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Sample records for pubmed growth patterns

  1. A Study on Pubmed Search Tag Usage Pattern: Association Rule Mining of a Full-day Pubmed Query Log

    PubMed Central

    2013-01-01

    Background The practice of evidence-based medicine requires efficient biomedical literature search such as PubMed/MEDLINE. Retrieval performance relies highly on the efficient use of search field tags. The purpose of this study was to analyze PubMed log data in order to understand the usage pattern of search tags by the end user in PubMed/MEDLINE search. Methods A PubMed query log file was obtained from the National Library of Medicine containing anonymous user identification, timestamp, and query text. Inconsistent records were removed from the dataset and the search tags were extracted from the query texts. A total of 2,917,159 queries were selected for this study issued by a total of 613,061 users. The analysis of frequent co-occurrences and usage patterns of the search tags was conducted using an association mining algorithm. Results The percentage of search tag usage was low (11.38% of the total queries) and only 2.95% of queries contained two or more tags. Three out of four users used no search tag and about two-third of them issued less than four queries. Among the queries containing at least one tagged search term, the average number of search tags was almost half of the number of total search terms. Navigational search tags are more frequently used than informational search tags. While no strong association was observed between informational and navigational tags, six (out of 19) informational tags and six (out of 29) navigational tags showed strong associations in PubMed searches. Conclusions The low percentage of search tag usage implies that PubMed/MEDLINE users do not utilize the features of PubMed/MEDLINE widely or they are not aware of such features or solely depend on the high recall focused query translation by the PubMed’s Automatic Term Mapping. The users need further education and interactive search application for effective use of the search tags in order to fulfill their biomedical information needs from PubMed/MEDLINE. PMID:23302604

  2. PUBMED OR NLM GATEWAY

    EPA Science Inventory

    PubMed, a service of the National Library of Medicine, provides access to over 12 million MEDLINE citations back to the mid-1960's and additional life science journals. PubMed includes links to many sites providing full text articles and other related resources. PubMed was design...

  3. Pattern, Growth and Control

    PubMed Central

    Lander, Arthur D.

    2011-01-01

    The view of biology as goal-directed engineering has deep historical roots in developmental biology, a field currently benefitting from an influx of ideas and methods from systems biology. Systems biology draws on non-biological paradigms to explain developmental mechanisms of control, the specific type of regulation that achieves or maintains a desired end. This review highlights some of the current efforts designed to elucidate basic design principles underlying the engineering objectives of robustness, precision, and scaling that are required during developmental control of growth and pattern formation. Examples from vertebrate and invertebrate development are used to illustrate general principles including the value of integral feedback in achieving set-point control; the usefulness of self-organizing behavior; the importance of recognizing and appropriately handling noise; and the No Free Lunch theory. Through the examination of such principles, systems biology offers a functional framework to make sense of the mechanistic complexity of organismal development. PMID:21414486

  4. Pattern formation with proportionate growth

    NASA Astrophysics Data System (ADS)

    Dhar, Deepak

    It is a common observation that as baby animals grow, different body parts grow approximately at same rate. This property, called proportionate growth is remarkable in that it is not encountered easily outside biology. The models of growth that have been studied in Physics so far, e.g diffusion -limited aggregation, surface deposition, growth of crystals from melt etc. involve only growth at the surface, with the inner structure remaining frozen. Interestingly, patterns formed in growing sandpiles provide a very wide variety of patterns that show proportionate growth. One finds patterns with different features, with sharply defined boundaries. In particular, even with very simple rules, one can produce patterns that show striking resemblance to those seen in nature. We can characterize the asymptotic pattern exactly in some special cases. I will discuss in particular the patterns grown on noisy backgrounds. Supported by J. C. Bose fellowship from DST (India).

  5. The concept of pattern in craniofacial growth.

    PubMed

    Moyers, R E; Bookstein, F L; Guire, K E

    1979-08-01

    1. There are semantic and associated problems with the word pattern in biology, particularly in orthodontics and facial growth. 2. Pattern, as we use the term, is invariance of relationships--"a set of constraints operating to preserve the integration of parts under varying conditions and through time." 3. Craniofacial pattern can be described and quantified by the identification of craniofacial constants, measures that are relatively invariant. 4. Growth is change and is best identified by studying those measures of size and shape that vary most sensitively through time over development stages. 5. The many traditional cephalometric measures that represent well neither pattern nor growth (mixed) are of less clinical utility than either pure pattern indices or growth indices. 6. The analytical and conceptual separation of pattern and growth seems useful in analysis of morphology, analysis of growth, prediction of growth, and clinical treatment planning. PMID:289292

  6. Exponential Growth through Pattern Exploration

    ERIC Educational Resources Information Center

    Brown, Betty

    2005-01-01

    Participants at the Summer Institute Pattern Exploration: Integration Math and Science in the Middle Grades used and developed a method treat arithmetic, algebra and geometry as one entity. The use of iterative geometric constructions is seen to reinforce the concepts of exponents, ratios and algebraic expressions for the nth stage of the…

  7. Orienteering: Growth Patterns in the United States.

    ERIC Educational Resources Information Center

    Jeffery, Charles F.

    The history of orienteering in the United States includes both military and civilian interest, with the period of greatest growth between 1970 and 1980. To investigate growth patterns in orienteering, questionnaires were mailed to 42 civilian orienteering clubs and 286 universities supporting senior Reserve Office Training Corps (ROTC)…

  8. Stochasticity in plant cellular growth and patterning

    PubMed Central

    Meyer, Heather M.; Roeder, Adrienne H. K.

    2014-01-01

    Plants, along with other multicellular organisms, have evolved specialized regulatory mechanisms to achieve proper tissue growth and morphogenesis. During development, growing tissues generate specialized cell types and complex patterns necessary for establishing the function of the organ. Tissue growth is a tightly regulated process that yields highly reproducible outcomes. Nevertheless, the underlying cellular and molecular behaviors are often stochastic. Thus, how does stochasticity, together with strict genetic regulation, give rise to reproducible tissue development? This review draws examples from plants as well as other systems to explore stochasticity in plant cell division, growth, and patterning. We conclude that stochasticity is often needed to create small differences between identical cells, which are amplified and stabilized by genetic and mechanical feedback loops to begin cell differentiation. These first few differentiating cells initiate traditional patterning mechanisms to ensure regular development. PMID:25250034

  9. Deciphering Dynamical Patterns of Growth Processes

    ERIC Educational Resources Information Center

    Kolakowska, A.

    2009-01-01

    Large systems of statistical physics often display properties that are independent of particulars that characterize their microscopic components. Universal dynamical patterns are manifested by the presence of scaling laws, which provides a common insight into governing physics of processes as vastly diverse as, e.g., growth of geological…

  10. Growth and patterning in the conodont skeleton

    PubMed Central

    Donoghue, P. C. J.

    1998-01-01

    Recent advances in our understanding of conodont palaeobiology and functional morphology have rendered established hypotheses of element growth untenable. In order to address this problem, hard tissue histology is reviewed paying particular attention to the relationships during growth of the component hard tissues comprising conodont elements, and ignoring a priori assumptions of the homologies of these tissues. Conodont element growth is considered further in terms of the pattern of formation, of which four distinct types are described, all possibly derived from a primitive condition after heterochronic changes in the timing of various developmental stages. It is hoped that this may provide further means of unravelling conodont phylogeny. The manner in which the tissues grew is considered homologous with other vertebrate hard tissues, and the elements appear to have grown in a way similar to the growing scales and growing dentition of other vertebrates.

  11. Instabilities and pattern formation in crystal growth

    NASA Astrophysics Data System (ADS)

    Langer, J. S.

    1980-01-01

    Several common modes of crystal growth provide particularly simple and elegant examples of spontaneous pattern formation in nature. Phenomena of interest here are those in which an advancing nonfaceted solidification front suffers an instability and subsequently reorganizes itself into a more complex mode of behavior. The purpose of this essay is to examine several such situations and, in doing this, to identify a few new theoretical ideas and a larger number of outstanding problems. The systems studied are those in which solidification is controlled entirely by a single diffusion process, either the flow of latent heat away from a moving interface or the analogous redistribution of chemical constituents. Convective effects are ignored, as are most effects of crystalline anisotropy. The linear theory of the Mullins-Sekerka instability is reviewed for simple planar and spherical cases and also for a special model of directional solidification. These techniques are then extended to the case of a freely growing dendrite, and it is shown how this analysis leads to an understanding of sidebranching and tip-splitting instabilities. A marginal-stability hypothesis is introduced; and it is argued that this intrinsically nonlinear theory, if valid, permits aone to use results of linear-stability analysis to predict dendritic growth rates. The review concludes with a discussion of nonlinear effects in directional solidication. The nonplanar, cellular interfaces which emerge in this situation have much in common with convection patterns in hydrodynamics. The cellular stability problem is discussed briefly, and some preliminary attempts to do calculations in the strongly nonlinear regime are summarized.

  12. Acta Informatica Medica Is Indexed In Pubmed And Archived In Pubmed Central

    PubMed Central

    Masic, Izet

    2013-01-01

    Acta Informatica Medica journal has been accepted for archiving in PubMed Central from 2011 onward. The journal started in 1993 as the official journal of the Society for Medical Informatics of Bosnia and Herzegovina. During the last 3 years, Acta Informatica Medica has een included in almost all prestigious online databases, including PubMed, Scopus and EMBASE. The 20th volume of the journal is fully international, with papers from 18 countries. PMID:23572852

  13. SPELLING CORRECTION IN THE PUBMED SEARCH ENGINE.

    PubMed

    Wilbur, W John; Kim, Won; Xie, Natalie

    2006-11-01

    It is known that users of internet search engines often enter queries with misspellings in one or more search terms. Several web search engines make suggestions for correcting misspelled words, but the methods used are proprietary and unpublished to our knowledge. Here we describe the methodology we have developed to perform spelling correction for the PubMed search engine. Our approach is based on the noisy channel model for spelling correction and makes use of statistics harvested from user logs to estimate the probabilities of different types of edits that lead to misspellings. The unique problems encountered in correcting search engine queries are discussed and our solutions are outlined. PMID:18080004

  14. Patterned Growth of Carbon Nanotubes or Nanofibers

    NASA Technical Reports Server (NTRS)

    Delzeit, Lance D.

    2004-01-01

    A method and apparatus for the growth of carbon nanotubes or nanofibers in a desired pattern has been invented. The essence of the method is to grow the nanotubes or nanofibers by chemical vapor deposition (CVD) onto a patterned catalyst supported by a substrate. The figure schematically depicts salient aspects of the method and apparatus in a typical application. A substrate is placed in a chamber that contains both ion-beam sputtering and CVD equipment. The substrate can be made of any of a variety of materials that include several forms of silicon or carbon, and selected polymers, metals, ceramics, and even some natural minerals and similar materials. Optionally, the substrate is first coated with a noncatalytic metal layer (which could be a single layer or could comprise multiple different sublayers) by ion-beam sputtering. The choice of metal(s) and thickness(es) of the first layer (if any) and its sublayers (if any) depends on the chemical and electrical properties required for subsequent deposition of the catalyst and the subsequent CVD of the carbon nanotubes. A typical first-sublayer metal is Pt, Pd, Cr, Mo, Ti, W, or an alloy of two or more of these elements. A typical metal for the second sublayer or for an undivided first layer is Al at a thickness .1 nm or Ir at a thickness .5 nm. Proper choice of the metal for a second sublayer of a first layer makes it possible to use a catalyst that is chemically incompatible with the substrate. In the next step, a mask having holes in the desired pattern is placed over the coated substrate. The catalyst is then deposited on the coated substrate by ion-beam sputtering through the mask. Optionally, the catalyst could be deposited by a technique other than sputtering and/or patterned by use of photolithography, electron- beam lithography, or another suitable technique. The catalytic metal can be Fe, Co, Ni, or an alloy of two or more of these elements, deposited to a typical thickness in the range from 0.1 to 20 nm.

  15. Secretory pattern of canine growth hormone

    SciTech Connect

    French, M.B.; Vaitkus, P.; Cukerman, E.; Sirek, A.; Sirek, O.V.

    1987-02-01

    The aim of this paper was to define the secretory pattern of growth hormone (GH) under basal conditions in fasted, conscious, male dogs accustomed to handling. Blood samples were withdrawn from a cephalic vein at 15-min intervals. In this way, any ultradian rhythms, if present, could be detected within the frequency range of 0.042-2 cycles/h. In addition, samples were drawn at either 1- or 2.5-min intervals for 2.5 or 5 h to determine whether frequency components greater than 2 cycles/h were present. GH was measured by radioimmunoassay and the raw data were submitted to time series analysis employing power spectral estimation by means of fast Fourier transformation techniques. Peak plasma levels were up to 12 times higher than the baseline concentration of approx. 1 ng/ml. Spectral analysis revealed an endogenous frequency of 0.22 cycles/h, i.e., a periodicity of 4.5 h/cycle. The results indicate that under basal conditions the secretory bursts of canine GH are limited to one peak every 4.5 h.

  16. The Growth Patterns of General Medical Achievement.

    ERIC Educational Resources Information Center

    Shen, Linjun

    This longitudinal study investigates the growth of medical achievement as a multilevel process and emphasizes the structure of the growth. Subjects were students in all 15 U.S. osteopathic medical schools, a total of 1,060 (78 percent of the 1987 osteopathic cohort). Students took appropriate portions of the National Board of Osteopathic Medical…

  17. Fast growth of graphene patterns by laser direct writing

    SciTech Connect

    Park, J. B.; Xiong, W.; Gao, Y.; Qian, M.; Xie, Z. Q.; Mitchell, M.; Zhou, Y. S.; Lu, Y. F.; Han, G. H.; Jiang, L.

    2011-03-21

    Rapid single-step fabrication of graphene patterns was developed using laser-induced chemical vapor deposition (LCVD). A laser beam irradiates a thin nickel foil in a CH{sub 4} and H{sub 2} environment to induce a local temperature rise, thereby allowing the direct writing of graphene patterns in precisely controlled positions at room temperature. Line patterns can be achieved with a single scan without pre- or postprocesses. Surprisingly, the growth rate is several thousand times faster than that of general CVD methods. The discovery and development of the LCVD growth process provide a route for the rapid fabrication of graphene patterns for various applications.

  18. Dinosaurian growth patterns and rapid avian growth rates.

    PubMed

    Erickson, G M; Rogers, K C; Yerby, S A

    2001-07-26

    Did dinosaurs grow in a manner similar to extant reptiles, mammals or birds, or were they unique? Are rapid avian growth rates an innovation unique to birds, or were they inherited from dinosaurian precursors? We quantified growth rates for a group of dinosaurs spanning the phylogenetic and size diversity for the clade and used regression analysis to characterize the results. Here we show that dinosaurs exhibited sigmoidal growth curves similar to those of other vertebrates, but had unique growth rates with respect to body mass. All dinosaurs grew at accelerated rates relative to the primitive condition seen in extant reptiles. Small dinosaurs grew at moderately rapid rates, similar to those of marsupials, but large species attained rates comparable to those of eutherian mammals and precocial birds. Growth in giant sauropods was similar to that of whales of comparable size. Non-avian dinosaurs did not attain rates like those of altricial birds. Avian growth rates were attained in a stepwise fashion after birds diverged from theropod ancestors in the Jurassic period. PMID:11473315

  19. Ordered Self-Similar Patterns in Anisotropic Stochastic Growth.

    PubMed

    Yao, Zhenwei; Olvera de la Cruz, Monica

    2016-07-01

    We propose an anisotropic stochastic growth model to rationalize the anisotropic self-assembly of supramolecules to form elongated two-dimensional ribbon structures in a recent experiment. The model exhibits distinct growth scenarios that are critically controlled by the ratio of the transverse and the longitudinal growth rate. In the regime of suppressed transverse growth, the model generates the experimentally observed elongated structures through layer-by-layer growing. We further observe the convergence of rough clusters toward smooth regular elliptic patterns by averaging over a number of independent growth processes. Remarkably, these resulting elliptic clusters are self-similar in each instantaneous moment in the growth process. Statistical analysis suggests that the realization of such ordered patterns does not rely on the delicate coordination of different parts in the cluster growth. The self-similarity phenomenon derived from this idealized model may have wider implications, notably in the designed clustering of various elementary building blocks with anisotropic interactions. PMID:27003104

  20. Growth Patterns Inferred from Anatomical Records 1

    PubMed Central

    Silk, Wendy Kuhn; Lord, Elizabeth M.; Eckard, Kathleen J.

    1989-01-01

    Our objective was to test whether accurate growth analyses can be obtained from anatomical records and some mathematical formulas. Roots of Zea mays L. were grown at one of two temperatures (19°C or 29°C) and were prepared with standard techniques for light microscopy. Positions of cell walls were digitized from micrographs. The digitized data were averaged and smoothed and used in formulas to estimate growth trajectories, Z(t), velocities, v(z), and strain rates, r(z), where Z(t) is the location occupied by the cellular particle at time t; and v(z) and r(z) are, respectively, the fields of growth velocity and strain rate. The relationships tested are: for Z(t), t = n * c; v(z) = l(z) * f; and r(z) = f * (∂/∂z (l(z))). In the formulas, n represents the number of cells between the origin and the position Z(t); l(z) is local cell length; the constant c, named the `cellochron,' denotes the time for successive cells to pass a spatial point distal to the meristem; l(z) is local cell length, and f is cell flux. Growth trajectories and velocity fields from the anatomical method are in good agreement with earlier analyses based on marking experiments at the two different temperatures. Growth strain rate fields show an unexpected oscillation which may be due to numerical artifacts or to a real oscillation in cell production rate. Images Figure 2 PMID:16666832

  1. Hair growth cycles and wave patterns in "nude" mice.

    PubMed

    Eaton, G J

    1976-09-01

    Hair growth cycles and waves were studied through five generations of hair growth in C57BL/6Icr "nude" mice. One group of nudes received thymus grafts, a second group was composed of athymid nudes and a third consisted of heterozygous (nu/&) haired littermates. The results showed that hair growth cycles and wave patterns were essentially the same in thymus-restored nudes and athymic nudes which indicated that thymus did not play a role in these phenomena. The time interval between hair cycles was considerably shorter in both groups of nude mice as compared to heterozygotes (nu/&). Finally, the hair growth wave pattern in nude mice did not change throughout the generation of hair growth whereas profound changes in wave patterns were observed in heterozygous (nu/&) littermates. PMID:788248

  2. Fish otoliths: daily growth layers and periodical patterns.

    PubMed

    Panella, G

    1971-09-17

    The early-stage annual rings in otoliths from some cold-temperate fish consist of thin growth bands, the number of which corresponds to that of the days in a year. This indicates that growth takes place by daily increments. Other recurrent patterns show a fortnightly and monthly periodicity. Spawning rings are microscopically distinguishable from winter rings. PMID:5098955

  3. The relationship between growth and pattern formation

    PubMed Central

    Bryant, Susan V.

    2016-01-01

    Abstract Successful development depends on the creation of spatial gradients of transcription factors within developing fields, and images of graded distributions of gene products populate the pages of developmental biology journals. Therefore the challenge is to understand how the graded levels of intracellular transcription factors are generated across fields of cells. We propose that transcription factor gradients are generated as a result of an underlying gradient of cell cycle lengths. Very long cell cycles will permit accumulation of a high level of a gene product encoded by a large transcription unit, whereas shorter cell cycles will permit progressively fewer transcripts to be completed due to gating of transcription by the cell cycle. We also propose that the gradients of cell cycle lengths are generated by gradients of extracellular morphogens/growth factors. The model of cell cycle gated transcriptional regulation brings focus back to the functional role of morphogens as cell cycle regulators, and proposes a specific and testable mechanism by which morphogens, in their roles as growth factors (how they were originally discovered), also determine cell fate. PMID:27499882

  4. Bosnian and Herzegovinian medical scientists in PubMed database.

    PubMed

    Masic, Izet

    2013-01-01

    In this paper it is shortly presented PubMed as one of the most important on-line databases of the scientific biomedical literature. Also, the author has analyzed the most cited authors, professors of the medical faculties in Bosnia and Herzegovina, from the published papers in the biomedical journals abstracted and indexed in PubMed. PMID:24341067

  5. Growth patterns of craniopharyngiomas: clinical analysis of 226 patients.

    PubMed

    Pan, Jun; Qi, Songtao; Liu, Yi; Lu, Yuntao; Peng, Junxiang; Zhang, XiAn; Xu, YiKai; Huang, Guang-Long; Fan, Jun

    2016-04-01

    OBJECT Craniopharyngiomas (CPs) are rare epithelial tumors that are often associated with an enigmatic and unpredictable growth pattern. Understanding the growth patterns of these tumors has a direct impact on surgical planning and may enhance the safety of radical tumor removal. The aim of this study was to analyze the growth patterns and surgical treatment of CPs with a focus on the involvement of the hypothalamopituitary axis and the relationship of the tumor to the arachnoid membrane and surrounding structures. METHODS Clinical data from 226 consecutive patients with primary CP were retrospectively reviewed. Tumor location and the relationship of the tumor to the third ventricle floor and the pituitary stalk were evaluated using preoperative MRI and intraoperative findings. A topographic classification scheme was proposed based on the site of tumor origin and tumor development. The clinical relevance of this classification on patient presentation and outcomes was also analyzed. RESULTS The growth of CPs can be broadly divided into 3 groups based on the site of tumor origin and on tumor-meningeal relationships: Group I, infrasellar/infradiaphragmatic CPs (Id-CPs), which mainly occurred in children; Group II, suprasellar subarachnoid extraventricular CPs (Sa-CPs), which were mainly observed in adults and rarely occurred in children; and Group III, suprasellar subpial ventricular CPs (Sp-CPs), which commonly occurred in both adults and children. Tumors in each group may develop complex growth patterns during vertical expansion along the pituitary stalk. Tumor growth patterns were closely related to both clinical presentation and outcomes. Patients with Sp-CPs had more prevalent weight gain than patients with Id-CPs or Sa-CPs; the rates of significant weight gain were 41.7% for children and 16.7% for adults with Sp-CPs, 2.2% and 7.1% for those with Id-CPs, and 12.5% and 2.6% for those with Sa-CPs (p < 0.001). Moreover, patients with Sp-CPs had increased

  6. Alveolar-filling growth pattern of sarcomatoid malignant pleural mesothelioma.

    PubMed

    Hayakawa, Takamitsu; Tajima, Shogo; Takanashi, Yusuke; Takahashi, Tsuyoshi; Neyatani, Hiroshi; Funai, Kazuhito

    2016-09-01

    A case of sarcomatoid malignant pleural mesothelioma showing extremely rare growth pattern is described. A 63-year-old man presented to our hospital with left pleural effusion. A computed tomography (CT) scan of the chest showed diffusely thickened left visceral and parietal pleura associated with intermingled pulmonary infiltrative shadowing. Biopsy of the pleura under general anaesthesia confirmed the diagnosis of sarcomatoid malignant pleural mesothelioma. The patient underwent left extra-pleural pneumonectomy. Histopathologically, the sarcomatoid spindle tumour cells changed their morphology to polygonal cells in the pulmonary parenchyma and grew upwards, filling the alveolar space without the destruction of its septa, showing an alveolar-filling growth pattern. The current report indicates a case of sarcomatoid pleural mesothelioma that shows an alveolar-filling growth pattern, despite having not been thoroughly categorized in the World Health Organization (WHO) classification. PMID:27516891

  7. Secretory pattern and regulatory mechanism of growth hormone in cattle.

    PubMed

    Kasuya, Etsuko

    2016-02-01

    The ultradian rhythm of growth hormone (GH) secretion has been known in several animal species for years and has recently been observed in cattle. Although the physiological significance of the rhythm is not yet fully understood, it appears essential for normal growth. In this review, previous studies concerning the GH secretory pattern in cattle, including its ultradian rhythm, are introduced and the regulatory mechanism is discussed on the basis of recent findings. PMID:26260675

  8. Recent growth of conifer species of western North America: Assessing spatial patterns of radial growth trends

    USGS Publications Warehouse

    McKenzie, D.; Hessl, Amy E.; Peterson, D.L.

