Toward Understanding Astrophysical Phenomena

Fast radio bursts (FRBs), a novel type of radio pulse, whose physics is not yet understood at all. Only a handful of FRBs had been detected when we started this project. Taking account of the scant observations, we put physical constraints on FRBs. We excluded proposals of a galactic origin for their extraordinarily high dispersion measures (DM), in particular stellar coronas and HII regions. Therefore our work supports an extragalactic origin for FRBs. We show that the resolved scattering tail of FRB 110220 is unlikely to be due to propagation through the intergalactic plasma. Instead the scattering is probably caused by the interstellar medium in the FRB's host galaxy, and indicates that this burst sits in the central region of that galaxy. Pulse durations of order $\ms$ constrain source sizes of FRBs implying enormous brightness temperatures and thus coherent emission. Electric fields near FRBs at cosmological distances would be so strong that they could accelerate free electrons from rest to relativistic energies in a single wave period. When we worked on FRBs, it was unclear whether they were genuine astronomical signals as distinct from `perytons', clearly terrestrial radio bursts, sharing some common properties with FRBs. Recently, in April 2015, astronomers discovered that perytons were emitted by microwave ovens. Radio chirps similar to FRBs were emitted when their doors opened while they were still heating. Evidence for the astronomical nature of FRBs has strengthened since our paper was published. Some bursts have been found to show linear and circular polarizations and Faraday rotation of the linear polarization has also been detected. I hope to resume working on FRBs in the near future. But after we completed our FRB paper, I decided to pause this project because of the lack of observational constraints.

The pulsar triple system, J0733+1715, has its orbital parameters fitted to high accuracy owing to the precise timing of the central $\ms$ pulsar. The two orbits are highly hierarchical, namely $P_{\mathrm{orb,1}}\ll P_{\mathrm{orb,2}}$, where 1 and 2 label the inner and outer white dwarf (WD) companions respectively. Moreover, their orbital planes almost coincide, providing a unique opportunity to study secular interaction associated purely with eccentricity beyond the solar system. Secular interaction only involves effect averaged over many orbits. Thus each companion can be represented by an elliptical wire with its mass distributed inversely proportional to its local orbital speed. Generally there exists a mutual torque, which vanishes only when their apsidal lines are parallel or anti-parallel. To maintain either mode, the eccentricity ratio, $e_1/e_2$, must be of the proper value, so that both apsidal lines precess together. For J0733+1715, $e_1\ll e_2$ for the parallel mode, while $e_1\gg e_2$ for the anti-parallel one. We show that the former precesses $\sim 10$ times slower than the latter. Currently the system is dominated by the parallel mode. Although only a little anti-parallel mode survives, both eccentricities especially $e_1$ oscillate on $\sim 10^3\yr$ timescale. Detectable changes would occur within $\sim 1\yr$. We demonstrate that the anti-parallel mode gets damped $\sim 10^4$ times faster than its parallel brother by any dissipative process diminishing $e_1$. If it is the tidal damping in the inner WD, we proceed to estimate its tidal quantity parameter ($Q$) to be $\sim 10^6$, which was poorly constrained by observations. However, tidal damping may also happen during the preceding low-mass X-ray binary (LMXB) phase or hydrogen thermal nuclear flashes. But, in both cases, the inner companion fills its Roche lobe and probably suffers mass/angular momentum loss, which might cause $e_1$ to grow rather than decay.

Several pairs of solar system satellites occupy mean motion resonances (MMRs). We divide these into two groups according to their proximity to exact resonance. Proximity is measured by the existence of a separatrix in phase space. MMRs between Io-Europa, Europa-Ganymede and Enceladus-Dione are too distant from exact resonance for a separatrix to appear. A separatrix is present only in the phase spaces of the Mimas-Tethys and Titan-Hyperion MMRs and their resonant arguments are the only ones to exhibit substantial librations. When a separatrix is present, tidal damping of eccentricity or inclination excites overstable librations that can lead to passage through resonance on the damping timescale. However, after investigation, we conclude that the librations in the Mimas-Tethys and Titan-Hyperion MMRs are fossils and do not result from overstability.

