bluuebunny/crossref_metadata_2025_split huggingface dataset:
TRF2-RAP1 is required to protect telomeres from engaging in homologous recombination-mediated deletions and fusions
Authors: Rai Rekha , Chen Yong , Lei Ming , Chang Sandy 
Published: March 2016

AbstractRepressor/activator protein 1 (RAP1) is a highly conserved telomere-interacting protein. Yeast Rap1 protects telomeres from non-homologous end joining (NHEJ), plays important roles in telomere length control and is involved in transcriptional gene regulation. However, a role for mammalian RAP1 in telomere end protection remains controversial. Here we present evidence that mammalian RAP1 is essential to protect telomere from homology directed repair (HDR) of telomeres. RAP1 cooperates with the basic domain of TRF2 (TRF2B) to repress PARP1 and SLX4 localization to telomeres. Without RAP1 and TRF2B, PARP1 and SLX4 HR factors promote rapid telomere resection, resulting in catastrophic telomere loss and the generation of telomere-free chromosome fusions in both mouse and human cells. The RAP1 Myb domain is required to repress both telomere loss and formation of telomere-free fusions. Our results highlight the importance of the RAP1-TRF2 heterodimer in protecting telomeres from inappropriate processing by the HDR pathway.
The ReaxFF reactive force-field: development, applications and future directions
Authors: Senftle Thomas P , Hong Sungwook , Islam Md Mahbubul , Kylasa Sudhir B , Zheng Yuanxia , Shin Yun Kyung , Junkermeier Chad , Engel-Herbert Roman , Janik Michael J , Aktulga Hasan Metin , Verstraelen Toon , Grama Ananth , van Duin Adri C T 
Published: March 2016

AbstractThe reactive force-field (ReaxFF) interatomic potential is a powerful computational tool for exploring, developing and optimizing material properties. Methods based on the principles of quantum mechanics (QM), while offering valuable theoretical guidance at the electronic level, are often too computationally intense for simulations that consider the full dynamic evolution of a system. Alternatively, empirical interatomic potentials that are based on classical principles require significantly fewer computational resources, which enables simulations to better describe dynamic processes over longer timeframes and on larger scales. Such methods, however, typically require a predefined connectivity between atoms, precluding simulations that involve reactive events. The ReaxFF method was developed to help bridge this gap. Approaching the gap from the classical side, ReaxFF casts the empirical interatomic potential within a bond-order formalism, thus implicitly describing chemical bonding without expensive QM calculations. This article provides an overview of the development, application, and future directions of the ReaxFF method.
Intratumoral heterogeneity identified at the epigenetic, genetic and transcriptional level in glioblastoma
Authors: Parker Nicole R. , Hudson Amanda L. , Khong Peter , Parkinson Jonathon F. , Dwight Trisha , Ikin Rowan J. , Zhu Ying , Cheng Zhangkai Jason , Vafaee Fatemeh , Chen Jason , Wheeler Helen R. , Howell Viive M. 
Published: March 2016

AbstractHeterogeneity is a hallmark of glioblastoma with intratumoral heterogeneity contributing to variability in responses and resistance to standard treatments. Promoter methylation status of the DNA repair enzyme O6-methylguanine DNA methyltransferase (MGMT) is the most important clinical biomarker in glioblastoma, predicting for therapeutic response. However, it does not always correlate with response. This may be due to intratumoral heterogeneity, with a single biopsy unlikely to represent the entire lesion. Aberrations in other DNA repair mechanisms may also contribute. This study investigated intratumoral heterogeneity in multiple glioblastoma tumors with a particular focus on the DNA repair pathways. Transcriptional intratumoral heterogeneity was identified in 40% of cases with variability in MGMT methylation status found in 14% of cases. As well as identifying intratumoral heterogeneity at the transcriptional and epigenetic levels, targeted next generation sequencing identified between 1 and 37 unique sequence variants per specimen. In-silico tools were then able to identify deleterious variants in both the base excision repair and the mismatch repair pathways that may contribute to therapeutic response. As these pathways have roles in temozolomide response, these findings may confound patient management and highlight the importance of assessing multiple tumor biopsies.
Macrophage Migration Inhibitory Factor (MIF) Deficiency Exacerbates Aging-Induced Cardiac Remodeling and Dysfunction Despite Improved Inflammation: Role of Autophagy Regulation
Authors: Xu Xihui , Pang Jiaojiao , Chen Yuguo , Bucala Richard , Zhang Yingmei , Ren Jun 
Published: March 2016