    2001-01-01

    We explored spatial patterns of low-frequency variability in radial tree growth among western North American conifer species and identified predictors of the variability in these patterns. Using 185 sites from the International Tree-Ring Data Bank, each of which contained 10a??60 raw ring-width series, we rebuilt two chronologies for each site, using two conservative methods designed to retain any low-frequency variability associated with recent environmental change. We used factor analysis to identify regional low-frequency patterns in site chronologies and estimated the slope of the growth trend since 1850 at each site from a combination of linear regression and time-series techniques. This slope was the response variable in a regression-tree model to predict the effects of environmental gradients and species-level differences on growth trends. Growth patterns at 27 sites from the American Southwest were consistent with quasi-periodic patterns of drought. Either 12 or 32 of the 185 sites demonstrated patterns of increasing growth between 1850 and 1980 A.D., depending on the standardization technique used. Pronounced growth increases were associated with high-elevation sites (above 3000 m) and high-latitude sites in maritime climates. Future research focused on these high-elevation and high-latitude sites should address the precise mechanisms responsible for increased 20th century growth.

  9. Cytometric patterns reveal growth states of Shewanella putrefaciens

    PubMed Central

    Melzer, Susanne; Winter, Gudrun; Jäger, Kathrin; Hübschmann, Thomas; Hause, Gerd; Syrowatka, Frank; Harms, Hauke; Tárnok, Attila; Müller, Susann

    2015-01-01

    Bacterial growth is often difficult to estimate beyond classical cultivation approaches. Low cell numbers, particles or coloured and dense media may disturb reliable growth assessment. Further difficulties appear when cells are attached to surfaces and detachment is incomplete. Therefore, flow cytometry was tested and used for analysis of bacterial growth on the single-cell level. Shewanella putrefaciens was cultivated as a model organism in planktonic or biofilm culture. Materials of smooth and rough surfaces were used for biofilm cultivation. Both aerobic and anaerobic as well as feast and famine conditions were applied. Visualization of growth was also done using Environmental Scanning and Phase Contrast Microscopy. Bioinformatic tools were applied for data interpretation. Cytometric proliferation patterns based on distributions of DNA contents per cell corresponded distinctly to the various lifestyles, electron acceptors and substrates tested. Therefore, cell cycling profiles of S. putrefaciens were found to mirror growth conditions. The cytometric patterns were consistently detectable with exception of some biofilm types whose resolution remained challenging. Corresponding heat maps proved to be useful for clear visualization of growth behaviour under all tested conditions. Therefore, flow cytometry in combination with bioinformatic tools proved to be powerful means to determine various growth states of S. putrefaciens, even in constrained environments. The approach is universal and will also be applicable for other bacterial species. PMID:25185955

  10. Influence of facial growth pattern on outcome of extraction therapy.

    PubMed

    Hirschfelder, U; Boulouchou, O; Müssig, D; Fleischer-Peters, A

    1997-01-01

    The present clinical-radiological study analyzes orthodontic casts and lateral cephalometric X-rays (at start and finish of orthodontic treatment) of 56 extraction cases, most of them adolescent patients who had 4 teeth extracted. The test group was classified into 3 morphological categories according to growth patterns. For comparison purposes, cephalometric findings of morphologically matching non-extraction groups as well as corresponding data from the literature were used. There was no deepening of overbite in any of the extraction cases in the different test groups. However, an average bite opening of 1.2 mm was found in patients with a neutral or horizontal growth pattern. Irrespective of the growth pattern, a significant increase in anterior and posterior facial height as well as a mean reduction of the ANB angle between 0.9 degrees and 1.3 degrees was found in the different extraction groups. These results matched those of the corresponding nonextraction control groups. At the end of treatment, the longitudinal axis of the upper incisors appeared too steep (retruded). Overall, the individual growth pattern was found to be of very little relevance to treatment results, provided a well considered treatment plan had been drawn up. PMID:9200891

  11. PubMed searches: overview and strategies for clinicians.

    PubMed

    Lindsey, Wesley T; Olin, Bernie R

    2013-04-01

    PubMed is a biomedical and life sciences database maintained by a division of the National Library of Medicine known as the National Center for Biotechnology Information (NCBI). It is a large resource with more than 5600 journals indexed and greater than 22 million total citations. Searches conducted in PubMed provide references that are more specific for the intended topic compared with other popular search engines. Effective PubMed searches allow the clinician to remain current on the latest clinical trials, systematic reviews, and practice guidelines. PubMed continues to evolve by allowing users to create a customized experience through the My NCBI portal, new arrangements and options in search filters, and supporting scholarly projects through exportation of citations to reference managing software. Prepackaged search options available in the Clinical Queries feature also allow users to efficiently search for clinical literature. PubMed also provides information regarding the source journals themselves through the Journals in NCBI Databases link. This article provides an overview of the PubMed database's structure and features as well as strategies for conducting an effective search. PMID:23442731

  12. Geological pattern formation by growth and dissolution in aqueous systems

    SciTech Connect

    Paul Meakin

    2010-03-01

    Although many geological processes take place on time scales that are very long compared with the human experience, essentially all geological processes, fast or slow, are far from equilibrium processes. Surprisingly often, geological processes lead to the formation of quite simple and distinctive patterns, which hint at an underlying simplicity in many complex geological systems.. The ability to predict the seasons was critically important to early human society, and Halley’s prediction of the return of the comet that bears his name is still considered to be a scientific milestone. Spatial patterns have also attracted attention because of their aesthetic appeal, which depends in subtle ways on a combination of regularity and irregularity. In recent decades, rapid growth in the capabilities of digital computers has facilitated the simulation of pattern formation processes, and computer simulations have become an important tool for evaluating theoretical concepts and for scientific discovery. Computer technology in combination with other technologies such as high resolution digital cameras, scanning microprobes (atomic force microscopy AFM), confocal microscopy, and scanning tunneling microscopy (STM), for example) has facilitated the quantitative characterization of patterns over a wide range of scales and has enabled rapid advances in our ability to understand the links between large scale pattern formation and microscopic processes. The ability to quantitatively characterize patterns is important because it enables a more rigorous comparison between the predictions of computer models and real world patterns and their formation.In some cases, the idea that patterns with a high degree of regularity have simple origins appears to be justified, but in other cases, such as the formation of almost perfectly circular stone rings due to freeze-thaw cycles simple patterns appear to be the consequence of quite complex processes. In other cases, it has been shown that

  13. The peptide growth factor, phytosulfokine, attenuates pattern-triggered immunity.

    PubMed

    Igarashi, Daisuke; Tsuda, Kenichi; Katagiri, Fumiaki

    2012-07-01

    Pattern-triggered immunity (PTI) is triggered by recognition of elicitors called microbe-associated molecular patterns (MAMPs). Although immune responses may provide good protection of plants from pathogen attack, excessive immune responses have negative impacts on plant growth and development. Thus, a good balance between positive and negative effects on the immune signaling network is important for plant fitness. However, little information is known about the molecular mechanisms that are involved in attenuation of PTI. Here, we describe a growth-promoting peptide hormone, phytosulfokine (PSK), as attenuating PTI signaling in Arabidopsis. This research was motivated by the observation that expression of the PSK Receptor 1 (PSKR1) gene was induced by MAMP treatment. Plants homozygous for pskr1 T-DNA insertions showed enhanced defense gene expression and seedling growth inhibition triggered by MAMPs. The pskr1 plants also showed enhanced PTI against the bacterial pathogen Pseudomonas syringae. These results indicate that the PSKR-mediated signaling attenuates immune responses. Tyrosyl protein sulfotransferase (TPST) is an enzyme required for production of the mature sulfated PSK. Like pskr1 mutants, a tpst T-DNA insertion line exhibited enhanced MAMP-triggered seedling growth inhibition, which was suppressed by exogenous application of PSK. Thus, PSK signaling mediated by PSKR1 attenuates PTI but stimulates growth. PMID:22353039

  14. Patterning of hydrogenated microcrystalline silicon growth by magnetic field

    SciTech Connect

    Fejfar, A.; Stuchlik, J.; Mates, T.; Ledinsky, M.; Honda, S.; Kocka, J.

    2005-07-04

    A way of influencing growth of silicon films by magnetic field is demonstrated. Permanent magnet(s) placed under the substrate influenced the discharge in a mixture of silane and hydrogen and led to formation of microcrystalline regions in otherwise amorphous film. The pattern of microcrystalline regions varied with the orientation of the magnetic field. Microscopic study by atomic force microscopy and by micro-Raman spectroscopy revealed that the microcrystalline regions resulted from a higher density of crystalline grain nuclei, increased at the locations where the magnetron effect could be expected. This phenomenon could be used to study the transition between amorphous and microcrystalline growth. Moreover, we suggest it as a kind of 'magnetic lithography' for the preparation of predefined microcrystalline patterns in otherwise amorphous silicon films.

  15. Fetal growth patterns in Beckwith-Wiedemann syndrome.

    PubMed

    Mussa, A; Russo, S; de Crescenzo, A; Freschi, A; Calzari, L; Maitz, S; Macchiaiolo, M; Molinatto, C; Baldassarre, G; Mariani, M; Tarani, L; Bedeschi, M F; Milani, D; Melis, D; Bartuli, A; Cubellis, M V; Selicorni, A; Silengo, M C; Larizza, L; Riccio, A; Ferrero, G B

    2016-07-01

    We provide data on fetal growth pattern on the molecular subtypes of Beckwith-Wiedemann syndrome (BWS): IC1 gain of methylation (IC1-GoM), IC2 loss of methylation (IC2-LoM), 11p15.5 paternal uniparental disomy (UPD), and CDKN1C mutation. In this observational study, gestational ages and neonatal growth parameters of 247 BWS patients were compared by calculating gestational age-corrected standard deviation scores (SDS) and proportionality indexes to search for differences among IC1-GoM (n = 21), UPD (n = 87), IC2-LoM (n = 147), and CDKN1C mutation (n = 11) patients. In IC1-GoM subgroup, weight and length are higher than in other subgroups. Body proportionality indexes display the following pattern: highest in IC1-GoM patients, lowest in IC2-LoM/CDKN1C patients, intermediate in UPD ones. Prematurity was significantly more prevalent in the CDKN1C (64%) and IC2-LoM subgroups (37%). Fetal growth patterns are different in the four molecular subtypes of BWS and remarkably consistent with altered gene expression primed by the respective molecular mechanisms. IC1-GoM cases show extreme macrosomia and severe disproportion between weight and length excess. In IC2-LoM/CDKN1C patients, macrosomia is less common and associated with more proportionate weight/length ratios with excess of preterm birth. UPD patients show growth patterns closer to those of IC2-LoM, but manifest a body mass disproportion rather similar to that seen in IC1-GoM cases. PMID:26857110

  16. Chemical vapor deposition growth of patterned graphene on copper

    NASA Astrophysics Data System (ADS)

    Gutierrez, Humberto; Wang, Bei; Zhu, J.

    2010-03-01

    Graphene possesses unique electronic properties and application potentials. However, the synthesis of high-quality, single-layer graphene on large scale remains challenging. Mechanical exfoliation from graphite crystals yields graphene of the highest quality but in an uncontrolled and non-scalable way. Epitaxial growth on SiC has made significant advances in large-scale synthesis, although the cost is relatively high. Very recently, chemical vapor deposition (CVD) is used to grow graphene on Ni and Cu surfaces and has also produced large-area graphene of reasonably high quality. Cracks and ripples, however, present considerable challenges to the CVD growth and transfer process. We report the CVD growth of single-layer graphene on patterned, micron-size copper templates. Raman spectra of the films show low D-band and relatively narrow 2D peak, suggesting high quality. We present and discuss the transport properties of graphene films transferred onto an insulating substrate.

  17. Gaps in affiliation indexing in Scopus and PubMed

    PubMed Central

    Schmidt, Cynthia M.; Cox, Roxanne; Fial, Alissa V.; Hartman, Teresa L.; Magee, Martha L.

    2016-01-01

    Objective The authors sought to determine whether unexpected gaps existed in Scopus's author affiliation indexing of publications written by the University of Nebraska Medical Center or Nebraska Medicine (UNMC/NM) authors during 2014. Methods First, we compared Scopus affiliation identifier search results to PubMed affiliation keyword search results. Then, we searched Scopus using affiliation keywords (UNMC, etc.) and compared the results to PubMed affiliation keyword and Scopus affiliation identifier searches. Results We found that Scopus's records for approximately 7% of UNMC/NM authors' publications lacked appropriate UNMC/NM author affiliation identifiers, and many journals' publishers were supplying incomplete author affiliation information to PubMed. Conclusions Institutions relying on Scopus to track their impact should determine whether Scopus's affiliation identifiers will, in fact, identify all articles published by their authors and investigators. PMID:27076801

  18. Key variables influencing patterns of lava dome growth and collapse

    NASA Astrophysics Data System (ADS)

    Husain, T.; Elsworth, D.; Voight, B.; Mattioli, G. S.; Jansma, P. E.

    2013-12-01

    Lava domes are conical structures that grow by the infusion of viscous silicic or intermediate composition magma from a central volcanic conduit. Dome growth can be characterized by repeated cycles of growth punctuated by collapse, as the structure becomes oversized for its composite strength. Within these cycles, deformation ranges from slow long term deformation to sudden deep-seated collapses. Collapses may range from small raveling failures to voluminous and fast-moving pyroclastic flows with rapid and long-downslope-reach from the edifice. Infusion rate and magma rheology together with crystallization temperature and volatile content govern the spatial distribution of strength in the structure. Solidification, driven by degassing-induced crystallization of magma leads to the formation of a continuously evolving frictional talus as a hard outer shell. This shell encapsulates the cohesion-dominated soft ductile core. Here we explore the mechanics of lava dome growth and failure using a two-dimensional particle-dynamics model. This meshless model follows the natural evolution of a brittle carapace formed by loss of volatiles and rheological stiffening and avoids difficulties of hour-glassing and mesh-entangelment typical in meshed models. We test the fidelity of the model against existing experimental and observational models of lava dome growth. The particle-dynamics model follows the natural development of dome growth and collapse which is infeasible using simple analytical models. The model provides insight into the triggers that lead to the transition in collapse mechasnism from shallow flank collapse to deep seated sector collapse. Increase in material stiffness due to decrease in infusion rate results in the transition of growth pattern from endogenous to exogenous. The material stiffness and strength are strongly controlled by the magma infusion rate. Increase in infusion rate decreases the time available for degassing induced crystallization leading to a

  19. Colony patterning and collective hyphal growth of filamentous fungi

    NASA Astrophysics Data System (ADS)

    Matsuura, Shu

    2002-11-01

    Colony morphology of wild and mutant strains of Aspergillus nidulans at various nutrient and agar levels was investigated. Two types of colony patterning were found for these strains. One type produced uniform colonies at all nutrient and agar levels tested, and the other exhibited morphological change into disordered ramified colonies at low nutrient levels. Both types showed highly condensed compact colonies at high nutrient levels on low agar media that was highly diffusive. Disordered colonies were found to develop with low hyphal extension rates at low nutrient levels. To understand basic pattern selection rules, a colony model with three parameters, i.e., the initial nutrient level and the step length of nutrient random walk as the external parameters, and the frequency of nutrient uptake as an internal parameter, was constructed. At low nutrient levels, with decreasing nutrient uptake frequency under diffusive conditions, the model colony exhibited onsets of disordered ramification. Further, in the growth process of A. nidulans, reduction of hyphal extension rate due to a population effect of hyphae was found when hyphae form three-dimensional dense colonies, as compared to the case in which hyphal growth was restricted into two-dimensional space. A hyphal population effect was introduced in the colony model. Thickening of colony periphery due to the population effect became distinctive as the nutrient diffusion effect was raised at high nutrient levels with low hyphal growth rate. It was considered that colony patterning and onset of disorder were strongly governed by the combination of nutrient diffusion and hyphal growth rate.

  20. pubmed.mineR: an R package with text-mining algorithms to analyse PubMed abstracts.

    PubMed

    Rani, Jyoti; Shah, A B Rauf; Ramachandran, Srinivasan

    2015-10-01

    The PubMed literature database is a valuable source of information for scientific research. It is rich in biomedical literature with more than 24 million citations. Data-mining of voluminous literature is a challenging task. Although several text-mining algorithms have been developed in recent years with focus on data visualization, they have limitations such as speed, are rigid and are not available in the open source. We have developed an R package, pubmed.mineR, wherein we have combined the advantages of existing algorithms, overcome their limitations, and offer user flexibility and link with other packages in Bioconductor and the Comprehensive R Network (CRAN) in order to expand the user capabilities for executing multifaceted approaches. Three case studies are presented, namely, 'Evolving role of diabetes educators', 'Cancer risk assessment' and 'Dynamic concepts on disease and comorbidity' to illustrate the use of pubmed.mineR. The package generally runs fast with small elapsed times in regular workstations even on large corpus sizes and with compute intensive functions. The pubmed.mineR is available at http://cran.rproject. org/web/packages/pubmed.mineR. PMID:26564970

  1. Pattern of variation in avian population growth rates.

    PubMed Central

    Saether, Bernt-Erik; Engen, Steinar

    2002-01-01

    A central question in population ecology is to understand why population growth rates differ over time. Here, we describe how the long-term growth of populations is not only influenced by parameters affecting the expected dynamics, for example form of density dependence and specific population growth rate, but is also affected by environmental and demographic stochasticity. Using long-term studies of fluctuations of bird populations, we show an interaction between the stochastic and the deterministic components of the population dynamics: high specific growth rates at small densities r(1) are typically positively correlated with the environmental variance sigma(e)(2). Furthermore, theta, a single parameter describing the form of the density regulation in the theta-logistic density-regulation model, is negatively correlated with r(1). These patterns are in turn correlated with interspecific differences in life-history characteristics. Higher specific growth rates, larger stochastic effects on the population dynamics and stronger density regulation at small densities are found in species with large clutch sizes or high adult mortality rates than in long-lived species. Unfortunately, large uncertainties in parameter estimates, as well as strong stochastic effects on the population dynamics, will often make even short-term population projections unreliable. We illustrate that the concept of population prediction interval can be useful in evaluating the consequences of these uncertainties in the population projections for the choice of management actions. PMID:12396511

  2. Discovering biomedical semantic relations in PubMed queries for information retrieval and database curation

    PubMed Central

    Huang, Chung-Chi; Lu, Zhiyong

    2016-01-01

    Identifying relevant papers from the literature is a common task in biocuration. Most current biomedical literature search systems primarily rely on matching user keywords. Semantic search, on the other hand, seeks to improve search accuracy by understanding the entities and contextual relations in user keywords. However, past research has mostly focused on semantically identifying biological entities (e.g. chemicals, diseases and genes) with little effort on discovering semantic relations. In this work, we aim to discover biomedical semantic relations in PubMed queries in an automated and unsupervised fashion. Specifically, we focus on extracting and understanding the contextual information (or context patterns) that is used by PubMed users to represent semantic relations between entities such as ‘CHEMICAL-1 compared to CHEMICAL-2.’ With the advances in automatic named entity recognition, we first tag entities in PubMed queries and then use tagged entities as knowledge to recognize pattern semantics. More specifically, we transform PubMed queries into context patterns involving participating entities, which are subsequently projected to latent topics via latent semantic analysis (LSA) to avoid the data sparseness and specificity issues. Finally, we mine semantically similar contextual patterns or semantic relations based on LSA topic distributions. Our two separate evaluation experiments of chemical-chemical (CC) and chemical–disease (CD) relations show that the proposed approach significantly outperforms a baseline method, which simply measures pattern semantics by similarity in participating entities. The highest performance achieved by our approach is nearly 0.9 and 0.85 respectively for the CC and CD task when compared against the ground truth in terms of normalized discounted cumulative gain (nDCG), a standard measure of ranking quality. These results suggest that our approach can effectively identify and return related semantic patterns in a ranked

  3. Discovering biomedical semantic relations in PubMed queries for information retrieval and database curation.

    PubMed

    Huang, Chung-Chi; Lu, Zhiyong

    2016-01-01

    Identifying relevant papers from the literature is a common task in biocuration. Most current biomedical literature search systems primarily rely on matching user keywords. Semantic search, on the other hand, seeks to improve search accuracy by understanding the entities and contextual relations in user keywords. However, past research has mostly focused on semantically identifying biological entities (e.g. chemicals, diseases and genes) with little effort on discovering semantic relations. In this work, we aim to discover biomedical semantic relations in PubMed queries in an automated and unsupervised fashion. Specifically, we focus on extracting and understanding the contextual information (or context patterns) that is used by PubMed users to represent semantic relations between entities such as 'CHEMICAL-1 compared to CHEMICAL-2' With the advances in automatic named entity recognition, we first tag entities in PubMed queries and then use tagged entities as knowledge to recognize pattern semantics. More specifically, we transform PubMed queries into context patterns involving participating entities, which are subsequently projected to latent topics via latent semantic analysis (LSA) to avoid the data sparseness and specificity issues. Finally, we mine semantically similar contextual patterns or semantic relations based on LSA topic distributions. Our two separate evaluation experiments of chemical-chemical (CC) and chemical-disease (CD) relations show that the proposed approach significantly outperforms a baseline method, which simply measures pattern semantics by similarity in participating entities. The highest performance achieved by our approach is nearly 0.9 and 0.85 respectively for the CC and CD task when compared against the ground truth in terms of normalized discounted cumulative gain (nDCG), a standard measure of ranking quality. These results suggest that our approach can effectively identify and return related semantic patterns in a ranked order

  4. Cortical Folding Pattern and its Consistency Induced by Biological Growth

    PubMed Central

    Jalil Razavi, Mir; Zhang, Tuo; Liu, Tianming; Wang, Xianqiao

    2015-01-01

    Cortical folding, characterized by convex gyri and concave sulci, has an intrinsic relationship to the brain’s functional organization. Understanding the mechanism of the brain’s convoluted patterns can provide useful clues into normal and pathological brain function. In this paper, the cortical folding phenomenon is interpreted both analytically and computationally, and, in some cases, the findings are validated with experimental observations. The living human brain is modeled as a soft structure with a growing outer cortex and inner core to investigate its developmental mechanism. Analytical interpretations of differential growth of the brain model provide preliminary insight into critical growth ratios for instability and crease formation of the developing brain. Since the analytical approach cannot predict the evolution of cortical complex convolution after instability, non-linear finite element models are employed to study the crease formation and secondary morphological folds of the developing brain. Results demonstrate that the growth ratio of the cortex to core of the brain, the initial thickness, and material properties of both cortex and core have great impacts on the morphological patterns of the developing brain. Lastly, we discuss why cortical folding is highly correlated and consistent by presenting an intriguing gyri-sulci formation comparison. PMID:26404042

  5. Cortical Folding Pattern and its Consistency Induced by Biological Growth

    NASA Astrophysics Data System (ADS)

    Jalil Razavi, Mir; Zhang, Tuo; Liu, Tianming; Wang, Xianqiao

    2015-09-01

    Cortical folding, characterized by convex gyri and concave sulci, has an intrinsic relationship to the brain’s functional organization. Understanding the mechanism of the brain’s convoluted patterns can provide useful clues into normal and pathological brain function. In this paper, the cortical folding phenomenon is interpreted both analytically and computationally, and, in some cases, the findings are validated with experimental observations. The living human brain is modeled as a soft structure with a growing outer cortex and inner core to investigate its developmental mechanism. Analytical interpretations of differential growth of the brain model provide preliminary insight into critical growth ratios for instability and crease formation of the developing brain. Since the analytical approach cannot predict the evolution of cortical complex convolution after instability, non-linear finite element models are employed to study the crease formation and secondary morphological folds of the developing brain. Results demonstrate that the growth ratio of the cortex to core of the brain, the initial thickness, and material properties of both cortex and core have great impacts on the morphological patterns of the developing brain. Lastly, we discuss why cortical folding is highly correlated and consistent by presenting an intriguing gyri-sulci formation comparison.