Rubble piles are common in the solar system. Monolithic elements touch their neighbors in small localized areas. Voids occupy a significant fraction of the volume. In a fluid-free environment, heat cannot conduct through voids; only radiation can transfer energy across them. We model the effective thermal conductivity of a rubble pile and show that it is proportional the square root of the pressure, $P$, for $P\leq \epsy^3\mu$ where $\epsy$ is the material's yield strain and $\mu$ its shear modulus. Our model provides an excellent fit to the depth dependence of the thermal conductivity in the top $140\,\mathrm{cm}$ of the lunar regolith. It also offers an explanation for the low thermal inertias of rocky asteroids and icy satellites. Lastly, we discuss how rubble piles slow down the cooling of small bodies such as asteroids.

Electromagnetic (EM) follow-up observations of gravitational wave (GW) events will help shed light on the nature of the sources, and more can be learned if the EM follow-ups can start as soon as the GW event becomes observable. In this paper, we propose a computationally efficient time-domain algorithm capable of detecting gravitational waves (GWs) from coalescing binaries of compact objects with nearly zero time delay. In case when the signal is strong enough, our algorithm also has the flexibility to trigger EM observation {\it before} the merger. The key to the efficiency of our algorithm arises from the use of chains of so-called Infinite Impulse Response (IIR) filters, which filter time-series data recursively. Computational cost is further reduced by a template interpolation technique that requires filtering to be done only for a much coarser template bank than otherwise required to sufficiently recover optimal signal-to-noise ratio. Towards future detectors with sensitivity extending to lower frequencies, our algorithm's computational cost is shown to increase rather insignificantly compared to the conventional time-domain correlation method. Moreover, at latencies of less than hundreds to thousands of seconds, this method is expected to be computationally more efficient than the straightforward frequency-domain method.

Nonvolatile holograms in LiNbO3 : Fe : Cu by use of the bleaching effect

We report our observation of a bleaching effect under an ultraviolet exposure in LiNbO3:Fe:Cu crystals. Two three-step recording-transferring-fixing schemes are proposed to record nonvolatile photorefractive holograms in such crystals. In the schemes two red laser beams and an ultraviolet illumination are used selectively to write the charge grating in the shallow-level Fe centers, to develop the charge grating in the deep-level Cu centers by transferring the charge grating in the Fe centers, and to fix only the charge grating in the Cu centers for unerasable read-out. Experimental results, verifications, and an optimal recording scheme are given. A comparison of the lithium niobate crystals of the same double-doping system of Fe:Mn, Ce:Mn, Ce:Cu, and Fe:Cu is outlined. (C) 2002 Optical Society of America.

Redução dos níveis de IL-18 no fundo gengival após tratamento periodontal não-cirúrgico

O objetivo desse estudo foi avaliar o efeito do tratamento não-cirúrgico sobre os níveis da IL-18 em sítios inflamados de pacientes com doença periodontal. Foram avaliados 14 pacientes com doença periodontal, sendo 9 pacientes com periodontite crônica generalizada (media 48,8 DP 7,4 anos) e 5 pacientes com gengivite (43,6 DP 11,8 anos). Nos pacientes com periodontite, os sítios foram divididos em: sem (GP) e com perda de inserção clínica (PP). Os sítios de pacientes com gengivite foram denominados GG. Os pacientes foram avaliados no dia 0, receberam tratamento periodontal não-cirúrgico, e foram novamente avaliados 30 dias depois. Os parâmetros clínicos utilizados no dia 0 e dia 30 foram: Índice de Placa (IP), Índice gengival (IG), Índice de placa visível (IPV), sangramento gengival a sondagem, profundidade de bolsa à sondagem (PBS) e nível de inserção (NI). Foram realizadas coletas de fluido gengival (FG) em 5 sítios GP, 5 sítios PP e em 5 sítios GG por paciente no dia 0 e dia 30. IPV reduziu significantemente de 33,7% para 10,7%. A % de sitos comPBS >4 mm reduziu significantemente de 81,7% para 53,4%. Quando todos os sítios (GG, GP, PP) foram analisados juntos, houve uma redução significante para os níveis de IL-18, IP, IG e PBS. Sendo assim, podemos concluir que houve uma redução significante dos níveis de IL-18 nos sítios inflamados de pacientes com doença periodontal acompanhado por uma melhora significante nos parâmetros clínicos periodontais.

