PseudoBase: a database with RNA pseudoknots

PseudoBase is a database containing structural, functional and sequence data related to RNA pseudo-knots. It can be reached at http://wwwbio.Leiden Univ.nl/ approximately Batenburg/PKB.html. This page will direct the user to a retrieval page from where a particular pseudoknot can be chosen, or to a submission page which enables the user to add pseudoknot information to the database or to an informative page that elaborates on the various aspects of the database. For each pseudoknot, 12 items are stored, e.g. the nucleotides of the region that contains the pseudoknot, the stem positions of the pseudoknot, the EMBL accession number of the sequence that contains this pseudoknot and the support that can be given regarding the reliability of the pseudoknot. Access is via a small number of steps, using 16 different categories. The development process was done by applying the evolutionary methodology for software development rather than by applying the methodology of the classical waterfall model or the more modern spiral model.     

The oldest illustration of Chinese crinoid calyx: Annotated translation of “Cupressocrinus abbreviatus” reported by Fritz Frech in 1911

The early history on the discovery of the first Chinese crinoid calyx of “Cupressocrinus abbreviatus” (now Halocrinites schlotheimii Steininger, 1831) remains unclear. The first record of “C. abbreviatus” was reported by Fritz Frech in 1911. It was included in the fifth and the last volume of the series titled China by the German traveler and explorer Ferdinand Freiherr von Richthofen. The cover page, title page, and prologue are informative; thus, they are explained and translated in detail. Richthofen's specimen is still the oldest documented cupressocrinitid calyx known in China today. Discovery of a second cupressocrinitid specimen confirms the existence of this family in China. Current taxonomic positions of the Chinese specimens are discussed.     

GSDS: 基因结构显示系统

构建了一个用于绘制基因结构示意图的网站系统(http://gsds.cbi.pku.edu.cn/)。用户可提交核酸序列、NCBI核酸序列号或基因外显子位置信息, 得到基因结构示意图; 并可指定在基因结构图上标注某些特定区域。系统允许用户同时输入多个基因, 并指定输出次序和标注区域。结果可用位图和矢量图两种图形格式显示。点击位图格式结果, 可以查看相应序列。系统提供中英文两种用户界面。     

Optimizing Home-Based Software DSM Protocols

Software DSMs can be categorized into homeless and home-based systems both have strengths and weaknesses when compared to each other. This paper introduces optimization methods to exploit advantages and offset disadvantages of the home-based protocol in the home-based software DSM JIAJIA. The first optimization reduces the overhead of writes to home pages through a lazy home page write detection scheme. The normal write detection scheme write-protects shared pages at the beginning of a synchronization interval, while the lazy home page write detection delays home page write-protecting until the page is first fetched in the interval so that home pages that are not cached by remote processors do not need to be write-protected. The second optimization avoids fetching the whole page on a page fault through dividing a page into blocks and fetching only those blocks that are dirty with respect to the faulting processor. A write vector table is maintained for each shared page in its home to record for each processor which block(s) has been modified since the processor fetched the page last time. The third optimization adaptively migrates home of a page to the processor most frequently writes to the page to reduce twin and diff overhead. Migration information is piggybacked on barrier messages and no additional communication is required for the migration. Performance evaluation with some well-accepted benchmarks and real applications shows that the above optimization methods can reduce page faults, message amounts, and diffs dramatically and consequently improve performance significantly.     

THEORY AND MEASUREMENT OF VISUAL MECHANISMS : XI. ON FLICKER WITH SUBDIVIDED FIELDS

In Vol. 27, No. 5, May 20, 1944, page 403, in the eighth line from the bottom of the page, the comma after "intensity" should be a semicolon. On page 413, in the second formula from the bottom of the page, for See PDF for Equation read See PDF for Equation On the same page, formula 2 should read See PDF for Equation On page 414, line 3, at the end of the line add "or" to read "of the level of I or of F." On page 422, in the first line below the figure legend, for "illuminate" read "illuminated." On page 430, line 22, for "lighteb dars" read "lighted bars."     

