因特网上的生物医学在线期刊与全文获取

近年来 ,有关Ｉｎｔｅｒｎｅｔ在生物医学中应用的文献逐渐增多 ,内容涉及医学研究的很多专业领域 ,为医学网络情报资源的利用提供了宝贵的经验。许多文献均谈到了网络资源的搜索、Ｍｅｄｌｉｎｅ等数据库的文献检索及相关学科的重要站点 ,但因特网上多数文献检索数据库一般只免费提供题录和摘要 ,查找到所需论文后还需根据文章出处到图书馆获取原文 ,前提是图书馆收录了该种期刊 ,有时通过Ｉｎｔｅｒｎｅｔ也有多种方式可方便地获取全文。1 .通过检索结果直接获取[1]ＰｕｂＭｅｄ(ｈｔｔｐ :/ /ｗｗｗ .ｎｃｂｉ.ｎｌｍ .ｎｉｈ .ｇｏｖ/Ｐ…     

Full Text Clustering and Relationship Network Analysis of Biomedical Publications

Rapid developments in the biomedical sciences have increased the demand for automatic clustering of biomedical publications. In contrast to current approaches to text clustering, which focus exclusively on the contents of abstracts, a novel method is proposed for clustering and analysis of complete biomedical article texts. To reduce dimensionality, Cosine Coefficient is used on a sub-space of only two vectors, instead of computing the Euclidean distance within the space of all vectors. Then a strategy and algorithm is introduced for Semi-supervised Affinity Propagation (SSAP) to improve analysis efficiency, using biomedical journal names as an evaluation background. Experimental results show that by avoiding high-dimensional sparse matrix computations, SSAP outperforms conventional k-means methods and improves upon the standard Affinity Propagation algorithm. In constructing a directed relationship network and distribution matrix for the clustering results, it can be noted that overlaps in scope and interests among BioMed publications can be easily identified, providing a valuable analytical tool for editors, authors and readers.     

Training Top-Down Attention Improves Performance on a Triple-Conjunction Search Task

Training has been shown to improve perceptual performance on limited sets of stimuli. However, whether training can generally improve top-down biasing of visual search in a target-nonspecific manner remains unknown. We trained subjects over ten days on a visual search task, challenging them with a novel target (top-down goal) on every trial, while bottom-up uncertainty (distribution of distractors) remained constant. We analyzed the changes in saccade statistics and visual behavior over the course of training by recording eye movements as subjects performed the task. Subjects became experts at this task, with twofold increased performance, decreased fixation duration, and stronger tendency to guide gaze toward items with color and spatial frequency (but not necessarily orientation) that resembled the target, suggesting improved general top-down biasing of search.     

Enhanced Text Spacing Improves Reading Performance in Individuals with Macular Disease

The search by many investigators for a solution to the reading problems encountered by individuals with no central vision has been long and, to date, not very fruitful. Most textual manipulations, including font size, have led to only modest gains in reading speed. Previous work on spatial integrative properties of peripheral retina suggests that ‘visual crowding’ may be a major factor contributing to inefficient reading. Crowding refers to the fact that juxtaposed targets viewed eccentrically may be difficult to identify. The purpose of this study was to assess the combined effects of line spacing and word spacing on the ability of individuals with age-related macular degeneration (ARMD) to read short passages of text that were printed with either high (87.5%) or low contrast (17.5%) letters. Low contrast text was used to avoid potential ceiling effects and to mimic a possible reduction in letter contrast with light scatter from media opacities. For both low and high contrast text, the fastest reading speeds we measured were for passages of text with double line and double word spacing. In comparison with standard single spacing, double word/line spacing increased reading speed by approximately 26% with high contrast text (p < 0.001), and by 46% with low contrast text (p < 0.001). In addition, double line/word spacing more than halved the number of reading errors obtained with single spaced text. We compare our results with previous reading studies on ARMD patients, and conclude that crowding is detrimental to reading and that its effects can be reduced with enhanced text spacing. Spacing is particularly important when the contrast of the text is reduced, as may occur with intraocular light scatter or poor viewing conditions. We recommend that macular disease patients should employ double line spacing and double-character word spacing to maximize their reading efficiency.     