  6. Phasic temperature change patterns affect growth and tuberization in potatoes

    SciTech Connect

    Cao, W.; Tibbitts, T.W. . Dept. of Horticulture)

    1994-07-01

    This study determined the response of potato (Solanum tuberosum L., cv. Norland) plants to various patterns of air temperature changes over different growth periods. In each of two experiments under controlled environments, eight treatments of temperature changes were carried out in two growth rooms maintained at 17 and 22 C and a constant vapor pressure deficit of 0.60 kPa and 14-hour photoperiod. Plants were grown for 63 days after transplanting of tissue culture plantlets in 20-liter pots containing peat-vermiculite mix. Temperature changes were imposed on days 21 and 42, which were essentially at the beginning of tuber initiation and tuber enlargement, respectively, for this cultivar. Plants were moved between two temperature rooms to obtain eight temperature change patterns: 17-17-17, 17-17-22, 17-22-17, 22-17-17, 17-22-22, 22-17-22, 22-22-17, and 22-22-22C over three 21-day growth periods. At harvest on day 63, total plant dry weight was higher for the treatments beginning with 22 C than for those beginning with 17C, with highest biomass obtained at 22-22-17 and 22-17-17C. Shoot dry weight increased with temperature increased from 17-17-17 to 22-22-22C during the three growth periods. Tuber dry weight was highest with 22-17-17C, and lowest with 17-17-22 and 17-22-22C. With 22-17-17C, both dry weights of stolons and roots were lowest. Total tuber number and number of small tubers were highest with 17-17-17 and 17-17-22C, and lowest with 17-22-22 and 22-22-22C, whereas number of medium tubers was highest with 22-17-22C, and number of large tubers was highest with 22-17-17C. This study indicates that tuber development of potatoes is optimized with a phasic pattern of high temperature during early growth and low temperature during later growth.

  7. PubMed Central Canada: Beyond an Open Access Repository?

    ERIC Educational Resources Information Center

    Nariani, Rajiv

    2013-01-01

    PubMed Central Canada (PMC Canada) represents a partnership between the Canadian Institutes of Health Research (CIHR), the National Research Council's Canada Institute for Scientific and Technical Information (NRC-CISTI), and the National Library of Medicine of the US. The present study was done to gauge faculty awareness about the CIHR Policy on…

  8. How Complementary and Alternative Medicine Practitioners Use PubMed

    PubMed Central

    Quint-Rapoport, Mia

    2007-01-01

    Background PubMed is the largest bibliographic index in the life sciences. It is freely available online and is used by professionals and the public to learn more about medical research. While primarily intended to serve researchers, PubMed provides an array of tools and services that can help a wider readership in the location, comprehension, evaluation, and utilization of medical research. Objective This study sought to establish the potential contributions made by a range of PubMed tools and services to the use of the database by complementary and alternative medicine practitioners. Methods In this study, 10 chiropractors, 7 registered massage therapists, and a homeopath (N = 18), 11 with prior research training and 7 without, were taken through a 2-hour introductory session with PubMed. The 10 PubMed tools and services considered in this study can be divided into three functions: (1) information retrieval (Boolean Search, Limits, Related Articles, Author Links, MeSH), (2) information access (Publisher Link, LinkOut, Bookshelf ), and (3) information management (History, Send To, Email Alert). Participants were introduced to between six and 10 of these tools and services. The participants were asked to provide feedback on the value of each tool or service in terms of their information needs, which was ranked as positive, positive with emphasis, negative, or indifferent. Results The participants in this study expressed an interest in the three types of PubMed tools and services (information retrieval, access, and management), with less well-regarded tools including MeSH Database and Bookshelf. In terms of their comprehension of the research, the tools and services led the participants to reflect on their understanding as well as their critical reading and use of the research. There was universal support among the participants for greater access to complete articles, beyond the approximately 15% that are currently open access. The abstracts provided by PubMed were

  9. Growth pattern and carcase development in male ducks selected for growth rate.

    PubMed

    Maruyama, K; Akbar, M K; Turk, C M

    1999-05-01

    1. Growth patterns of the whole body, eviscerated carcases, breast muscle, leg and thigh muscles and abdominal fat pads were compared in 4 lines (Lines A, B, C, and D) of male ducks selected for market weight (n = 1305) using growth curve analysis, allometric growth analysis and repeated measure analysis. At 49 d of age, Line A was heaviest, followed by Line B, Line C and Line D. 2. Ducks were fed ad libitum under 24-h lighting and 12 or 24 ducks were killed to determine body, carcase, breast-muscle, leg and thigh-muscle, and abdominal fat weights at time points from hatching until 53 d of age. 3. The Weibull function was chosen for growth curve analysis. The asymptote and inflection point from the Weibull growth curves identified 3 lines (Lines B, C, and D) with discrete body and carcase growth patterns but did not distinguish Line A from Line B. In all 4 lines the asymptote ranged from 4437 g to 3008 g for body weight and from 3334 g to 2098 g for carcase weight; the inflection point ranged from 22.5 d to 25.3 d for body weight and from 25.4 d to 29.6 d for carcase weight. 4. The allometric growth coefficient, relative to whole-body growth, was higher than 1.00 for breast muscle and lower than 1.00 for leg and thigh muscles during from 4 d to 53 d of age. 5. Body fat accumulation was estimated by abdominal fat. Line D accumulated more abdominal fat than other lines. The pattern of fat accumulation in Line D was different from Lines A, B and C and there were no differences between Lines A, B and C. PMID:10465391

  10. Dynamics of rod eutectic growth patterns in confined geometry

    NASA Astrophysics Data System (ADS)

    Şerefoǧlu, Melis; Bottin-Rousseau, S.; Akamatsu, S.; Faivre, G.

    2012-01-01

    The dynamics of rod-like eutectics are examined using a directional solidification setup, which allows real-time observation of the whole solidification front in specimens of transparent eutectic alloys -here, succinonitrile-(D)camphor. In steady-state, rod eutectic growth patterns consist of triangular arrays, more or less disturbed by topological defects. In the absence of strong convection and of crystallographic anisotropy, the long-time evolution of the pattern is dominated by "imperfections" of the system, such as misalignment of the temperature gradient, and finite-size. In this study, we present experimental results on the finite-size effects on rod eutectics and show that a rod to lamella transition takes place as a result of finite-size effect only, at a given alloy concentration.

  11. Modelling spatial patterns of urban growth in Africa.

    PubMed

    Linard, Catherine; Tatem, Andrew J; Gilbert, Marius

    2013-10-01

    The population of Africa is predicted to double over the next 40 years, driving exceptionally high urban expansion rates that will induce significant socio-economic, environmental and health changes. In order to prepare for these changes, it is important to better understand urban growth dynamics in Africa and better predict the spatial pattern of rural-urban conversions. Previous work on urban expansion has been carried out at the city level or at the global level with a relatively coarse 5-10 km resolution. The main objective of the present paper was to develop a modelling approach at an intermediate scale in order to identify factors that influence spatial patterns of urban expansion in Africa. Boosted Regression Tree models were developed to predict the spatial pattern of rural-urban conversions in every large African city. Urban change data between circa 1990 and circa 2000 available for 20 large cities across Africa were used as training data. Results showed that the urban land in a 1 km neighbourhood and the accessibility to the city centre were the most influential variables. Results obtained were generally more accurate than results obtained using a distance-based urban expansion model and showed that the spatial pattern of small, compact and fast growing cities were easier to simulate than cities with lower population densities and a lower growth rate. The simulation method developed here will allow the production of spatially detailed urban expansion forecasts for 2020 and 2025 for Africa, data that are increasingly required by global change modellers. PMID:25152552

  12. Modelling spatial patterns of urban growth in Africa

    PubMed Central

    Linard, Catherine; Tatem, Andrew J.; Gilbert, Marius

    2013-01-01

    The population of Africa is predicted to double over the next 40 years, driving exceptionally high urban expansion rates that will induce significant socio-economic, environmental and health changes. In order to prepare for these changes, it is important to better understand urban growth dynamics in Africa and better predict the spatial pattern of rural-urban conversions. Previous work on urban expansion has been carried out at the city level or at the global level with a relatively coarse 5–10 km resolution. The main objective of the present paper was to develop a modelling approach at an intermediate scale in order to identify factors that influence spatial patterns of urban expansion in Africa. Boosted Regression Tree models were developed to predict the spatial pattern of rural-urban conversions in every large African city. Urban change data between circa 1990 and circa 2000 available for 20 large cities across Africa were used as training data. Results showed that the urban land in a 1 km neighbourhood and the accessibility to the city centre were the most influential variables. Results obtained were generally more accurate than results obtained using a distance-based urban expansion model and showed that the spatial pattern of small, compact and fast growing cities were easier to simulate than cities with lower population densities and a lower growth rate. The simulation method developed here will allow the production of spatially detailed urban expansion forecasts for 2020 and 2025 for Africa, data that are increasingly required by global change modellers. PMID:25152552

  13. Transgenic plants changed in carbon allocation pattern display a shift in diurnal growth pattern.

    PubMed

    Kehr, J; Hustiak, F; Walz, C; Willmitzer, L; Fisahn, J

    1998-11-01

    Photosynthesis, partitioning of carbohydrates and growth have to be highly orchestrated to enable an efficient performance of plants. To study the diurnal relationships between carbon distribution and growth, we analysed transgenic potato plants with altered carbon allocation patterns. To modify carbohydrate supply of growing sinks, we used plants that accumulated starch as a consequence of inhibition in triose-phosphate export from chloroplasts and plants that were genetically inhibited in starch production. Carbon assimilation was analysed by gas exchange and single cell analysis of source leaves. Export was determined by microanalysis of phloem exudates and internodal growth rates were measured by displacement transducers. Gas exchange measurements showed similar assimilation rates in the wild-type and transgenic plants during the light period. Sugar analysis of phloem exudates and epidermal cells revealed a severe shift of sucrose concentrations in the individual plant lines. Moreover, epidermal cells turned out to be a potential storage site for carbohydrates in potato. Finally, we could demonstrate that changing the diurnal rhythm of carbon allocation results in a change in the diurnal growth pattern. PMID:9881169

  14. Fractal patterns formed by growth of radial viscous fingers*

    NASA Astrophysics Data System (ADS)

    Praud, Olivier

    2004-03-01

    We examine fractal patterns formed by the injection of air into oil in a thin (0.13 mm) layer contained between two cylindrical glass plates of 288 mm diameter (a Hele-Shaw cell) [1]. The resultant radially grown patterns are similar to those formed in Diffusion Limited Aggregation (DLA), but the relation between the continuum limit of DLA and continuum (Laplacian) growth remains an open question. Our viscous fingering patterns in the limit of very high pressure difference reach an asymptotic state in which they exhibit a fractal dimension of 1.70± 0.02, in good agreement with a calculation of the fractal dimension of a DLA cluster, 1.713± 0.003 [2]. The generalized dimensions are also computed and show that the observed pattern is self-similar with Dq = 1.70 for all q. Further, the probability density function of shielding angles suggests the existence of a critical angle close to 75 degrees. This result is in accord with numerical and analytical evidence of a critical angle in DLA [3]. Thus fractal viscous fingering patterns and Diffusion Limited Aggregation clusters have a similar geometrical structure. *Work conducted in collaboration with H.L. Swinney, M.G. Moore and Eran Sharon [1] E. Sharon, M. G. Moore, W. D. McCormick, and H. L. Swinney, Phys. Rev. Lett. 91, 205504 (2003). [2] B.Davidovitch et A. Levermann and I. Procaccia, Phys. Rev. E 62, 5919 (2000). [3] D. A. Kessler et al., Phys. Rev. E 57, 6913 (1998).

  15. Pattern Formation and Growth Kinetics in Eutectic Systems

    SciTech Connect

    Teng, Jing

    2007-01-01

    Growth patterns during liquid/solid phase transformation are governed by simultaneous effects of heat and mass transfer mechanisms, creation of new interfaces, jump of the crystallization units from liquid to solid and their rearrangement in the solid matrix. To examine how the above processes influence the scale of microstructure, two eutectic systems are chosen for the study: a polymeric system polyethylene glycol-p-dibromobenzene (PEG-DBBZ) and a simple molecular system succinonitrile (SCN)-camphor. The scaling law for SCN-camphor system is found to follow the classical Jackson-Hunt model of circular rod eutectic, where the diffusion in the liquid and the interface energy are the main physics governing the two-phase pattern. In contrast, a significantly different scaling law is observed for the polymer system. The interface kinetics of PEG phase and its solute concentration dependence thus have been critically investigated for the first time by directional solidification technique. A model is then proposed that shows that the two-phase pattern in polymers is governed by the interface diffusion and the interface kinetics. In SCN-camphor system, a new branch of eutectic, elliptical shape rodl, is found in thin samples where only one layer of camphor rods is present. It is found that the orientation of the ellipse can change from the major axis in the direction of the thickness to the direction of the width as the velocity and/or the sample thickness is decreased. A theoretical model is developed that predicts the spacing and orientation of the elliptical rods in a thin sample. The single phase growth patterns of SCN-camphor system were also examined with emphasis on the three-dimensional single cell and cell/dendrite transition. For the 3D single cell in a capillary tube, the entire cell shape ahead of the eutectic front can be described by the Saffmann-Taylor finger only at extremely low growth rate. A 3D directional solidification model is developed to

  16. Characterizing growth patterns in longitudinal MRI using image contrast

    NASA Astrophysics Data System (ADS)

    Vardhan, Avantika; Prastawa, Marcel; Vachet, Clement; Piven, Joseph; Gerig, Guido

    2014-03-01

    Understanding the growth patterns of the early brain is crucial to the study of neuro-development. In the early stages of brain growth, a rapid sequence of biophysical and chemical processes take place. A crucial component of these processes, known as myelination, consists of the formation of a myelin sheath around a nerve fiber, enabling the effective transmission of neural impulses. As the brain undergoes myelination, there is a subsequent change in the contrast between gray matter and white matter as observed in MR scans. In this work, gray-white matter contrast is proposed as an effective measure of appearance which is relatively invariant to location, scanner type, and scanning conditions. To validate this, contrast is computed over various cortical regions for an adult human phantom. MR (Magnetic Resonance) images of the phantom were repeatedly generated using different scanners, and at different locations. Contrast displays less variability over changing conditions of scan compared to intensity-based measures, demonstrating that it is less dependent than intensity on external factors. Additionally, contrast is used to analyze longitudinal MR scans of the early brain, belonging to healthy controls and Down's Syndrome (DS) patients. Kernel regression is used to model subject-specific trajectories of contrast changing with time. Trajectories of contrast changing with time, as well as time-based biomarkers extracted from contrast modeling, show large differences between groups. The preliminary applications of contrast based analysis indicate its future potential to reveal new information not covered by conventional volumetric or deformation-based analysis, particularly for distinguishing between normal and abnormal growth patterns.

  17. The growth patterns of three hindlimb muscles in the chicken.

    PubMed Central

    Helmi, C; Cracraft, J

    1977-01-01

    This study was designed to investigate the growth patterns of three hindlimb muscles of the chicken relative to the functional-biomechanical demands of increasing body size. The biceps femoris, a bipennate non-postural muscle, grew relatively faster in terms of wet and dry weight than did the parallel-fibred adductor superficialis or the unipennate adductor profundus, both postural muscles. All three muscles exhibited positive allometry (relative to body weight) in muscle length but only biceps femoris and adductor profundus showed positive allometry in cross sectional area adductor superficialis having isometric growth in this parameter. In biceps femoris and adductor superficialis the lengths of the longest and shortest fasciculi grew at equal rates, whereas in adductor profundus the shortest fasciculi grew faster than the longest. We conclude that muscle weight alone is an insufficient indicator of changing function in growing muscle. Hence, growth studies should include other functionally relevant parameters such as cross sectional area, which is proportional to the force-producing capabilities of the muscle, or fibre (fasciculus) length, which is indicative of the absolute amount of stretching or shortening that is possible and of the contraction velocity. PMID:885779

  18. Studying PubMed usages in the field for complex problem solving: Implications for tool design.

    PubMed

    Mirel, Barbara; Song, Jean; Tonks, Jennifer Steiner; Meng, Fan; Xuan, Weijian; Ameziane, Rafiqa

    2013-05-01

    Many recent studies on MEDLINE-based information seeking have shed light on scientists' behaviors and associated tool innovations that may improve efficiency and effectiveness. Few if any studies, however, examine scientists' problem-solving uses of PubMed in actual contexts of work and corresponding needs for better tool support. Addressing this gap, we conducted a field study of novice scientists (14 upper level undergraduate majors in molecular biology) as they engaged in a problem solving activity with PubMed in a laboratory setting. Findings reveal many common stages and patterns of information seeking across users as well as variations, especially variations in cognitive search styles. Based on findings, we suggest tool improvements that both confirm and qualify many results found in other recent studies. Our findings highlight the need to use results from context-rich studies to inform decisions in tool design about when to offer improved features to users. PMID:24376375

  19. Studying PubMed usages in the field for complex problem solving: Implications for tool design

    PubMed Central

    Song, Jean; Tonks, Jennifer Steiner; Meng, Fan; Xuan, Weijian; Ameziane, Rafiqa

    2012-01-01

    Many recent studies on MEDLINE-based information seeking have shed light on scientists’ behaviors and associated tool innovations that may improve efficiency and effectiveness. Few if any studies, however, examine scientists’ problem-solving uses of PubMed in actual contexts of work and corresponding needs for better tool support. Addressing this gap, we conducted a field study of novice scientists (14 upper level undergraduate majors in molecular biology) as they engaged in a problem solving activity with PubMed in a laboratory setting. Findings reveal many common stages and patterns of information seeking across users as well as variations, especially variations in cognitive search styles. Based on findings, we suggest tool improvements that both confirm and qualify many results found in other recent studies. Our findings highlight the need to use results from context-rich studies to inform decisions in tool design about when to offer improved features to users. PMID:24376375

  20. Morphologic and molecular evaluation of Chlamydia trachomatis growth in human endocervix reveals distinct growth patterns

    PubMed Central

    Lewis, Maria E.; Belland, Robert J.; AbdelRahman, Yasser M.; Beatty, Wandy L.; Aiyar, Ashok A.; Zea, Arnold H.; Greene, Sheila J.; Marrero, Luis; Buckner, Lyndsey R.; Tate, David J.; McGowin, Chris L.; Kozlowski, Pamela A.; O'Brien, Michelle; Lillis, Rebecca A.; Martin, David H.; Quayle, Alison J.

    2014-01-01

    In vitro models of Chlamydia trachomatis growth have long been studied to predict growth in vivo. Alternative or persistent growth modes in vitro have been shown to occur under the influence of numerous stressors but have not been studied in vivo. Here, we report the development of methods for sampling human infections from the endocervix in a manner that permits a multifaceted analysis of the bacteria, host and the endocervical environment. Our approach permits evaluating total bacterial load, transcriptional patterns, morphology by immunofluorescence and electron microscopy, and levels of cytokines and nutrients in the infection microenvironment. By applying this approach to two pilot patients with disparate infections, we have determined that their contrasting growth patterns correlate with strikingly distinct transcriptional biomarkers, and are associated with differences in local levels of IFNγ. Our multifaceted approach will be useful to dissect infections in the human host and be useful in identifying patients at risk for chronic disease. Importantly, the molecular and morphological analyses described here indicate that persistent growth forms can be isolated from the human endocervix when the infection microenvironment resembles the in vitro model of IFNγ-induced persistence. PMID:24959423

  1. Complex event extraction at PubMed scale

    PubMed Central

    Björne, Jari; Ginter, Filip; Pyysalo, Sampo; Tsujii, Jun'ichi; Salakoski, Tapio

    2010-01-01

    Motivation: There has recently been a notable shift in biomedical information extraction (IE) from relation models toward the more expressive event model, facilitated by the maturation of basic tools for biomedical text analysis and the availability of manually annotated resources. The event model allows detailed representation of complex natural language statements and can support a number of advanced text mining applications ranging from semantic search to pathway extraction. A recent collaborative evaluation demonstrated the potential of event extraction systems, yet there have so far been no studies of the generalization ability of the systems nor the feasibility of large-scale extraction. Results: This study considers event-based IE at PubMed scale. We introduce a system combining publicly available, state-of-the-art methods for domain parsing, named entity recognition and event extraction, and test the system on a representative 1% sample of all PubMed citations. We present the first evaluation of the generalization performance of event extraction systems to this scale and show that despite its computational complexity, event extraction from the entire PubMed is feasible. We further illustrate the value of the extraction approach through a number of analyses of the extracted information. Availability: The event detection system and extracted data are open source licensed and available at http://bionlp.utu.fi/. Contact: jari.bjorne@utu.fi PMID:20529932

  2. Rhone deep-sea fan: morphostructure and growth pattern

    SciTech Connect

    Droz, L.; Bellaiche, G.

    1985-03-01

    A detailed bathymetric survey of the Rhone deep-sea fan and its feeder canyon using Sea-Beam, reveals morphologic features such as very tight meanders of the canyon and channel courses, cutoff meanders, and downslope narrowing of the inner channel floor. Striking similarities exist between these deep-sea features and some continental landforms, especially in alluvial plain areas or desert environments. Sea-Beam also reveals evidence of huge slump scars affecting the slope and fan. The superficial structure of the Rhone Fan results from the stacking of numerous lenticular acoustic units displaying specific seismic characters in which the authors recognized channel and levee facies. Except in the upper fan area, these units have not been constant; they have generally migrated, owing to shifting of the channel throughout fan evolution. Construction of the fan probably began as early as the early Pliocene and continued to the close of the Wurmian (late Wisconsinian). The fan's growth pattern could be associated with climatic fluctuations. The principal sedimentary mechanism responsible for the growth of the fan appears to be turbidity currents, but mass gravity flows have also been an important factor in building the fan by occasionally blocking the main channel and forcing it to migrate.

  3. Biological traits and growth patterns of pejerrey Odontesthes argentinensis.

    PubMed

    Llompart, F M; Colautti, D C; Maiztegui, T; Cruz-Jiménez, A M; Baigún, C R M

    2013-02-01

    This study assesses for the first time the relationship between annual cycles of different biological indices with growth patterns of a marine pejerrey Odontesthes argentinensis population near its southern-distribution boundary in North Patagonia. The reproductive period is between September and November evidenced by an increase in the gonado-somatic index with a peak in October corresponding to spawning. The reproductive cycle was also coupled with metabolic processes related to energy allocation as shown by changes in the hepato-somatic index and body condition. Total length (L(T) ) at maturity was 270 for females and 282 mm for males, whereas fecundity was estimated at mean ±s.d. = 9380 ± 1797 mature oocytes. Based on the marginal increment analysis, most of the scales showed a maximum value during summer, with a sharp decline thereafter during autumn and winter, indicating that scale rings are formed during the latter period and only once a year. Growth fitted by the von Bertalanffy model for both males and females did not show significant differences and showed a rapid growth during the first 2 years. The shorter reproductive period compared with that of the northern O. argentinensis populations inhabiting tropical and subtropical areas was interpreted as an adjustment to temperate environmental conditions. The larger maximum L(T) and L(T) at first maturity are in agreement with the counter-gradient hypothesis and could be related to the selective effects of low temperature and a shorter growing season. This latitude dependency argues strongly against the application of the same fishing regulations for different O. argentinensis populations as a whole and reinforces the need to assess basic biological features at a population scale to promote local sustainable fisheries management. PMID:23398062

  4. Bioconvective patterns, synchrony, and survival. [in light-limited growth model of motile algae culture

    NASA Technical Reports Server (NTRS)

    Noever, David A.

    1990-01-01

    With and without bioconvective pattern formation, a theoretical model predicts growth in light-limited cultures of motile algae. At the critical density for pattern formation, the resulting doubly exponential population curves show an inflection. Such growth corresponds quantitatively to experiments in mechanically unstirred cultures. This attaches survival value to synchronized pattern formation.