Structure-function analysis of USP1: insights into the role of Ser313 phosphorylation site and the effect of cancer-associated mutations on autocleavage

Background: In complex with its cofactor UAF1, the USP1 deubiquitinase plays an important role in cellular processes related to cancer, including the response to DNA damage. The USP1/UAF1 complex is emerging as a novel target in cancer therapy, but several aspects of its function and regulation remain to be further clarified. These include the role of the serine 313 phosphorylation site, the relative contribution of different USP1 sequence motifs to UAF1 binding, and the potential effect of cancer-associated mutations on USP1 regulation by autocleavage. Methods: We have generated a large set of USP1 structural variants, including a catalytically inactive form (C90S), non-phosphorylatable (S313A) and phosphomimetic (S313D) mutants, deletion mutants lacking potential UAF1 binding sites, a mutant (GG/AA) unable to undergo autocleavage at the well-characterized G670/G671 diglycine motif, and four USP1 mutants identified in tumor samples that cluster around this cleavage site (G667A, L669P, K673T and A676T). Using cell-based assays, we have determined the ability of these mutants to bind UAF1, to reverse DNA damage-induced monoubiquitination of PCNA, and to undergo autocleavage. Results: A non-phosphorylatable S313A mutant of USP1 retained the ability to bind UAF1 and to reverse PCNA ubiquitination in cell-based assays. Regardless of the presence of a phosphomimetic S313D mutation, deletion of USP1 fragment 420-520 disrupted UAF1 binding, as determined using a nuclear relocation assay. The UAF1 binding site in a second UAF1-interacting DUB, USP46, was mapped to a region homologous to USP1(420-520). Regarding USP1 autocleavage, co-expression of the C90S and GG/AA mutants did not result in cleavage, while the cancer-associated mutation L669P was found to reduce cleavage efficiency. Conclusions: USP1 phosphorylation at S313 is not critical for PCNA deubiquitination, neither for binding to UAF1 in a cellular environment. In this context, USP1 amino acid motif 420-520 is necessary and sufficient for UAF1 binding. This motif, and a homologous amino acid segment that mediates USP46 binding to UAF1, map to the Fingers sub-domain of these DUBs. On the other hand, our results support the view that USP1 autocleavage may occur in cis, and can be altered by a cancer-associated mutation.

Influência do polimorfismo genético de citocinas na hepatite C crônica em uma população do Rio de Janeiro

