bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor
Authors: Nobu Masaru K , Narihiro Takashi , Rinke Christian , Kamagata Yoichi , Tringe Susannah G , Woyke Tanja , Liu Wen-Tso 
Published: January 2015

Abstract
Ecogenomic investigation of a methanogenic bioreactor degrading terephthalate (TA) allowed elucidation of complex synergistic networks of uncultivated microorganisms, including those from candidate phyla with no cultivated representatives. Our previous metagenomic investigation proposed that Pelotomaculum and methanogens may interact with uncultivated organisms to degrade TA; however, many members of the community remained unaddressed because of past technological limitations. In further pursuit, this study employed state-of-the-art omics tools to generate draft genomes and transcriptomes for uncultivated organisms spanning 15 phyla and reports the first genomic insight into candidate phyla Atribacteria, Hydrogenedentes and Marinimicrobia in methanogenic environments. Metabolic reconstruction revealed that these organisms perform fermentative, syntrophic and acetogenic catabolism facilitated by energy conservation revolving around H2 metabolism. Several of these organisms could degrade TA catabolism by-products (acetate, butyrate and H2) and syntrophically support Pelotomaculum. Other taxa could scavenge anabolic products (protein and lipids) presumably derived from detrital biomass produced by the TA-degrading community. The protein scavengers expressed complementary metabolic pathways indicating syntrophic and fermentative step-wise protein degradation through amino acids, branched-chain fatty acids and propionate. Thus, the uncultivated organisms may interact to form an intricate syntrophy-supported food web with Pelotomaculum and methanogens to metabolize catabolic by-products and detritus, whereby facilitating holistic TA mineralization to CO2 and CH4.
Ecophysiology of uncultivated marine euryarchaea is linked to particulate organic matter
Authors: Orsi William D , Smith Jason M , Wilcox Heather M , Swalwell Jarred E , Carini Paul , Worden Alexandra Z , Santoro Alyson E 
Published: January 2015

Abstract
Particles in aquatic environments host distinct communities of microbes, yet the evolution of particle-specialized taxa and the extent to which specialized microbial metabolism is associated with particles is largely unexplored. Here, we investigate the hypothesis that a widely distributed and uncultivated microbial group—the marine group II euryarchaea (MGII)—interacts with living and detrital particulate organic matter (POM) in the euphotic zone of the central California Current System. Using fluorescent in situ hybridization, we verified the association of euryarchaea with POM. We further quantified the abundance and distribution of MGII 16 S ribosomal RNA genes in size-fractionated seawater samples and compared MGII functional capacity in metagenomes from the same fractions. The abundance of MGII in free-living and &gt;3 μm fractions decreased with increasing distance from the coast, whereas MGII abundance in the 0.8–3 μm fraction remained constant. At several offshore sites, MGII abundance was highest in particle fractions, indicating that particle-attached MGII can outnumber free-living MGII under oligotrophic conditions. Compared with free-living MGII, the genome content of MGII in particle-associated fractions exhibits an increased capacity for surface adhesion, transcriptional regulation and catabolism of high molecular weight substrates. Moreover, MGII populations in POM fractions are phylogenetically distinct from and more diverse than free-living MGII. Eukaryotic phytoplankton additions stimulated MGII growth in bottle incubations, providing the first MGII net growth rate measurements. These ranged from 0.47 to 0.54 d−1. However, MGII were not recovered in whole-genome amplifications of flow-sorted picoeukaryotic phytoplankton and heterotrophic nanoflagellates, suggesting that MGII in particle fractions are not physically attached to living POM. Collectively, our results support a linkage between MGII ecophysiology and POM, implying that marine archaea have a role in elemental cycling through interactions with particles.
Evidence for a small hole pocket in the Fermi surface of underdoped YBa2Cu3Oy
Authors: Doiron-Leyraud N. , Badoux S. , René de Cotret S. , Lepault S. , LeBoeuf D. , Laliberté F. , Hassinger E. , Ramshaw B. J. , Bonn D. A. , Hardy W. N. , Liang R. , Park J.-H.. , Vignolles D. , Vignolle B. , Taillefer L. , Proust C. 
Published: January 2015

