bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long-duration animal tracking in difficult lighting conditions
Authors: Stern Ulrich , Zhu Edward Y. , He Ruo , Yang Chung-Hui 
Published: July 2015

AbstractHigh-throughput analysis of animal behavior requires software to analyze videos. Such software typically depends on the experiments’ being performed in good lighting conditions, but this ideal is difficult or impossible to achieve for certain classes of experiments. Here, we describe techniques that allow long-duration positional tracking in difficult lighting conditions with strong shadows or recurring “on”/“off” changes in lighting. The latter condition will likely become increasingly common, e.g., for Drosophila due to the advent of red-shifted channelrhodopsins. The techniques enabled tracking with good accuracy in three types of experiments with difficult lighting conditions in our lab. Our technique handling shadows relies on single-animal tracking and on shadows’ and flies’ being accurately distinguishable by distance to the center of the arena (or a similar geometric rule); the other techniques should be broadly applicable. We implemented the techniques as extensions of the widely-used tracking software Ctrax; however, they are relatively simple, not specific to Drosophila and could be added to other trackers as well.
Low-bias phosphopeptide enrichment from scarce samples using plastic antibodies
Authors: Chen Jing , Shinde Sudhirkumar , Koch Markus-Hermann , Eisenacher Martin , Galozzi Sara , Lerari Thilo , Barkovits Katalin , Subedi Prabal , Krüger Rejko , Kuhlmann Katja , Sellergren Börje , Helling Stefan , Marcus Katrin 
Published: July 2015

AbstractPhosphospecific enrichment techniques and mass spectrometry (MS) are essential tools for comprehending the cellular phosphoproteome. Here, we report a fast and simple approach for low sequence-bias phosphoserine (pS) peptide capture and enrichment that is compatible with low biological or clinical sample input. The approach exploits molecularly imprinted polymers (MIPs, “plastic antibodies”) featuring tight neutral binding sites for pS or pY that are capable of cross-reacting with phosphopeptides of protein proteolytic digests. The versatility of the resulting method was demonstrated with small samples of whole-cell lysate from human embryonic kidney (HEK) 293T cells, human neuroblastoma SH-SY5Y cells, mouse brain or human cerebrospinal fluid (CSF). Following pre-fractionation of trypsinized proteins by strong cation exchange (SCX) chromatography, pS-MIP enrichment led to the identification of 924 phosphopeptides in the HEK 293T whole-cell lysate, exceeding the number identified by TiO2-based enrichment (230). Moreover, the phosphopeptides were extracted with low sequence bias and showed no evidence for the characteristic preference of TiO2 for acidic amino acids (aspartic and glutamic acid). Applying the method to human CSF led to the discovery of 47 phosphopeptides belonging to 24 proteins and revealed three previously unknown phosphorylation sites.
RETRACTED ARTICLE: Large-Area Semiconducting Graphene Nanomesh Tailored by Interferometric Lithography
Authors: Kazemi Alireza , He Xiang , Alaie Seyedhamidreza , Ghasemi Javad , Dawson Noel Mayur , Cavallo Francesca , Habteyes Terefe G. , Brueck Steven R. J. , Krishna Sanjay 
Published: July 2015

AbstractGraphene nanostructures are attracting a great deal of interest because of newly emerging properties originating from quantum confinement effects. We report on using interferometric lithography to fabricate uniform, chip-scale, semiconducting graphene nanomesh (GNM) with sub-10 nm neck widths (smallest edge-to-edge distance between two nanoholes). This approach is based on fast, low-cost and high-yield lithographic technologies and demonstrates the feasibility of cost-effective development of large-scale semiconducting graphene sheets and devices. The GNM is estimated to have a room temperature energy bandgap of ~30 meV. Raman studies showed that the G band of the GNM experiences a blue shift and broadening compared to pristine graphene, a change which was attributed to quantum confinement and localization effects. A single-layer GNM field effect transistor exhibited promising drive current of ~3.9 μA/μm and ON/OFF current ratios of ~35 at room temperature. The ON/OFF current ratio of the GNM-device displayed distinct temperature dependence with about 24-fold enhancement at 77 K.
Diversity and evolution of cytochrome P450 monooxygenases in Oomycetes
Authors: Sello Mopeli Marshal , Jafta Norventia , Nelson David R , Chen Wanping , Yu Jae-Hyuk , Parvez Mohammad , Kgosiemang Ipeleng Kopano Rosinah , Monyaki Richie , Raselemane Seiso Caiphus , Qhanya Lehlohonolo Benedict , Mthakathi Ntsane Trevor , Sitheni Mashele Samson , Syed Khajamohiddin 
Published: July 2015