AbstractAging leads to unfavorable geometric and functional sequelae in the heart. The proinflammatory cytokine macrophage migration inhibitory factor (MIF) plays a role in the maintenance of cardiac homeostasis under stress conditions although its impact in cardiac aging remains elusive. This study was designed to evaluate the role of MIF in aging-induced cardiac anomalies and the underlying mechanism involved. Cardiac geometry, contractile and intracellular Ca2+ properties were examined in young (3–4 mo) or old (24 mo) wild type and MIF knockout (MIF−/−) mice. Our data revealed that MIF knockout exacerbated aging-induced unfavorable structural and functional changes in the heart. The detrimental effect of MIF knockout was associated with accentuated loss in cardiac autophagy with aging. Aging promoted cardiac inflammation, the effect was attenuated by MIF knockout. Intriguingly, aging-induced unfavorable responses were reversed by treatment with the autophagy inducer rapamycin, with improved myocardial ATP availability in aged WT and MIF−/− mice. Using an in vitro model of senescence, MIF knockdown exacerbated doxorubicin-induced premature senescence in H9C2 myoblasts, the effect was ablated by MIF replenishment. Our data indicated that MIF knockout exacerbates aging-induced cardiac remodeling and functional anomalies despite improved inflammation, probably through attenuating loss of autophagy and ATP availability in the heart.
Vision-based Nano Robotic System for High-throughput Non-embedded Cell Cutting
Authors: Shang Wanfeng , Lu Haojian , Wan Wenfeng , Fukuda Toshio , Shen Yajing 
Published: March 2016

AbstractCell cutting is a significant task in biology study, but the highly productive non-embedded cell cutting is still a big challenge for current techniques. This paper proposes a vision-based nano robotic system and then realizes automatic non-embedded cell cutting with this system. First, the nano robotic system is developed and integrated with a nanoknife inside an environmental scanning electron microscopy (ESEM). Then, the positions of the nanoknife and the single cell are recognized, and the distance between them is calculated dynamically based on image processing. To guarantee the positioning accuracy and the working efficiency, we propose a distance-regulated speed adapting strategy, in which the moving speed is adjusted intelligently based on the distance between the nanoknife and the target cell. The results indicate that the automatic non-embedded cutting is able to be achieved within 1–2 mins with low invasion benefiting from the high precise nanorobot system and the sharp edge of nanoknife. This research paves a way for the high-throughput cell cutting at cell’s natural condition, which is expected to make significant impact on the biology studies, especially for the in-situ analysis at cellular and subcellular scale, such as cell interaction investigation, neural signal transduction and low invasive cell surgery.
Forest dynamics and its driving forces of sub-tropical forest in South China
Authors: Ma Lei , Lian Juyu , Lin Guojun , Cao Honglin , Huang Zhongliang , Guan Dongsheng 
Published: March 2016