  5. Growth Patterns and E-Moderating Supports in Asynchronous Online Discussions in an Undergraduate Blended Course

    ERIC Educational Resources Information Center

    Ghadirian, Hajar; Ayub, Ahmad Fauzi Mohd; Bakar, Kamariah Binti Abu; Hassanzadeh, Maryam

    2016-01-01

    This study presents a case study of asynchronous online discussions' (AOD) growth patterns in an undergraduate blended course to address the gap in our current understanding of how threads are developed in peer-moderated AODs. Building on a taxonomy of thread pattern proposed by Chan, Hew and Cheung (2009), growth patterns of thirty-six forums…

  6. Clinicopathological correlates of extrasellar growth patterns in pituitary adenomas.

    PubMed

    Sarkar, Sauradeep; Chacko, Ari G; Chacko, Geeta

    2015-07-01

    We reviewed clinical, imaging and histopathology details of 297 patients who underwent surgery for pituitary adenomas, with an equal distribution of functional and non-functioning tumors, to examine clinicopathological correlates of extrasellar growth. Knosp grades of 3 and 4 on MRI defined cavernous sinus invasion, Hardy grades of C and D defined significant suprasellar/subfrontal extension, and intraoperative evidence of tumor eroding through the clivus or sellar floor defined infrasellar invasion. Disease status at follow-up was known in 246 patients overall, including 35 patients who were evaluated for progression of residual disease on serial imaging. On univariate analysis, we found several statistically significant associations (p < 0.05) including adenoma size with age, sex and tumor protein p53 reactivity; cavernous sinus invasion with size, non-functional status, increased mitotic activity, an elevated MIB-1 proliferation index and p53 reactivity; suprasellar/subfrontal extension with p53 reactivity; and infrasellar invasion with age and tumor size. When adjusting for confounders with logistic regression, several significant associations were evident including adenoma size with male sex and p53 reactivity; cavernous sinus invasion with size and elevated MIB-1 proliferation index; suprasellar/subfrontal extension with p53 reactivity; and infrasellar invasion with adenoma size alone. Patients with early progression of postoperative residual tumor were younger with a non-significant trend towards higher MIB-1 proliferation indices. Individual patterns of extrasellar growth in pituitary adenomas are associated with unique clinical and immunohistochemical profiles. Younger patients with elevated MIB-1 values are probably at high risk for early recurrence of non-functioning tumors. Definitions of atypia must be standardized before more robust assumptions about tumor biology can be established. PMID:25979255

  7. Invited Article: Plasmonic growth of patterned metamaterials with fractal geometry

    NASA Astrophysics Data System (ADS)

    Takeyasu, Nobuyuki; Taguchi, Natsuo; Nishimura, Naoki; Cheng, Bo Han; Kawata, Satoshi

    2016-08-01

    Large-scale metallic three-dimensional (3D) structures composed of sub-wavelength fine details, called metamaterials, have attracted optical scientists and materials scientists because of their unconventional and extraordinary optical properties that are not seen in nature. However, existing nano-fabrication technologies including two-photon fabrication, e-beam, focused ion-beam, and probe microscopy are not necessarily suitable for fabricating such large-scale 3D metallic nanostructures. In this article, we propose a different method of fabricating metamaterials, which is based on a bottom-up approach. We mimicked the generation of wood forest under the sunlight and rain in nature. In our method, a silver nano-forest is grown from the silver seeds (nanoparticles) placed on the glass substrate in silver-ion solution. The metallic nano-forest is formed only in the area where ultraviolet light is illuminated. The local temperature increases at nano-seeds and tips of nano-trees and their branches due to the plasmonic heating as a result of UV light excitation of localized mode of surface plasmon polaritons. We have made experiments of growth of metallic nano-forest patterned by the light distribution. The experimental results show a beautiful nano-forest made of silver with self-similarity. Fractal dimension and spectral response of the grown structure are discussed. The structures exhibit a broad spectral response from ultraviolet to infrared, which was used for surface-enhanced Raman detection of molecules.

  8. Growth patterns for etiolated soybeans germinated under spaceflight conditions

    NASA Astrophysics Data System (ADS)

    Levine, Howard G.; Piastuch, William C.

    In the GENEX (GENe EXpression) spaceflight experiment (flown on STS-87), six surface sterilized soybean seeds ( Glycine max cv McCall) were inserted into each of 32 autoclaved plastic seed growth pouches containing an inner germination paper sleeve (for a total of 192 seeds). The pouches were stowed within a mid-deck locker until Mission Flight Day 10, at which time an astronaut added water to initiate the process of seed germination on-orbit and subsequently transferred them to four light-tight aluminum canisters called BRIC-60s (Biological Research In Canisters). We report here on the morphological characteristics of: (1) the recovered flight plants ( N = 177), (2) the corresponding ground control population ( N = 183), plus (3) additional controls grown on the ground under clinostat conditions ( N = 93). No significant morphological differences were found between the flight, ground control and clinorotated treatments for either the cotyledons or hypocotyls. There were, however, significantly longer primary roots produced in the flight population relative to the ground control population, which in turn had significantly longer primary roots than the clinorotated population. This same pattern was observed relative to the production of lateral roots (flight > control > clinorotated). Taken together with previous literature reports, we believe that there is now sufficient evidence to conclude that plants grown under conditions of microgravity will generally exhibit enhanced root production relative to their ground control counterparts. Some causes underlying this phenomenon are speculated on.

  9. [Effects of substrate-aeration cultivation pattern on tomato growth].

    PubMed

    Zhao, Xu; Li, Tian-Lai; Sun, Zhou-Ping

    2010-01-01

    Aeroponics can increase the fruit yield of tomato plant, but its cost is very high. In this paper, tomato seedlings were planted with three cultures, i. e., whole perlite culture (CK), perlite-aeration culture (T1), and aeroponics (T2), and a comparative study was made on the seedlings growth. Compared with CK, T1 improved the gas environment in root zone significantly, with the CO2 and O2 concentrations in root zone being 0.2 and 1.17 times higher, and increased the plant height and stem diameter after 60 days of transplanting by 5.1% and 8.4%, respectively. The plant net photosynthetic rate of T1 was significantly higher than that of CK, with the maximum value after transplanting 45 days increased by 13%. T1 also increased the root activity and ion absorbing ability significantly, with the root activity after transplanting 45 days being 1.23 times of CK, and the root K, Ca, and Mg contents after transplanting 60 days increased by 31%, 37%, and 27%, respectively. The fruit yield of T1 was 1.16 times of CK. No significant differences in these indices were observed between T1 and T2, and less difference in the fruit soluble sugar and organic acid contents as well as the sugar-acid ratio was found among CK, T1, and T2. It was suggested that perlite-aeration cultivation pattern was an easy and feasible way to markedly improve the fruit yield of tomato plant. PMID:20387426

  10. Temporal consistency of spatial pattern in growth of the mussel, Mytilus edulis: Implications for predictive modelling

    NASA Astrophysics Data System (ADS)

    Bergström, Per; Lindegarth, Susanne; Lindegarth, Mats

    2013-10-01

    Human pressures on coastal seas are increasing and methods for sustainable management, including spatial planning and mitigative actions, are therefore needed. In coastal areas worldwide, the development of mussel farming as an economically and ecologically sustainable industry requires geographic information on the growth and potential production capacity. In practice this means that coherent maps of temporally stable spatial patterns of growth need to be available in the planning process and that maps need to be based on mechanistic or empirical models. Therefore, as a first step towards development of models of growth, we assessed empirically the fundamental requirement that there are temporally consistent spatial patterns of growth in the blue mussel, Mytilus edulis. Using a pilot study we designed and dimensioned a transplant experiment, where the spatial consistency in the growth of mussels was evaluated at two resolutions. We found strong temporal and scale-dependent spatial variability in growth but patterns suggested that spatial patterns were uncoupled between growth of shell and that of soft tissue. Spatial patterns of shell growth were complex and largely inconsistent among years. Importantly, however, the growth of soft tissue was qualitatively consistent among years at the scale of km. The results suggest that processes affecting the whole coastal area cause substantial differences in growth of soft tissue among years but that factors varying at the scale of km create strong and persistent spatial patterns of growth, with a potential doubling of productivity by identifying the most suitable locations. We conclude that the observed spatial consistency provides a basis for further development of predictive modelling and mapping of soft tissue growth in these coastal areas. Potential causes of observed patterns, consequences for mussel-farming as a tool for mitigating eutrophication, aspects of precision of modelling and sampling of mussel growth as well

  11. Connecting the Dots between PubMed Abstracts

    PubMed Central

    Hossain, M. Shahriar; Gresock, Joseph; Edmonds, Yvette; Helm, Richard; Potts, Malcolm; Ramakrishnan, Naren

    2012-01-01

    Background There are now a multitude of articles published in a diversity of journals providing information about genes, proteins, pathways, and diseases. Each article investigates subsets of a biological process, but to gain insight into the functioning of a system as a whole, we must integrate information from multiple publications. Particularly, unraveling relationships between extra-cellular inputs and downstream molecular response mechanisms requires integrating conclusions from diverse publications. Methodology We present an automated approach to biological knowledge discovery from PubMed abstracts, suitable for “connecting the dots” across the literature. We describe a storytelling algorithm that, given a start and end publication, typically with little or no overlap in content, identifies a chain of intermediate publications from one to the other, such that neighboring publications have significant content similarity. The quality of discovered stories is measured using local criteria such as the size of supporting neighborhoods for each link and the strength of individual links connecting publications, as well as global metrics of dispersion. To ensure that the story stays coherent as it meanders from one publication to another, we demonstrate the design of novel coherence and overlap filters for use as post-processing steps. Conclusions We demonstrate the application of our storytelling algorithm to three case studies: i) a many-one study exploring relationships between multiple cellular inputs and a molecule responsible for cell-fate decisions, ii) a many-many study exploring the relationships between multiple cytokines and multiple downstream transcription factors, and iii) a one-to-one study to showcase the ability to recover a cancer related association, viz. the Warburg effect, from past literature. The storytelling pipeline helps narrow down a scientist's focus from several hundreds of thousands of relevant documents to only around a hundred

  12. History and Trends of "Personal Health Record" Research in PubMed

    PubMed Central

    Kim, Jeongeun; Bates, David W.

    2011-01-01

    Objectives The purpose of this study was to review history and trends of personal health record research in PubMed and to provide accurate understanding and categorical analysis of expert opinions. Methods For the search strategy, PubMed was queried for 'personal health record, personal record, and PHR' in the title and abstract fields. Those containing different definitions of the word were removed by one-by-one analysis from the results, 695 articles. In the end, total of 229 articles were analyzed in this research. Results The results show that the changes in terms over the years and the shift to patient centeredness and mixed usage. And we identified history and trend of PHR research in some category that the number of publications by year, topic, methodologies and target diseases. Also from analysis of MeSH terms, we can show the focal interest in regards the PHR boundaries and related subjects. Conclusions For PHRs to be efficiently used by general public, initial understanding of the history and trends of PHR research may be helpful. Simultaneously, accurate understanding and categorical analysis of expert opinions that can lead to the development and growth of PHRs will be valuable to their adoption and expansion. PMID:21818452

  13. GeneView: a comprehensive semantic search engine for PubMed.

    PubMed

    Thomas, Philippe; Starlinger, Johannes; Vowinkel, Alexander; Arzt, Sebastian; Leser, Ulf

    2012-07-01

    Research results are primarily published in scientific literature and curation efforts cannot keep up with the rapid growth of published literature. The plethora of knowledge remains hidden in large text repositories like MEDLINE. Consequently, life scientists have to spend a great amount of time searching for specific information. The enormous ambiguity among most names of biomedical objects such as genes, chemicals and diseases often produces too large and unspecific search results. We present GeneView, a semantic search engine for biomedical knowledge. GeneView is built upon a comprehensively annotated version of PubMed abstracts and openly available PubMed Central full texts. This semi-structured representation of biomedical texts enables a number of features extending classical search engines. For instance, users may search for entities using unique database identifiers or they may rank documents by the number of specific mentions they contain. Annotation is performed by a multitude of state-of-the-art text-mining tools for recognizing mentions from 10 entity classes and for identifying protein-protein interactions. GeneView currently contains annotations for >194 million entities from 10 classes for ∼21 million citations with 271,000 full text bodies. GeneView can be searched at http://bc3.informatik.hu-berlin.de/. PMID:22693219

  14. Growth patterns in the orbital region: a morphometric study.

    PubMed

    Farkas, L G; Posnick, J C; Hreczko, T M; Pron, G E

    1992-07-01

    Data for analysis of age-related changes in growth in the intercanthal (en-en) and biocular (ex-ex) widths were obtained from 1,594 healthy North American Caucasians in age groups from 1 to 18 years, divided equally between males and females. At 1 year, the degree of development of the intercanthal width reached 84.1%, and that of the biocular width 85.9% of adults in both sexes. The levels of growth achieved by 5 years of age rose to 93.3% in the intercanthal width and 88.1% in the biocular width, in both sexes. The average total growth increments achieved between ages 1 and 18 years were 5.2 mm in the intercanthal width and 12.5 mm in the biocular. The intercanthal width showed very little growth after 1 year of age; in contrast, the biocular width showed significantly greater growth increments both before and after 5 years of age. Rapid growth was observed between 3 and 4 years in the intercanthal width of both sexes. The age-related growth observed in the biocular width was small but continuous up to maturation time. The intercanthal width reached full maturation at 8 years in females and 11 years in males, and the biocular width at 13 years in females and 15 years in males. PMID:1643059

  15. Hormone-Mediated Pattern Formation in Seedling of Plants: a Competitive Growth Dynamics Model

    NASA Astrophysics Data System (ADS)

    Kawaguchi, Satoshi; Mimura, Masayasu; Ohya, Tomoyuki; Oikawa, Noriko; Okabe, Hirotaka; Kai, Shoichi

    2001-10-01

    An ecologically relevant pattern formation process mediated by hormonal interactions among growing seedlings is modeled based on the experimental observations on the effects of indole acetic acid, which can act as an inhibitor and activator of root growth depending on its concentration. In the absence of any lateral root with constant hormone-sensitivity, the edge effect phenomenon is obtained depending on the secretion rate of hormone from the main root. Introduction of growth-stage-dependent hormone-sensitivity drastically amplifies the initial randomness, resulting in spatially irregular macroscopic patterns. When the lateral root growth is introduced, periodic patterns are obtained whose periodicity depends on the length of lateral roots. The growth-stage-dependent hormone-sensitivity and the lateral root growth are crucial for macroscopic periodic-pattern formation.

  16. Growth of SiC single crystals on patterned seeds by a sublimation method

    NASA Astrophysics Data System (ADS)

    Yang, Xianglong; Chen, Xiufang; Peng, Yan; Xu, Xiangang; Hu, Xiaobo

    2016-04-01

    Growth of 6H-SiC on patterned seeds with the vertical sidewalls composed of {11-20} and {1-100} faces by a sublimation method at 1700-2000 °C was studied. Anisotropy in lateral growth rates was observed, i.e the growth rate towards <11-20> was faster than that along <1-100>. It was found that free lateral growth on mesas was accompanied by a sharp decrease in the density of threading dislocation. The dependence of lateral growth rate on growth conditions such as reactor pressure and growth temperature was investigated. The factors governing the process of lateral growth of 6H-SiC on patterned seeds were discussed.

  17. Water Control on Vegetation Growth Pattern in Eurasia from GRACE

    NASA Astrophysics Data System (ADS)

    A, G.; Velicogna, I.; Kimball, J. S.; Kim, Y.

    2014-12-01

    High latitude ecosystem productivity is constrained by cold temperature and moisture limitations to plant growth, while these environmental restrictions may be changing with global warming. Satellite data driven assessments indicate that over the past three decades, rapid warming in the northern high latitudes has resulted in earlier and longer potential growing seasons and widespread greening, due to general relaxation of cold temperature constraints to vegetation productivity. However, warming may have also increased water stress limitations to growth. In this study, we use GRACE (Gravity Recovery and Climate Experiment) derived total water storage (TWS), 2-m air temperature (T) from ERA-interim reanalysis, normalized difference vegetation index (NDVI) data from MODIS (Collection 5) and satellite data driven vegetation gross primary productivity (GPP) estimates as surrogates for vegetation growth, for the period August 2002-December 2013 to evaluate terrestrial water supply controls to vegetation growth changes over the three major river basins of northern Eurasia. We find that during the analyzed period, the apparent growth response follows regional vegetation, moisture and temperature gradients and is spatially complex. In the drier southwest characterized by grassland, vegetation growth is mainly controlled by TWS availability. In the central region, dominated by cold temperature and water limited boreal forest, T is the main control on vegetation growth. In the Lena basin, where vegetation includes both boreal forest and water limited grassland, both T and TWS impact vegetation growth. We suggest that GRACE TWS estimates provide reliable observational constraints on water availability to vegetation that supplement sparse soil moisture observations and satellite precipitation estimates with unknown bias.

  18. Numerical computations of faceted pattern formation in snow crystal growth.

    PubMed

    Barrett, John W; Garcke, Harald; Nürnberg, Robert

    2012-07-01

    Faceted growth of snow crystals leads to a rich diversity of forms with remarkable sixfold symmetry. Snow crystal structures result from diffusion-limited crystal growth in the presence of anisotropic surface energy and anisotropic attachment kinetics. It is by now well understood that the morphological stability of ice crystals strongly depends on supersaturation, crystal size, and temperature. Until very recently it was very difficult to perform numerical simulations of this highly anisotropic crystal growth. In particular, obtaining facet growth in combination with dendritic branching is a challenging task. We present numerical simulations of snow crystal growth in two and three spacial dimensions using a computational method recently introduced by the present authors. We present both qualitative and quantitative computations. In particular, a linear relationship between tip velocity and supersaturation is observed. In our computations, surface energy effects, although small, have a pronounced effect on crystal growth. We compute solid plates, solid prisms, hollow columns, needles, dendrites, capped columns, and scrolls on plates. Although all these forms appear in nature, it is a significant challenge to reproduce them with the help of numerical simulations for a continuum model. PMID:23005427

  19. Numerical computations of faceted pattern formation in snow crystal growth

    NASA Astrophysics Data System (ADS)

    Barrett, John W.; Garcke, Harald; Nürnberg, Robert

    2012-07-01

    Faceted growth of snow crystals leads to a rich diversity of forms with remarkable sixfold symmetry. Snow crystal structures result from diffusion-limited crystal growth in the presence of anisotropic surface energy and anisotropic attachment kinetics. It is by now well understood that the morphological stability of ice crystals strongly depends on supersaturation, crystal size, and temperature. Until very recently it was very difficult to perform numerical simulations of this highly anisotropic crystal growth. In particular, obtaining facet growth in combination with dendritic branching is a challenging task. We present numerical simulations of snow crystal growth in two and three spacial dimensions using a computational method recently introduced by the present authors. We present both qualitative and quantitative computations. In particular, a linear relationship between tip velocity and supersaturation is observed. In our computations, surface energy effects, although small, have a pronounced effect on crystal growth. We compute solid plates, solid prisms, hollow columns, needles, dendrites, capped columns, and scrolls on plates. Although all these forms appear in nature, it is a significant challenge to reproduce them with the help of numerical simulations for a continuum model.

  20. MICROTASK CROWDSOURCING FOR DISEASE MENTION ANNOTATION IN PUBMED ABSTRACTS

    PubMed Central

    Good, Benjamin M; Nanis, Max; Wu, Chunlei; Su, Andrew I

    2014-01-01

    Identifying concepts and relationships in biomedical text enables knowledge to be applied in computational analyses. Many biological natural language processing (BioNLP) projects attempt to address this challenge, but the state of the art still leaves much room for improvement. Progress in BioNLP research depends on large, annotated corpora for evaluating information extraction systems and training machine learning models. Traditionally, such corpora are created by small numbers of expert annotators often working over extended periods of time. Recent studies have shown that workers on microtask crowdsourcing platforms such as Amazon’s Mechanical Turk (AMT) can, in aggregate, generate high-quality annotations of biomedical text. Here, we investigated the use of the AMT in capturing disease mentions in PubMed abstracts. We used the NCBI Disease corpus as a gold standard for refining and benchmarking our crowdsourcing protocol. After several iterations, we arrived at a protocol that reproduced the annotations of the 593 documents in the ‘training set’ of this gold standard with an overall F measure of 0.872 (precision 0.862, recall 0.883). The output can also be tuned to optimize for precision (max = 0.984 when recall = 0.269) or recall (max = 0.980 when precision = 0.436). Each document was completed by 15 workers, and their annotations were merged based on a simple voting method. In total 145 workers combined to complete all 593 documents in the span of 9 days at a cost of $.066 per abstract per worker. The quality of the annotations, as judged with the F measure, increases with the number of workers assigned to each task; however minimal performance gains were observed beyond 8 workers per task. These results add further evidence that microtask crowdsourcing can be a valuable tool for generating well-annotated corpora in BioNLP. Data produced for this analysis are available at http

  1. Prediction of fatigue crack-growth patterns and lives in three-dimensional cracked bodies

    NASA Technical Reports Server (NTRS)

    Newman, J. C., Jr.; Raju, I. S.

    1984-01-01

    Fatigue crack growth patterns and lives for surface cracks, surface cracks at holes, and corner cracks at holes in three dimensional bodies were predicted using linear-elastic fracture mechanics concepts that were modified to account for crack-closure behavior. The predictions were made by using stress intensity factor equations for these crack configurations and the fatigue crack-growth (delta K against rate) relationship for the material of interest. The crack configurations were subjected to constant-amplitude fatigue loading under either remote tension or bending loads. The predicted crack growth patterns and crack growth lives for aluminum alloys agreed well with test data from the literature.

  2. Increased monolayer domain size and patterned growth of tungsten disulfide through controlling surface energy of substrates

    NASA Astrophysics Data System (ADS)

    Godin, Kyle; Kang, Kyungnam; Fu, Shichen; Yang, Eui-Hyeok

    2016-08-01

    We report a surface energy-controlled low-pressure chemical vapor deposition growth of WS2 monolayers on SiO2 using pre-growth oxygen plasma treatment of substrates, facilitating increased monolayer surface coverage and patterned growth without lithography. Oxygen plasma treatment of the substrate caused an increase in the average domain size of WS2 monolayers by 78%  ±  2% while having a slight reduction in nucleation density, which translates to increased monolayer surface coverage. This substrate effect on growth was exploited to grow patterned WS2 monolayers by patterned plasma treatment on patterned substrates and by patterned source material with resolutions less than 10 µm. Contact angle-based surface energy measurements revealed a dramatic increase in polar surface energy. A growth model was proposed with lowered activation energies for growth and increased surface diffusion length consistent with the range of results observed. WS2 samples grown with and without oxygen plasma were similar high quality monolayers verified through transmission electron microscopy, selected area electron diffraction, atomic force microscopy, Raman, and photoluminescence measurements. This technique enables the production of large-grain size, patterned WS2 without a post-growth lithography process, thereby providing clean surfaces for device applications.

  3. Growth pattern from birth to adulthood in African pygmies of known age

    PubMed Central

    Rozzi, Fernando V. Ramirez; Koudou, Yves; Froment, Alain; Le Bouc, Yves; Botton, Jérémie

    2015-01-01

    The African pygmy phenotype stems from genetic foundations and is considered to be the product of a disturbance in the growth hormone–insulin-like growth factor (GH–IGF) axis. However, when and how the pygmy phenotype is acquired during growth remains unknown. Here we describe growth patterns in Baka pygmies based on two longitudinal studies of individuals of known age, from the time of birth to the age of 25 years. Body size at birth among the Baka is within standard limits, but their growth rate slows significantly during the first two years of life. It then more or less follows the standard pattern, with a growth spurt at adolescence. Their life history variables do not allow the Baka to be distinguished from other populations. Therefore, the pygmy phenotype in the Baka is the result of a change in growth that occurs during infancy, which differentiates them from East African pygmies revealing convergent evolution. PMID:26218408

  4. Nonlinear and Quasi-Simplex Patterns in Latent Growth Models

    ERIC Educational Resources Information Center

    Bianconcini, Silvia

    2012-01-01

    In the SEM literature, simplex and latent growth models have always been considered competing approaches for the analysis of longitudinal data, even if they are strongly connected and both of specific importance. General dynamic models, which simultaneously estimate autoregressive structures and latent curves, have been recently proposed in the…

  5. Annual growth patterns of baldcypress (Taxodium distichum) along salinity gradients

    USGS Publications Warehouse

    Thomas, Brenda L.; Doyle, Thomas W.; Krauss, Ken W.

