bluuebunny/crossref_metadata_2025 huggingface dataset:
Simultaneous Observation of Cells and Nuclear Tracks from the Boron Neutron Capture Reaction by UV-C Sensitization of Polycarbonate
Authors: Portu Agustina , Rossini Andrés Eugenio , Thorp Silvia Inés , Curotto Paula , Pozzi Emiliano César Cayetano , Granell Pablo , Golmar Federico , Cabrini Rómulo Luis , Martin Gisela Saint
Published: July 2015

The distribution of boron in tissue samples coming from boron neutron capture therapy protocols can be determined through the analysis of its autoradiography image on a nuclear track detector. A more precise knowledge of boron atom location on the microscopic scale can be attained by the observation of nuclear tracks superimposed on the sample image on the detector. A method to produce an “imprint” of cells cultivated on a polycarbonate detector was developed, based on the photodegradation properties of UV-C radiation on this material. Optimal conditions to generate an appropriate monolayer of Mel-J cells incubated with boronophenylalanine were found. The best images of both cells and nuclear tracks were obtained for a neutron fluence of 1013cm−2, 6 h UV-C (254 nm) exposure, and 4 min etching time with a KOH solution. The imprint morphology was analyzed by both light and scanning electron microscopy. Similar samples, exposed to UV-A (360 nm) revealed no cellular imprinting. Etch pits were present only inside the cell imprints, indicating a preferential boron uptake (about threefold the incubation concentration). Comparative studies of boron absorption in different cell lines andin vitroevaluation of the effect of diverse boron compounds are feasible with this methodology.
First record and range extension of the Antarctic coral Flabellum (Flabellum) impensum Squires, 1962 (Cnidaria: Scleractinia) in Argentinean coastal waters
Authors: Schejter Laura , Bremec Claudia
Published: July 2015

The present paper reports the occurrence of the Antarctic coralFlabellum impensumin Tierra del Fuego Province, Argentina, and extends its distribution northwards in the south-west Atlantic Ocean. Nine individuals were found in Argentinean coastal waters in 2014, also representing one of the shallowest records of the species.
First record of Norwegian killer whales attacking and feeding on a harbour porpoise
Authors: Cosentino A. Mel
Published: July 2015

Orcinus orcais a cosmopolitan species and the most widely distributed marine mammal. Its diet includes over 140 species of fish, cephalopods, sea birds and marine mammals. However, many populations are specialised on certain specific prey items. Three genetically distinct populations have been described in the North Atlantic. Population A (that includes the Icelandic and Norwegian sub-populations) is believed to be piscivorous, as is population C, which includes fish-eating killer whales from the Strait of Gibraltar. In contrast, population B feeds on both fish and marine mammals. Norwegian killer whales follow the Norwegian spring spawning herring stock. The only description in the literature of Norwegian killer whales feeding on another cetacean species is a predation event on northern bottlenose whales in 1968. Daily land-based surveys targeting sperm whales were conducted from the Andenes lighthouse using BigEyes®binoculars (25×, 80 mm). The location of animals at sea was approximated through the use of an internal reticule system and a graduated wheel. On 24 June 2012 at 3:12 am, an opportunistic sighting of 11 killer whales was made off Andenes harbour. The whales hunted and fed on a harbour porpoise. Despite these species having overlapping distributions in Norwegian waters, this is the first predatory event reported in the literature.
Learning Geoscience by Doing Geoscience
Authors: Murray Laura
Published: July 2015

A pilot project helps teachers bring scientific practice into the classroom.
Targeting neddylation induces DNA damage and checkpoint activation and sensitizes chronic lymphocytic leukemia B cells to alkylating agents
Authors: Paiva C , Godbersen J C , Berger A , Brown J R , Danilov A V
Published: July 2015

Microenvironment-mediated upregulation of the B-cell receptor (BCR) and nuclear factor-κB (NF-κB) signaling in CLL cells resident in the lymph node and bone marrow promotes apoptosis evasion and clonal expansion. We recently reported that MLN4924 (pevonedistat), an investigational agent that inhibits the NEDD8-activating enzyme (NAE), abrogates stromal-mediated NF-κB pathway activity and CLL cell survival. However, the NAE pathway also assists degradation of multiple other substrates. MLN4924 has been shown to induce DNA damage and cell cycle arrest, but the importance of this mechanism in primary neoplastic B cells has not been studied. Here we mimicked the lymph node microenvironment using CD40 ligand (CD40L)-expressing stroma and interleukin-21 (IL-21) to find that inducing proliferation of the primary CLL cells conferred enhanced sensitivity to NAE inhibition. Treatment of the CD40-stimulated CLL cells with MLN4924 resulted in deregulation of Cdt1, a DNA replication licensing factor, and cell cycle inhibitors p21 and p27. This led to DNA damage, checkpoint activation and G2 arrest. Alkylating agents bendamustine and chlorambucil enhanced MLN4924-mediated DNA damage and apoptosis. These events were more prominent in cells stimulated with IL-21 compared with CD40L alone, indicating that, following NAE inhibition, the culture conditions were able to direct CLL cell fate from an NF-κB inhibition to a Cdt1 induction program. Our data provide insight into the biological consequences of targeting NAE in CLL and serves as further rationale for studying the clinical activity of MLN4924 in CLL, particularly in combination with alkylating agents.
Alpha-Synuclein affects neurite morphology, autophagy, vesicle transport and axonal degeneration in CNS neurons
Authors: Koch J C , Bitow F , Haack J , d'Hedouville Z , Zhang J-N , Tönges L , Michel U , Oliveira L M A , Jovin T M , Liman J , Tatenhorst L , Bähr M , Lingor P
Published: July 2015

