However, although some functionally redundant species exhibited response diversity, this was not consistent across functional groups and aggregate abundances within each functional group were rarely stabilized. This shows functional redundancy and response diversity do not always operate in concert. Hence, despite exotic species becoming increasingly dominant in human-modified systems, they cannot replace the functional composition of native species.
A new giant titanosaur sheds light on body mass evolution among sauropod dinosaurs
Authors: Carballido José L. , Pol Diego , Otero Alejandro , Cerda Ignacio A. , Salgado Leonardo , Garrido Alberto C. , Ramezani Jahandar , Cúneo Néstor R. , Krause Javier M.
Published: August 2017

Titanosauria was the most diverse and successful lineage of sauropod dinosaurs. This clade had its major radiation during the middle Early Cretaceous and survived up to the end of that period. Among sauropods, this lineage has the most disparate values of body mass, including the smallest and largest sauropods known. Although recent findings have improved our knowledge on giant titanosaur anatomy, there are still many unknown aspects about their evolution, especially for the most gigantic forms and the evolution of body mass in this clade. Here we describe a new giant titanosaur, which represents the largest species described so far and one of the most complete titanosaurs. Its inclusion in an extended phylogenetic analysis and the optimization of body mass reveals the presence of an endemic clade of giant titanosaurs inhabited Patagonia between the Albian and the Santonian. This clade includes most of the giant species of titanosaurs and represents the major increase in body mass in the history of Titanosauria.
Increased prenatal maternal investment reduces inbreeding depression in offspring
Authors: Ihle Kate E. , Hutter Pascale , Tschirren Barbara
Published: August 2017

Inbreeding depression refers to the reduction of fitness that results from matings between relatives. Evidence for reduced fitness in inbred individuals is widespread, but the strength of inbreeding depression varies widely both within and among taxa. Environmental conditions can mediate this variation in the strength of inbreeding depression, with environmental stress exacerbating the negative consequences of inbreeding. Parents can modify the environment experienced by offspring, and have thus the potential to mitigate the negative consequences of inbreeding. While such parental effects have recently been demonstrated during the postnatal period, the role of prenatal parental effects in influencing the expression of inbreeding depression remains unexplored. To address this gap, we performed matings between full-sibs or unrelated individuals in replicated lines of Japanese quail (
Coturnix japonica
) experimentally selected for high and low maternal egg provisioning. We show that in the low maternal investment lines hatching success was strongly reduced when parents were related. In the high maternal investment lines, however, this negative effect of inbreeding on hatching success was absent, demonstrating that prenatal maternal provisioning can alleviate the negative fitness consequences of inbreeding.
Multimodal Study of Resting-State Functional Connectivity Networks using EEG electrodes position as seed
Authors: Rojas Gonzalo M. , Alvarez Carolina , Montoya Carlos , de la Iglesia-Vayá María , Cisternas Jaime , Gálvez Marcelo
Published: August 2017

Electroencephalography (EEG) is the standard diagnosis method for a wide variety of diseases such as epilepsy, sleep disorders, encephalopathies, and coma, among others. Resting-state functional magnetic resonance (rs-fMRI) is currently a technique used in research in both healthy individuals as well as patients. EEG and fMRI are procedures used to obtain direct and indirect measurements of brain neural activity: EEG measures the electrical activity of the brain using electrodes placed on the scalp, and fMRI detects the changes in blood oxygenation that occur in response to neural activity. EEG has a high temporal resolution and low spatial resolution, while fMRI has high spatial resolution and low temporal resolution. Thus, the combination of EEG with rs-fMRI using different methods could be very useful for research and clinical applications. In this article, we describe and show the results of a new methodology for processing rs-fMRI using seeds positioned according to the 10-10 EEG standard. We analyze the functional connectivity and adjacency matrices obtained using 65 seeds based on 10-10 EEG scheme and 21 seeds based on 10-20 EEG. Connectivity networks are created using each 10-20 EEG seeds and are analyzed by comparisons to the seven networks that have been found in recent studies. The proposed method captures high correlation between contralateral seeds, ipsilateral and contralateral occipital seeds, and some in the frontal lobe.
Expanding primary cells from mucoepidermoid and other salivary gland neoplasms for genetic and chemosensitivity testing
Authors: Alamri Ahmad M. , Liu Xuefeng , Blancato Jan K. , Haddad Bassem R. , Wang Weisheng , Zhong Xiaogang , Choudhary Sujata , Krawczyk Ewa , Kallakury Bhaskar V. , Davidson Bruce J. , Furth Priscilla A.
Published: August 2017

Restricted availability of cell and animal models is a rate-limiting step for investigation of salivary gland neoplasm pathophysiology and therapeutic response. Conditionally reprogrammed cell (CRC) technology enables establishment of primary epithelial cell cultures from patient material. This study tested a translational workflow for acquisition, expansion and testing of CRC-derived primary cultures of salivary gland neoplasms from patients presenting to an academic surgical practice. Results showed cultured cells were sufficient for epithelial cell-specific transcriptome characterization to detect candidate therapeutic pathways and fusion genes in addition to screening for cancer-risk-associated single nucleotide polymorphisms (SNPs) and driver gene mutations through exome sequencing. Focused study of primary cultures of a low-grade mucoepidermoid carcinoma demonstrated Amphiregulin-Mechanistic Target of Rapamycin-AKT/Protein kinase B (AKT) pathway activation, identified through bioinformatics and subsequently confirmed as present in primary tissue and preserved through different secondary 2D and 3D culture media and xenografts. Candidate therapeutic testing showed that the allosteric AKT inhibitor MK2206 reproducibly inhibited cell survival across different culture formats. In contrast, the cells appeared resistant to the adenosine triphosphate competitive AKT inhibitor GSK690693. Procedures employed here illustrate an approach for reproducibly obtaining material for pathophysiological studies of salivary gland neoplasms, and other less common epithelial cancer types, that can be executed without compromising pathological examination of patient specimens. The approach permits combined genetic and cell-based physiological and therapeutic investigations in addition to more traditional pathologic studies and can be used to build sustainable bio-banks for future inquiries.