Escherichia coliSkp Chaperone Coexpression Improves Solubility and Phage Display of Single-Chain Antibody Fragments

Expression of single-chain antibody fragments (scAb)in the periplasm ofEscherichia colioften results in low soluble product yield and cell lysis. We have increased scAb solubility and prevented cell culture lysis by coexpressing theE. coliSkp chaperone gene. A mutant Skp cistron was linked to a bacteriophage T7 gene 10 translational initiation region and placed either downstream of a scAb gene within an isopropyl β- -thiogalactopyranoside-inducible expression cassette or on a separate colE1-compatible arabinose-inducible vector. Increases in scAb solubility reflected the amount of coexpressed Skp. A bacteriophage display vector that was also engineered to coexpress Skp permitted display of a virtually undisplayable scAb and should prove useful in expanding library sizes.     

The Breakdown of Sucrose During Translocation: With two Plates and one Figure in the Text

When a vine petiole is carrying labelled sucrose away from thelamina, the quantity of labelled carbon dioxide lost from thepetiole bears a constant relation to the quantity of labelledsucrose inside the petiole. Sucrose is virtually the only labelledsugar in the petiole, and the labelled sucrose is confined topart of the phloem. Calculations based on these measurementsand some assumptions suggest that the rate of breakdown of thetranslocated sucrose is about 0·5 mg. per c.c. of phloemper hour. The bearings of these findings on the problem of energysupply to translocation are discussed.     

Using Confidence Set Heuristics During Topology Search Improves the Robustness of Phylogenetic Inference

We examine the impact of likelihood surface characteristics on phylogenetic inference. Amino acid data sets simulated from topologies with branch length features chosen to represent varying degrees of difficulty for likelihood maximization are analyzed. We present situations where the tree found to achieve the global maximum in likelihood is often not equal to the true tree. We use the program covSEARCH to demonstrate how the use of adaptively sized pools of candidate trees that are updated using confidence tests results in solution sets that are highly likely to contain the true tree. This approach requires more computation than traditional maximum likelihood methods, hence covSEARCH is best suited to small to medium-sized alignments or large alignments with some constrained nodes. The majority rule consensus tree computed from the confidence sets also proves to be different from the generating topology. Although low phylogenetic signal in the input alignment can result in large confidence sets of trees, some biological information can still be obtained based on nodes that exhibit high support within the confidence set. Two real data examples are analyzed: mammal mitochondrial proteins and a small tubulin alignment. We conclude that the technique of confidence set optimization can significantly improve the robustness of phylogenetic inference at a reasonable computational cost. Additionally, when either very short internal branches or very long terminal branches are present, confident resolution of specific bipartitions or subtrees, rather than whole-tree phylogenies, may be the most realistic goal for phylogenetic methods. [Reviewing Editor: Dr. Nicolas Galtier]     

Inhibition of Rooting of Cuttings by Gibberellic Acid: With one Figure in the Text

Gibberellic acid inhibited rooting but increased extension ofpea and bean stem cuttings. Indolylacetic acid usually had acontrary effect both on extension and on root initiation. Itwas found possible to separate the effects of gibberellic acidon extension and rooting. Small doses of gibberellic acid appliedto the bases of cuttings reduced rooting without increasingextension. Small apical doses increased extension without reducingrooting. Disbudding cuttings prevented extension, but gibberellicacid inhibited rooting of disbudded cuttings as strongly asthat of normal cuttings. It has thus been found necessary todiscard an earlier hypothesis that inhibition of rooting bygibberellic acid was a consequence of a diversion of essentialmetabolites to the extending apical regions of the cutting.The antagonism between gibberellic acid and indolylacetic acidwas non-competitive. Gibberellin A₁, known to occur naturallyin Phaseolus, was as active a rooting inhibitor as gibberellicacid. It is now believed that inhibition of rooting of cuttingsby gibberellins is a direct local effect, preventing those earlycell divisions involved in transformation of mature stem tissuesto a meristematic condition.     