Many neuropathological and experimental studies suggest that the degeneration of dopaminergic terminals and axons precedes the demise of dopaminergic neurons in the substantia nigra, which finally results in the clinical symptoms of Parkinson disease (PD). The mechanisms underlying this early axonal degeneration are, however, still poorly understood. Here, we examined the effects of overexpression of human wildtype alpha-synuclein (αSyn-WT), a protein associated with PD, and its mutant variantsαSyn-A30P and -A53T on neurite morphology and functional parameters in rat primary midbrain neurons (PMN). Moreover, axonal degeneration after overexpression ofαSyn-WT and -A30P was analyzed by live imaging in the rat optic nervein vivo. We found that overexpression ofαSyn-WT and of its mutants A30P and A53T impaired neurite outgrowth of PMN and affected neurite branching assessed by Sholl analysis in a variant-dependent manner. Surprisingly, the number of primary neurites per neuron was increased in neurons transfected withαSyn. Axonal vesicle transport was examined by live imaging of PMN co-transfected with EGFP-labeled synaptophysin. Overexpression of allαSyn variants significantly decreased the number of motile vesicles and decelerated vesicle transport compared with control. Macroautophagic flux in PMN was enhanced byαSyn-WT and -A53T but not byαSyn-A30P. Correspondingly, colocalization ofαSyn and the autophagy marker LC3 was reduced forαSyn-A30P compared with the otherαSyn variants. The number of mitochondria colocalizing with LC3 as a marker for mitophagy did not differ among the groups. In the rat optic nerve, bothαSyn-WT and -A30P accelerated kinetics of acute axonal degeneration following crush lesion as analyzed byin vivolive imaging. We conclude thatαSyn overexpression impairs neurite outgrowth and augments axonal degeneration, whereas axonal vesicle transport and autophagy are severely altered.
Multiple sclerosis: getting personal with induced pluripotent stem cells
Authors: Di Ruscio A , Patti F , Welner R S , Tenen D G , Amabile G
Published: July 2015

Human induced pluripotent stem (iPS) cells can be derived from lineage-restricted cells and represent an important tool to develop novel patient-specific cell therapies and research models for inherited and acquired diseases. Recently, patient-derived iPS cells, containing donor genetic background, have offered a breakthrough approach to study human genetics of neurodegenerative diseases. By offering an unlimited source of patient-specific disease-relevant cells, iPS cells hold great promise for understanding disease mechanisms, identifying molecular targets and developing phenotypic screens for drug discovery. This review will discuss the potential impact of using iPS cell-derived models in multiple sclerosis (MS) research and highlight some of the current challenges and prospective for generating novel therapeutic treatments for MS patients.
Estrogen receptor α regulates non-canonical autophagy that provides stress resistance to neuroblastoma and breast cancer cells and involves BAG3 function
Authors: Felzen V , Hiebel C , Koziollek-Drechsler I , Reißig S , Wolfrum U , Kögel D , Brandts C , Behl C , Morawe T
Published: July 2015

Breast cancer is a heterogeneous disease and approximately 70% of newly diagnosed breast cancers are estrogen receptor (ER) positive. Out of the two ER types, α and β, ERα is the only ER that is detectable by immunohistochemistry in breast cancer biopsies and is the predominant subtype expressed in breast tumor tissue. ER-positive tumors are currently treated with anti-hormone therapy to inhibit ER signaling. It is well known that breast cancer cells can develop endocrine resistance and resistance to anti-hormone therapy and this can be facilitated via the autophagy pathway, but so far the description of a detailed autophagy expression profile of ER-positive cancer cells is missing. In the present study, we characterized tumor cell lines ectopically expressing ERα or ERβ as well as the breast cancer-derived MCF-7 cell line endogenously expressing ERα but being ERβ negative. We could show that ERα-expressing cells have a higher autophagic activity than cells expressing ERβ and cells lacking ER expression. Additionally, for autophagy-related gene expression we describe an ERα-specific ‘autophagy-footprint’ that is fundamentally different to tumor cells expressing ERβ or lacking ER expression. This newly described ERα-mediated and estrogen response element (ERE)-independent non-canonical autophagy pathway, which involves the function of the co-chaperone Bcl2-associated athanogene 3 (BAG3), is independent of classical mammalian target of rapamycin (mTOR) and phosphatidylinositol 3 kinase (PI3K) signaling networks and provides stress resistance in our model systems. Altogether, our study uncovers a novel non-canonical autophagy pathway that might be an interesting target for personalized medicine and treatment of ERα-positive breast cancer cells that do not respond to anti-hormone therapy and classical autophagy inhibitors.
Single-cell imaging of inflammatory caspase dimerization reveals differential recruitment to inflammasomes
Authors: Sanders M G , Parsons M J , Howard A G A , Liu J , Fassio S R , Martinez J A , Bouchier-Hayes L
Published: July 2015