AbstractTree mortality and recruitment are key factors influencing forest dynamics, but the driving mechanisms of these processes remain unclear. To better understand these driving mechanisms, we studied forest dynamics over a 5-year period in a 20-ha sub-tropical forest in the Dinghushan Nature Reserve, South China. The goal was to identify determinants of tree mortality/recruitment at the local scale using neighborhood analyses on some locally dominant tree species. Results show that the study plot was more dynamic than some temperate and tropical forests in a comparison to large, long-term forest dynamics plots. Over the 5-year period, mortality rates ranged from 1.67 to 12.33% per year while recruitment rates ranged from 0 to 20.26% per year. Tree size had the most consistent effect on mortality across species. Recruitment into the ≥1-cm size class consistently occurred where local con-specific density was high. This suggests that recruitment may be limited by seed dispersal. Hetero-specific individuals also influenced recruitment significantly for some species. Canopy species had low recruitment into the ≥1-cm size class over the 5-year period. In conclusion, tree mortality and recruitment for sixteen species in this plot was likely limited by seed dispersal and density-dependence.
Intra-epidemic evolutionary dynamics of a Dengue virus type 1 population reveal mutant spectra that correlate with disease transmission
Authors: Hapuarachchi Hapuarachchige Chanditha , Koo Carmen , Kek Relus , Xu Helen , Lai Yee Ling , Liu Lilac , Kok Suet Yheng , Shi Yuan , Chuen Raphael Lee Tze , Lee Kim-Sung , Maurer-Stroh Sebastian , Ng Lee Ching 
Published: March 2016

AbstractDengue virus (DENV) is currently the most prevalent mosquito-borne viral pathogen. DENVs naturally exist as highly heterogeneous populations. Even though the descriptions on DENV diversity are plentiful, only a few studies have narrated the dynamics of intra-epidemic virus diversity at a fine scale. Such accounts are important to decipher the reciprocal relationship between viral evolutionary dynamics and disease transmission that shape dengue epidemiology. In the current study, we present a micro-scale genetic analysis of a monophyletic lineage of DENV-1 genotype III (epidemic lineage) detected from November 2012 to May 2014. The lineage was involved in an unprecedented dengue epidemic in Singapore during 2013–2014. Our findings showed that the epidemic lineage was an ensemble of mutants (variants) originated from an initial mixed viral population. The composition of mutant spectrum was dynamic and positively correlated with case load. The close interaction between viral evolution and transmission intensity indicated that tracking genetic diversity through time is potentially a useful tool to infer DENV transmission dynamics and thereby, to assess the epidemic risk in a disease control perspective. Moreover, such information is salient to understand the viral basis of clinical outcome and immune response variations that is imperative to effective vaccine design.
High-order random Raman lasing in a PM fiber with ultimate efficiency and narrow bandwidth
Authors: Babin Sergey A. , Zlobina Ekaterina A. , Kablukov Sergey I. , Podivilov Evgeniy V. 
Published: March 2016

AbstractRandom Raman lasers attract now a great deal of attention as they operate in non-active turbid or transparent scattering media. In the last case, single mode fibers with feedback via Rayleigh backscattering generate a high-quality unidirectional laser beam. However, such fiber lasers have rather poor spectral and polarization properties, worsening with increasing power and Stokes order. Here we demonstrate a linearly-polarized cascaded random Raman lasing in a polarization-maintaining fiber. The quantum efficiency of converting the pump (1.05 μm) into the output radiation is almost independent of the Stokes order, amounting to 79%, 83% and 77% for the 1st (1.11 μm), 2nd (1.17 μm) and 3rd (1.23 μm) order, respectively, at the polarization extinction ratio >22 dB for all orders. The laser bandwidth grows with increasing order, but it is almost independent of power in the 1–10 W range, amounting to ~1, ~2 and ~3 nm for orders 1–3, respectively. So, the random Raman laser exhibits no degradation of output characteristics with increasing Stokes order. A theory adequately describing the unique laser features has been developed. Thus, a full picture of the cascaded random Raman lasing in fibers is shown.
Photodynamic killing of cancer cells by a Platinum(II) complex with cyclometallating ligand
Authors: Doherty Rachel E. , Sazanovich Igor V. , McKenzie Luke K. , Stasheuski Alexander S. , Coyle Rachel , Baggaley Elizabeth , Bottomley Sarah , Weinstein Julia A. , Bryant Helen E. 
Published: March 2016