AbstractCytochrome P450 monooxygenases (P450s) are heme-thiolate proteins whose role as drug targets against pathogens, as well as in valuable chemical production and bioremediation, has been explored. In this study we performed comprehensive comparative analysis of P450s in 13 newly explored oomycete pathogens. Three hundred and fifty-six P450s were found in oomycetes. These P450s were grouped into 15 P450 families and 84 P450 subfamilies. Among these, nine P450 families and 31 P450 subfamilies were newly found in oomycetes. Research revealed that oomycetes belonging to different orders contain distinct P450 families and subfamilies in their genomes. Evolutionary analysis and sequence homology data revealed P450 family blooms in oomycetes. Tandem arrangement of a large number of P450s belonging to the same family indicated that P450 family blooming is possibly due to its members’ duplications. A unique combination of amino acid patterns was observed at EXXR and CXG motifs for the P450 families CYP5014, CYP5015 and CYP5017. A novel P450 fusion protein (CYP5619 family) with an N-terminal P450 domain fused to a heme peroxidase/dioxygenase domain was discovered in Saprolegnia declina. Oomycete P450 patterns suggested host influence in shaping their P450 content. This manuscript serves as reference for future P450 annotations in newly explored oomycetes.
Energy landscape scheme for an intuitive understanding of complex domain dynamics in ferroelectric thin films
Authors: Heon Kim Tae , Yoon Jong-Gul , Hyub Baek Seung , Park Woong-kyu , Mo Yang Sang , Yup Jang Seung , Min Taeyuun , Chung Jin-Seok , Eom Chang-Beom , Won Noh Tae 
Published: July 2015

AbstractFundamental understanding of domain dynamics in ferroic materials has been a longstanding issue because of its relevance to many systems and to the design of nanoscale domain-wall devices. Despite many theoretical and experimental studies, a full understanding of domain dynamics still remains incomplete, partly due to complex interactions between domain-walls and disorder. We report domain-shape-preserving deterministic domain-wall motion, which directly confirms microscopic return point memory, by observing domain-wall breathing motion in ferroelectric BiFeO3 thin film using stroboscopic piezoresponse force microscopy. Spatial energy landscape that provides new insights into domain dynamics is also mapped based on the breathing motion of domain walls. The evolution of complex domain structure can be understood by the process of occupying the lowest available energy states of polarization in the energy landscape which is determined by defect-induced internal fields. Our result highlights a pathway for the novel design of ferroelectric domain-wall devices through the engineering of energy landscape using defect-induced internal fields such as flexoelectric fields.
Highly homologous proteins exert opposite biological activities by using different interaction interfaces
Authors: Iosub Amir Anat , van Rosmalen Martijn , Mayer Guy , Lebendiker Mario , Danieli Tsafi , Friedler Assaf 
Published: July 2015

AbstractWe present a possible molecular basis for the opposite activity of two homologues proteins that bind similar ligands and show that this is achieved by fine-tuning of the interaction interface. The highly homologous ASPP proteins have opposite roles in regulating apoptosis: ASPP2 induces apoptosis while iASPP inhibits it. The ASPP proteins are regulated by an autoinhibitory interaction between their Ank-SH3 and Pro domains. We performed a detailed biophysical and molecular study of the Pro – Ank-SH3 interaction in iASPP and compared it to the interaction in ASPP2. We found that iASPP Pro is disordered and that the interaction sites are entirely different: iASPP Ank-SH3 binds iASPP Pro via its fourth Ank repeat and RT loop while ASPP2 Ank-SH3 binds ASPP2 Pro via its first Ank repeat and the n-src loop. It is possible that by using different moieties in the same interface, the proteins can have distinct and specific interactions resulting in differential regulation and ultimately different biological activities.
Molecular evolution of haemagglutinin (H) gene in measles virus
Authors: Kimura Hirokazu , Saitoh Mika , Kobayashi Miho , Ishii Haruyuki , Saraya Takeshi , Kurai Daisuke , Tsukagoshi Hiroyuki , Shirabe Komei , Nishina Atsuyoshi , Kozawa Kunihisa , Kuroda Makoto , Takeuchi Fumihiko , Sekizuka Tsuyoshi , Minakami Hisanori , Ryo Akihide , Takeda Makoto 
Published: July 2015