The human inflammatory caspases, including caspase-1, -4, -5 and -12, are considered as key regulators of innate immunity protecting from sepsis and numerous inflammatory diseases. Caspase-1 is activated by proximity-induced dimerization following recruitment to inflammasomes but the roles of the remaining inflammatory caspases in inflammasome assembly are unclear. Here, we use caspase bimolecular fluorescence complementation to visualize the assembly of inflammasomes and dimerization of inflammatory caspases in single cells. We observed caspase-1 dimerization induced by the coexpression of a range of inflammasome proteins and by lipospolysaccharide (LPS) treatment in primary macrophages. Caspase-4 and -5 were only dimerized by select inflammasome proteins, whereas caspase-12 dimerization was not detected by any investigated treatment. Strikingly, we determined that certain inflammasome proteins could induce heterodimerization of caspase-1 with caspase-4 or -5. Caspase-5 homodimerization and caspase-1/-5 heterodimerization was also detected in LPS-primed primary macrophages in response to cholera toxin subunit B. The subcellular localization and organization of the inflammasome complexes varied markedly depending on the upstream trigger and on which caspase or combination of caspases were recruited. Three-dimensional imaging of the ASC (apoptosis-associated speck-like protein containing a caspase recruitment domain)/caspase-1 complexes revealed a large spherical complex of ASC with caspase-1 dimerized on the outer surface. In contrast, NALP1 (NACHT leucine-rich repeat protein 1)/caspase-1 complexes formed large filamentous structures. These results argue that caspase-1, -4 or -5 can be recruited to inflammasomes under specific circumstances, often leading to distinctly organized and localized complexes that may impact the functions of these proteases.
Rapid neodymium release to marine waters from lithogenic sediments in the Amazon estuary
Authors: Rousseau Tristan C. C. , Sonke Jeroen E. , Chmeleff Jérôme , van Beek Pieter , Souhaut Marc , Boaventura Geraldo , Seyler Patrick , Jeandel Catherine
Published: July 2015

Rare earth element (REE) concentrations and neodymium isotopic composition (ɛNd) are tracers for ocean circulation and biogeochemistry. Although models suggest that REE release from lithogenic sediment in river discharge may dominate all other REE inputs to the oceans, the occurrence, mechanisms and magnitude of such a source are still debated. Here we present the first simultaneous observations of dissolved (<0.45 μm), colloidal and particulate REE and ɛNd in the Amazon estuary. A sharp drop in dissolved REE in the low-salinity zone is driven by coagulation of colloidal matter. At mid-salinities, total dissolved REE levels slightly increase, while ɛNd values are shifted from the dissolved Nd river endmember (−8.9) to values typical of river suspended matter (−10.6). Combining a Nd isotope mass balance with apparent radium isotope ages of estuarine waters suggests a rapid (3 weeks) and globally significant Nd release by dissolution of lithogenic suspended sediments.
New streams and springs after the 2014 Mw6.0 South Napa earthquake
Authors: Wang Chi-Yuen , Manga Michael
Published: July 2015

Many streams and springs, which were dry or nearly dry before the 2014 Mw6.0 South Napa earthquake, started to flow after the earthquake. A United States Geological Survey stream gauge also registered a coseismic increase in discharge. Public interest was heightened by a state of extreme drought in California. Since the new flows were not contaminated by pre-existing surface water, their composition allowed unambiguous identification of their origin. Following the earthquake we repeatedly surveyed the new flows, collecting data to test hypotheses about their origin. We show that the new flows originated from groundwater in nearby mountains released by the earthquake. The estimated total amount of new water is ∼106 m3, about 1/40 of the annual water use in the Napa–Sonoma area. Our model also makes a testable prediction of a post-seismic decrease of seismic velocity in the shallow crust of the affected region.
Ubiquitous healthy diatoms in the deep sea confirm deep carbon injection by the biological pump
Authors: Agusti S. , González-Gordillo J. I. , Vaqué D. , Estrada M. , Cerezo M. I. , Salazar G. , Gasol J. M. , Duarte C. M.
Published: July 2015

The role of the ocean as a sink for CO2 is partially dependent on the downward transport of phytoplankton cells packaged within fast-sinking particles. However, whether such fast-sinking mechanisms deliver fresh organic carbon down to the deep bathypelagic sea and whether this mechanism is prevalent across the ocean requires confirmation. Here we report the ubiquitous presence of healthy photosynthetic cells, dominated by diatoms, down to 4,000 m in the deep dark ocean. Decay experiments with surface phytoplankton suggested that the large proportion (18%) of healthy photosynthetic cells observed, on average, in the dark ocean, requires transport times from a few days to a few weeks, corresponding to sinking rates (124–732 m d−1) comparable to those of fast-sinking aggregates and faecal pellets. These results confirm the expectation that fast-sinking mechanisms inject fresh organic carbon into the deep sea and that this is a prevalent process operating across the global oligotrophic ocean.
Lansoprazole is an antituberculous prodrug targeting cytochrome bc1
Authors: Rybniker Jan , Vocat Anthony , Sala Claudia , Busso Philippe , Pojer Florence , Benjak Andrej , Cole Stewart T.
Published: July 2015

Better antibiotics capable of killing multi-drug-resistant Mycobacterium tuberculosis are urgently needed. Despite extensive drug discovery efforts, only a few promising candidates are on the horizon and alternative screening protocols are required. Here, by testing a panel of FDA-approved drugs in a host cell-based assay, we show that the blockbuster drug lansoprazole (Prevacid), a gastric proton-pump inhibitor, has intracellular activity against M. tuberculosis. Ex vivo pharmacokinetics and target identification studies reveal that lansoprazole kills M. tuberculosis by targeting its cytochrome bc1 complex through intracellular sulfoxide reduction to lansoprazole sulfide. This novel class of cytochrome bc1 inhibitors is highly active against drug-resistant clinical isolates and spares the human H+K+-ATPase thus providing excellent opportunities for targeting the major pathogen M. tuberculosis. Our finding provides proof of concept for hit expansion by metabolic activation, a powerful tool for antibiotic screens.
Crucial roles of RSK in cell motility by catalysing serine phosphorylation of EphA2
Authors: Zhou Yue , Yamada Naoki , Tanaka Tomohiro , Hori Takashi , Yokoyama Satoru , Hayakawa Yoshihiro , Yano Seiji , Fukuoka Junya , Koizumi Keiichi , Saiki Ikuo , Sakurai Hiroaki
Published: July 2015