AbstractPhotodynamic therapy that uses photosensitizers which only become toxic upon light-irradiation provides a strong alternative to conventional cancer treatment due to its ability to selectively target tumour material without affecting healthy tissue. Transition metal complexes are highly promising PDT agents due to intense visible light absorption, yet the majority are toxic even without light. This study introduces a small, photostable, charge-neutral platinum-based compound, Pt(II) 2,6-dipyrido-4-methyl-benzenechloride, complex 1, as a photosensitizer, which works under visible light. Activation of the new photosensitizer at low concentrations (0.1–1 μM) by comparatively low dose of 405 nm light (3.6 J cm−2) causes significant cell death of cervical, colorectal and bladder cancer cell lines, and, importantly, a cisplatin resistant cell line EJ-R. The photo-index of the complex is 8. We demonstrate that complex 1 induces irreversible DNA single strand breaks following irradiation, and that oxygen is essential for the photoinduced action. Neither light, nor compound alone led to cell death. The key advantages of the new drug include a remarkably fast accumulation time (diffusion-controlled, minutes), and photostability. This study demonstrates a highly promising new agent for photodynamic therapy, and attracts attention to photostable metal complexes as viable alternatives to conventional chemotherapeutics, such as cisplatin.
High throughput sequencing of small RNAs transcriptomes in two Crassostrea oysters identifies microRNAs involved in osmotic stress response
Authors: Zhao Xuelin , Yu Hong , Kong Lingfeng , Liu Shikai , Li Qi 
Published: March 2016

AbstractIncreasing evidence suggests that microRNAs post-transcriptionally regulate gene expression and are involved in responses to biotic and abiotic stress. However, the role of miRNAs involved in osmotic plasticity remains largely unknown in marine bivalves. In the present study, we performed low salinity challenge with two Crassostrea species (C. gigas and C. hongkongensis), and conducted high-throughput sequencing of four small RNA libraries constructed from the gill tissues. A total of 202 and 87 miRNAs were identified from C. gigas and C. hongkongensis, respectively. Six miRNAs in C. gigas and two in C. hongkongensis were differentially expressed in response to osmotic stress. The expression profiles of these eight miRNAs were validated by qRT-PCR. Based on GO enrichment and KEGG pathway analysis, genes associated with microtubule-based process and cellular component movement were enriched in both species. In addition, five miRNA-mRNA interaction pairs that showed opposite expression patterns were identified in the C. hongkongensis, Differential expression analysis identified the miRNAs that play important regulatory roles in response to low salinity stress, providing insights into molecular mechanisms that are essential for salinity tolerance in marine bivalves.
Direct manufacturing of ultrathin graphite on three-dimensional nanoscale features
Authors: Pacios Mercè , Hosseini Peiman , Fan Ye , He Zhengyu , Krause Oliver , Hutchison John , Warner Jamie H. , Bhaskaran Harish 
Published: March 2016

AbstractThere have been many successful attempts to grow high-quality large-area graphene on flat substrates. Doing so at the nanoscale has thus far been plagued by significant scalability problems, particularly because of the need for delicate transfer processes onto predefined features, which are necessarily low-yield processes and which can introduce undesirable residues. Herein we describe a highly scalable, clean and effective, in-situ method that uses thin film deposition techniques to directly grow on a continuous basis ultrathin graphite (uG) on uneven nanoscale surfaces. We then demonstrate that this is possible on a model system of atomic force probe tips of various radii. Further, we characterize the growth characteristics of this technique as well as the film’s superior conduction and lower adhesion at these scales. This sets the stage for such a process to allow the use of highly functional graphite in high-aspect-ratio nanoscale components.
Compact UWB monopole antenna for internet of things applications
Authors: Bekasiewicz A. , Koziel S. 
Published: March 2016

A structure of a compact ultra‐wideband monopole antenna has been presented. The antenna consists of a microstrip‐fed rectangle radiator as well as a ground plane with a rectangle slit and an L‐shaped stub. The critical factor in achieving a small size is a careful design procedure involving numerical optimisation of all geometry parameters of the antenna aiming at explicit size reduction while maintaining acceptable electrical performance. The final design exhibits dimensions of only 9.45 × 18.5 mm and a footprint of 175 mm2. Experimental validation and comparisons with competitive designs are also provided.
Three‐phase double auxiliary resonant commutated pole inverter topology and analysis of its working principle
Authors: Chu Enhui , Zhang Xing , Sun Qiuye , Li Si , Xiong Huiming , Yang Xiaochen 
Published: March 2016