Corrections

Vol. 30, parts 1 and 2 page 45, line 7 for "Canyon" read "Cayman". page 46 line 27for "2G; 7.xi.l937" read "36; 2.vi.l938". page 50 line 5 for "31" read "27". delete "dredged at 3 &metres". page 50 line 32 for "26; 7.xi.l937" read "30; 2.vi.l938". page 53 line 6 for "19.x.l937" read "8.v.l938". page 10, line 35, for "niiudula" read nitidula. page 21, figure 29, for "L. 8248" read "L. 82482". page 61, line 12, for "holotype (B.M. 43100)" read "syntypes(B.M. 43106, L. 82350)". page 64, line 23, for "Coriopsis" read "Cordiopsis". p. 64, lines 34 and 3G, for "lyell" read "lyellii". page 76, line 37, "Rzymowska 1914" should follow "Taylor (1900)"in line 36. page 77, line 43, for "Xerotrhicha" read "Xerotricha". page 87, line 1, for "twelve" read "ten". page 90, lines 44 and 45, for "marginal (M)" read "lateral",and for "two lateral teeth (L₁ L₂)" read "two marginal teeth".In figure 2, for "esehalent" read "exhalent". pp. 123, 125, 127, 129, headings, for "Pseudoneptunia" read"Pseudoneptunea" p. 124, line 34, for "highgatenis" read "highgatensis". p. 125, The locality of the Sedgwick Museum specimens C. 12891of Siphonalia ferroviae should be given as Titchfield, Hants.,and not as Portsmouth Dock.     

Some correlations between development and respiration in the sand dollar egg,as shown by cyanide inhibition studies

Cyanide is a valuable tool for studying respiratory mechanisms and their r?le in embryonic development: it is relatively specific in its action, penetrates cell membranes readily, is active in low concentration, and may be controlled quantitatively (page 217). Echinarachnius is extremely sensitive to cyanide and the oxygen consumption of both eggs and of sperm is almost completely inhibited by 10(-5)M HCN (pages 219 and 221). Cell division is likewise arrested by the same concentration (page 223). One of the pronounced effects of an irreversible dosage of cyanide is the marked cytolysis or breakdown of the egg, both internally and at the cell membrane. This cytolysis appears to be related to the state of metabolism, and its occurrence varies with both the respiratory and developmental activity of the cell (page 224). The lethal dosage of cyanide varies with the state of development of the egg: the unfertilized egg is less susceptible than the fertilized one, and the susceptibility increases as the development of the fertilized egg proceeds (page 228). The Echinarachnius egg differs from that of Arbacia in respiratory behavior chiefly in its inability to survive prolonged anoxia: the sea urchin egg will tolerate for 24 hours a concentration of cyanide that kills the sand dollar eggs in 30 minutes (page 229). The Echinarachnius egg is apparently completely dependent upon cyanide-sensitive catalytic systems for its normal functioning and maintenance. Interference with this aerobic energy release mechanism results in irreversible damage to the egg (page 231).     

THE ELECTRICAL CHARGE OF MAMMALIAN RED BLOOD CELLS

In Vol. 19, No. 4, March 20, 1936, page 603, in the eleventh line from the bottom of the page for "z_j = 2, z_jj = 1", read "z_j = 1, z_jj = 2". On the same page in the fourteenth line from the bottom of the page for "jj(HPO₄-)" read "jj(HPO₄--)".     

THE POLARIZATION CAPACITY AND RESISTANCE OF VALONIA : I. ALTERNATING CURRENT MEASUREMENTS

On page 685, at the end of the fourth line of the legend for Fig. 4, the sentence should begin "Δr derived" instead of "r derived". On page 690 in the paragraph beginning in the middle of the page, in the second sentence the reference should be to footnote 12, instead of to footnote 11.     

优化AFLP阳性带回收克隆技术

通过将AFLP聚丙烯酰胺变性胶切小、适当曝光过量、以聚丙烯酰胺凝胶电泳代替琼脂糖电泳检测克隆片段大小的方法 ,增加了回收克隆AFLP阳性带的准确性。该方法对于从变性和非变性大page胶上回收克隆目的片段具有普遍意义。     

学术类科技期刊正文转接的原则与技巧

通过编辑实践经验,对学术类科技期刊正文转接的原则和技巧进行总结提炼。阐述了尽量避免跳页排印、以少接多、顺势接排、尽量避免逆向转接、分段或分句转接、不能出现背题的接排、含图表和公式部分不宜转接、应避免转接错误和字体混乱等8条原则以及具体实施的技巧,认为处理正文转接的最适宜时期是清样"定版"环节,其目的在于不断提高编辑工作的效率和期刊的编辑质量。     