AbstractWe studied the molecular evolution of the haemagglutinin (H) gene (full length) in all genotypes (24 genotypes, 297 strains) of measles virus (MeV). The gene’s evolutionary timescale was estimated by the Bayesian Markov chain Monte Carlo (MCMC) method. We also analysed positive selection sites. The MCMC tree indicated that the MeV H gene diverged from the rinderpest virus (same genus) about 250 years ago and that 24 MeV genotypes formed 3 lineages dating back to a 1915 ancestor (95% highest posterior density [HPD] 1882–1941) with relatively rapid evolution (mean rate: 9.02 × 10−4 substitutions/site/year). The 3 lineages diverged in 1915 (lineage 1, 95% HPD 1882–1941), 1954 (lineage 2, 95% HPD 1937–1969) and 1940 (lineage 3, 95% HPD 1927–1952). These 24 genotypes may have diverged and emerged between the 1940s and 1990s. Selective pressure analysis identified many negative selection sites on the H protein but only a few positive selection sites, suggesting strongly operated structural and/or functional constraint of changes on the H protein. Based on the molecular evolution of H gene, an ancestor MeV of the 24 genotypes emerged about 100 years ago and the structure of H protein has been well conserved.
Late-glacial elevated dust deposition linked to westerly wind shifts in southern South America
Authors: Vanneste Heleen , De Vleeschouwer François , Martínez-Cortizas Antonio , von Scheffer Clemens , Piotrowska Natalia , Coronato Andrea , Le Roux Gaël 
Published: July 2015

AbstractAtmospheric dust loadings play a crucial role in the global climate system. Southern South America is a key dust source, however, dust deposition rates remain poorly quantified since the last glacial termination (~17 kyr ago), an important timeframe to anticipate future climate changes. Here we use isotope and element geochemistry in a peat archive from Tierra del Fuego, to reconstruct atmospheric dust fluxes and associated environmental and westerly wind changes for the past 16.2 kyr. Dust depositions were elevated during the Antarctic Cold Reversal (ACR) and second half of the Younger Dryas (YD) stadial, originating from the glacial Beagle Channel valley. This increase was most probably associated with a strengthening of the westerlies during both periods as dust source areas were already available before the onset of the dust peaks and remained present throughout. Congruent with glacier advances across Patagonia, this dust record indicates an overall strengthening of the wind belt during the ACR. On the other hand, we argue that the YD dust peak is linked to strong and poleward shifted westerlies. The close interplay between dust fluxes and climatic changes demonstrates that atmospheric circulation was essential in generating and sustaining present-day interglacial conditions.
Quantum-confinement and Structural Anisotropy result in Electrically-Tunable Dirac Cone in Few-layer Black Phosphorous
Authors: Dolui Kapildeb , Quek Su Ying 
Published: July 2015

AbstractTwo-dimensional (2D) materials are well-known to exhibit interesting phenomena due to quantum confinement. Here, we show that quantum confinement, together with structural anisotropy, result in an electric-field-tunable Dirac cone in 2D black phosphorus. Using density functional theory calculations, we find that an electric field, Eext, applied normal to a 2D black phosphorus thin film, can reduce the direct band gap of few-layer black phosphorus, resulting in an insulator-to-metal transition at a critical field, Ec. Increasing Eext beyond Ec can induce a Dirac cone in the system, provided the black phosphorus film is sufficiently thin. The electric field strength can tune the position of the Dirac cone and the Dirac-Fermi velocities, the latter being similar in magnitude to that in graphene. We show that the Dirac cone arises from an anisotropic interaction term between the frontier orbitals that are spatially separated due to the applied field, on different halves of the 2D slab. When this interaction term becomes vanishingly small for thicker films, the Dirac cone can no longer be induced. Spin-orbit coupling can gap out the Dirac cone at certain electric fields; however, a further increase in field strength reduces the spin-orbit-induced gap, eventually resulting in a topological-insulator-to-Dirac-semimetal transition.
Beta-cell regeneration from vimentin+/MafB+ cells after STZ-induced extreme beta-cell ablation
Authors: Cheng Yu , Kang Hongjun , Shen Jing , Hao Haojie , Liu Jiejie , Guo Yelei , Mu Yiming , Han Weidong 
Published: July 2015