A infecção pelo vírus da hepatite C (VHC) é uma das mais comuns infecções ao redor do mundo. Aproximadamente, 20% dos pacientes infectados eliminam espontaneamente o vírus, porém a maioria dos indivíduos infectados desenvolve infecção crônica com amplo espectro de lesões hepáticas, desde inflamação leve até cirrose. A resposta imune do hospedeiro exerce grande influência sobre o desfecho da infecção pelo VHC. O objetivo deste trabalho foi analisar a influência dos polimorfismos genéticos de citocinas na susceptibilidade ou persistência da infecção por VHC e no clareamento espontâneo em uma amostra de pacientes da população do Rio de Janeiro (Brasil). Os polimorfismos genéticos das citocinas TNFA (-308), TGFB1 (codon 10 e 25), IL10 (-1082, -592), IL6 (-174) e IFNG (+874) foram analisados por PCR-SSP em 245 pacientes com hepatite C crônica (HCC), 41 pacientes que alcançaram o clareamento viral espontâneo e 189 indivíduos controle saudáveis. Além disso, os polimorfismos próximos ao gene da citocina IL28B (rs12979860, rs12980275 e rs8099917) foram analisados por PCR em tempo real em todos os grupos. O grau de fibrose e inflamação, a resposta ao tratamento e o genótipo do vírus também foram levados em consideração quanto ao desfecho da HCC Os genótipos IL28B rs12979860 CC e CT e rs12980275 AA e AG foram significativamente associados ao clareamento espontâneo e à resposta à terapia anti-viral. Da mesma forma, o alelo C (rs12979860) e o alelo A (rs12980275) foram significativamente maior no grupo Clareamento. O alelo C de IL6 (-174) foi associado com o Clareamento. Nenhuma associação entre as demais citocinas e o desfecho da HCC foi encontrada. O Genótipo TNFA (-308) GG parece estar associado com menor grau de inflamação. Além disso, a etnia auto declarada influencia a distribuição dos polimorfismos em IL6 (-174) e IL28B rs12979860 e rs8099917. Nossas observações indicam que os polimorfismos próximos ao gene da IL28B estão associados com o clareamento viral e resposta ao tratamento na população do Rio de Janeiro. Além disso, nossos resultados podem ser úteis para futuras investigações entre os polimorfismos de citocinas e a infecção por VHC numa população heterogênea como a Brasileira.

稻属Oryza officinalis复合体基因组研究－兼论基因组原位杂交的原理和方法

稻属（Oryza L.）属于禾本科稻族（Oryzeae Dumortier）。本属包括AA，BB，BBCC，CC，CCDD，EE，FF，GG，HHJJ和HHKK十个基因组，二十余种。其中Oryza officinalis复合体包括BB，BBCC，CC，CCDD和EE五个基因组，九个种。众多的学者对该复合体进行了广泛深入的研究，为后续研究奠定了坚实的基础。然而，迄今为止，多倍体物种形成问题许多没有解决，基因组间的关系尚未完全阐明，甚至有些多倍体物种的基因组组成仍未确认。 本文评述了Oryza officinalis复合体中基因组研究的历史和现状，用基因组原位杂位（GISH）的方法，对该复合体四倍体物种的基因组组成作了验证;对B，C，D和E四个基因组间的关系进行了研究。同时对基因组原位杂交的方法，原位杂交鉴定多倍体基因组的组成以及研究基因组间关系的方法作了一些探讨。其主要研究结果如下： 一. 原杂交方法的研究：1）染色体制片：比较研究了不同的制片方法，发现压片法适用于大染色体的材料;将酶解/空气干燥法（Fukui et al., 1992）加以改进后，特别适宜于小染色体植物材料的制片。2）根尖储存时间和条件对原位杂交的影响：发现在-20 ℃的酒精（70%）中储存8个月以内的根尖材料，可用于原位杂交;而在-20 ℃的固定液中储藏18个月的根尖，DNA降解严重，不能用于GISH。3）探针标记：比较了随机引物法、缺口平移法和两步标记法（先用随机引物标记后，再用缺口平移法进行标记的方法）的优缺点。结果显示两步标记法是最佳标记方法。 二. GISH鉴定异源多倍体的方法：用两个异源四倍体Oryza minuta和Scilla sinensis (2n = 34)做染色体制片，进行原位杂交实验，结果表明：1）用二倍体亲本基因组之一做探针而不用封阻DNA， 可以鉴别Oryza minuta而不能鉴别Scilla sinensis中的基因组。2）用一个二倍体亲本做探针而用另一个做封阻，能够区分Scilla sinensis的两个基因组;但过量的封阻DNA将可以造成一些实验假象。3）同时用两个亲本的DNA做探针，不仅能够有效分辨不同的基因组，还能够根据交叉杂交程度推测基因组间的分化程度，是鉴别异源多倍体最有效的方法。 三. GISH鉴定稻属四倍体的基因组组成：1）Oryza minuta, O. punctata和O. malampuzhaensis的基因组的组成都为BBCC。2）Oryza minuta中B基因组和二倍体O. punctata中的B基因组之间存在着明显的基因组内分化。3）O. alta是一个异源多倍体，其基因组组成为CCDD。但C和D之间的分化不彻底，可以认为它不是一个严格意义上的异源多倍体。 四. GISH研究B，C，D和E基因组间的关系：1）B基因组和C基因组之间的关系最远;E和C之间的分化同E和B之间的分化程度接近，但E和C之间的分化比E和D之间的分化要小一些;C和D之间的分化不彻底，关系最近。