Meristem Initial Cells in Irradiated Roots of Vicia faba: With one Figure in the Text

Beans (Vicia faba) were germinated for 24 hours and irradiatedwith X-rays. Primary roots were fixed after 9, 11, and 21 days.Aberrant chromosome complements, the result of chromosome changesinduced by irradiation, were present. They were used as cellmarkers to estimate the number of cell types present in themeristem initial cells of the growing root and the number ofprimordium initial cells from which root regeneration occurred.Up to 9 cell types occur as meristem initials. From the relativefrequencies of the different cell types, it is estimated thatthere are at least 32 actual meristem initial cells in regeneratingirradiated primary roots. This result is compatible with observationsmade on normal roots. The chimaerical nature of the regeneratingroot apparently does not interfere with the normal organizationof the meristem, but it serves to reveal what part of the organizationis.     

An Unsupervised Text Mining Method for Relation Extraction from Biomedical Literature

The wealth of interaction information provided in biomedical articles motivated the implementation of text mining approaches to automatically extract biomedical relations. This paper presents an unsupervised method based on pattern clustering and sentence parsing to deal with biomedical relation extraction. Pattern clustering algorithm is based on Polynomial Kernel method, which identifies interaction words from unlabeled data; these interaction words are then used in relation extraction between entity pairs. Dependency parsing and phrase structure parsing are combined for relation extraction. Based on the semi-supervised KNN algorithm, we extend the proposed unsupervised approach to a semi-supervised approach by combining pattern clustering, dependency parsing and phrase structure parsing rules. We evaluated the approaches on two different tasks: (1) Protein–protein interactions extraction, and (2) Gene–suicide association extraction. The evaluation of task (1) on the benchmark dataset (AImed corpus) showed that our proposed unsupervised approach outperformed three supervised methods. The three supervised methods are rule based, SVM based, and Kernel based separately. The proposed semi-supervised approach is superior to the existing semi-supervised methods. The evaluation on gene–suicide association extraction on a smaller dataset from Genetic Association Database and a larger dataset from publicly available PubMed showed that the proposed unsupervised and semi-supervised methods achieved much higher F-scores than co-occurrence based method.     

荧光成像技术及其在生命科学中的应用

近年来,荧光成像技术发展迅速,其成像系统通常为目前最先进的分析检测仪器之一的激光共聚焦显微镜,荧光探针是荧光成像技术的核心之一。作为新兴光学成像技术,荧光成像技术在生命科学领域中应用广泛,可用于蛋白质及金属离子检测,肿瘤疾病的诊断,并为药物新剂型的研究提供了新思路。     

Studies on the Membrane of the Almond Endosperm Haustorium: With six Plates and one Figure in the Text

The endosperm of Primus amygdalus develops after fertilizationinto a long narrow tube reaching the chalaza. This tubular formationdoes not become cellular and functions as a haustorium. Cellularizationoccurs at the micropilar end of the endosperm and, after theseed has reached its definite size, the cellular endosperm growsat the expense of the nucellus pushing toward the chalaza thehaustorial portion. The membrane of the haustorium is mainly cellulosic and clearlylamellated as shown by electron micrographs of its sections.The X-ray diagrams show lack of orientation through the thicknessof the membrane and indicate some slight difference in spacingsbetween the haustorial cellulose and the cellulose of Cladophorarupestris An interesting feature of the haustorial membrane is the presenceof numerous roundish structures, about 4µ in diameter,which show an irregular maltese cross when observed under crossednicols. The electron micrographs show that these structurescorrespond to regions of the membrane where the regular lamellationis disturbed, the membrane appearing swollen and the interiorof the ‘bubble’ being occupied by irregular spiral-likecoils. In some cases, through stripping of the membrane, somerather thick coiled strands have been isolated.     

The Growth of Cacao (Theobroma cacao) With and Without Shade: With one Figure in the Text

Evidence is presented that young plants of cacao can toleratehigh light intensities if provided with adequate water and nutrientsupplies.     