Crosstalk between inflammatory signalling pathways and receptor tyrosine kinases has been revealed as an indicator of cancer malignant progression. In the present study, we focus on EphA2 receptor tyrosine kinase, which is overexpressed in many human cancers. It has been reported that ligand-independent phosphorylation of EphA2 at Ser-897 is induced by Akt. We show that inflammatory cytokines promote RSK-, not Akt-, dependent phosphorylation of EphA2 at Ser-897. In addition, the RSK–EphA2 signalling pathway controls cell migration and invasion of metastatic breast cancer cells. Moreover, Ser-897-phosphorylated EphA2 co-localizes with phosphorylated active form of RSK in various human tumour specimens, and this double positivity is related to poor survival in lung cancer patients, especially those with a smoking history. Taken together, these results indicate that the phosphorylation of EphA2 at Ser-897 is controlled by RSK and the RSK–EphA2 axis might contribute to cell motility and promote tumour malignant progression.
Significant radiative impact of volcanic aerosol in the lowermost stratosphere
Authors: Andersson Sandra M. , Martinsson Bengt G. , Vernier Jean-Paul , Friberg Johan , Brenninkmeijer Carl A. M. , Hermann Markus , van Velthoven Peter F. J. , Zahn Andreas
Published: July 2015

Despite their potential to slow global warming, until recently, the radiative forcing associated with volcanic aerosols in the lowermost stratosphere (LMS) had not been considered. Here we study volcanic aerosol changes in the stratosphere using lidar measurements from the NASA CALIPSO satellite and aircraft measurements from the IAGOS-CARIBIC observatory. Between 2008 and 2012 volcanism frequently affected the Northern Hemisphere stratosphere aerosol loadings, whereas the Southern Hemisphere generally had loadings close to background conditions. We show that half of the global stratospheric aerosol optical depth following the Kasatochi, Sarychev and Nabro eruptions is attributable to LMS aerosol. On average, 30% of the global stratospheric aerosol optical depth originated in the LMS during the period 2008–2011. On the basis of the two independent, high-resolution measurement methods, we show that the LMS makes an important contribution to the overall volcanic forcing.
Point nodes persisting far beyond Tc in Bi2212
Authors: Kondo Takeshi , Malaeb W. , Ishida Y. , Sasagawa T. , Sakamoto H. , Takeuchi Tsunehiro , Tohyama T. , Shin S.
Published: July 2015

In contrast to a complex feature of antinodal state, suffering from competing orders, the pairing gap of cuprates is obtained in the nodal region, which therefore holds the key to the superconducting mechanism. One of the biggest question is whether the point nodal state as a hallmark of d-wave pairing collapses at Tc like the BCS-type superconductors, or it instead survives above Tc turning into the preformed pair state. A difficulty in this issue comes from the small magnitude of the nodal gap, which has been preventing experimentalists from solving it. Here we use a laser ARPES capable of ultrahigh-energy resolution, and detect the point nodes surviving far beyond Tc in Bi2212. By tracking the temperature evolution of spectra, we reveal that the superconductivity occurs when the pair-breaking rate is suppressed smaller than the single-particle scattering rate on cooling, which governs the value of Tc in cuprates.
Biotin starvation causes mitochondrial protein hyperacetylation and partial rescue by the SIRT3-like deacetylase Hst4p
Authors: Madsen Christian T. , Sylvestersen Kathrine B. , Young Clifford , Larsen Sara C. , Poulsen Jon W. , Andersen Marianne A. , Palmqvist Eva A. , Hey-Mogensen Martin , Jensen Per B. , Treebak Jonas T. , Lisby Michael , Nielsen Michael L.
Published: July 2015

The essential vitamin biotin is a covalent and tenaciously attached prosthetic group in several carboxylases that play important roles in the regulation of energy metabolism. Here we describe increased acetyl-CoA levels and mitochondrial hyperacetylation as downstream metabolic effects of biotin deficiency. Upregulated mitochondrial acetylation sites correlate with the cellular deficiency of the Hst4p deacetylase, and a biotin-starvation-induced accumulation of Hst4p in mitochondria supports a role for Hst4p in lowering mitochondrial acetylation. We show that biotin starvation and knockout of Hst4p cause alterations in cellular respiration and an increase in reactive oxygen species (ROS). These results suggest that Hst4p plays a pivotal role in biotin metabolism and cellular energy homeostasis, and supports that Hst4p is a functional yeast homologue of the sirtuin deacetylase SIRT3. With biotin deficiency being involved in various metabolic disorders, this study provides valuable insight into the metabolic effects biotin exerts on eukaryotic cells.
Vibronic origin of long-lived coherence in an artificial molecular light harvester
Authors: Lim James , Paleček David , Caycedo-Soler Felipe , Lincoln Craig N. , Prior Javier , von Berlepsch Hans , Huelga Susana F. , Plenio Martin B. , Zigmantas Donatas , Hauer Jürgen
Published: July 2015