AbstractIn underdoped cuprate superconductors, the Fermi surface undergoes a reconstruction that produces a small electron pocket, but whether there is another, as yet, undetected portion to the Fermi surface is unknown. Establishing the complete topology of the Fermi surface is key to identifying the mechanism responsible for its reconstruction. Here we report evidence for a second Fermi pocket in underdoped YBa2Cu3Oy, detected as a small quantum oscillation frequency in the thermoelectric response and in the c-axis resistance. The field-angle dependence of the frequency shows that it is a distinct Fermi surface, and the normal-state thermopower requires it to be a hole pocket. A Fermi surface consisting of one electron pocket and two hole pockets with the measured areas and masses is consistent with a Fermi-surface reconstruction by the charge–density–wave order observed in YBa2Cu3Oy, provided other parts of the reconstructed Fermi surface are removed by a separate mechanism, possibly the pseudogap.
Site- and allele-specific polycomb dysregulation in T-cell leukaemia
Authors: Navarro Jean-Marc , Touzart Aurore , Pradel Lydie C. , Loosveld Marie , Koubi Myriam , Fenouil Romain , Le Noir Sandrine , Maqbool Muhammad Ahmad , Morgado Ester , Gregoire Claude , Jaeger Sebastien , Mamessier Emilie , Pignon Charles , Hacein-Bey-Abina Salima , Malissen Bernard , Gut Marta , Gut Ivo G. , Dombret Hervé , Macintyre Elizabeth A. , Howe Steven J. , Gaspar H. Bobby , Thrasher Adrian J. , Ifrah Norbert , Payet-Bornet Dominique , Duprez Estelle , Andrau Jean-Christophe , Asnafi Vahid , Nadel Bertrand 
Published: January 2015

AbstractT-cell acute lymphoblastic leukaemias (T-ALL) are aggressive malignant proliferations characterized by high relapse rates and great genetic heterogeneity. TAL1 is amongst the most frequently deregulated oncogenes. Yet, over half of the TAL1+ cases lack TAL1 lesions, suggesting unrecognized (epi)genetic deregulation mechanisms. Here we show that TAL1 is normally silenced in the T-cell lineage, and that the polycomb H3K27me3-repressive mark is focally diminished in TAL1+ T-ALLs. Sequencing reveals that >20% of monoallelic TAL1+ patients without previously known alterations display microinsertions or RAG1/2-mediated episomal reintegration in a single site 5′ to TAL1. Using ‘allelic-ChIP’ and CrispR assays, we demonstrate that such insertions induce a selective switch from H3K27me3 to H3K27ac at the inserted but not the germline allele. We also show that, despite a considerable mechanistic diversity, the mode of oncogenic TAL1 activation, rather than expression levels, impact on clinical outcome. Altogether, these studies establish site-specific epigenetic desilencing as a mechanism of oncogenic activation.
Suppression of Mic60 compromises mitochondrial transcription and oxidative phosphorylation
Authors: Yang Rui-Feng , Sun Li-Hong , Zhang Ran , Zhang Yuan , Luo Yu-Xuan , Zheng Wei , Zhang Zhu-Qin , Chen Hou-Zao , Liu De-Pei 
Published: January 2015

AbstractPrecise regulation of mtDNA transcription and oxidative phosphorylation (OXPHOS) is crucial for human health. As a component of mitochondrial contact site and cristae organizing system (MICOS), Mic60 plays a central role in mitochondrial morphology. However, it remains unclear whether Mic60 affects mitochondrial transcription. Here, we report that Mic60 interacts with mitochondrial transcription factors TFAM and TFB2M. Furthermore, we found that Mic60 knockdown compromises mitochondrial transcription and OXPHOS activities. Importantly, Mic60 deficiency decreased TFAM binding and mitochondrial RNA polymerase (POLRMT) recruitment to the mtDNA promoters. In addition, through mtDNA immunoprecipitation (mIP)-chromatin conformation capture (3C) assays, we found that Mic60 interacted with mtDNA and was involved in the architecture of mtDNA D-loop region. Taken together, our findings reveal a previously unrecognized important role of Mic60 in mtDNA transcription.
Evaluating Language Environment Analysis System Performance for Chinese: A Pilot Study in Shanghai
Authors: Gilkerson Jill , Zhang Yiwen , Xu Dongxin , Richards Jeffrey A. , Xu Xiaojuan , Jiang Fan , Harnsberger James , Topping Keith 
Published: January 2015

Purpose
The purpose of this study was to evaluate performance of the Language Environment Analysis (LENA) automated language-analysis system for the Chinese Shanghai dialect and Mandarin (SDM) languages.