AbstractLoss of functional beta-cells is fundamental in both type 1 and type 2 diabetes. In situ beta-cell regeneration therefore has garnered great interest as an approach to diabetes therapy. Here, after elimination of pre-existing beta cells by a single high-dose of streptozotocin (STZ), we demonstrated that a considerable amount of beta-like-cells was generated within 48 hrs. But the newly formed insulin producing cells failed to respond to glucose challenge at this time and diminished afterwards. Insulin treatment to normalize the glucose level protected the neogenic beta-like cells and the islet function was also gradually matured. Strikingly, intermediate cells lacking epithelial marker E-cadherin but expressing mesenchymal cell-specific marker vimentin appeared within 16 hrs following STZ exposure, which served as the major source of insulin-producing cells observed at 24 hrs. Moreover, these intermediate cells strongly expressed alpha-cell-specific marker MafB. In summary, the data presented here identified a novel intermediate cell type as beta-cell progenitors, showing mesenchymal cell feature as well as alpha-cell marker MafB. Our results might have important implications for efforts to stimulate beta-cell regeneration.
New Insulating Antiferromagnetic Quaternary Iridates MLa10Ir4O24 (M = Sr, Ba)
Authors: Zhao Qingbiao , Han Fei , Stoumpos Constantinos C. , Han Tian-Heng , Li Hao , Mitchell J. F. 
Published: July 2015

AbstractRecently, oxides of Ir4+ have received renewed attention in the condensed matter physics community, as it has been reported that certain iridates have a strongly spin-orbital coupled (SOC) electronic state, Jeff = ½, that defines the electronic and magnetic properties. The canonical example is the Ruddlesden-Popper compound Sr2IrO4, which has been suggested as a potential route to a new class of high temperature superconductor due to the formal analogy between Jeff = ½ and the S = ½ state of the cuprate superconductors. The quest for other iridium oxides that present tests of the underlying SOC physics is underway. In this spirit, here we report the synthesis and physical properties of two new quaternary tetravalent iridates, MLa10Ir4O24 (M = Sr, Ba). The crystal structure of both compounds features isolated IrO6 octahedra in which the electronic configuration of Ir is d5. Both compounds order antiferromagnetically despite the lack of obvious superexchange pathways and resistivity measurement shows that SrLa10Ir4O24 is an insulator.
Characterization of Three Tetrabromobisphenol-S Derivatives in Mollusks from Chinese Bohai Sea: A Strategy for Novel Brominated Contaminants Identification
Authors: Liu Ai-feng , Tian Yong , Yin Nuo-ya , Yu Miao , Qu Guang-bo , Shi Jian-bo , Du Yu-guo , Jiang Gui-bin 
Published: July 2015

AbstractIdentification of novel brominated contaminants in the environment, especially the derivatives and byproducts of brominated flame retardants (BFRs), has become a wide concern because of their adverse effects on human health. Herein, we qualitatively and quantitatively identified three byproducts of tetrabromobisphenol-S bis(2,3-dibromopropyl ether) (TBBPS-BDBPE), including TBBPS mono(allyl ether) (TBBPS-MAE), TBBPS mono(2-bromoallyl ether) (TBBPS-MBAE) and TBBPS mono(2,3-dibromopropyl ether) (TBBPS-MDBPE) as novel brominated contaminants. Meanwhile, the mass spectra and analytical method for determination of TBBPS-BDBPE byproducts were presented for the first time. The detectable concentrations (dry weight) of TBBPS-MAE, TBBPS-MBAE and TBBPS-MDBPE were in the ranges 28–394 μg/g in technical TBBPS-BDBPE and 0.1–4.1 ng/g in mollusks collected from the Chinese Bohai Sea. The detection frequencies in mollusk samples were 5%, 39%, 95% for TBBPS-MAE, TBBPS-MBAE and TBBPS-MDBPE, respectively, indicating their prevailing in the environment. The results showed that they could be co-produced and leaked into the environment with production process and might be more bioaccumulative and toxic than TBBPS-BDBPE. Therefore, the production and use of TBBPS derivatives lead to unexpected contamination to the surrounding environment. This study also provided an effective approach for identification of novel contaminants in the environment with synthesized standards and Orbitrap high resolution mass spectrometry.
Defect-Engineered Heat Transport in Graphene: A Route to High Efficient Thermal Rectification
Authors: Zhao Weiwei , Wang Yanlei , Wu Zhangting , Wang Wenhui , Bi Kedong , Liang Zheng , Yang Juekuan , Chen Yunfei , Xu Zhiping , Ni Zhenhua 
Published: July 2015