Natural and artificial light-harvesting processes have recently gained new interest. Signatures of long-lasting coherence in spectroscopic signals of biological systems have been repeatedly observed, albeit their origin is a matter of ongoing debate, as it is unclear how the loss of coherence due to interaction with the noisy environments in such systems is averted. Here we report experimental and theoretical verification of coherent exciton–vibrational (vibronic) coupling as the origin of long-lasting coherence in an artificial light harvester, a molecular J-aggregate. In this macroscopically aligned tubular system, polarization-controlled 2D spectroscopy delivers an uncongested and specific optical response as an ideal foundation for an in-depth theoretical description. We derive analytical expressions that show under which general conditions vibronic coupling leads to prolonged excited-state coherence.
Patient perceptions of severe COPD and transitions towards death: a qualitative study identifying milestones and developing key opportunities
Authors: Landers Amanda , Wiseman Rachel , Pitama Suzanne , Beckert Lutz
Published: July 2015

Background:

Chronic obstructive pulmonary disease (COPD) is a slowly disabling illness, with functional limitations and a high burden of symptoms. Palliative care services focus on quality of life for those facing life-limiting illness. Patients with COPD often see their illness as a ‘way of life’, not as a life-threatening illness, which makes the interface difficult.

Aims:

The aim of this study was to explore the experience of patients with advanced COPD after a life-threatening event, particularly focusing on end-of-life issues.

Methods:

Qualitative methods were used to capture patient experiences. Patients admitted for noninvasive ventilation for COPD were recruited and interviewed in their homes following discharge. The interview schedule explored the participants' understanding of their illness, concerns and plans, exploring end-of-life issues and perceptions of palliative care.

Results:

Participants were recruited until themes were saturated. Six transition points or milestones emerged: loss of recreation, home environment, episodes of acute care, long-term oxygen treatment, panic attacks, and assistance with self-care were common themes throughout the narratives.

Conclusions:

Milestones accumulate in no particular order. They can be easily recognised and allow health professionals to develop a common language with their patients. In advancing COPD, milestones may trigger the reassessment of goals of care and integration of a palliative approach.
Revealing Missing Human Protein Isoforms Based on Ab Initio Prediction, RNA-seq and Proteomics
Authors: Hu Zhiqiang , Scott Hamish S. , Qin Guangrong , Zheng Guangyong , Chu Xixia , Xie Lu , Adelson David L. , Oftedal Bergithe E. , Venugopal Parvathy , Babic Milena , Hahn Christopher N. , Zhang Bing , Wang Xiaojing , Li Nan , Wei Chaochun
Published: July 2015

Biological and biomedical research relies on comprehensive understanding of protein-coding transcripts. However, the total number of human proteins is still unknown due to the prevalence of alternative splicing. In this paper, we detected 31,566 novel transcripts with coding potential by filtering our ab initio predictions with 50 RNA-seq datasets from diverse tissues/cell lines. PCR followed by MiSeq sequencing showed that at least 84.1% of these predicted novel splice sites could be validated. In contrast to known transcripts, the expression of these novel transcripts were highly tissue-specific. Based on these novel transcripts, at least 36 novel proteins were detected from shotgun proteomics data of 41 breast samples. We also showed L1 retrotransposons have a more significant impact on the origin of new transcripts/genes than previously thought. Furthermore, we found that alternative splicing is extraordinarily widespread for genes involved in specific biological functions like protein binding, nucleoside binding, neuron projection, membrane organization and cell adhesion. In the end, the total number of human transcripts with protein-coding potential was estimated to be at least 204,950.
A High Throughput Ambient Mass Spectrometric Approach to Species Identification and Classification from Chemical Fingerprint Signatures
Authors: Musah Rabi A. , Espinoza Edgard O. , Cody Robert B. , Lesiak Ashton D. , Christensen Earl D. , Moore Hannah E. , Maleknia Simin , Drijfhout Falko P.
Published: July 2015

A high throughput method for species identification and classification through chemometric processing of direct analysis in real time (DART) mass spectrometry-derived fingerprint signatures has been developed. The method entails introduction of samples to the open air space between the DART ion source and the mass spectrometer inlet, with the entire observed mass spectral fingerprint subjected to unsupervised hierarchical clustering processing. A range of both polar and non-polar chemotypes are instantaneously detected. The result is identification and species level classification based on the entire DART-MS spectrum. Here, we illustrate how the method can be used to: (1) distinguish between endangered woods regulated by the Convention for the International Trade of Endangered Flora and Fauna (CITES) treaty; (2) assess the origin and by extension the properties of biodiesel feedstocks; (3) determine insect species from analysis of puparial casings; (4) distinguish between psychoactive plants products; and (5) differentiate between Eucalyptus species. An advantage of the hierarchical clustering approach to processing of the DART-MS derived fingerprint is that it shows both similarities and differences between species based on their chemotypes. Furthermore, full knowledge of the identities of the constituents contained within the small molecule profile of analyzed samples is not required.
Production of graphene oxide from pitch-based carbon fiber
Authors: Lee Miyeon , Lee Jihoon , Park Sung Young , Min Byunggak , Kim Bongsoo , In Insik
Published: July 2015