Method
Volunteer parents of 22 children aged 3–23 months were recruited in Shanghai. Families provided daylong in-home audio recordings using LENA. A native speaker listened to 15 min of randomly selected audio samples per family to label speaker regions and provide Chinese character and SDM word counts for adult speakers. LENA segment labeling and counts were compared with rater-based values.

Results
LENA demonstrated good sensitivity in identifying adult and child; this sensitivity was comparable to that of American English validation samples. Precision was strong for adults but less so for children. LENA adult word count correlated strongly with both Chinese characters and SDM word counts. LENA conversational turn counts correlated similarly with rater-based counts after the exclusion of three unusual samples. Performance related to some degree to child age.

Conclusions
LENA adult word count and conversational turn provided reasonably accurate estimates for SDM over the age range tested. Theoretical and practical considerations regarding LENA performance in non-English languages are discussed. Despite the pilot nature and other limitations of the study, results are promising for broader cross-linguistic applications.
Fast superpixel segmentation by iterative edge refinement
Authors: Zhu Song , Cao Danhua , Jiang Shixiong , Wu Yubin , Hu Pan 
Published: January 2015

The superpixel, as an important pre‐processing technique, has been successfully used in many vision applications. Introduced is a fast superpixel method called iterative edge refinement (IER). The image was first initialised as regular grids, and then concentration was on unstable pixels and relabelling them iteratively so called unstable pixels, are edge pixels around the moving boundary. It is found that the unstable pixels decrease rapidly during the iterative process, which results in a high speed‐up. Experimental results on the Berkeley BSDS500 dataset show that IER achieves a segmentation performance comparable with the state‐of‐the‐art, and moreover, runs in real‐time on a single Intel i3 CPU at 2.5 GHz.
Compact lowpass filter with wide stopband using coupled rhombic stubs
Authors: Zhang Bo , Li Shaosheng , Huang Jianming 
Published: January 2015

A compact and high selective lowpass filter (LPF) with wide stopband is presented using coupled rhombic stubs. The proposed LPF unit is constructed by loading a rhombic stub on a transmission line. Then, a folded three‐element LPF is proposed to achieve compact size and high selectivity by introducing coupling between adjacent rhombic stubs. The operating mechanism of the filter is investigated and explained, by adopting the physically‐based LC‐equivalent circuit model. The implemented final LPF exhibits a wide stopband of up to 11.5 fc with a rejection level of better than 35 dB. Furthermore, the final LPF features a compact size of 0.12λg × 0.10λg, where λg is the guide wavelength of fc, and a very high figure‐of‐merit (FOM) of 27 142.
High‐resolution time of arrival estimation for OFDM‐based transceivers
Authors: Makki A. , Siddig A. , Saad M.M. , Bleakley C.J. , Cavallaro J.R. 
Published: January 2015

A novel algorithm for time of arrival (TOA) estimation for OFDM‐based transceivers is presented. The algorithm processes the sampled baseband signal to obtain a high‐resolution estimate of the TOA of the OFDM symbol. In the first step, the algorithm obtains a sample‐resolution estimate of the TOA by finding the peak of the absolute value of the cross‐correlation of the in‐phase and quadrature received signals with the known transmitted symbol. In the second step, the algorithm refines this estimate to sub‐sample resolution by estimating the phase delay of the received signal based on the gradient of a linear fit to the phase difference between the transmitted and received sub‐carriers (in the frequency domain). The algorithm was applied to the long training sequence (LTS) symbol of the IEEE wireless local area network (WLAN) 802.11 g preamble. In real‐world experiments, the algorithm was found to achieve a mean TOA estimation error of 49 cm in a low multi‐path line‐of‐sight environment for ranges of 1–7 m.
Compact algorithmic time‐to‐digital converter
Authors: Li Shuo , Salthouse Christopher D. 
Published: January 2015

Time‐to‐digital converters (TDCs) are an important circuit block in time‐of‐flight sensors, fluorescence lifetime sensors, and self‐calibrating digital circuits. Fine‐resolution TDCs are usually built with chains of delay elements, but this architecture requires large area, conversion time, and power consumption. A novel compact TDC architecture based on the cyclic comparison algorithm is presented, which implemented and tested in the TSMC, 0.35 μm process within a 200 × 200 μm area is demonstrated that the proposed TDC achieves a conversion rate of 10 ns/bit and sub‐picosecond resolution. The measured power is 0.7 mW, taking 100 ns for each bit.
Design of dual‐band transmission line with flexible phase shifts and its applications
Authors: Ren Han , Shao Jin , Zhou Mi , Arigong Bayaner , Ding Jun , Zhang Hualiang 
Published: January 2015