    2015-01-01

    The effects of salinity on Taxodium distichum seedlings have been well documented, but few studies have examined mature trees in situ. We investigated the environmental drivers of T. distichum growth along a salinity gradient on the Waccamaw (South Carolina) and Savannah (Georgia) Rivers. On each river, T. distichum increment cores were collected from a healthy upstream site (Upper), a moderately degraded mid-reach site (Middle), and a highly degraded downstream site (Lower). Chronologies were successfully developed for Waccamaw Upper and Middle, and Savannah Middle. Correlations between standardized chronologies and environmental variables showed significant relationships between T. distichum growth and early growing season precipitation, temperature, and Palmer Drought Severity Index (PDSI). Savannah Middle chronology correlated most strongly with August river salinity levels. Both lower sites experienced suppression/release events likely in response to local anthropogenic impacts rather than regional environmental variables. The factors that affect T. distichum growth, including salinity, are strongly synergistic. As sea-level rise pushes the freshwater/saltwater interface inland, salinity becomes more limiting to T. distichum growth in tidal freshwater swamps; however, salinity impacts are exacerbated by locally imposed environmental modifications.

  6. Experiments on LICHEN growth. 1. Seasonal patterns and environmental controls

    SciTech Connect

    Benedict, J.B. )

    1990-08-01

    Radial growth of mature Xanthoparmelia lineola and X. subdecipiens thalli (n = 10 thalli, 170 lobes) was measured bimonthly for 2 yr at a transplant locality on the East Slope of the Colorado Front Range (altitude 2,565 m). Growth occurred during every measurement period, but was most rapid in May, June, July, and August. Ninety-three percent of seasonal growth-rate variation during the first year of the study, and 92% during the second year, are explained by differences in the duration of daytime, snow-free thallus moisture (moisture available for photosynthesis); the strength of the relationship suggests that a positive net carbon assimilation rate is translated almost immediately into lobe elongation. No negative correlation was found between radial growth and thallus moisture recorded at night or beneath snow. In the cool, continental environment of the study area, duration of photosynthetically significant thallus moisture is influenced more strongly by air temperature, day length, and snow cover than by total precipitation. At higher altitudes and latitudes, where lichenometry is used for dating, these factors will have even greater importance.

  7. Literature Growth and Author Productivity Patterns in Indian Physics.

    ERIC Educational Resources Information Center

    Gupta, B. M.; Sharma, Lalita; Kumar, Suresh

    1998-01-01

    Explores the applicability of selected technology diffusion models to the growth of literature in Indian and World physics (1900-50). Focuses on the applicability and validity of two forms of Lotka's Law and negative binomial distribution model to the cumulative author productivity data on Indian physics. Looks at linkages between…

  8. Growth patterns of the nasolabial region: a morphometric study.

    PubMed

    Farkas, L G; Posnick, J C; Hreczko, T M; Pron, G E

    1992-07-01

    Age-related growth changes in the nasolabial region were analyzed through six measurements taken between 1 year and 18 years of age in 1,593 North American Caucasians. By 1 year of age, the length of the cutaneous portion of the upper lip and the width of the nose showed the highest levels of development compared with their adult size, 80.3 and 79.5%, respectively. By 5 years, the developmental level of the nasolabial region except nasal tip protrusion approached their maturation level. Our nasal measurements indicated that growth of the nose between 5 and 18 years was significantly greater than that of the upper lip, which revealed significantly greater growth increments between 1 and 5 years of age. The cutaneous upper lip height reached its adult size in 3-year-old females (12.7 mm) and 6-year-old males (14.4 mm). Nose width and height were fully developed in females by age 12 and in males by age 14 or 15. Rapid growth occurred in the upper lip, nose height, and nasal tip protrusion between the ages of 1 and 4 years. Knowledge of these age-related morphologic variations within the nose and upper lip may be useful in planning the time and type of reconstructive surgery and in anticipating further change in the operated regions after the surgical reconstruction. PMID:1643060

  9. Phototropic growth control of nanoscale pattern formation in photoelectrodeposited Se–Te films

    PubMed Central

    Sadtler, Bryce; Burgos, Stanley P.; Batara, Nicolas A.; Beardslee, Joseph A.; Atwater, Harry A.; Lewis, Nathan S.

    2013-01-01

    Photoresponsive materials that adapt their morphologies, growth directions, and growth rates dynamically in response to the local incident electromagnetic field would provide a remarkable route to the synthesis of complex 3D mesostructures via feedback between illumination and the structure that develops under optical excitation. We report the spontaneous development of ordered, nanoscale lamellar patterns in electrodeposited selenium–tellurium (Se–Te) alloy films grown under noncoherent, uniform illumination on unpatterned substrates in an isotropic electrolyte solution. These inorganic nanostructures exhibited phototropic growth in which lamellar stripes grew toward the incident light source, adopted an orientation parallel to the light polarization direction with a period controlled by the illumination wavelength, and showed an increased growth rate with increasing light intensity. Furthermore, the patterns responded dynamically to changes during growth in the polarization, wavelength, and angle of the incident light, enabling the template-free and pattern-free synthesis, on a variety of substrates, of woodpile, spiral, branched, or zigzag structures, along with dynamically directed growth toward a noncoherent, uniform intensity light source. Full-wave electromagnetic simulations in combination with Monte Carlo growth simulations were used to model light–matter interactions in the Se–Te films and produced a model for the morphological evolution of the lamellar structures under phototropic growth conditions. The experiments and simulations are consistent with a phototropic growth mechanism in which the optical near-field intensity profile selects and reinforces the dominant morphological mode in the emergent nanoscale patterns. PMID:24218617

  10. Cellular and Muscular Growth Patterns During Sipunculan Development

    PubMed Central

    KRISTOF, ALEN; WOLLESEN, TIM; MAIOROVA, ANASTASSYA S.; WANNINGER, ANDREAS

    2015-01-01

    Sipuncula is a lophotrochozoan taxon with annelid affinities, albeit lacking segmentation of the adult body. Here, we present data on cell proliferation and myogenesis during development of three sipunculan species, Phascolosoma agassizii, Thysanocardia nigra, and Themiste pyroides. The first anlagen of the circular body wall muscles appear simultaneously and not subsequently as in the annelids. At the same time, the rudiments of four longitudinal retractor muscles appear. This supports the notion that four introvert retractors were part of the ancestral sipunculan bodyplan. The longitudinal muscle fibers form a pattern of densely arranged fibers around the retractor muscles, indicating that the latter evolved from modified longitudinal body wall muscles. For a short time interval, the distribution of S-phase mitotic cells shows a metameric pattern in the developing ventral nerve cord during the pelagosphera stage. This pattern disappears close to metamorphic competence. Our findings are congruent with data on sipunculan neurogenesis, as well as with recent molecular analyses that place Sipuncula within Annelida, and thus strongly support a segmental ancestry of Sipuncula. PMID:21246707

  11. A Preliminary Investigation of Within-Year Growth Patterns in Reading and Mathematics Curriculum-Based Measures

    ERIC Educational Resources Information Center

    Graney, Suzanne B.; Missall, Kristen N.; Martinez, Rebecca S.; Bergstrom, Melissa

    2009-01-01

    This study examined patterns of growth across benchmark assessments for curriculum-based measures (CBM) over 2 academic years, with the twofold purpose of replicating earlier findings of growth patterns on R-CBM and conducting a preliminary investigation of growth patterns on M-CBM and CBM-Maze. The sample included 898 cases from 3rd through 5th…

  12. Spontaneous Pattern Formation of Surface Nanodroplets from Competitive Growth

    NASA Astrophysics Data System (ADS)

    Peng, Shuhua; Lohse, Detlef; Zhang, Xuehua; Xuehua Zhang Team; Detlef Lohse Collaboration

    2015-11-01

    Nanoscale droplets on a substrate are of great interest because of their relevance for droplet-based technologies for light manipulation, lab-on-chip devices, miniaturised reactors, encapsulation and many others. In this work, we establish a basic principle for the symmetrical arrangement of surface nanodroplets during their growth under simple flow conditions. In our model system, nanodroplets nucleate at the rim of spherical cap microstructures on a substrate, as a pulse of oversaturation is supplied by a solvent exchange process. We find that, while growing, the nanodroplets self-organise into highly symmetric arrangements, with respect to position, size, and mutual distance. The angle between the neighbouring droplets is four times the ratio between the base radii of the droplets and the spherical caps. We show and explain how the nanodroplets acquire the symmetrical spatial arrangement during their competitive growth and why and how the competition enhances the overall growth rate of the nucleated nanodroplets. This mechanism behind the nanodroplet self-organisation promises a simple approach for the location control of droplets with a volume down to attoliters.

  13. Spontaneous Pattern Formation of Surface Nanodroplets from Competitive Growth.

    PubMed

    Peng, Shuhua; Lohse, Detlef; Zhang, Xuehua

    2015-12-22

    Nanoscale droplets on a substrate are of great interest because of their relevance for droplet-based technologies for light manipulation, lab-on-chip devices, miniaturized reactors, encapsulation, and many others. In this work, we establish a basic principle for symmetrical arrangements of surface nanodroplets during their growth out of oversaturated solution established through solvent exchange, which takes place under simple and controlled flow conditions. In our model system, nanodroplets nucleate at the rim of spherical cap microstructures on a substrate, due to a pulse of oversaturation supplied by a solvent exchange process. We find that, while growing at the rim of the microcap, the nanodroplets self-organize into highly symmetric arrangements, with respect to position, size, and mutual distance. The angle between the neighboring droplets is 4 times the ratio between the base radii of the droplets and the spherical caps. We show and explain how the nanodroplets acquire the symmetrical spatial arrangement during their competitive growth and why and how the competition enhances the overall growth rate of the nucleated nanodroplets. This mechanism behind the nanodroplet self-organization promises a simple approach to control the location of droplets with a volume down to attoliters. PMID:26502340

  14. Spontaneous Pattern Formation of Surface Nanodroplets from Competitive Growth

    NASA Astrophysics Data System (ADS)

    Lohse, Detlef; Peng, Shuhua; Zhang, Xuehua

    Nanoscale droplets on a substrate are of great interest because of their relevance for droplet-based technologies for light manipulation, lab-on-chip devices, miniaturised reactors, encapsulation and many others. In this work, we establish a basic principle for the symmetrical arrangement of surface nanodroplets during their growth under simple flow conditions. In our model system, nanodroplets nucleate at the rim of spherical cap microstructures on a substrate, due to a pulse of oversaturation is supplied by a solvent exchange process. We find that, while growing at the rim of the microcap, the nanodroplets self-organise into highly symmetric arrangements, with respect to position, size, and mutual distance. The angle between the neighbouring droplets is four times the ratio between the base radii of the droplets and the spherical caps. We show and explain how the nanodroplets acquire the symmetrical spatial arrangement during their competitive growth and why and how the competition enhances the overall growth rate of the nucle- ated nanodroplets. This mechanism behind the nanodroplet self-organisation promises a simple approach for the location control of droplets with a volume down to attoliters.

  15. Growth patterns and life-history strategies in Placodontia (Diapsida: Sauropterygia)

    PubMed Central

    Klein, Nicole; Neenan, James M.; Scheyer, Torsten M.; Griebeler, Eva Maria

    2015-01-01

    Placodontia is a clade of durophagous, near shore marine reptiles from Triassic sediments of modern-day Europe, Middle East and China. Although much is known about their primary anatomy and palaeoecology, relatively little has been published regarding their life history, i.e. ageing, maturation and growth. Here, growth records derived from long bone histological data of placodont individuals are described and modelled to assess placodont growth and life-history strategies. Growth modelling methods are used to confirm traits documented in the growth record (age at onset of sexual maturity, age when asymptotic length was achieved, age at death, maximum longevity) and also to estimate undocumented traits. Based on these growth models, generalized estimates of these traits are established for each taxon. Overall differences in bone tissue types and resulting growth curves indicate different growth patterns and life-history strategies between different taxa of Placodontia. Psephoderma and Paraplacodus grew with lamellar-zonal bone tissue type and show growth patterns as seen in modern reptiles. Placodontia indet. aff. Cyamodus and some Placodontia indet. show a unique combination of fibrolamellar bone tissue regularly stratified by growth marks, a pattern absent in modern sauropsids. The bone tissue type of Placodontia indet. aff. Cyamodus and Placodontia indet. indicates a significantly increased basal metabolic rate when compared with modern reptiles. Double lines of arrested growth, non-annual rest lines in annuli, and subcycles that stratify zones suggest high dependence of placodont growth on endogenous and exogenous factors. Histological and modelled differences within taxa point to high individual developmental plasticity but sexual dimorphism in growth patterns and the presence of different taxa in the sample cannot be ruled out. PMID:26587259

  16. Growth patterns and life-history strategies in Placodontia (Diapsida: Sauropterygia).

    PubMed

    Klein, Nicole; Neenan, James M; Scheyer, Torsten M; Griebeler, Eva Maria

    2015-07-01

    Placodontia is a clade of durophagous, near shore marine reptiles from Triassic sediments of modern-day Europe, Middle East and China. Although much is known about their primary anatomy and palaeoecology, relatively little has been published regarding their life history, i.e. ageing, maturation and growth. Here, growth records derived from long bone histological data of placodont individuals are described and modelled to assess placodont growth and life-history strategies. Growth modelling methods are used to confirm traits documented in the growth record (age at onset of sexual maturity, age when asymptotic length was achieved, age at death, maximum longevity) and also to estimate undocumented traits. Based on these growth models, generalized estimates of these traits are established for each taxon. Overall differences in bone tissue types and resulting growth curves indicate different growth patterns and life-history strategies between different taxa of Placodontia. Psephoderma and Paraplacodus grew with lamellar-zonal bone tissue type and show growth patterns as seen in modern reptiles. Placodontia indet. aff. Cyamodus and some Placodontia indet. show a unique combination of fibrolamellar bone tissue regularly stratified by growth marks, a pattern absent in modern sauropsids. The bone tissue type of Placodontia indet. aff. Cyamodus and Placodontia indet. indicates a significantly increased basal metabolic rate when compared with modern reptiles. Double lines of arrested growth, non-annual rest lines in annuli, and subcycles that stratify zones suggest high dependence of placodont growth on endogenous and exogenous factors. Histological and modelled differences within taxa point to high individual developmental plasticity but sexual dimorphism in growth patterns and the presence of different taxa in the sample cannot be ruled out. PMID:26587259

  17. Spontaneous extraskeletal osteosarcoma with various histological growth patterns in the abdominal wall of an ICR mouse

    PubMed Central

    Ito, Tsuyoshi; Katoh, Yoshitaka; Shimada, Yuko; Ohnuma-Koyama, Aya; Takahashi, Naofumi; Kuwahara, Maki; Harada, Takanori

    2015-01-01

    Extraskeletal osteosarcoma is extremely rare in mice. This case report demonstrates a spontaneous murine extraskeletal osteosarcoma that exhibited various histological growth patterns in an ICR mouse. At necropsy, the tumor mass was located in the abdominal wall and was 45 × 30 × 25 mm in size. Histopathologically, the tumor showed the following four growth patterns: a solid pattern of polygonal cells embedded in an osteoid eosinophilic matrix with calcification, an irregular sheet pattern of short spindle cells accompanying some eosinophilic multinucleated cells, a fascicular pattern of spindle cells and a cystic pattern lined by short spindle cells. Immunohistochemically, most of the tumor cells were positive for vimentin, proliferating cell nuclear antigen and osterix. The multinucleated cells mentioned above were desmin positive and were regarded as regenerative striated muscles but not tumor cells. Since no clear continuity with normal bone tissues was observed, the tumor was diagnosed as an “extraskeletal osteosarcoma.” PMID:26989300

  18. Patterns of postnatal growth in HIV-infected and HIV-exposed children

    PubMed Central

    Isanaka, Sheila; Duggan, Christopher; Fawzi, Wafaie W.

    2009-01-01

    HIV infection can contribute to disturbances in both linear growth and weight gain in early childhood, with disturbances often apparent as early as 3 mo of age. There is little evidence for a difference in the early growth of HIV-exposed but uninfected children compared to healthy controls. Owing to the close association of growth with immune function and clinical progression, an understanding of growth patterns may be an important tool to ensure the provision of appropriate care to HIV-infected and exposed children. Timely growth monitoring may be used to improve the clinical course and quality of life of these children. PMID:19519675

  19. Effects of Atypical Patterns of Fetal Growth on Newborn (NBAS) Behavior.

    ERIC Educational Resources Information Center

    Lester, Barry M.; And Others

    1986-01-01

    Newborn infants showing anthropometric signs of atypical patterns of fetal growth were compared with infants of appropriate growth on the Neonatal Behavioral Assessment Scale and on recently developed supplementary items. The sample consisted of lower-socioeconomic-status families in San Juan, Puerto Rico, and included teenage and older mothers.…

  20. Bacterial locomotion, adsorption and growth over chemically patterned surfaces

    NASA Astrophysics Data System (ADS)

    Jalali, Maryam; Molaei, Mehdi; Sheng, Jian

    2013-11-01

    Complex dynamic interactions between bacteria and chemically patched interface that mimics the heterogeneous energy landscape of a real-life interfacial environment are studied in the paper. We explore effects of these spatially varying chemical patches on bacterial locomotion, adsorption, biofilm formation and the film growth rate. Using micro-fabrication and soft-lithography, we have fabricated PDMS microfluidic channels with a solid substrate covered by micro-scale chemical patches. Arrays of 2D geometries of characteristic scales varying from 10 to 50 μm are transferred onto a glass substrate by soft-lithography. The substrate is functionalized to generate alternating hydrophobic and hydrophilic regions and bonded with the channel. The 3D swimming characteristics near these surfaces, such as swimming velocity, linear and angular dispersions, are measured in-situ using 3D digital holographic microscopy. The observations are used to examine the mechanisms involved in adsorption and desorption of swimming bacteria onto the substrate. Long-term experiments are conducted to quantify the growth rate and structures of colony. A correlation between various length scales of the substrate and bacteria motility are observed.

  1. Publication Productivity of Faculty of Medicine, Mansoura University Indexed in PubMed

    PubMed Central

    Helal, RM; Abou-ElWafa, HS; El-Gilany, AH

    2014-01-01

    Background: Analysis of PubMed publications as an indicator of the research productivity of individual countries, regions, or institutions has recently become a field of interest. Aim: The aim was to assess the past trends in PubMed-indexed medical publications from Mansoura Faculty of Medicine and to have an idea about the current situation in medical research. Materials and Methods: PubMed was searched for publications affiliated to Mansoura from the end of the calendar year 2012 and earlier. Results: Of 2798 papers related to Mansoura, 1756 publications were included in the analysis, and 1042 publications were excluded (false positives). The highest number of publications was in 2011 (10.6%, 187/1756) followed by 2012 (10.2%, 179/1756). There was an increase of the publication rate over 5-years period until it reaches 47.0% (826/1756) during the period from 2008 to 2012. The main high-producing department was Urology and Nephrology, which accounted for 35.9% (631/1756) of the total publications followed by Pediatrics and Parasitology. The median number of authors participated in the researches was four ranging from 1 to 23. Most of the publications were in the form of intervention/clinical trials (38.4%, 662/1756) followed by descriptive/cross-sectional study (38.3%, 659/1756). The median of the impact factor was 1.99 ranging from 0.27 to 53.3. Conclusion: The publication productivity of Mansoura Faculty of Medicine showed fluctuating pattern from the end of the calendar year 2012 and earlier. Future prospects for increasing research productivity should be considered to increase the number and quality of publications and academic staff participating in high-quality international researches. PMID:25364602

  2. Pattern formation in crystal growth under parabolic shear flow.

    PubMed

    Ueno, K

    2003-08-01

    Morphological instability of the solid-liquid interface occurring in a crystal growing from an undercooled thin liquid bounded on one side by a free surface and flowing down inclined plane, is investigated by a linear stability analysis under shear flow. It is found that restoring forces due to gravity and surface tension is an important factor for stabilization of the solid-liquid interface on long length scales. This is a stabilizing effect different from the Gibbs-Thomson effect. A particular long wavelength mode of about 1 cm of wavy pattern, observed on the surface of icicles covered with a thin layer of flowing water is obtained from the dispersion relation, including the effect of flow and restoring forces. PMID:14524982

  3. Non-Linear Pattern Formation in Bone Growth and Architecture

    PubMed Central

    Salmon, Phil

    2014-01-01

    The three-dimensional morphology of bone arises through adaptation to its required engineering performance. Genetically and adaptively bone travels along a complex spatiotemporal trajectory to acquire optimal architecture. On a cellular, micro-anatomical scale, what mechanisms coordinate the activity of osteoblasts and osteoclasts to produce complex and efficient bone architectures? One mechanism is examined here – chaotic non-linear pattern formation (NPF) – which underlies in a unifying way natural structures as disparate as trabecular bone, swarms of birds flying, island formation, fluid turbulence, and others. At the heart of NPF is the fact that simple rules operating between interacting elements, and Turing-like interaction between global and local signals, lead to complex and structured patterns. The study of “group intelligence” exhibited by swarming birds or shoaling fish has led to an embodiment of NPF called “particle swarm optimization” (PSO). This theoretical model could be applicable to the behavior of osteoblasts, osteoclasts, and osteocytes, seeing them operating “socially” in response simultaneously to both global and local signals (endocrine, cytokine, mechanical), resulting in their clustered activity at formation and resorption sites. This represents problem-solving by social intelligence, and could potentially add further realism to in silico computer simulation of bone modeling. What insights has NPF provided to bone biology? One example concerns the genetic disorder juvenile Pagets disease or idiopathic hyperphosphatasia, where the anomalous parallel trabecular architecture characteristic of this pathology is consistent with an NPF paradigm by analogy with known experimental NPF systems. Here, coupling or “feedback” between osteoblasts and osteoclasts is the critical element. This NPF paradigm implies a profound link between bone regulation and its architecture: in bone the architecture is the regulation. The former is the

  4. Non-linear pattern formation in bone growth and architecture.

    PubMed

    Salmon, Phil

    2014-01-01

    The three-dimensional morphology of bone arises through adaptation to its required engineering performance. Genetically and adaptively bone travels along a complex spatiotemporal trajectory to acquire optimal architecture. On a cellular, micro-anatomical scale, what mechanisms coordinate the activity of osteoblasts and osteoclasts to produce complex and efficient bone architectures? One mechanism is examined here - chaotic non-linear pattern formation (NPF) - which underlies in a unifying way natural structures as disparate as trabecular bone, swarms of birds flying, island formation, fluid turbulence, and others. At the heart of NPF is the fact that simple rules operating between interacting elements, and Turing-like interaction between global and local signals, lead to complex and structured patterns. The study of "group intelligence" exhibited by swarming birds or shoaling fish has led to an embodiment of NPF called "particle swarm optimization" (PSO). This theoretical model could be applicable to the behavior of osteoblasts, osteoclasts, and osteocytes, seeing them operating "socially" in response simultaneously to both global and local signals (endocrine, cytokine, mechanical), resulting in their clustered activity at formation and resorption sites. This represents problem-solving by social intelligence, and could potentially add further realism to in silico computer simulation of bone modeling. What insights has NPF provided to bone biology? One example concerns the genetic disorder juvenile Pagets disease or idiopathic hyperphosphatasia, where the anomalous parallel trabecular architecture characteristic of this pathology is consistent with an NPF paradigm by analogy with known experimental NPF systems. Here, coupling or "feedback" between osteoblasts and osteoclasts is the critical element. This NPF paradigm implies a profound link between bone regulation and its architecture: in bone the architecture is the regulation. The former is the emergent

  5. Tree growth and competition in an old-growth Picea abies forest of boreal Sweden: influence of tree spatial patterning

    USGS Publications Warehouse

    Fraver, Shawn; D'Amato, Anthony W.; Bradford, John B.; Jonsson, Bengt Gunnar; Jönsson, Mari; Esseen, Per-Anders

    2013-01-01

    Question: What factors best characterize tree competitive environments in this structurally diverse old-growth forest, and do these factors vary spatially within and among stands? Location: Old-growth Picea abies forest of boreal Sweden. Methods: Using long-term, mapped permanent plot data augmented with dendrochronological analyses, we evaluated the effect of neighbourhood competition on focal tree growth by means of standard competition indices, each modified to include various metrics of trees size, neighbour mortality weighting (for neighbours that died during the inventory period), and within-neighbourhood tree clustering. Candidate models were evaluated using mixed-model linear regression analyses, with mean basal area increment as the response variable. We then analysed stand-level spatial patterns of competition indices and growth rates (via kriging) to determine if the relationship between these patterns could further elucidate factors influencing tree growth. Results: Inter-tree competition clearly affected growth rates, with crown volume being the size metric most strongly influencing the neighbourhood competitive environment. Including neighbour tree mortality weightings in models only slightly improved descriptions of competitive interactions. Although the within-neighbourhood clustering index did not improve model predictions, competition intensity was influenced by the underlying stand-level tree spatial arrangement: stand-level clustering locally intensified competition and reduced tree growth, whereas in the absence of such clustering, inter-tree competition played a lesser role in constraining tree growth. Conclusions: Our findings demonstrate that competition continues to influence forest processes and structures in an old-growth system that has not experienced major disturbances for at least two centuries. The finding that the underlying tree spatial pattern influenced the competitive environment suggests caution in interpreting traditional tree

  6. Correlations between polyamine ratios and growth patterns in seedling roots

    NASA Technical Reports Server (NTRS)

    Shen, H. J.; Galston, A. W.