This study presents a double auxiliary resonant commutated pole (ARCP) inverter topology and modulation strategy. In the proposed inverter, the zero‐voltage‐switching (ZVS) turn‐off of auxiliary switches influenced by parasitic circuit elements from the wiring process can be avoided. It is assured that the auxiliary switches achieve ZVS turn‐off reliably. Hence, the reliability of the ARCP inverter is improved, especially in high‐power application. According to the equivalent circuits in different operation modes under the proposed modulation strategy, the working principle, soft‐switching implementation condition, and parameter design procedure of the proposed inverter are analysed successively in this study. Finally, a 10 kW, 16 kHz double ARCP inverter prototype is built. Experimental results are given to demonstrate the validity of the proposed inverter.
Giardia
- significance of zoonotic routes in human infections.
Authors: Ballweber L. R. 
Published: March 2016

Abstract

Giardia
are flagellated protozoan parasites of numerous animals. Species of
Giardia
were originally described based, primarily, on the host from which they were isolated; later, isolates that were morphologically identical with
Giardia duodenalis
were synonymized with that species. Accumulating genetic evidence, however, indicates that
G. duodenalis
is a species complex in which members are morphologically identical, but, genetically distinct. At least eight distinct groups (=assemblages) have been identified, all of which likely constitute unique species. Although zoonotic transmission may occur in discrete circumstances, people to people transmission is likely much more important. However, the human disease burden associated with zoonotic transmission still needs to be assessed, including differences in the biology and clinical manifestations associated with the various types. Genetic targets for typing have been identified but do not work well for all assemblages, particularly assemblage B; thus, the search for appropriate targets must continue. Multilocus genotyping and standardized terminology is highly recommended as interpretations based on single markers may lead to incomplete conclusions. Combining appropriate genetic markers with well-designed epidemiological studies will be necessary to further our understanding of
Giardia
transmission patterns and infection sources for both people and animals.
The Genetic Relationship between Anadromous and Resident Oncorhynchus mykiss at a Putative Barrier with Implications for Habitat Improvement
Authors: Bowersox Brett , Wickersham Thea , Redfield Laura , Ackerman Michael W. 
Published: March 2016

AbstractBig Bear Creek in the Potlatch River system, Idaho, contains an Endangered Species Act‐listed wild population of steelhead Oncorhynchus mykiss (anadromous Rainbow Trout) that is the focus of extensive habitat restoration actions intended to increase population abundance. Both anadromous and resident O. mykiss populations occur in the Big Bear Creek drainage; however, anadromous individuals are known to spawn and rear only in the lower drainage, whereas putative resident fish occur in the headwaters. Big Bear Falls is a potential upstream migration barrier that is located between the two populations. Oncorhynchus mykiss of unknown origin are present within 1 km above the falls. We used analyses of genetic diversity, structure, and sibship reconstruction to determine whether Big Bear Falls limited the movement of steelhead to headwater areas. Known resident O. mykiss were sampled in headwater areas, known anadromous adults were sampled at a weir in the lower drainage, and juveniles of unknown life history were collected from areas below and above the falls. Allele frequency data indicated that anadromous and headwater resident populations were highly differentiated and that exchange of genetic material between populations was limited. However, juvenile O. mykiss in the above‐waterfall collection were found to be the offspring or recent descendants of steelhead that successfully navigated above Big Bear Falls, demonstrating that the falls is not a complete barrier. We also identified evidence of limited downstream gene flow, suggesting that resident fish contributed genetic material to the downstream anadromous population. This study documented the successful passage of adult steelhead above Big Bear Falls and the downstream movement of resident fish from the headwaters. However, uncertainties still exist regarding the annual variability in passage and the habitat limitations that impact O. mykiss utilization of areas immediately above the falls.Received March 14, 2015; accepted October 27, 2015