Pitch-based graphene oxide (p-GO) whose compositional/structural features are comparable to those of graphene oxide (GO) was firstly produced by chemical exfoliation of pitch-based carbon fiber rather than natural graphite. Incorporation of p-GO as nanofillers into poly(methyl methacrylate) (PMMA) as a matrix polymer resulted in excellent mechanical reinforcement. p-GO/PMMA nanocomposite (1 wt.-% p-GO) demonstrated 800% higher modulus of toughness of neat PMMA.
Dynamic phase coexistence in glass–forming liquids
Authors: Pastore Raffaele , Coniglio Antonio , Ciamarra Massimo Pica
Published: July 2015

One of the most controversial hypotheses for explaining the heterogeneous dynamics of glasses postulates the temporary coexistence of two phases characterized by a high and by a low diffusivity. In this scenario, two phases with different diffusivities coexist for a time of the order of the relaxation time and mix afterwards. Unfortunately, it is difficult to measure the single-particle diffusivities to test this hypothesis. Indeed, although the non-Gaussian shape of the van-Hove distribution suggests the transient existence of a diffusivity distribution, it is not possible to infer from this quantity whether two or more dynamical phases coexist. Here we provide the first direct observation of the dynamical coexistence of two phases with different diffusivities, by showing that in the deeply supercooled regime the distribution of the single-particle diffusivities acquires a transient bimodal shape. We relate this distribution to the heterogeneity of the dynamics and to the breakdown of the Stokes-Einstein relation and we show that the coexistence of two dynamical phases occurs up to a timescale growing faster than the relaxation time on cooling, for some of the considered models. Our work offers a basis for rationalizing the dynamics of supercooled liquids and for relating their structural and dynamical properties.
Demographic comparison of sweetpotato weevil reared on a major host, Ipomoea batatas, and an alternative host, I. triloba
Authors: Reddy Gadi V. P. , Chi Hisn
Published: July 2015

In this study, we collected life table data for the sweetpotato weevil,Cylas formicarius,grown onIpomoea batatasandIpomoea trilobaand analyzed them using an age-stage, two-sex life table. We also demonstrated the growth potential ofC. formicariuson these two host plants by using population projection. These data will be useful to the growers to the selection or eradication of host plants in an integrated control strategy forC. formicariusfor the entire area of the targeted areas. We found thatC. formicariusdeveloped faster onI. batatasthan onI. triloba. The developmental times of the larval and pupal stages onI. batatasthan onI. trilobawere 37.01 and 8.3 days. The adult females emerged before and began to produce eggs at 42 days earlier when reared onI. batatas. The fecundity of females was 90.0 eggs onI. batatassignificantly higher than the mean fecundity of 68.5 eggs onI. triloba. Although this insect has a higher intrinsic rate of increase onI. batatas, the study indicated thatC. formicariuscan successfully survive and reproduce on both host plants.
In vivo efficacy and molecular docking of designed peptide that exhibits potent antipneumococcal activity and synergises in combination with penicillin
Authors: Le Cheng-Foh , Yusof Mohd Yasim Mohd , Hassan Mahmood Ameen Abdulla , Lee Vannajan Sanghiran , Isa Diyana Mohd , Sekaran Shamala Devi
Published: July 2015

We have previously designed a series of antimicrobial peptides (AMPs) and in the current study, thein vivotherapeutic efficacy and toxicity were investigated. Among all the peptides, DM3 conferred protection to a substantial proportion of the lethally infected mice caused by a strain of penicillin-resistantStreptococcus pneumoniae.Synergism was reported and therapeutic efficacy was significantly enhanced when DM3 was formulated in combination with penicillin (PEN). No toxicity was observed in mice receiving these treatments. Thein silicomolecular docking study results showed that, DM3 has a strong affinity towards three protein targets; autolysin and pneumococcal surface protein A (pspA). Thus AMPs could serve as supporting therapeutics in combination with conventional antibiotics to enhance treatment outcome.
Magnetic patterning: local manipulation of the intergranular exchange coupling via grain boundary engineering
Authors: Huang Kuo-Feng , Liao Jung-Wei , Hsieh Cheng-Yu , Wang Liang-Wei , Huang Yen-Chun , Wen Wei-Chih , Chang Mu-Tung , Lo Shen-Chuan , Yuan Jun , Lin Hsiu-Hau , Lai Chih-Huang
Published: July 2015

Magnetic patterning, with designed spatial profile of the desired magnetic properties, has been a rising challenge for developing magnetic devices at nanoscale. Most existing methods rely on locally modifying magnetic anisotropy energy or saturation magnetization and thus post stringent constraints on the adaptability in diverse applications. We propose an alternative route for magnetic patterning: by manipulating the local intergranular exchange coupling to tune lateral magnetic properties. As demonstration, the grain boundary structure of Co/Pt multilayers is engineered by thermal treatment, where the stress state of the multilayers and thus the intergranular exchange coupling can be modified. With Ag passivation layers on top of the Co/Pt multilayers, we can hinder the stress relaxation and grain boundary modification. Combining the pre-patterned Ag passivation layer with thermal treatment, we can design spatial variations of the magnetic properties by tuning the intergranular exchange coupling, which diversifies the magnetic patterning process and extends its feasibility for varieties of new devices.
Involvement of PrPC in kainate-induced excitotoxicity in several mouse strains
Authors: Carulla Patricia , Llorens Franc , Matamoros-Angles Andreu , Aguilar-Calvo Patricia , Espinosa Juan Carlos , Gavín Rosalina , Ferrer Isidre , Legname Giuseppe , Torres Juan Maria , del Río José A.
Published: July 2015