DeTEXT: A Database for Evaluating Text Extraction from Biomedical Literature Figures

Hundreds of millions of figures are available in biomedical literature, representing important biomedical experimental evidence. Since text is a rich source of information in figures, automatically extracting such text may assist in the task of mining figure information. A high-quality ground truth standard can greatly facilitate the development of an automated system. This article describes DeTEXT: A database for evaluating text extraction from biomedical literature figures. It is the first publicly available, human-annotated, high quality, and large-scale figure-text dataset with 288 full-text articles, 500 biomedical figures, and 9308 text regions. This article describes how figures were selected from open-access full-text biomedical articles and how annotation guidelines and annotation tools were developed. We also discuss the inter-annotator agreement and the reliability of the annotations. We summarize the statistics of the DeTEXT data and make available evaluation protocols for DeTEXT. Finally we lay out challenges we observed in the automated detection and recognition of figure text and discuss research directions in this area. DeTEXT is publicly available for downloading at http://prir.ustb.edu.cn/DeTEXT/.     

The Role of Leaves as Inhibitors of Flower Induction in Strawberry: With one Figure in the Text

The effects of various defoliation treatments on flower initiationwere studied in the strawberry var. Talisman, which is a facultativeshort-day plant, with particular reference to differences inthe inductive capacity of leaves of differing maturity. Plants from which all mature leaves had been removed to leaveonly two immature leaves flowered in longer photoperiods thanintact controls, and conversely plants bearing only three fullymature and no immature leaves required a shorter photoperiodfor flower initiation than intact plants. Intact plants in constant darkness and totally defoliated plantsin continuous light both initiated flowers, but intact plantsin continuous light failed to flower. It is submitted that these results provide evidence that thephotoperiodic control of flowering in this plant operates througha flower inhibitor produced in the leaves. They also show that although leaves of any maturity are ableto inhibit flower initiation, under some conditions mature leavesare more inhibitory than immature, and that the inhibitory activityof any leaf decreases with decreasing photoperiod.     

CEE-ing is believing: Bioscience ventures in Central and Eastern Europe

Bioscience ventures in Central and Eastern Europe are becoming a presence in world healthcare markets despite a perennially short supply of venture funding and other support mechanisms relative to other world economic regions. Here are three up-and-coming CEE stories worth keeping an eye on.Innovations in bioscience happen every day all over the world—in laboratories, on university campuses, in rich and poor nations alike—coming to life somewhere in the minds of inspired scientists who think they just might have a breakthrough solution to some daunting healthcare problem. The vast majority of these innovations, unfortunately, never make it to commercial markets, where they could be applied to solve actual medical challenges. This is true for a variety of reasons: intellectual property stuck in the recesses of academia; lack of practical know-how in running a business on the part of the innovators; but perhaps most of all because of the absence, in most parts of the world, of a supporting ecosystem of institutions and individuals that encourage and invest in highly risky early stage opportunities. There are very few localities that can replicate the intellectual know-how and financial resources on tap in places like Silicon Valley, and for all that the world economy has globalized over the last twenty years, venture capital is still very much a local backyard business.That being said, there are stories out there demonstrating that you don''t have to live in Palo Alto and sign a major venture capital backer to bring a worthwhile idea into fruition, establish a solid commercial value proposition and position yourself on a potentially robust growth trajectory. This article is about three such stories. The common thread between them is that they all took root in Central and Eastern Europe. This is a region with a relatively short history of modern free market economics and plenty of bumps in the road since the Berlin Wall came down in 1989 but at the same time one that retains a longstanding tradition of commitment to research and scientific excellence. Now the knowledge and expertise resident in what was once the bleak landscape stuck behind the Iron Curtain has the potential to help solve important healthcare challenges the world over. The founders of these three companies—an eclectic group of individuals from different backgrounds who perceived opportunities and accepted the daunting risks involved in choosing to pursue them—have brought themselves into a position where they may yet reap significant rewards for their labors.