    1985-01-01

    The levels of putrescine, cadaverine, spermidine and spermine were determined in seedling roots of pea, tomato, millet and corn, as well as in corn coleoptiles and pea internodes. In all roots, putrescine content increased as elongation progressed, and the putrescine/spermine ratio closely paralleled the sigmoid growth curve up until the time of lateral root initiation. Spermidine and spermine were most abundant near the apices and declined progressively with increasing age of the cells. In the zone of differentiation of root hairs in pea roots, putrescine rose progressively with increasing age, while cadaverine declined. In both pea internodes and corn coleoptiles, the putrescine/spermidine ratio rises with increasing age and elongation. Thus, a block in the conversion of the diamine putrescine to the triamine spermidine may be an important step in the change from cell division to cell elongation.

  7. Clinical significance of subepithelial growth patterns in non-muscle invasive bladder cancer

    PubMed Central

    2011-01-01

    Background We evaluated the clinical significance and prognostic value of histopathological features of bladder cancer, such as subepithelial growth patterns and tumor growth pattern at the invasion front. Methods In total, 130 patients newly diagnosed with non-muscle invasive bladder cancer and underwent transurethral resection between 1998 and 2009 were enrolled. Subepithelial growth patterns consisting of endophytic growth pattern (EGP) and von Brunn's nest involvement (VBNI) were investigated using hematoxylin and eosin-stained slides, and their frequency of occurrence, prognostic value, and correlation with other clinicopathological features was evaluated. Results EGP and VBNI were found in 40 (30.8%) and 5 (3.9%) of the 130 cases, respectively. Of the 26 pT1 tumors, the growth pattern at the invasion front was trabecular in 17 (65.4%) and infiltrative in 9 (34.6%). Although 8 (47.1%) of 17 trabecular tumors coexisted with EGP, no cases with infiltrative tumors had EGP (p = 0.023). VBNI correlated with high tumor grades (p = 0.006) and lymphovascular involvement (p = 0.026). The multivariate Cox proportional hazards analysis revealed that tumor diameter less than 3 cm (p = 0.04) and intravesical bacillus Calmette-Guérin therapy (p = 0.004) were independent favorable prognostic factors for recurrence-free survival, whereas tumor stage was an independent poor prognostic factor for disease progression (p = 0.006). Conclusions Subepithelial growth patterns were not a significant prognostic factor in this study. Additionally, no tumors with an infiltrative growth pattern coexisted with EGP, suggesting that determining the presence of EGP might be helpful for managing non-muscle invasive bladder cancers. PMID:21816111

  8. Secondary Growth and Carbohydrate Storage Patterns Differ between Sexes in Juniperus thurifera.

    PubMed

    DeSoto, Lucía; Olano, José M; Rozas, Vicente

    2016-01-01

    Differences in reproductive costs between male and female plants have been shown to foster sex-related variability in growth and C-storage patterns. The extent to which differential secondary growth in dioecious trees is associated with changes in stem carbohydrate storage patterns, however, has not been fully assessed. We explored the long-term radial growth and the seasonal variation of non-structural carbohydrate (NSC) content in sapwood of 40 males and 40 females Juniperus thurifera trees at two sites. NSC content was analyzed bimonthly for 1 year, and tree-ring width was measured for the 1931-2010 period. Sex-related differences in secondary growth and carbohydrate storage were site-dependent. Under less restrictive environmental conditions females grew more and stored more non-soluble sugars than males. Our results reinforce that sex-related differences in growth and resource storage may be a consequence of local adaptation to environmental conditions. Seasonal variation in soluble sugars concentration was opposite to cambial activity, with minima seen during periods of maximal secondary growth, and did not differ between the sexes or sites. Trees with higher stem NSC levels at critical periods showed higher radial growth, suggesting a common mechanism irrespective of site or sex. Sex-related patterns of secondary growth were linked to differences in non-soluble sugars content indicating sex-specific strategies of long-term performance. PMID:27303418

  9. Secondary Growth and Carbohydrate Storage Patterns Differ between Sexes in Juniperus thurifera

    PubMed Central

    DeSoto, Lucía; Olano, José M.; Rozas, Vicente

    2016-01-01

    Differences in reproductive costs between male and female plants have been shown to foster sex-related variability in growth and C-storage patterns. The extent to which differential secondary growth in dioecious trees is associated with changes in stem carbohydrate storage patterns, however, has not been fully assessed. We explored the long-term radial growth and the seasonal variation of non-structural carbohydrate (NSC) content in sapwood of 40 males and 40 females Juniperus thurifera trees at two sites. NSC content was analyzed bimonthly for 1 year, and tree-ring width was measured for the 1931–2010 period. Sex-related differences in secondary growth and carbohydrate storage were site-dependent. Under less restrictive environmental conditions females grew more and stored more non-soluble sugars than males. Our results reinforce that sex-related differences in growth and resource storage may be a consequence of local adaptation to environmental conditions. Seasonal variation in soluble sugars concentration was opposite to cambial activity, with minima seen during periods of maximal secondary growth, and did not differ between the sexes or sites. Trees with higher stem NSC levels at critical periods showed higher radial growth, suggesting a common mechanism irrespective of site or sex. Sex-related patterns of secondary growth were linked to differences in non-soluble sugars content indicating sex-specific strategies of long-term performance. PMID:27303418

  10. Simple Growth Patterns Can Create Complex Trajectories for the Ontogeny of Constitutive Chemical Defences in Seaweeds

    PubMed Central

    Paul, Nicholas A.; Svensson, Carl Johan; de Nys, Rocky; Steinberg, Peter D.

    2014-01-01

    All of the theory and most of the data on the ecology and evolution of chemical defences derive from terrestrial plants, which have considerable capacity for internal movement of resources. In contrast, most macroalgae – seaweeds – have no or very limited capacity for resource translocation, meaning that trade-offs between growth and defence, for example, should be localised rather than systemic. This may change the predictions of chemical defence theories for seaweeds. We developed a model that mimicked the simple growth pattern of the red seaweed Asparagopsis armata which is composed of repeating clusters of somatic cells and cells which contain deterrent secondary chemicals (gland cells). To do this we created a distinct growth curve for the somatic cells and another for the gland cells using empirical data. The somatic growth function was linked to the growth function for defence via differential equations modelling, which effectively generated a trade-off between growth and defence as these neighbouring cells develop. By treating growth and defence as separate functions we were also able to model a trade-off in growth of 2–3% under most circumstances. However, we found contrasting evidence for this trade-off in the empirical relationships between growth and defence, depending on the light level under which the alga was cultured. After developing a model that incorporated both branching and cell division rates, we formally demonstrated that positive correlations between growth and defence are predicted in many circumstances and also that allocation costs, if they exist, will be constrained by the intrinsic growth patterns of the seaweed. Growth patterns could therefore explain contrasting evidence for cost of constitutive chemical defence in many studies, highlighting the need to consider the fundamental biology and ontogeny of organisms when assessing the allocation theories for defence. PMID:24497991

  11. Environmental effects on spatial and temporal patterns of leaf and root growth.

    PubMed

    Walter, Achim; Silk, Wendy K; Schurr, Ulrich

    2009-01-01

    Leaves and roots live in dramatically different habitats, but are parts of the same organism. Automated image processing of time-lapse records of these organs has led to understanding of spatial and temporal patterns of growth on time scales from minutes to weeks. Growth zones in roots and leaves show distinct patterns during a diel cycle (24 h period). In dicot leaves under nonstressful conditions these patterns are characterized by endogenous rhythms, sometimes superimposed upon morphogenesis driven by environmental variation. In roots and monocot leaves the growth patterns depend more strongly on environmental fluctuations. Because the impact of spatial variations and temporal fluctuations of above- and belowground environmental parameters must be processed by the plant body as an entire system whose individual modules interact on different levels, growth reactions of individual modules are often highly nonlinear. A mechanistic understanding of plant resource use efficiency and performance in a dynamically fluctuating environment therefore requires an accurate analysis of leaf and root growth patterns in conjunction with knowledge of major intraplant communication systems and metabolic pathways. PMID:19575584

  12. Selective pattern of cancer cell accumulation and growth using UV modulating printing of hydrogels.

    PubMed

    Yang, Wenguang; Yu, Haibo; Wei, Fanan; Li, Gongxin; Wang, Yuechao; Liu, Lianqing

    2015-12-01

    Fabrication of extracellular microenvironment for cancer cell growth in vitro is an indispensable technique to precisely control the cell spatial arrangement and proliferation for cell-behavior research. Current micropatterning methods usually require relatively complicated operations, which makes it difficult to investigate the effects of different cell growth patterns. This manuscript proposes a DMD-based projection technique to quickly pattern a poly(ethylene) glycol diacrylate (PEGDA)-based hydrogel on a common glass substrate. Using this method, we can effectively control the growth patterns of cells. Compared with these traditional methods which employ digital dynamic mask, polymerization of PEGDA solution can be used to create arbitrary shaped microstructures with high efficiency, flexibility and repeatability. The duration of UV exposure is less than 10 s through controlling the projected illumination pattern. The ability of patterned PEGDA-coated film to hinder cell adhesion makes it possible to control area over which cells attach. In our experiments, we take advantage of the blank area to pattern cells, which allows cells to grow in various pre-designed shapes and sizes. And the patterning cells have a high viability after culturing for several days. Interestingly, we found that the restricted space could stiffen and strengthen the cells. These results indicate that cells and extracellular microenvironment can influence each other. PMID:26458559

  13. Literature Mapping with PubAtlas — extending PubMed with a ‘BLASTing interface’ *

    PubMed Central

    Parker, D.S.; Chu, W.W.; Sabb, F.W.; Toga, A.W.; Bilder, R.M.

    2009-01-01

    PubAtlas (www.pubatlas.org) is a web service and standalone program providing literature maps for the biomedical research literature. It accepts user-defined sets of terms (PubMed queries) as input, and permits ‘BLASTing’ of one set against another: for all terms x and y in these sets, deriving the results of the pairwise intersections x AND y. This all vs. all capability extends PubMed with a literature analysis interface. Correspondingly, the basic form of literature map that PubAtlas provides for exploring associations among sets of terms is an interactive tabular display, in heatmap/microarray format. PubAtlas supports development of specialized lexica -- hierarchies of controlled terminology that can represent sets of related concepts or a ‘user-defined query language’. PubAtlas also provides historical perspectives on the literature, with temporal query features that highlight historical patterns. Generally, it is a framework for extending the PubMed interface, and an extensible platform for producing interactive literature maps. PMID:21347177

  14. Spatial Patterning of Newly-Inserted Material during Bacterial Cell Growth

    NASA Astrophysics Data System (ADS)

    Ursell, Tristan

    2012-02-01

    In the life cycle of a bacterium, rudimentary microscopy demonstrates that cell growth and elongation are essential characteristics of cellular reproduction. The peptidoglycan cell wall is the main load-bearing structure that determines both cell shape and overall size. However, simple imaging of cellular growth gives no indication of the spatial patterning nor mechanism by which material is being incorporated into the pre-existing cell wall. We employ a combination of high-resolution pulse-chase fluorescence microscopy, 3D computational microscopy, and detailed mechanistic simulations to explore how spatial patterning results in uniform growth and maintenance of cell shape. We show that growth is happening in discrete bursts randomly distributed over the cell surface, with a well-defined mean size and average rate. We further use these techniques to explore the effects of division and cell wall disrupting antibiotics, like cephalexin and A22, respectively, on the patterning of cell wall growth in E. coli. Finally, we explore the spatial correlation between presence of the bacterial actin-like cytoskeletal protein, MreB, and local cell wall growth. Together these techniques form a powerful method for exploring the detailed dynamics and involvement of antibiotics and cell wall-associated proteins in bacterial cell growth.[4pt] In collaboration with Kerwyn Huang, Stanford University.

  15. The inclusion of an online journal in PubMed central - a difficult path.

    PubMed

    Grech, Victor

    2016-01-01

    The indexing of a journal in a prominent database (such as PubMed) is an important imprimatur. Journals accepted for inclusion in PubMed Central (PMC) are automatically indexed in PubMed but must provide the entire contents of their publications as XML-tagged (Extensible Markup Language) data files compliant with PubMed's document type definition (DTD). This paper describes the various attempts that the journal Images in Paediatric Cardiology made in its efforts to convert the journal contents (including all of the extant backlog) to PMC-compliant XML for archiving and indexing in PubMed after the journal was accepted for inclusion by the database. PMID:27244254

  16. Retrieving Clinical Evidence: A Comparison of PubMed and Google Scholar for Quick Clinical Searches

    PubMed Central

    Bejaimal, Shayna AD; Sontrop, Jessica M; Iansavichus, Arthur V; Haynes, R Brian; Weir, Matthew A; Garg, Amit X

    2013-01-01

    Background Physicians frequently search PubMed for information to guide patient care. More recently, Google Scholar has gained popularity as another freely accessible bibliographic database. Objective To compare the performance of searches in PubMed and Google Scholar. Methods We surveyed nephrologists (kidney specialists) and provided each with a unique clinical question derived from 100 renal therapy systematic reviews. Each physician provided the search terms they would type into a bibliographic database to locate evidence to answer the clinical question. We executed each of these searches in PubMed and Google Scholar and compared results for the first 40 records retrieved (equivalent to 2 default search pages in PubMed). We evaluated the recall (proportion of relevant articles found) and precision (ratio of relevant to nonrelevant articles) of the searches performed in PubMed and Google Scholar. Primary studies included in the systematic reviews served as the reference standard for relevant articles. We further documented whether relevant articles were available as free full-texts. Results Compared with PubMed, the average search in Google Scholar retrieved twice as many relevant articles (PubMed: 11%; Google Scholar: 22%; P<.001). Precision was similar in both databases (PubMed: 6%; Google Scholar: 8%; P=.07). Google Scholar provided significantly greater access to free full-text publications (PubMed: 5%; Google Scholar: 14%; P<.001). Conclusions For quick clinical searches, Google Scholar returns twice as many relevant articles as PubMed and provides greater access to free full-text articles. PMID:23948488

  17. Graphene Growth on Pre-patterned Copper Film with Nickel as a Buffer Layer

    NASA Astrophysics Data System (ADS)

    Li, Yang; Deng, Wu-Zhu; Wang, Dong-Zhao; Chen, Yang-Yang; Zhou, Wen-Li

    2015-11-01

    Selective graphene growth has been simultaneously achieved on oxidized silicon substrate with three kinds of pre-patterned rectangular metal films, i.e., Cu/Ni double layer, and Ni and Cu single layer film, by atmospheric chemical vapor deposition at 1020°C. The top graphene maintains the micron-scale patterning of the metal film underneath. It was found that single layer graphene growth is more favorable on the Cu/Ni double layer film than on either single layer. The morphology and structure study of the pre-patterned metal substrates before and after graphene growth indicated that Ni functions as a buffer layer to significantly weaken the lattice mismatch between the copper and silicon substrate, resulting in a smoother and larger grain-sized Cu surface. It is also suggested that Ni diffuses to the Cu surface and participates in the graphene growth during the chemical vapor deposition (CVD) process. Defect-free single layer graphene growth can be obtained when the ratio of Cu/Ni is appropriate with respect to their thickness and the feature size of rectangular patterning.

  18. Characteristics of proportionate growth observed in instability patterns of miscible fluids

    NASA Astrophysics Data System (ADS)

    Bischofberger, Irmgard; Ramachandran, Radha; Nagel, Sidney R.; Nagel lab Team

    2014-11-01

    As a baby mammal grows, different parts of its body develop at the nearly the same rate and thus to a good approximation in direct proportion to one another. This type of growth is called proportionate growth. As familiar as it appears to us, it is very rarely found in physical systems outside of the biological world. We here show an example of proportionate growth that occurs in the instability formed when a less viscous liquid, of viscosity ηin displaces a more viscous miscible one, of viscosity ηout. We investigate the growth of these patterns in a quasi-two-dimensional geometry. Within a range of viscosity ratios 0.1 <ηin /ηout <0.3, we observe the formation of small blunt structures that form at the edges of an inner circular region devoid of fingers. As the pattern grows, the size of these structures increases in proportion to the size of the inner circle, such that even small details in the shape of the pattern remain essentially unchanged during growth. These characteristics of proportionate growth are reflected in the shape of the interface in the third dimension as well.

  19. Postnatal changes in the growth dynamics of the human face revealed from bone modelling patterns

    PubMed Central

    Martinez-Maza, Cayetana; Rosas, Antonio; Nieto-Díaz, Manuel

    2013-01-01

    Human skull morphology results from complex processes that involve the coordinated growth and interaction of its skeletal components to keep a functional and structural balance. Previous histological works have studied the growth of different craniofacial regions and their relationship to functional spaces in humans up to 14 years old. Nevertheless, how the growth dynamics of the facial skeleton and the mandible are related and how this relationship changes through the late ontogeny remain poorly understood. To approach these two questions, we have compared the bone modelling activities of the craniofacial skeleton from a sample of subadult and adult humans. In this study, we have established for the first time the bone modelling pattern of the face and the mandible from adult humans. Our analyses reveal a patchy distribution of the bone modelling fields (overemphasized by the presence of surface islands with no histological information) reflecting the complex growth dynamics associated to the individual morphology. Subadult and adult specimens show important differences in the bone modelling patterns of the anterior region of the facial skeleton and the posterior region of the mandible. These differences indicate developmental changes in the growth directions of the whole craniofacial complex, from a predominantly downward growth in subadults that turns to a forward growth observed in the adult craniofacial skeleton. We hypothesize that these ontogenetic changes would respond to the physiological and physical requirements to enlarge the oral and nasal cavities once maturation of the brain and the closure of the cranial sutures have taken place during craniofacial development. PMID:23819603

  20. New Patterns of American Metropolitan Population Growth in the 1970s.

    ERIC Educational Resources Information Center

    Phillips, Phillip D.

    1978-01-01

    Discusses three aspects of post-1970 American metropolitan population trends: the general dimensions of change between pre- and post-1970 population growth patterns are presented; possible causes of these changes are examined; college or high school level classroom exercises that generate awareness of recent trends and their causes are outlined.…

  1. Effect of weather patterns on preweaning growth of beef calves in the Northern Great Plains

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Beef production records collected over a 76-year investigation into effects of linebreeding and selection of Hereford cattle, and concurrent weather records were used to assess effects of weather patterns on the growth of calves from birth to weaning. Data were simultaneously adjusted for trends in ...

  2. Catalyst-free growth of nanocrystalline graphene/graphite patterns from photoresist.

    PubMed

    Zhang, Zengxing; Ge, Binghui; Guo, Yunxian; Tang, Dongsheng; Wang, Xiaojuan; Wang, Fengli

    2013-04-01

    Catalyst-free growth of a nanocrystalline few-layer graphene (or graphite) film from photoresist on variable substrates was demonstrated. The thickness of the film can be easily controlled from 1 nm to hundreds of nanometers. With this method, graphene/graphite patterns with different thicknesses have been designed for integrated electronics. PMID:23439870

  3. The Homeobox Transcription Factor Cut Coordinates Patterning and Growth During Drosophila Airway Remodeling

    PubMed Central

    Pitsouli, Chrysoula; Perrimon, Norbert

    2014-01-01

    A fundamental question in developmental biology is how tissue growth and patterning are coordinately regulated to generate complex organs with characteristic shapes and sizes. We showed that in the developing primordium that produces the Drosophila adult trachea, the homeobox transcription factor Cut regulates both growth and patterning, and its effects depend on its abundance. Quantification of the abundance of Cut in the developing airway progenitors during late larval stage 3 revealed that the cells of the developing trachea had different amounts of Cut, with the most proliferative region having an intermediate amount of Cut and the region lacking Cut exhibiting differentiation. By manipulating Cut abundance, we showed that Cut functioned in different regions to regulate proliferation or patterning. Transcriptional profiling of progenitor populations with different amounts of Cut revealed the Wingless (known as Wnt in vertebrates) and Notch signaling pathways as positive and negative regulators of cut expression, respectively. Furthermore, we identified the gene encoding the receptor Breathless (Btl, known as fibroblast growth factor receptor in vertebrates) as a transcriptional target of Cut. Cut inhibited btl expression and tracheal differentiation to maintain the developing airway cells in a progenitor state. Thus, Cut functions in the integration of patterning and growth in a developing epithelial tissue. PMID:23423438

  4. Controlled neuronal cell patterning and guided neurite growth on micropatterned nanofiber platforms

    NASA Astrophysics Data System (ADS)

    Malkoc, Veysi; Gallego-Perez, Daniel; Nelson, Tyler; Lannutti, John J.; Hansford, Derek J.

    2015-12-01

    Patterning neuronal cells and guiding neurite growth are important for applications such as prosthetics, cell based biosensors, and tissue engineering. In this paper, a microdevice is presented that provides neuronal cell patterning and guided neurite growth on a collagen coated gelatin/PCL nanofiber mat. The pattern consisted of a grid of polystyrene microwells/nodes to confine the cell bodies and orthogonal grooves to guide neurite growth from each node. Vacuum assisted cell seeding was used to localize cell bodies in the microwells and physically separate the cells during seeding. The electrospun nanofiber mats under the polystyrene microstructures were coated with collagen to enhance the cellular attachment and enhance differentiation. We evaluated the performance of our device using adhesion, viability, and differentiation assays of neuron-like PC12 cells compared to controls for vacuum seeding, spatial isolation and guidance, and collagen coating of the fibers. The device provided PC12 cell patterning with increased adhesion, differentiation, and guided neurite outgrowth compared to controls, demonstrating its potential for in vitro neuronal cell patterning studies.

  5. Patterned growth of neuronal cells on modified diamond-like carbon substrates.

    PubMed

    Kelly, Stephen; Regan, Edward M; Uney, James B; Dick, Andrew D; McGeehan, Joseph P; Mayer, Eric J; Claeyssens, Frederik

    2008-06-01

    Diamond-like carbon (DLC) has been explored as a biomaterial with potential use for coating implantable devices and surgical instruments. In this study the interaction of DLC with mammalian neuronal cells has been studied along with its modifications to improve its function as a biomaterial. We describe the use of DLC, oxidised DLC and phosphorus-doped DLC to support the growth and survival of primary central nervous system neurones and neuroblastoma cells. None of these substrates were cytotoxic and primary neurones adhered better to phosphorus-doped DLC than unmodified DLC. This property was used to culture cortical neurones in a predetermined micropattern. This raises the potential of DLC as a biomaterial for central nervous system (CNS) implantation. Furthermore, patterned DLC and phosphorus-doped DLC can direct neuronal growth, generating a powerful tool to study neuronal networks in a spatially distinct way. This study reports the generation of nerve cell patterns via patterned deposition of DLC. PMID:18359076

  6. Using Si(100) - 2 x 1:H as a Platform for Patterned Silicon Growth

    NASA Astrophysics Data System (ADS)

    Sztelle, Matthew M.; Schmucker, Scott W.; Lyding, Joseph W.