The cellular prion protein (PrPC) has been associated with a plethora of cellular functions ranging from cell cycle to neuroprotection. Mice lacking PrPC show an increased susceptibility to epileptic seizures; the protein, then, is neuroprotective. However, lack of experimental reproducibility has led to considering the possibility that other factors besides PrPC deletion, such as the genetic background of mice or the presence of so-called “Prnp flanking genes”, might contribute to the reported susceptibility. Here, we performed a comparative analysis of seizure-susceptibility using characterized Prnp+/+ and Prnp0/0 mice of B6129, B6.129, 129/Ola or FVB/N genetic backgrounds. Our study indicates that PrPC plays a role in neuroprotection in KA-treated cells and mice. For this function, PrPC should contain the aa32–93 region and needs to be linked to the membrane. In addition, some unidentified “Prnp-flanking genes” play a role parallel to PrPC in the KA-mediated responses in B6129 and B6.129 Prnp0/0 mice.
Growth kinetics of white graphene (h-BN) on a planarised Ni foil surface
Authors: Cho Hyunjin , Park Sungchan , Won Dong-Il , Kang Sang Ook , Pyo Seong-Soo , Kim Dong-Ik , Kim Soo Min , Kim Hwan Chul , Kim Myung Jong
Published: July 2015

The morphology of the surface and the grain orientation of metal catalysts have been considered to be two important factors for the growth of white graphene (h-BN) by chemical vapour deposition (CVD). We report a correlation between the growth rate of h-BN and the orientation of the nickel grains. The surface of the nickel (Ni) foil was first polished by electrochemical polishing (ECP) and subsequently annealed in hydrogen at atmospheric pressure to suppress the effect of the surface morphology. Atmospheric annealing with hydrogen reduced the nucleation sites of h-BN, which induced a large crystal size mainly grown from the grain boundary with few other nucleation sites in the Ni foil. A higher growth rate was observed from the Ni grains that had the {110} or {100} orientation due to their higher surface energy.
Plasmakinetic resection technology for the treatment of benign prostatic hyperplasia: evidence from a systematic review and meta-analysis
Authors: Li Sheng , Kwong Joey S.W. , Zeng Xian-Tao , Ruan Xiao-Lan , Liu Tong-Zu , Weng Hong , Guo Yi , Xu Chang , Yan Jin-Zhu , Meng Xiang-Yu , Wang Xing-Huan
Published: July 2015

The aim of this study was to compare plasmakinetic resection of the prostate (PKRP) with transurethral resection of the prostate (TURP) for benign prostatic hyperplasia (BPH) in terms of efficacy and safety. Published RCTs were searched from PubMed, Embase, Science Citation Index and Cochrane Library up to April 10, 2014. After methodological quality assessment and data extraction, meta-analysis was performed using the STATA 12.0 software. 18 reports of 16 RCTs were included in this analysis. Meta-analyses showed that PKRP significantly improved Qmax at 12 months, but no significant difference was found for other efficacy outcomes. In terms of safety, treatment of PKRP was associated with reduced drop in serum sodium, lower TUR syndrome, reduced need of blood transfusion, clot retention and shorter catheterization time and hospital stay; in contrast, there were no significant differences in the analysis of operative time, postoperative fever and long-term postoperative complications. In summary, current evidence suggests that, although PKRP and TURP are both effective for BPH, PKRP is associated with additional potential benefits in efficacy and more favorable safety profile. It may be possible that PKRP may replace the TURP in the future and become a new standard surgical procedure.
To brood or not to brood: Are marine invertebrates that protect their offspring more resilient to ocean acidification?
Authors: Lucey Noelle Marie , Lombardi Chiara , DeMarchi Lucia , Schulze Anja , Gambi Maria Cristina , Calosi Piero
Published: July 2015

Anthropogenic atmospheric carbon dioxide (CO2) is being absorbed by seawater resulting in increasingly acidic oceans, a process known as ocean acidification (OA). OA is thought to have largely deleterious effects on marine invertebrates, primarily impacting early life stages and consequently, their recruitment and species’ survival. Most research in this field has been limited to short-term, single-species and single-life stage studies, making it difficult to determine which taxa will be evolutionarily successful under OA conditions. We circumvent these limitations by relating the dominance and distribution of the known polychaete worm species living in a naturally acidic seawater vent system to their life history strategies. These data are coupled with breeding experiments, showing all dominant species in this natural system exhibit parental care. Our results provide evidence supporting the idea that long-term survival of marine species in acidic conditions is related to life history strategies where eggs are kept in protected maternal environments (brooders) or where larvae have no free swimming phases (direct developers). Our findings are the first to formally validate the hypothesis that species with life history strategies linked to parental care are more protected in an acidifying ocean compared to their relatives employing broadcast spawning and pelagic larval development.
DNA-dependent targeting of cell nuclei by a lupus autoantibody
Authors: Weisbart Richard H. , Chan Grace , Jordaan Gwen , Noble Philip W. , Liu Yanfeng , Glazer Peter M. , Nishimura Robert N. , Hansen James E.
Published: July 2015

A nuclear-penetrating lupus anti-DNA autoantibody, 3E10, has been found to inhibit DNA repair and selectively kill certain cancer cells that are highly vulnerable to DNA damage. In addition, a 3E10 single chain variable fragment (scFv) has been developed for use as a delivery vehicle to carry therapeutic cargo proteins into cell nuclei. A greater understanding of the mechanism by which 3E10 penetrates cell nuclei is needed to help determine the scope of its potential therapeutic applications. Here we show that the presence of extracellular DNA significantly enhances the nuclear uptake of 3E10 scFv. In addition, we find that 3E10 scFv preferentially localizes into tumor cell nuclei in vivo, likely due to increased DNA in the local environment released from ischemic and necrotic regions of tumor. These data provide insight into the mechanism of nuclear penetration by 3E10 and demonstrate the potential for use of 3E10 in therapeutic approaches to diseases ranging from malignancy to ischemic conditions such as stroke.
Inactivation of group II intron RmInt1 in the Sinorhizobium meliloti genome
Authors: Dolores Molina-Sánchez María , Toro Nicolás
Published: July 2015