A novel dual‐band transmission line with flexible phase shifts is presented. To realise dual‐band operations, the proposed transmission line is constructed by series‐connected coupled lines and open‐ended stubs. Using this structure, flexible characteristic impedances and electrical lengths can be designed to operate at two frequencies. Moreover, the proposed dual‐band transmission line features a wide range of realisable frequency ratios and a flexible structure. For practical applications, a planar dual‐band 3 dB branch‐line coupler operating at 2/5.2 GHz is designed using the proposed dual‐band transmission line. The simulation and measurement results agree very well with the design theory.
Synthesis and biological activities of the amide derivative of aplog-1, a simplified analog of aplysiatoxin with anti-proliferative and cytotoxic activities
Authors: Hanaki Yusuke , Yanagita Ryo C , Sugahara Takahiro , Aida Misako , Tokuda Harukuni , Suzuki Nobutaka , Irie Kazuhiro 
Published: January 2015

Abstract
Aplog-1 is a simplified analog of the tumor-promoting aplysiatoxin with anti-proliferative and cytotoxic activities against several cancer cell lines. Our recent findings have suggested that protein kinase Cδ (PKCδ) could be one of the target proteins of aplog-1. In this study, we synthesized amide-aplog-1 (3), in which the C-1 ester group was replaced with an amide group, to improve chemical stability in vivo. Unfortunately, 3 exhibited seventy-fold weaker binding affinity to the C1B domain of PKCδ than that of aplog-1, and negligible anti-proliferative and cytotoxic activities even at 10−4 M. A conformational analysis and density functional theory calculations indicated that the stable conformation of 3 differed from that of aplog-1. Since 27-methyl and 27-methoxy derivatives (1, 2) without the ability to bind to PKC isozymes exhibited marked anti-proliferative and cytotoxic activities at 10−4 M, 3 may be an inactive control to identify the target proteins of aplogs.
Screening for a gene deletion mutant whose temperature sensitivity is suppressed by FK506 in budding yeast and its application for a positive screening for drugs inhibiting calcineurin
Authors: Kume Kazunori , Koyano Takayuki , Takata Junpei , Wakabayashi Ko , Mizunuma Masaki , Miyakawa Tokichi , Hirata Dai 
Published: January 2015

AbstractCalcineurin, which is a Ca2+/calmodulin-dependent protein phosphatase, is a key mediator in calcium signaling in diverse biological processes and of clinical importance as the target of the immunosuppressant FK506. To identify a mutant(s) in which calcineurin is activated, inhibiting cellular growth as a result, we screened for a mutant(s) whose temperature sensitivity would be suppressed by FK506 from the budding yeast non-essential gene deletion library. We found that the temperature sensitivity of cells in which the conserved Verprolin VRP1 gene had been deleted, which gene is required for actin organization and endocytosis, was suppressed by either FK506 or by cnb1 deletion. Indeed, the calcineurin activity increased significantly in the ∆vrp1 cells. Finally, we demonstrated that the ∆vrp1 strain to be useful as an indicator in a positive screening for bioactive compounds inhibiting calcineurin.
Incorporating the patient’s voice into electronic health records through patient-reported outcomes as the “review of systems”
Authors: Chung Arlene E , Basch Ethan M 
Published: January 2015

Abstract
Owing to lack of standardization for eliciting patient symptoms, the limited time available during clinical encounters, and the often-competing priorities of patients and providers, providers may not appreciate the full spectrum of the patient’s symptom experience. Using electronically collected patient-reported outcomes to capture the review of system outside of the clinic visit may not only improve the efficiency, completeness, and accuracy of data collection for the review of system, but also provide the opportunity to operationalize incorporating the patient’s voice into the electronic health record. While the necessary technology is already available, multiple stakeholders, including electronic health record vendors, clinicians, researchers, and professional societies, need to align their interests before this can become a widespread reality.
Resurrection of Two Species From Synonymy of Anopheles (Nyssorhynchus) strodei Root, and Characterization of a Distinct Morphological Form From the Strodei Complex (Diptera: Culicidae)
Authors: Sallum Maria Anice Mureb , Foster Peter G. , Santos Cecilia L. S. Dos , Flores Daniel C. , Motoki Maysa T. , Bergo Eduardo S. 
Published: January 2015