    2006-03-01

    An ultra-high vacuum scanning tunneling microscope (UHV-STM) is used to create patterns at the atomic level by desorbing hydrogen atoms from the Si(100) -- 2 x 1:H surface thereby creating a clean silicon template for selective area chemical vapor deposition (CVD). Disilane (Si2H6) gas, when introduced, repassivates the clean silicon pattern with an inert mix of hydride and silicon-hydride species. Subsequent layers can be grown through repeated patterning allowing controlled silicon growth at the nanometer scale. Amorphous silicon growth has been demonstrated at room temperature with nanometer scale control over feature sizes. Results will also be presented on our attempts to grow single crystal silicon features by performing these experiments at elevated temperatures to promote silicon surface diffusion.

  7. Selective Growth of α-Sexithiophene by Using Silicon Oxides Patterns

    PubMed Central

    Albonetti, Cristiano; Barbalinardo, Marianna; Milita, Silvia; Cavallini, Massimiliano; Liscio, Fabiola; Moulin, Jean-François; Biscarini, Fabio

    2011-01-01

    A process for fabricating ordered organic films on large area is presented. The process allows growing sexithiophene ultra-thin films at precise locations on patterned Si/SiOx substrates by driving the orientation of growth. This process combines the parallel local anodic oxidation of Si/SiOx substrates with the selective arrangement of molecular ultra-thin film. The former is used to fabricate silicon oxide arrays of parallel lines of 400 nm in width over an area of 1 cm2. Selective growth arises from the interplay between kinetic growth parameters and preferential interactions with the patterned surface. The result is an ultra-thin film of organic molecules that is conformal to the features of the fabricated motives. PMID:22016622

  8. Pattern Selection in Plants: Coupling Chemical Dynamics to Surface Growth in Three Dimensions

    PubMed Central

    Holloway, David M.; Harrison, Lionel G.

    2008-01-01

    Background and Aims A study is made by computation of the interplay between the pattern formation of growth catalysts on a plant surface and the expansion of the surface to generate organismal shape. Consideration is made of the localization of morphogenetically active regions, and the occurrence within them of symmetry-breaking processes such as branching from an initially dome-shaped tip or meristem. Representation of a changing and growing three-dimensional shape is necessary, as two-dimensional work cannot distinguish, for example, formation of an annulus from dichotomous branching. Methods For the formation of patterns of chemical concentrations, the Brusselator reaction-diffusion model is used, applied on a hemispherical shell and generating patterns that initiate as surface spherical harmonics. The initial shape is hemispherical, represented as a mesh of triangles. These are combined into finite elements, each made up of all the triangles surrounding each node. Chemical pattern is converted into shape change by moving nodes outwards according to the concentration of growth catalyst at each, to relieve misfits caused by area increase of the finite element. New triangles are added to restore the refinement of the mesh in rapidly growing regions. Key Results The postulated mechanism successfully generates: tip growth (or stalk extension by an apical meristem) to ten times original hemisphere height; tip flattening and resumption of apical advance; and dichotomous branching and higher-order branching to make whorled structures. Control of the branching plane in successive dichotomous branchings is tackled with partial success and clarification of the issues. Conclusions The representation of a growing plant surface in computations by an expanding mesh that has no artefacts constraining changes of shape and symmetry has been achieved. It is shown that one type of pattern-forming mechanism, Turing-type reaction-diffusion, acting within a surface to pattern a

  9. [Use of PubMed to improve evidence-based medicine in routine urological practice].

    PubMed

    Rink, M; Kluth, L A; Shariat, S F; Chun, F K; Fisch, M; Dahm, P

    2013-03-01

    Applying evidence-based medicine in daily clinical practice is the basis of patient-centered medicine and knowledge of accurate literature acquisition skills is necessary for informed clinical decision-making. PubMed is an easy accessible, free bibliographic database comprising over 21 million citations from the medical field, life-science journals and online books. The article summarizes the effective use of PubMed in routine urological clinical practice based on a common case scenario. This article explains the simple use of PubMed to obtain the best search results with the highest evidence. Accurate knowledge about the use of PubMed in routine clinical practice can improve evidence-based medicine and also patient treatment. PMID:23503794

  10. Patterning Expression of Regenerative Growth Factors Using High Intensity Focused Ultrasound

    PubMed Central

    Wilson, Christopher G.; Martín-Saavedra, Francisco M.; Padilla, Frédéric; Fabiilli, Mario L.; Zhang, Man; Baez, Alexander M.; Bonkowski, Christopher J.; Kripfgans, Oliver D.; Voellmy, Richard; Vilaboa, Nuria; Fowlkes, J. Brian

    2014-01-01

    Temporal and spatial control of growth factor gradients is critical for tissue patterning and differentiation. Reinitiation of this developmental program is also required for regeneration of tissues during wound healing and tissue regeneration. Devising methods for reconstituting growth factor gradients remains a central challenge in regenerative medicine. In the current study we develop a novel gene therapy approach for temporal and spatial control of two important growth factors in bone regeneration, vascular endothelial growth factor, and bone morphogenetic protein 2, which involves application of high intensity focused ultrasound to cells engineered with a heat-activated- and ligand-inducible gene switch. Induction of transgene expression was tightly localized within cell-scaffold constructs to subvolumes of ∼30 mm3, and the amplitude and projected area of transgene expression was tuned by the intensity and duration of ultrasound exposure. Conditions for ultrasound-activated transgene expression resulted in minimal cytotoxicity and scaffold damage. Localized regions of growth factor expression also established gradients in signaling activity, suggesting that patterns of growth factor expression generated by this method will have utility in basic and applied studies on tissue development and regeneration. PMID:24460731

  11. Patterning expression of regenerative growth factors using high intensity focused ultrasound.

    PubMed

    Wilson, Christopher G; Martín-Saavedra, Francisco M; Padilla, Frédéric; Fabiilli, Mario L; Zhang, Man; Baez, Alexander M; Bonkowski, Christopher J; Kripfgans, Oliver D; Voellmy, Richard; Vilaboa, Nuria; Fowlkes, J Brian; Franceschi, Renny T

    2014-10-01

    Temporal and spatial control of growth factor gradients is critical for tissue patterning and differentiation. Reinitiation of this developmental program is also required for regeneration of tissues during wound healing and tissue regeneration. Devising methods for reconstituting growth factor gradients remains a central challenge in regenerative medicine. In the current study we develop a novel gene therapy approach for temporal and spatial control of two important growth factors in bone regeneration, vascular endothelial growth factor, and bone morphogenetic protein 2, which involves application of high intensity focused ultrasound to cells engineered with a heat-activated- and ligand-inducible gene switch. Induction of transgene expression was tightly localized within cell-scaffold constructs to subvolumes of ∼30 mm³, and the amplitude and projected area of transgene expression was tuned by the intensity and duration of ultrasound exposure. Conditions for ultrasound-activated transgene expression resulted in minimal cytotoxicity and scaffold damage. Localized regions of growth factor expression also established gradients in signaling activity, suggesting that patterns of growth factor expression generated by this method will have utility in basic and applied studies on tissue development and regeneration. PMID:24460731

  12. Eye Size at Birth in Prosimian Primates: Life History Correlates and Growth Patterns

    PubMed Central

    Cummings, Joshua R.; Muchlinski, Magdalena N.; Kirk, E. Christopher; Rehorek, Susan J.; DeLeon, Valerie B.; Smith, Timothy D.

    2012-01-01

    Background Primates have large eyes relative to head size, which profoundly influence the ontogenetic emergence of facial form. However, growth of the primate eye is only understood in a narrow taxonomic perspective, with information biased toward anthropoids. Methodology/Principal Findings We measured eye and bony orbit size in perinatal prosimian primates (17 strepsirrhine taxa and Tarsius syrichta) to infer the extent of prenatal as compared to postnatal eye growth. In addition, multiple linear regression was used to detect relationships of relative eye and orbit diameter to life history variables. ANOVA was used to determine if eye size differed according to activity pattern. In most of the species, eye diameter at birth measures more than half of that for adults. Two exceptions include Nycticebus and Tarsius, in which more than half of eye diameter growth occurs postnatally. Ratios of neonate/adult eye and orbit diameters indicate prenatal growth of the eye is actually more rapid than that of the orbit. For example, mean neonatal transverse eye diameter is 57.5% of the adult value (excluding Nycticebus and Tarsius), compared to 50.8% for orbital diameter. If Nycticebus is excluded, relative gestation age has a significant positive correlation with relative eye diameter in strepsirrhines, explaining 59% of the variance in relative transverse eye diameter. No significant differences were found among species with different activity patterns. Conclusions/Significance The primate developmental strategy of relatively long gestations is probably tied to an extended period of neural development, and this principle appears to apply to eye growth as well. Our findings indicate that growth rates of the eye and bony orbit are disassociated, with eyes growing faster prenatally, and the growth rate of the bony orbit exceeding that of the eyes after birth. Some well-documented patterns of orbital morphology in adult primates, such as the enlarged orbits of nocturnal species

  13. Spatially controlled simultaneous patterning of multiple growth factors in three-dimensional hydrogels

    NASA Astrophysics Data System (ADS)

    Wylie, Ryan G.; Ahsan, Shoeb; Aizawa, Yukie; Maxwell, Karen L.; Morshead, Cindi M.; Shoichet, Molly S.

    2011-10-01

    Three-dimensional (3D) protein-patterned scaffolds provide a more biomimetic environment for cell culture than traditional two-dimensional surfaces, but simultaneous 3D protein patterning has proved difficult. We developed a method to spatially control the immobilization of different growth factors in distinct volumes in 3D hydrogels, and to specifically guide differentiation of stem/progenitor cells therein. Stem-cell differentiation factors sonic hedgehog (SHH) and ciliary neurotrophic factor (CNTF) were simultaneously immobilized using orthogonal physical binding pairs, barnase-barstar and streptavidin-biotin, respectively. Barnase and streptavidin were sequentially immobilized using two-photon chemistry for subsequent concurrent complexation with fusion proteins barstar-SHH and biotin-CNTF, resulting in bioactive 3D patterned hydrogels. The technique should be broadly applicable to the patterning of a wide range of proteins.

  14. Unraveling a generic growth pattern in structure evolution of thiolate-protected gold nanoclusters

    NASA Astrophysics Data System (ADS)

    Xu, Wen Wu; Li, Yadong; Gao, Yi; Zeng, Xiao Cheng

    2016-03-01

    Precise control of the growth of thiolate-protected gold nanoclusters is a prerequisite for their applications in catalysis and bioengineering. Here, we bring to bear a new series of thiolate-protected nanoclusters with a unique growth pattern, i.e., Au20(SR)16, Au28(SR)20, Au36(SR)24, Au44(SR)28, and Au52(SR)32. These nanoclusters can be viewed as resulting from the stepwise addition of a common structural motif [Au8(SR)4]. The highly negative values of the nucleus-independent chemical shift (NICS) in the center of the tetrahedral Au4 units suggest that the overall stabilities of these clusters stem from the local stability of each tetrahedral Au4 unit. Generalization of this growth-pattern rule to large-sized nanoclusters allows us to identify the structures of three new thiolate-protected nanoclusters, namely, Au60(SR)36, Au68(SR)40, and Au76(SR)44. Remarkably, all three large-sized nanoclusters possess relatively large HOMO-LUMO gaps and negative NICS values, suggesting their high chemical stability. Further extension of the growth-pattern rule to the infinitely long nanowire limit results in a one-dimensional (1D) thiolate-protected gold nanowire (RS-AuNW) with a band gap of 0.78 eV. Such a unique growth-pattern rule offers a guide for precise synthesis of a new class of large-sized thiolate-protected gold nanoclusters or even RS-AuNW which, to our knowledge, has not been reported in the literature.Precise control of the growth of thiolate-protected gold nanoclusters is a prerequisite for their applications in catalysis and bioengineering. Here, we bring to bear a new series of thiolate-protected nanoclusters with a unique growth pattern, i.e., Au20(SR)16, Au28(SR)20, Au36(SR)24, Au44(SR)28, and Au52(SR)32. These nanoclusters can be viewed as resulting from the stepwise addition of a common structural motif [Au8(SR)4]. The highly negative values of the nucleus-independent chemical shift (NICS) in the center of the tetrahedral Au4 units suggest that the overall

  15. A simple method for understanding the triangular growth patterns of transition metal dichalcogenide sheets

    NASA Astrophysics Data System (ADS)

    Zhu, Siya; Wang, Qian

    2015-10-01

    Triangular nanoflake growth patterns have been commonly observed in synthesis of transition metal dichalcogenide sheets and their hybrid structures. Triangular nanoflakes not only show exceptional properties, but also can serve as building blocks for two or three dimensional structures. In this study, taking the MoS2 system as a test case, we propose a Matrix method to understand the mechanism of such unique growth pattern. Nanoflakes with different edge types are mathematically described with configuration matrices, and the total formation energy is calculated as the sum of the edge formation energies and the chemical potentials of sulfur and molybdenum. Based on energetics, we find that three triangular patterns with the different edge configurations are energetically more favorable in different ranges of the chemical potential of sulfur, which are in good agreement with experimental observations. Our algorithm has high efficiency and can deal with nanoflakes in microns which are beyond the ability of ab-initio method. This study not only elucidates the mechanism of triangular nanoflake growth patterns in experiment, but also provides a clue to control the geometric configurations in synthesis.

  16. A simple method for understanding the triangular growth patterns of transition metal dichalcogenide sheets

    SciTech Connect

    Zhu, Siya; Wang, Qian

    2015-10-15

    Triangular nanoflake growth patterns have been commonly observed in synthesis of transition metal dichalcogenide sheets and their hybrid structures. Triangular nanoflakes not only show exceptional properties, but also can serve as building blocks for two or three dimensional structures. In this study, taking the MoS{sub 2} system as a test case, we propose a Matrix method to understand the mechanism of such unique growth pattern. Nanoflakes with different edge types are mathematically described with configuration matrices, and the total formation energy is calculated as the sum of the edge formation energies and the chemical potentials of sulfur and molybdenum. Based on energetics, we find that three triangular patterns with the different edge configurations are energetically more favorable in different ranges of the chemical potential of sulfur, which are in good agreement with experimental observations. Our algorithm has high efficiency and can deal with nanoflakes in microns which are beyond the ability of ab-initio method. This study not only elucidates the mechanism of triangular nanoflake growth patterns in experiment, but also provides a clue to control the geometric configurations in synthesis.

  17. Patterned growth of carbon nanotubes obtained by high density plasma chemical vapor deposition

    NASA Astrophysics Data System (ADS)

    Mousinho, A. P.; Mansano, R. D.

    2015-03-01

    Patterned growth of carbon nanotubes by chemical vapor deposition represents an assembly approach to place and orient nanotubes at a stage as early as when they are synthesized. In this work, the carbon nanotubes were obtained at room temperature by High Density Plasmas Chemical Vapor Deposition (HDPCVD) system. This CVD system uses a new concept of plasma generation, where a planar coil coupled to an RF system for plasma generation was used with an electrostatic shield for plasma densification. In this mode, high density plasmas are obtained. We also report the patterned growth of carbon nanotubes on full 4-in Si wafers, using pure methane plasmas and iron as precursor material (seed). Photolithography processes were used to pattern the regions on the silicon wafers. The carbon nanotubes were characterized by micro-Raman spectroscopy, the spectra showed very single-walled carbon nanotubes axial vibration modes around 1590 cm-1 and radial breathing modes (RBM) around 120-400 cm-1, confirming that high quality of the carbon nanotubes obtained in this work. The carbon nanotubes were analyzed by atomic force microscopy and scanning electron microscopy too. The results showed that is possible obtain high-aligned carbon nanotubes with patterned growth on a silicon wafer with high reproducibility and control.

  18. Estimated in vivo postnatal surface growth patterns of the ovine main pulmonary artery and ascending aorta.

    PubMed

    Fata, Bahar; Gottlieb, Danielle; Mayer, John E; Sacks, Michael S

    2013-07-01

    Delineating the normal postnatal development of the pulmonary artery (PA) and ascending aorta (AA) can inform our understanding of congenital abnormalities, as well as pulmonary and systolic hypertension. We thus conducted the following study to delineate the PA and AA postnatal growth deformation characteristics in an ovine model. MR images were obtained from endoluminal surfaces of 11 animals whose ages ranged from 1.5 months/15.3 kg mass (very young) to 12 months/56.6 kg mass (adult). A bicubic Hermite finite element surface representation was developed for the each artery from each animal. Under the assumption that the relative locations of surface points were retained during growth, the individual animal surface fits were subsequently used to develop a method to estimate the time-evolving local effective surface growth (relative to the youngest measured animal) in the end-diastolic state. Results indicated that the spatial and temporal surface growth deformation patterns of both arteries, especially in the circumferential direction, were heterogeneous, leading to an increase in taper and increase in cross-sectional ellipticity of the PA. The longitudinal PA growth stretch of a large segment on the posterior wall reached 2.57 ± 0.078 (mean ± SD) at the adult stage. In contrast, the longitudinal growth of the AA was smaller and more uniform (1.80 ± 0.047). Interestingly, a region of the medial wall of both arteries where both arteries are in contact showed smaller circumferential growth stretches-specifically 1.12 ± 0.012 in the PA and 1.43 ± 0.071 in the AA at the adult stage. Overall, our results indicated that contact between the PA and AA resulted in increasing spatial heterogeneity in postnatal growth, with the PA demonstrating the greatest changes. Parametric studies using simplified geometric models of curved arteries during growth suggest that heterogeneous effective surface growth deformations must occur to account for the

  19. Morphogen-based simulation model of ray growth and joint patterning during fin development and regeneration.

    PubMed

    Rolland-Lagan, Anne-Gaëlle; Paquette, Mathieu; Tweedle, Valerie; Akimenko, Marie-Andrée

    2012-03-01

    The fact that some organisms are able to regenerate organs of the correct shape and size following amputation is particularly fascinating, but the mechanism by which this occurs remains poorly understood. The zebrafish (Danio rerio) caudal fin has emerged as a model system for the study of bone development and regeneration. The fin comprises 16 to 18 bony rays, each containing multiple joints along its proximodistal axis that give rise to segments. Experimental observations on fin ray growth, regeneration and joint formation have been described, but no unified theory has yet been put forward to explain how growth and joint patterns are controlled. We present a model for the control of fin ray growth during development and regeneration, integrated with a model for joint pattern formation, which is in agreement with published, as well as new, experimental data. We propose that fin ray growth and joint patterning are coordinated through the interaction of three morphogens. When the model is extended to incorporate multiple rays across the fin, it also accounts for how the caudal fin acquires its shape during development, and regains its correct size and shape following amputation. PMID:22318227

  20. Quantifying Two-Dimensional Filamentous and Invasive Growth Spatial Patterns in Yeast Colonies

    PubMed Central

    Binder, Benjamin J.; Sundstrom, Joanna F.; Gardner, Jennifer M.; Jiranek, Vladimir; Oliver, Stephen G.

    2015-01-01

    The top-view, two-dimensional spatial patterning of non-uniform growth in a Saccharomyces cerevisiae yeast colony is considered. Experimental images are processed to obtain data sets that provide spatial information on the cell-area that is occupied by the colony. A method is developed that allows for the analysis of the spatial distribution with three metrics. The growth of the colony is quantified in both the radial direction from the centre of the colony and in the angular direction in a prescribed outer region of the colony. It is shown that during the period of 100–200 hours from the start of the growth of the colony there is an increasing amount of non-uniform growth. The statistical framework outlined in this work provides a platform for comparative quantitative assays of strain-specific mechanisms, with potential implementation in inferencing algorithms used for parameter-rate estimation. PMID:25719406

  1. [Postnatal growth patterns in eight species of herons and egrets (Ciconiiformes: Ardeidae)].

    PubMed

    Avila, Dennis Denis

    2011-06-01

    Avian postnatal growth has received considerable attention and its ecological implications have been deeply analyzed. In this current paper, I describe the patterns of culmen and tarsus growth, as well as of weight gain patterns in eight species of herons and egrets (Aves: Ardeidae) found in the Birama Swamp in Eastern Cuba. Between 1998 and 2006,714 nestlings of the following species were measured every two days: Butorides virescens, Bubulcus ibis, Egretta thula, E. tricolor, E. caerulea, E. rufescens, Ardea alba and Nycticorax nycticorax. Logistic and Gompertz equations were adjusted to data using non-lineal regression models with adult values as the asymptote. For each species, the following were determined and recorded: growth rate, age at inflexion, instantaneous growth rates at each age interval, and time taken to reach 90% of adult size. Reported hatchling sizes were similar in other localities, with a variation coefficient ranging between 10-19%. At hatch, each species exhibited differing sizes relative to adult values. In all cases, Gompertz equations were best fitted to explain more variance and lesser residuals. Rates of weight change and tarsus growth were alometrically related to the log of adult weight. Two main growth processes were identified: a physical extension in dimensions of each measurement reflecting inter-specific morphometric differences, and a lineal increase of the growth period from Green Heron to Great Egret. The Black-crowned Night Heron, Cattle Egret and Reddish Egret exhibited some unique measurement characteristics in comparison to the remaining members of the family. All results support the hypothesis that hypermorphosis, as the main evolutionary process in the microevolution of Ardeidae, is caused by a delayed final moment of growth. PMID:21721238

  2. Growth plate cartilage shows different strain patterns in response to static versus dynamic mechanical modulation.

    PubMed

    Kaviani, Rosa; Londono, Irene; Parent, Stefan; Moldovan, Florina; Villemure, Isabelle

    2016-08-01

    Longitudinal growth of long bones and vertebrae occurs in growth plate cartilage. This process is partly regulated by mechanical forces, which are one of the underlying reasons for progression of growth deformities such as idiopathic adolescent scoliosis and early-onset scoliosis. This concept of mechanical modulation of bone growth is also exploited in the development of fusionless treatments of these deformities. However, the optimal loading condition for the mechanical modulation of growth plate remains to be identified. The objective of this study was to evaluate the effects of in vitro static versus dynamic modulation and of dynamic loading parameters, such as frequency and amplitude, on the mechanical responses and histomorphology of growth plate explants. Growth plate explants from distal ulnae of 4-week-old swines were extracted and randomly distributed among six experimental groups: baseline ([Formula: see text]), control ([Formula: see text]), static ([Formula: see text]) and dynamic ([Formula: see text]). For static and dynamic groups, mechanical modulation was performed in vitro using an Indexed CartiGen bioreactor. A stress relaxation test combined with confocal microscopy and digital image correlation was used to characterize the mechanical responses of each explant in terms of peak stress, equilibrium stress, equilibrium modulus of elasticity and strain pattern. Histomorphometrical measurements were performed on toluidine blue tissue sections using a semi-automatic custom-developed MATLAB toolbox. Results suggest that compared to dynamic modulation, static modulation changes the strain pattern of the tissue and thus is more detrimental for tissue biomechanics, while the histomorphological parameters are not affected by mechanical modulation. Also, under dynamic modulation, changing the frequency or amplitude does not affect the biomechanical response of the tissue. Results of this study will be useful in finding optimal and non-damaging parameters

  3. Control of bacterial adhesion and growth on honeycomb-like patterned surfaces.

    PubMed

    Yang, Meng; Ding, Yonghui; Ge, Xiang; Leng, Yang

    2015-11-01

    It is a great challenge to construct a persistent bacteria-resistant surface even though it has been demonstrated that several surface features might be used to control bacterial behavior, including surface topography. In this study, we develop micro-scale honeycomb-like patterns of different sizes (0.5-10 μm) as well as a flat area as the control on a single platform to evaluate the bacterial adhesion and growth. Bacteria strains, Escherichia coli and Staphylococcus aureus with two distinct shapes (rod and sphere) are cultured on the platforms, with the patterned surface-up and surface-down in the culture medium. The results demonstrate that the 1 μm patterns remarkably reduce bacterial adhesion and growth while suppressing bacterial colonization when compared to the flat surface. The selective adhesion of the bacterial cells on the patterns reveals that the bacterial adhesion is cooperatively mediated by maximizing the cell-substrate contact area and minimizing the cell deformation, from a thermodynamic point of view. Moreover, study of bacterial behaviors on the surface-up vs. surface-down samples shows that gravity does not apparently affect the spatial distribution of the adherent cells although it indeed facilitates bacterial adhesion. Furthermore, the experimental results suggest that two major factors, i.e. the availability of energetically favorable adhesion sites and the physical confinements, contribute to the anti-bacterial nature of the honeycomb-like patterns. PMID:26302067

  4. Instability growth patterns of a shock-accelerated thin fluid layer

    SciTech Connect

    Jacobs, J.W. ); Klein, D.L.; Jenkins, D.G.; Benjamin, R.F. )

    1993-02-01

    Laser-induced fluorescence imaging of a shock-accelerated thin gas layer, produced by a planar SF[sub 6] jet in air, shows multiple flow evolutions. Richtmyer-Meshkov instability causes spatially periodic perturbations initially imposed on the jet to develop into one of three distinct flow patterns, indicating nonlinear instability growth. Slight differences in the vorticity distribution deposited on the air-SF[sub 6] interfaces by the shock interaction produce a bifurcated flow, observed as mushroom-shaped or sinuous-shaped interfacial patterns.