AbstractLow-dimensional materials such as graphene provide an ideal platform to probe the correlation between thermal transport and lattice defects, which could be engineered at the molecular level. In this work, we perform molecular dynamics simulations and non-contact optothermal Raman measurements to study this correlation. We find that oxygen plasma treatment could reduce the thermal conductivity of graphene significantly even at extremely low defect concentration (∼83% reduction for ∼0.1% defects), which could be attributed mainly to the creation of carbonyl pair defects. Other types of defects such as hydroxyl, epoxy groups and nano-holes demonstrate much weaker effects on the reduction where the sp2 nature of graphene is better preserved. With the capability of selectively functionalizing graphene, we propose an asymmetric junction between graphene and defective graphene with a high thermal rectification ratio of ∼46%, as demonstrated by our molecular dynamics simulation results. Our findings provide fundamental insights into the physics of thermal transport in defective graphene and two-dimensional materials in general, which could help on the future design of functional applications such as optothermal and electrothermal devices.
Interaction of mercury and selenium in the larval stage zebrafish vertebrate model
Authors: MacDonald Tracy C , Korbas Malgorzata , James Ashley K , Sylvain Nicole J , Hackett Mark J , Nehzati Susan , Krone Patrick H , George Graham N , Pickering Ingrid J 
Published: July 2015

Abstract
The compounds of mercury can be more toxic than those of any other non-radioactive heavy element. Despite this, environmental mercury pollution and human exposure to mercury are widespread, and are increasing. While the unusual ability of selenium to cancel the toxicity of mercury compounds has been known for nearly five decades, only recently have some aspects of the molecular mechanisms begun to be understood. We report herein a study of the interaction of mercury and selenium in the larval stage zebrafish, a model vertebrate system, using X-ray fluorescence imaging. Exposure of larval zebrafish to inorganic mercury shows nano-scale structures containing co-localized mercury and selenium. No such co-localization is seen with methylmercury exposure under similar conditions. Micro X-ray absorption spectra support the hypothesis that the co-localized deposits are most likely comprised of highly insoluble mixed chalcogenide HgSxSe(1−x) where x is 0.4–0.9, probably with the cubic zincblende structure.
GABA-mediated repulsive coupling between circadian clock neurons in the SCN encodes seasonal time
Authors: Myung Jihwan , Hong Sungho , DeWoskin Daniel , De Schutter Erik , Forger Daniel B. , Takumi Toru 
Published: July 2015

SignificanceHow animals track the seasons has long been a mystery. We found a mechanism that explains how day length is encoded within the neuronal network of suprachiasmatic nucleus (SCN). Using an integrated approach combining experiments and modeling, we find evidence for changes in the coupling in the SCN that divides the clock oscillations into two clusters as a function of day length. We show that asymmetric distribution of intracellular chloride across the SCN causes this coupling change. Blocking GABA or chloride import erases the oscillator organization formed by day-length entrainment. These demonstrate that coupling through GABA is a key ingredient of day-length encoding in the SCN.
Brook Trout Distribution, Genetics, and Population Characteristics in the Driftless Area of Minnesota
Authors: Hoxmeier R. John H. , Dieterman Douglas J. , Miller Loren M. 
Published: July 2015

Abstract
The Driftless Area in southeastern Minnesota is on the southwestern edge of the native range of Brook Trout Salvelinus fontinalis. It was assumed that native Brook Trout were extirpated from this region in the early 1900s due to degraded stream conditions and stockings of eastern-origin Brook Trout and European Brown Trout Salmo trutta. Our objectives were to examine Brook Trout populations in the region to determine their spatial and genetic distribution and quantify population characteristics. Information on presence or absence of Brook Trout was gathered by electrofishing 174 streams in southeastern Minnesota. Brook Trout were present in 68% of coldwater streams compared with only in 3% in the early 1970s. The increase is likely due to increasing stream discharge throughout the Driftless Area, enabling recolonization or successful establishment of stocked populations. Streams with higher base flow discharge also had higher abundance, larger size at maturity, and larger Brook Trout present. Genetic data on 74 populations were analyzed to characterize genetic variation within populations, assess genetic structure among populations, and determine possible origins. Numerous populations were not associated with known hatchery sources but were primarily composed of geographic groupings that could represent remnant lineages. Although population characteristics were similar among genetic origins, potentially remnant populations should be given conservation priority because they have proven their ability to sustain themselves in this region. Management actions that emphasize maintaining or increasing stream base flows throughout the region will likely enhance remnant Brook Trout populations in the Driftless Area.
Received July 25, 2014; accepted March 17, 2015