大尺度环境梯度上羊草种群适应性研究

　　由于全球气候变化，干旱化问题已经成为制约植物生存、影响农作物产量的主要环境因子，因此有关植物在大尺度环境梯度上对环境因子变化的适应性研究已经成为生态学研究的热点。目前环境变化对植被生产力的影响已经有了广泛研究，但是关于植物在形态解剖和渗透调节等生理特征上对大尺环境梯度变化的适应机制研究报道却很少。本研究以北纬43°16′-44°36′；东经125°17′-115°43′范围内的羊草草地为研究对象，探讨羊草主要形态解剖特征、生理渗透调节特征等的变化规律及其与环境因子的关系，以期揭示大尺度环境梯度上羊草种群对环境变化的响应规律和适应策略。本研究的主要结果如下： 在大尺度环境梯度下，羊草种群的气孔密度和气孔指数表现出非常相似的变化趋势，均为由东向西呈先降后升的变化趋势，且与降水等因子的相关关系为V型二次曲线。这是因为气孔的蒸腾作用是植物散失水分的主要途径，同时蒸腾作用产生的蒸腾拉力是植物根部吸收水分的主要动力，因此这种V型曲线正是它在野外对如何调节体内失水和吸水的一种权衡的结果。由于羊草叶片的营养生长和器官建成主要在7月份，这也导致了该月的平均降水对气孔密度和气孔指数有很重要的影响作用。 在该梯度下，羊草叶片厚度和LMA（Leaf mass per unit area, 单位面积叶重）等形态性状指标、叶片解剖学特征等表现出有规律的变化趋势。具体表现为从东向西随着气候由湿润到干旱的变化，叶片厚度、LMA呈增加趋势；同样维管束、木质部及导管直径和叶片厚度等变化趋势相似，从东向西逐渐增加,它们均与七月份温度显著相关。这说明外界环境变化对羊草的形态性状和解剖特征等产生了显著的影响，而且羊草也会通过改变形态解剖特征等来适应大尺度环境梯度变化。 在本研究中，羊草叶片脯氨酸和可溶糖份含量等生理指标也随着环境梯度的变化呈现出明显的规律变化，主要表现为由东至西随降水量的减少而逐渐增加；叶片钠离子和钾离子含量虽然有一定变化，但是它们与气候因子变化并不一致，而分别与土壤里钠离子和钾离子含量呈显著的相关关系。这说明自东向西随着干旱程度的增加，脯氨酸和可溶糖份含量对羊草适应环境变化起着主要的渗透调节作用。 自然条件下，羊草主要有两种生态型，根据叶片颜色的差异分别为灰绿型(GG)和黄绿型(YG)。它们在分布上也表现出很大的差异，其中灰绿型羊草分布范围更广，且更耐盐碱。我们分别选取查干花和绍根两个样点镶嵌生长的两种生态型羊草，对它们的叶片形态解剖特征和渗透调节特征进行比较。结果显示无论是在查干花还是绍根地区，在同一生境条件下，黄绿型羊草叶片厚度、LMA、及维管束直径、木质部直径和导管直径等均比灰绿型高，而气孔密度和气孔指数比灰绿型低，在形态上表现出明显的旱生化特征。而灰绿型羊草叶片则有较高的脯氨酸含量、可溶糖份含量及钾离子含量，较低的钠离子含量，表现出较强的渗透调节能力、更强的选择性排钠离子和吸收钾离子的能力。为此我们推断在相同生境下两种生态型羊草在应对干旱和盐碱胁迫时在形态和生理上采取不同的适应策略，而且这两种策略是互相补充，这就解释了两种生态型羊草能够镶嵌生长的现象。