THE QUANTIC AND STATISTICAL BASES OF VISUAL EXCITATION

In the article entitled "The quantic and statistical bases of visual excitation" (J. Gen. Physiol., 1947–48, 31, 269), in footnote 1, at the bottom of page 274, read, The product k (k–1) ..., may be written See PDF for Equation. On page 284, in equation (1) add, t = mτ; m = 1,2,3.... I take this occasion to call attention to the fact that in 1944 van der Velden developed two equations, one of which described the variation of liminal energy with the flash time and the other this variation with the visual angle of the spot; both of them apply in the case of homogeneous populations of receptors (rods). These equations are very similar to mine, obtained in an entirely different manner and published nearly 4 years later. In fact, until very recently I was not aware of the equations of van der Velden, published in Physica, 1944, 11, 179, because the papers published in that journal, and particularly those which are written in Dutch, generally become known to French physiologists as abstracts which are often incomplete. Thus the priority of the theoretical basis of the empirical laws which are directly related to the two equations in question belongs entirely to van der Velden. ERNEST L. M. BAUMGARDT In Vol. 31, No. 3, January 20, 1948, page 261, in equation (1) for H ₂ read H ₁. On page 262, in equation (5) for H read H ₂. On page 265, in the third line from the bottom of the page, for 4 c.mm. read 5.24 c.mm. On the same page, in the second line from the bottom of the page, for 5 c.mm. read 6.86 c.mm.     

The effects of adaptation on the perception of similar and dissimilar odors

The Pubishers wish to apologise for the inadvertent mis-spellingof Charles J. Wysocki and other errors in the above article,which should be corrected as follows. On Page 471, Table I, the first Number in the second columnshould read 2:6. On page 477, Table II, the results under d-limonene should readas below. On page 481, the NIH grant number to CJW is DC00298.     

Detecting Memory and Structure in Human Navigation Patterns Using Markov Chain Models of Varying Order

One of the most frequently used models for understanding human navigation on the Web is the Markov chain model, where Web pages are represented as states and hyperlinks as probabilities of navigating from one page to another. Predominantly, human navigation on the Web has been thought to satisfy the memoryless Markov property stating that the next page a user visits only depends on her current page and not on previously visited ones. This idea has found its way in numerous applications such as Google''s PageRank algorithm and others. Recently, new studies suggested that human navigation may better be modeled using higher order Markov chain models, i.e., the next page depends on a longer history of past clicks. Yet, this finding is preliminary and does not account for the higher complexity of higher order Markov chain models which is why the memoryless model is still widely used. In this work we thoroughly present a diverse array of advanced inference methods for determining the appropriate Markov chain order. We highlight strengths and weaknesses of each method and apply them for investigating memory and structure of human navigation on the Web. Our experiments reveal that the complexity of higher order models grows faster than their utility, and thus we confirm that the memoryless model represents a quite practical model for human navigation on a page level. However, when we expand our analysis to a topical level, where we abstract away from specific page transitions to transitions between topics, we find that the memoryless assumption is violated and specific regularities can be observed. We report results from experiments with two types of navigational datasets (goal-oriented vs. free form) and observe interesting structural differences that make a strong argument for more contextual studies of human navigation in future work.     

A THEORY OF INJURY AND RECOVERY : I. EXPERIMENTS WITH PURE SALTS.

In addition to the Correction in Vol. iii, No. 3, January 20, 1921, on page 149, Vol. iii, No. 2, November 20, 1920, line 13, for 92.57 read 89.10; page 154, lines 15, 28, and 32, for O read O+10; page 155, line 3 of the figure legend, for O read O+10.     

Authors index

Hydrobiologia 361: 201–223, 1998. Due to technical problems, Figures 91–94 on page 217 of the above volume were poorly reproduced. We now present the correct figures with their captions, on page 218 of this volume.     

A HyperCard program for the identification of biological specimens

The authors with to make the following corrections to the abovepaper:

• page 64 and References: Omodeo, (1956) not (1965)
• page 68and References: Rosa, (1893) not (1981)
• Table I. Line 1. Cognetti,not Cogneni Line 20. delete (1906) Line 28. Kvavadze (1985)not (1975) Line 29. Kvavadze (1971) not (1981) Line 44.delete (1906) Line 52. delete (1906)
• page 68 in Note sectionthe address given should read ‘A.Colosimo,Departmentof Biochemical Sciences, University of Rome (La Sapienza),PiazzaleA.Moro I-00185, Rome, Italy.’

     

Erratum: Human Demography in the Pleistocene: Do Mitochondrial and Nuclear Genes Tell the Same Story? Evol. Anthropol. 8: 81–86.

Eugene E. Harris and Jody Hey (1999). Human Demography in the Pleistocene: Do Mitochondrial and Nuclear Genes Tell the Same Story? Evol. Anthropol. 8: 81–86. On page 84 at the end of 1st paragraph of the 2nd column should read “. . .intergenetic variation Xq 13.3 to about 535,000 years,³⁹. . .” On page 84 in the 2nd paragraph of the 3rd column should read “. . .and seem to indicate widespread or restricted gene flow among populations.”^19,48,49 On page 85 in the 2nd paragraph of the 1st column should read “. . .united by gene flow at zones of overlap.”⁵³