Abstract
Anopheles albertoi Unti and Anopheles arthuri Unti are revived from the synonymy with Anopheles strodei Root, and a distinct morphological form (designated in this study as Anopheles CP Form) from the Strodei Complex of Anopheles (Nyssorhynchus) is characterized. The male genitalia of An. arthuri and An. albertoi are described and illustrated for the first time. An. strodei, An. arthuri, and An. albertoi were first distinguished based on scanning electron microphotos of the eggs, and then each egg type was associated with diagnostic characters of the male genitalia. Identification of Anopheles CP Form was based on morphological characters of the male genitalia, characterized and illustrated in this study. Molecular phylogenetic analysis was most clear when an outgroup was not included, in which case using the nuclear white gene, or the white gene in combination with the mitochondrial cytochrome c oxidase subunit I (COI) gene, clearly separated these four taxa. When Anopheles quadrimaculatus Say and Anopheles stephensi Liston were included as an outgroup, combined white and COI data resolved An. strodei and An. albertoi, whereas An. arthuri was not well resolved. The single sequence of Anopheles CP Form was recovered well separated from other groups in all analyses.
The KaVA and KVN pulsar project
Authors: Dodson Richard , Kim Chunglee , Sohn Bongwon , Rioja María J. , Jung Taehyun , Seymour Andrew , Raja Wasim 
Published: January 2015

Abstract
We present our work towards using the Korean VLBI (Very Long Baseline Interferometer) Network (KVN) and VLBI Exploration of Radio Astronomy (VERA) arrays combined into the KVN and VERA Array (KaVA) for observations of radio pulsars at high frequencies (≃ 22 GHz). Pulsar astronomy is generally focused at frequencies approximately 0.3 to several GHz and pulsars are usually discovered and monitored with large, single-dish, radio telescopes. For most pulsars, reduced radio flux is expected at high frequencies due to their steep spectrum, but there are exceptions where high frequency observations can be useful. Moreover, some pulsars are observable at high frequencies only, such as those close to the Galactic Center. The discoveries of a radio-bright magnetar and a few dozen extended Chandra sources within 15′ of the Galactic Center provide strong motivations to make use of the KaVA frequency band to search for pulsars in this region. Here, we describe the science targets and report progress made from the KVN test observations for known pulsars. We then discuss why KaVA pulsar observations are compelling.
Does Morphological and Anatomical Plasticity during the Vegetative Stage Make Wheat More Tolerant of Water Deficit Stress Than Rice?
Authors: Kadam Niteen N. , Yin Xinyou , Bindraban Prem S. , Struik Paul C. , Jagadish Krishna S.V. 
Published: January 2015

AbstractWater scarcity and the increasing severity of water deficit stress are major challenges to sustaining irrigated rice (Oryza sativa) production. Despite the technologies developed to reduce the water requirement, rice growth is seriously constrained under water deficit stress compared with other dryland cereals such as wheat (Triticum aestivum). We exposed rice cultivars with contrasting responses to water deficit stress and wheat cultivars well adapted to water-limited conditions to the same moisture stress during vegetative growth to unravel the whole-plant (shoot and root morphology) and organ/tissue (root anatomy) responses. Wheat cultivars followed a water-conserving strategy by reducing specific leaf area and developing thicker roots and moderate tillering. In contrast, rice ‘IR64’ and ‘Apo’ adopted a rapid water acquisition strategy through thinner roots under water deficit stress. Root diameter, stele and xylem diameter, and xylem number were more responsive and varied with different positions along the nodal root under water deficit stress in wheat, whereas they were relatively conserved in rice cultivars. Increased metaxylem diameter and lower metaxylem number near the root tips and exactly the opposite phenomena at the root-shoot junction facilitated the efficient use of available soil moisture in wheat. Tolerant rice ‘Nagina 22’ had an advantage in root morphological and anatomical attributes over cultivars IR64 and Apo but lacked plasticity, unlike wheat cultivars exposed to water deficit stress. The key traits determining the adaptation of wheat to dryland conditions have been summarized and discussed.