Focused ion beam etching of GaN

We have investigated the use of focused ion beam (FIB) etching for the fabrication of GaN-based devices. Although work has shown that conventional reactive ion etching (RIE) is in most cases appropriate for the GaN device fabrication, the direct write facility of FIB etching - a well-established technique for optical mask repair and for IC failure analysis and repair - without the requirement for depositing an etch mask is invaluable. A gallium ion beam of about 20nm diameter was used to sputter GaN material. The etching rate depends linearly on the ion dose per area with a slope of 3.5×10 -4μm3/pC. At a current of 3nA, for example, this corresponds to an etch rate of 1.05μm3/s. Good etching qualities have been achieved with a side wall roughness significantly below 0.1μm. Changes in the roughness of the etched surface plane stay below 8nm.

RNA processing and Arabidopsis flowering time control.

Plants control their flowering time in order to ensure that they reproduce under favourable conditions. The components involved in this complex process have been identified using a molecular genetic approach in Arabidopsis and classified into genetically separable pathways. The autonomous pathway controls the level of mRNA encoding a floral repressor, FLC, and comprises three RNA-binding proteins, FCA, FPA and FLK. FCA interacts with the 3'-end RNA-processing factor FY to autoregulate its own expression post-transcriptionally and to control FLC. Other components of the autonomous pathway, FVE and FLD, regulate FLC epigenetically. This combination of epigenetic and post-transcriptional control gives precision to the control of FLC expression and flowering time.

FY is an RNA 3' end-processing factor that interacts with FCA to control the Arabidopsis floral transition

The nuclear RNA binding protein, FCA, promotes Arabidopsis reproductive development. FCA contains a WW protein interaction domain that is essential for FCA function. We have identified FY as a protein partner for this domain. FY belongs to a highly conserved group of eukaryotic proteins represented in Saccharomyces cerevisiae by the RNA 3' end-processing factor, Pfs2p. FY regulates RNA 3' end processing in Arabidopsis as evidenced through its role in FCA regulation. FCA expression is autoregulated through the use of different polyadenylation sites within the FCA pre-mRNA, and the FCA/FY interaction is required for efficient selection of the promoter-proximal polyadenylation site. The FCA/FY interaction is also required for the downregulation of the floral repressor FLC. We propose that FCA controls 3' end formation of specific transcripts and that in higher eukaryotes, proteins homologous to FY may have evolved as sites of association for regulators of RNA 3' end processing.

An allelic series reveals essential roles for FY in plant development in addition to flowering-time control

The autonomous pathway functions to promote flowering in Arabidopsis by limiting the accumulation of the floral repressor FLOWERING LOCUS C (FLC). Within this pathway FCA is a plant-specific, nuclear RNA-binding protein, which interacts with FY, a highly conserved eukaryotic polyadenylation factor. FCA and FY function to control polyadenylation site choice during processing of the FCA transcript. Null mutations in the yeast FY homologue Pfs2p are lethal. This raises the question as to whether these essential RNA processing functions are conserved in plants. Characterisation of an allelic series of fy mutations reveals that null alleles are embryo lethal. Furthermore, silencing of FY, but not FCA, is deleterious to growth in Nicotiana. The late-flowering fy alleles are hypomorphic and indicate a requirement for both intact FY WD repeats and the C-terminal domain in repression of FLC. The FY C-terminal domain binds FCA and in vitro assays demonstrate a requirement for both C-terminal FY-PPLPP repeats during this interaction. The expression domain of FY supports its roles in essential and flowering-time functions. Hence, FY may mediate both regulated and constitutive RNA 3'-end processing.