Group II introns are self-splicing catalytic RNAs that probably originated in bacteria and act as mobile retroelements. The dispersal and dynamics of group II intron spread within a bacterial genome are thought to follow a selection-driven extinction model. Likewise, various studies on the evolution of group II introns have suggested that they are evolving toward an inactive form by fragmentation, with the loss of the intron 3′-terminus, but with some intron fragments remaining and continuing to evolve in the genome. RmInt1 is a mobile group II intron that is widespread in natural populations of Sinorhizobium meliloti, but some strains of this species have no RmInt1 introns. We studied the splicing ability and mobility of the three full-length RmInt1 copies harbored by S. meliloti 1021 and obtained evidence suggesting that specific mutations may lead to the impairment of intron splicing and retrohoming. Our data suggest that the RmInt1 copies in this strain are undergoing a process of inactivation.
Coherent control of radiation patterns of nonlinear multiphoton processes in nanoparticles
Authors: Papoff Francesco , McArthur Duncan , Hourahine Ben
Published: July 2015

We propose a scheme for the coherent control of light waves and currents in metallic nanospheres which applies independently of the nonlinear multiphoton processes at the origin of waves and currents. We derive conditions on the external control field which enable us to change the radiation pattern and suppress radiative losses or to reduce absorption, enabling the particle to behave as a perfect scatterer or as a perfect absorber. The control introduces narrow features in the response of the particles that result in high sensitivity to small variations in the local environment, including subwavelength spatial shifts.
Mammalian ranges are experiencing erosion of natural darkness
Authors: Duffy James P. , Bennie Jonathan , Durán América P. , Gaston Kevin J.
Published: July 2015

The continuous increase in the intensity and extent of anthropogenic artificial light has significantly shaped Earth’s nighttime environment. This environmental change has effects across the natural world, with consequences for organismal physiology and behaviour and the abundances and distributions of species. Here, we evaluate for the first time the relations between the spatio-temporal patterns of anthropogenic nighttime light and the distribution of terrestrial mammals, one of the most endangered species groups and one that expresses varying time partitioning strategies. Using descriptive statistics, trend tests and spatial prioritization analysis we show that in most places on earth there is a terrestrial mammal species whose range is experiencing detectable artificial light. For most species this tends only to be for small parts of their range and those affected across large parts are typically rare. Over time (1992–2012), an increase in mean light intensity was found for the ranges of the majority of species, with very few experiencing a decrease. Moreover, nocturnal species are more likely to experience an increase in light within their ranges. This is of conservation concern as many terrestrial mammals are nocturnal and therefore often particularly vulnerable to a pressure such as artificial light at night.
Using Benford’s law to investigate Natural Hazard dataset homogeneity
Authors: Joannes-Boyau Renaud , Bodin Thomas , Scheffers Anja , Sambridge Malcolm , May Simon Matthias
Published: July 2015

Working with a large temporal dataset spanning several decades often represents a challenging task, especially when the record is heterogeneous and incomplete. The use of statistical laws could potentially overcome these problems. Here we apply Benford’s Law (also called the “First-Digit Law”) to the traveled distances of tropical cyclones since 1842. The record of tropical cyclones has been extensively impacted by improvements in detection capabilities over the past decades. We have found that, while the first-digit distribution for the entire record follows Benford’s Law prediction, specific changes such as satellite detection have had serious impacts on the dataset. The least-square misfit measure is used as a proxy to observe temporal variations, allowing us to assess data quality and homogeneity over the entire record and at the same time over specific periods. Such information is crucial when running climatic models and Benford’s Law could potentially be used to overcome and correct for data heterogeneity and/or to select the most appropriate part of the record for detailed studies.
Regulation rewiring analysis reveals mutual regulation between STAT1 and miR-155-5p in tumor immunosurveillance in seven major cancers
Authors: Lin Chen-Ching , Jiang Wei , Mitra Ramkrishna , Cheng Feixiong , Yu Hui , Zhao Zhongming
Published: July 2015

Transcription factors (TFs) and microRNAs (miRNAs) form a gene regulatory network (GRN) at the transcriptional and post-transcriptional level in living cells. However, this network has not been well characterized, especially in regards to the mutual regulations between TFs and miRNAs in cancers. In this study, we collected those regulations inferred by ChIP-Seq or CLIP-Seq to construct the GRN formed by TFs, miRNAs and target genes. To increase the reliability of the proposed network and examine the regulation activity of TFs and miRNAs, we further incorporated the mRNA and miRNA expression profiles in seven cancer types using The Cancer Genome Atlas data. We observed that regulation rewiring was prevalent during tumorigenesis and found that the rewired regulatory feedback loops formed by TFs and miRNAs were highly associated with cancer. Interestingly, we identified one regulatory feedback loop between STAT1 and miR-155-5p that is consistently activated in all seven cancer types with its function to regulate tumor-related biological processes. Our results provide insights on the losing equilibrium of the regulatory feedback loop between STAT1 and miR-155-5p influencing tumorigenesis.