  5. Self-Assembly, Pattern Formation and Growth Phenomena in Nano-Systems

    NASA Astrophysics Data System (ADS)

    Golovin, Alexander A.; Nepomnyashchy, Alexander A.

    Nano-science and nano-technology are rapidly developing scientific and technological areas that deal with physical, chemical and biological processes that occur on nano-meter scale -- one millionth of a millimeter. Self-organization and pattern formation play crucial role on nano-scales and promise new, effective routes to control various nano-scales processes. This book contains lecture notes written by the lecturers of the NATO Advanced Study Institute "Self-Assembly, Pattern Formation and Growth Phenomena in Nano-Systems" that took place in St Etienne de Tinee, France, in the fall 2004.

  6. Flexible and fixed mathematical models describing growth patterns of chukar partridges

    NASA Astrophysics Data System (ADS)

    Aygün, Ali; Narinç, Doǧan

    2016-04-01

    In animal science, the nonlinear regression models for growth curve analysis ofgrowth patterns are separated into two groups called fixed and flexible according to their point of inflection. The aims of this study were to compare fixed and flexible growth functions and to determine the best fit model for the growth data of chukar partridges. With this aim, the growth data of partridges were modeled with widely used models, such as Gompertz, Logistic, Von Bertalanffy as well as the flexible functions, such as, Richards, Janoschek, Levakovich. So as to evaluate growth functions, the R2 (coefficient of determination), adjusted R2 (adjusted coefficient of determination), MSE (mean square error), AIC (Akaike's information criterion) and BIC (Bayesian information criterion) goodness of fit criteria were used. It has been determined that the best fit model from the point of chukar partridge growth data according to mentioned goodness of fit criteria is Janoschek function which has a flexible structure. The Janoschek model is not only important because it has a higher number of parameters with biological meaning than the other functions (the mature weight and initial weight parameters), but also because it was not previously used in the modeling of the chukar partridge growth.

  7. Self-organized MBE growth of II VI epilayers on patterned GaSb substrates

    NASA Astrophysics Data System (ADS)

    Wissmann, H.; Tran Anh, T.; Rogaschewski, S.; von Ortenberg, M.

    1999-05-01

    We report on the self-organized MBE growth of II-VI epilayers on patterned and unpatterned GaSb substrates resulting in quantum wires and quantum wells, respectively. The HgSe : Fe quantum wires were grown on (0 0 1)GaSb substrates with a buffer of lattice-matched ZnTe 1- xSe x. Due to the anisotropic growth of HgSe on the A-oriented stripes roof-like overgrowth with a definite ridge was obtained. Additional Fe doping in the direct vicinity of the ridge results in a highly conductive quantum wire.

  8. Divergent selection for shape of growth curve in Japanese quail. 5. Growth pattern and low protein level in starter diet.

    PubMed

    Hyankova, L; Knizetova, H

    2009-07-01

    1. The effect of crude protein (CP) concentration in starter diet (259 or 216 g CP and 11.7 MJ ME/kg, fed from 0 to 21 d of age) on postnatal growth pattern (from hatching to 70 d of age) was analysed in Japanese quail lines divergently selected for high (HG) and low (LG) relative gain of body weight (BW) between 11 and 28 d of age, and constant BW at 49 d of age. 2. Males and females of both lines fed on the low CP diet showed a transient BW retardation between 7 and 28 d of age, and 7 and 35 d of age, respectively, when compared with their counterparts receiving the standard CP diet. 3. Although the negative effect of low CP concentration on growth rate was observed in both lines, a lower tolerance of young HG vs. LG quail to the reduction of CP level in food was evident from their (i) stronger BW retardation at 14 d of age (16 vs. 7%), (ii) more delayed onset of compensatory growth (21 vs. 7 d of age) and (iii) greater prolongation of the acceleration growth phase (3 vs. 1 d of age) following insufficient dietary CP. 4. The line differences in early growth rate were accompanied by significant differences in food intake. The LG line consumed more food than the HG line on both CP diets and consumption was not influenced by food quality. In contrast, HG quail reduced food intake with the decrease of dietary CP concentration. On both CP diets, this was associated with a higher body fatness of LG vs. HG quail. 5. The protein-deficient food could thus represent an important factor contributing to the selection advantage of developmentally accelerated genotypes during the selection for high BW in young age categories. PMID:19735014

  9. Template-Assisted Direct Growth of 1 Td/in(2) Bit Patterned Media.

    PubMed

    Yang, En; Liu, Zuwei; Arora, Hitesh; Wu, Tsai-Wei; Ayanoor-Vitikkate, Vipin; Spoddig, Detlef; Bedau, Daniel; Grobis, Michael; Gurney, Bruce A; Albrecht, Thomas R; Terris, Bruce

    2016-07-13

    We present a method for growing bit patterned magnetic recording media using directed growth of sputtered granular perpendicular magnetic recording media. The grain nucleation is templated using an epitaxial seed layer, which contains Pt pillars separated by amorphous metal oxide. The scheme enables the creation of both templated data and servo regions suitable for high density hard disk drive operation. We illustrate the importance of using a process that is both topographically and chemically driven to achieve high quality media. PMID:27295317

  10. Non-equilibrium growth patterns of carbohydrate and saccharin in gel media

    NASA Astrophysics Data System (ADS)

    Das, Ishwar; Sharma, Archana; Kumar, Anuj; Lall, R. S.

    1997-02-01

    Non-equilibrium growth patterns of mono-, di-saccharides and a sweetener saccharin have been developed on microslides in the presence of a dense matrix. Scanned pictures were analyzed and fractal dimensions calculated by a box counting method. Morphologies and fractal dimension were found to depend on the compound-dense matrix composition. In case of di-saccharides, the morphology depends on a linkage between the monomer units.

  11. Selective growth of ZnO nanowires on substrates patterned by photolithography and inkjet printing

    NASA Astrophysics Data System (ADS)

    Laurenti, M.; Verna, A.; Fontana, M.; Quaglio, M.; Porro, S.

    2014-05-01

    Zinc oxide nanowires (ZnO NWs) were grown by a two-step growth method, involving the deposition of a patterned ZnO thin seeding layer and the chemical vapor deposition (CVD) of ZnO NWs. Two ways of patterning the seed layer were performed. The seeding solution containing ZnO precursors was deposited by sol-gel/spin-coating technique and patterned by photolithography. In the other case, the seeding solution was directly printed by inkjet printing only on selected portion of the substrate areas. In both cases, crystallization of the seed layer was achieved by thermal annealing in ambient air. Vertically aligned ZnO NWs were then grown by CVD on patterned, seeded substrates. The structure and morphology of ZnO NWs was analyzed by means of X-ray diffraction and field emission scanning electron microscopy measurements, respectively, while the vibrational properties were evaluated through Raman spectroscopy. Results showed that less-defective, vertically aligned, c-axis oriented ZnO NWs were grown on substrates patterned by photolithography while more defective nanostructures were grown on printed seed layer. A feature size of 30 µm was transferred into the patterned seed layer, and a good selectivity in growing ZnO NWs was obtained.

  12. Tree growth rates in an Amazonian evergreen forest: seasonal patterns and correlations with leaf phenology

    NASA Astrophysics Data System (ADS)

    Wu, J.; Silva Campos, K.; Prohaska, N.; Ferreira, M. L.; Nelson, B. W.; Saleska, S. R.; da Silva, R.

    2014-12-01

    Metabolism and phenology of tropical forests significantly influence global dynamics of climate, carbon and water. However, there is still lack of mechanistic understanding of the controls on tropical forest metabolism, particularly at individual tree level. In this study, we are interested in investigating (1) what is the seasonal pattern of woody growth for tropical trees and (2) what is the mechanistic controls onwoody growth at individual level?To explore the above questions,we use two data sources from an evergreen tropical forest KM67 site (near Santarem, Brazil). They are: (1) image time series from a tower mounted RGB imaging system, with images recordedin10 minutes interval since October 2013.Images near local noon homogeneous diffuse lighting were selectedfor leaf phenologymonitoring; (2) ground based bi-weekly biometry survey (via dendrometry band technique) for 25 trees from random sampling since September 2013. 12 among 25 trees are within the tower mounted camera image view. Our preliminary resultsdemonstrate that 20 trees among 25 trees surveyed significantly increase woody growth (or "green up") in dry season. Our results also find thatamong those 20 trees, 12 trees reaches the maximum woody increment rate in late dry season with a mean DBH (Diameter at Breast Height) around 30 cm,while 8 trees reaching the maximum in the middle of wet season, with a mean DBH around 90 cm. This study,though limited in the sample size, mightprovide another line of evidence that Amazon rainforests "green up" in dry season. As for mechanistic controls on tropical tree woody control, we hypothesize both climate and leaf phenology control individual woody growth. We would like to link both camera based leaf phenology and climate data in the next to explorethe reason as to the pattern found in this study that bigger trees might have different seasonal growth pattern as smaller trees.

  13. MET network in PubMed: a text-mined network visualization and curation system

    PubMed Central

    Dai, Hong-Jie; Su, Chu-Hsien; Lai, Po-Ting; Huang, Ming-Siang; Jonnagaddala, Jitendra; Rose Jue, Toni; Rao, Shruti; Chou, Hui-Jou; Milacic, Marija; Singh, Onkar; Syed-Abdul, Shabbir; Hsu, Wen-Lian

    2016-01-01

    Metastasis is the dissemination of a cancer/tumor from one organ to another, and it is the most dangerous stage during cancer progression, causing more than 90% of cancer deaths. Improving the understanding of the complicated cellular mechanisms underlying metastasis requires investigations of the signaling pathways. To this end, we developed a METastasis (MET) network visualization and curation tool to assist metastasis researchers retrieve network information of interest while browsing through the large volume of studies in PubMed. MET can recognize relations among genes, cancers, tissues and organs of metastasis mentioned in the literature through text-mining techniques, and then produce a visualization of all mined relations in a metastasis network. To facilitate the curation process, MET is developed as a browser extension that allows curators to review and edit concepts and relations related to metastasis directly in PubMed. PubMed users can also view the metastatic networks integrated from the large collection of research papers directly through MET. For the BioCreative 2015 interactive track (IAT), a curation task was proposed to curate metastatic networks among PubMed abstracts. Six curators participated in the proposed task and a post-IAT task, curating 963 unique metastatic relations from 174 PubMed abstracts using MET. Database URL: http://btm.tmu.edu.tw/metastasisway PMID:27242035

  14. Measuring Medical Student Preference: A Comparison of Classroom Versus Online Instruction for Teaching Pubmed*EC

    PubMed Central

    Schimming, Laura M.

    2008-01-01

    Objective: The research analyzed evaluation data to assess medical student satisfaction with the learning experience when required PubMed training is offered entirely online. Methods: A retrospective study analyzed skills assessment scores and student feedback forms from 455 first-year medical students who completed PubMed training either through classroom sessions or an online tutorial. The class of 2006 (n = 99) attended traditional librarian-led sessions in a computer classroom. The classes of 2007 (n = 120), 2008 (n = 121), and 2009 (n = 115) completed the training entirely online through a self-paced tutorial. PubMed skills assessment scores and student feedback about the training were compared for all groups. Results: As evidenced by open-ended comments about the training, students who took the online tutorial were equally or more satisfied with the learning experience than students who attended classroom sessions, with the classes of 2008 and 2009 reporting greater satisfaction (P<0.001) than the other 2 groups. The mean score on the PubMed skills assessment (91%) was the same for all groups of students. Conclusions: Student satisfaction improved and PubMed assessment scores did not change when instruction was offered online to first-year medical students. Comments from the students who received online training suggest that the increased control and individual engagement with the web-based content led to their satisfaction with the online tutorial. PMID:18654658

  15. MET network in PubMed: a text-mined network visualization and curation system.

    PubMed

    Dai, Hong-Jie; Su, Chu-Hsien; Lai, Po-Ting; Huang, Ming-Siang; Jonnagaddala, Jitendra; Rose Jue, Toni; Rao, Shruti; Chou, Hui-Jou; Milacic, Marija; Singh, Onkar; Syed-Abdul, Shabbir; Hsu, Wen-Lian

    2016-01-01

    Metastasis is the dissemination of a cancer/tumor from one organ to another, and it is the most dangerous stage during cancer progression, causing more than 90% of cancer deaths. Improving the understanding of the complicated cellular mechanisms underlying metastasis requires investigations of the signaling pathways. To this end, we developed a METastasis (MET) network visualization and curation tool to assist metastasis researchers retrieve network information of interest while browsing through the large volume of studies in PubMed. MET can recognize relations among genes, cancers, tissues and organs of metastasis mentioned in the literature through text-mining techniques, and then produce a visualization of all mined relations in a metastasis network. To facilitate the curation process, MET is developed as a browser extension that allows curators to review and edit concepts and relations related to metastasis directly in PubMed. PubMed users can also view the metastatic networks integrated from the large collection of research papers directly through MET. For the BioCreative 2015 interactive track (IAT), a curation task was proposed to curate metastatic networks among PubMed abstracts. Six curators participated in the proposed task and a post-IAT task, curating 963 unique metastatic relations from 174 PubMed abstracts using MET.Database URL: http://btm.tmu.edu.tw/metastasisway. PMID:27242035

  16. Successive selective growth of semipolar (11-22) GaN on patterned sapphire substrate

    NASA Astrophysics Data System (ADS)

    Tendille, Florian; Hugues, Maxime; Vennéguès, Philippe; Teisseire, Monique; De Mierry, Philippe

    2015-06-01

    Thanks to the use of two successive selective growths by metal organic chemical vapor deposition reactor, high quality semipolar (11-22) GaN with a homogenous defect repartition over the surface was achieved. The procedure starts with a first selective growth on a patterned sapphire substrate, leading to continuous stripes of three dimensional (3D) GaN crystals of low defect density. Then, a second selective growth step is achieved by depositing a SiNx nano-mask and a low temperature GaN nano-layer on the top of the GaN stripes. Hereby, we demonstrate an original way to obtain a homoepitaxial selective growth on 3D GaN crystals by taking advantage of the different crystallographic planes available. Basal stacking faults (BSFs) are generated during this second selective growth but could be eliminated by using a three-step growth method in which elongated voids are created above the defective area. For a fully coalesced sample grown using the 2 step method, dislocation density of 1.2 × 108 cm-2 and BSFs density of 154 cm-1 with a homogenous distribution have been measured by cathodoluminescence at 80 K. Consequently the material quality of this coalesced semipolar layer is comparable to the one of polar GaN on c-plane sapphire.

  17. Prediction of competitive microbial growth in mixed culture at dynamic temperature patterns.

    PubMed

    Fujikawa, Hiroshi; Sakha, Mohammad Z

    2014-01-01

    A novel competition model developed with the new logistic model and the Lotka-Volterra model successfully predicted the growth of bacteria in mixed culture using the mesophiles Staphylococcus aureus, Escherichia coli, and Salmonella at a constant temperature in our previous studies. In this study, we further studied the prediction of the growth of those bacteria in mixed culture at dynamic temperatures with various initial populations with the competition model. First, we studied the growth kinetics of the species in a monoculture at various constant temperatures ranging from 16℃ to 32℃. With the analyzed data in the monoculture, we then examined the prediction of bacterial growth in mixed culture with two and three species. The growth of the bacteria in the mixed culture at dynamic temperatures was successfully predicted with the model. The residuals between the observed and predicted populations at the data points were <0.5 log at most points, being 83.3% and 84.2% for the two-species mixture and the three-species mixture, respectively. The present study showed that the model could be applied to the competitive growth in mixed culture at dynamic temperature patterns. PMID:25252643

  18. Regularly patterned multi-section GaN nanorod arrays grown with a pulsed growth technique

    NASA Astrophysics Data System (ADS)

    Tu, Charng-Gan; Su, Chia-Ying; Liao, Che-Hao; Hsieh, Chieh; Yao, Yu-Feng; Chen, Hao-Tsung; Lin, Chun-Han; Weng, Chi-Ming; Kiang, Yean-Woei; Yang, C. C.

    2016-01-01

    The growth of regularly patterned multi-section GaN nanorod (NR) arrays based on a pulsed growth technique with metalorganic chemical vapor deposition is demonstrated. Such an NR with multiple sections of different cross-sectional sizes is formed by tapering a uniform cross section to another through stepwise decreasing of the Ga supply duration to reduce the size of the catalytic Ga droplet. Contrast line structures are observed in either a scanning electron microscopy or transmission electron microscopy image of an NR. Such a contrast line-marker corresponds to a thin Ga-rich layer formed at the beginning of GaN precipitation of a pulsed growth cycle and illustrates the boundary between two successive growth cycles in pulsed growth. By analyzing the geometry variation of the contrast line-markers, the morphology evolution in the growth of a multi-section NR, including a tapering process, can be traced. Such a morphology variation is controlled by the size of the catalytic Ga droplet and its coverage range on the slant facets at the top of an NR. The comparison of emission spectra between single-, two-, and three-section GaN NRs with sidewall InGaN/GaN quantum wells indicates that a multi-section NR can lead to a significantly broader sidewall emission spectrum.

  19. Digital Transfer Growth of Patterned 2D Metal Chalcogenides by Confined Nanoparticle Evaporation

    SciTech Connect

    Mahjouri-Samani, Masoud; Tian, Mengkun; Wang, Kai; Boulesbaa, Abdelaziz; Rouleau, Christopher M.; Puretzky, Alexander A.; McGuire, Michael A.; Srijanto, Bernadeta R.; Xiao, Kai; Eres, Gyula; Duscher, Gerd; Geohegan, David B.

    2014-10-19

    Developing methods for the facile synthesis of two-dimensional (2D) metal chalcogenides and other layered materials is crucial for emerging applications in functional devices. Controlling the stoichiometry, number of the layers, crystallite size, growth location, and areal uniformity is challenging in conventional vapor phase synthesis. Here, we demonstrate a new route to control these parameters in the growth of metal chalcogenide (GaSe) and dichalcogenide (MoSe2) 2D crystals by precisely defining the mass and location of the source materials in a confined transfer growth system. A uniform and precise amount of stoichiometric nanoparticles are first synthesized and deposited onto a substrate by pulsed laser deposition (PLD) at room temperature. This source substrate is then covered with a receiver substrate to form a confined vapor transport growth (VTG) system. By simply heating the source substrate in an inert background gas, a natural temperature gradient is formed that evaporates the confined nanoparticles to grow large, crystalline 2D nanosheets on the cooler receiver substrate, the temperature of which is controlled by the background gas pressure. Large monolayer crystalline domains (~ 100 m lateral sizes) of GaSe and MoSe2 are demonstrated, as well as continuous monolayer films through the deposition of additional precursor materials. This novel PLD-VTG synthesis and processing method offers a unique approach for the controlled growth of large-area, metal chalcogenides with a controlled number of layers in patterned growth locations for optoelectronics and energy related applications.

  20. Trophic interactions and population growth rates: describing patterns and identifying mechanisms.

    PubMed Central

    Hudson, Peter J; Dobson, Andy P; Cattadori, Isabella M; Newborn, David; Haydon, Dan T; Shaw, Darren J; Benton, Tim G; Grenfell, Bryan T

    2002-01-01

    While the concept of population growth rate has been of central importance in the development of the theory of population dynamics, few empirical studies consider the intrinsic growth rate in detail, let alone how it may vary within and between populations of the same species. In an attempt to link theory with data we take two approaches. First, we address the question 'what growth rate patterns does theory predict we should see in time-series?' The models make a number of predictions, which in general are supported by a comparative study between time-series of harvesting data from 352 red grouse populations. Variations in growth rate between grouse populations were associated with factors that reflected the quality and availability of the main food plant of the grouse. However, while these results support predictions from theory, they provide no clear insight into the mechanisms influencing reductions in population growth rate and regulation. In the second part of the paper, we consider the results of experiments, first at the individual level and then at the population level, to identify the important mechanisms influencing changes in individual productivity and population growth rate. The parasitic nematode Trichostrongylus tenuis is found to have an important influence on productivity, and when incorporated into models with their patterns of distribution between individuals has a destabilizing effect and generates negative growth rates. The hypothesis that negative growth rates at the population level were caused by parasites was demonstrated by a replicated population level experiment. With a sound and tested model framework we then explore the interaction with other natural enemies and show that in general they tend to stabilize variations in growth rate. Interestingly, the models show selective predators that remove heavily infected individuals can release the grouse from parasite-induced regulation and allow equilibrium populations to rise. By contrast, a

  1. Patterned epitaxial vapor-liquid-solid growth of silicon nanowires on Si(111) using silane

    NASA Astrophysics Data System (ADS)

    Schmid, H.; Björk, M. T.; Knoch, J.; Riel, H.; Riess, W.; Rice, P.; Topuria, T.

    2008-01-01

    We have carried out a detailed study on the vapour-liquid-solid growth of silicon nanowires (SiNWs) on (111)-oriented Si substrates using Au as catalytic seed material. Arrays of individual seeds were patterned by electron-beam lithography, followed by Au evaporation and lift-off. SiNWs were grown using diluted silane as precursor gas in a low-pressure chemical vapor deposition system. The silane partial pressure, substrate temperature, and seed diameter were systematically varied to obtain the growth rate of the NWs and the rate of sidewall deposition. Activation energies of 19kcal/mol for the axial SiNW growth and 29kcal/mol for the radial deposition on the SiNW surface are derived from the data. SiNW growth at elevated temperatures is accompanied by significant Au surface diffusion, leading to a loss of Au from the tips of the SiNWs that depends on the layout and density of the Au seeds patterned. In contrast to NWs grown from a thin-film-nucleated substrate, the deterministic patterning of identical Au seeds of varying diameters allows accurate measurements of the nucleation yield of the SiNW, which is close to 100%, and analysis of the epitaxial relationship with the substrate. In addition to the vertical and the three 70.5°-inclined ⟨111⟩ epitaxial growth directions, we observe three additional 70.5°-inclined directions, which are rotated by 60°. The 60° rotation is explained by the occurrence of stacking faults in the SiNWs. The overall yield of vertically grown ⟨111⟩ NWs depends sensitively on the partial pressure of the silane and, to a lesser extent, on the growth temperature. At 80mTorr partial pressure and 470°C, up to 60% of the SiNWs grow in the vertical ⟨111⟩ direction. In situ doping of SiNWs using arsine resulted in a significant reduction of nucleation and wire growth, whereas doping with trimethylboron and phosphine exhibited no difference in growth and epitaxy compared with undoped samples.

  2. Growth of AlN layer on patterned sapphire substrate by hydride vapor phase epitaxy

    NASA Astrophysics Data System (ADS)

    Lee, Gang Seok; Lee, Chanmi; Jeon, Hunsoo; Lee, Chanbin; Bae, Sung Geun; Ahn, Hyung Soo; Yang, Min; Yi, Sam Nyung; Yu, Young Moon; Lee, Jae Hak; Honda, Yoshio; Sawaki, Nobuhiko; Kim, Suck-Whan

    2016-05-01

    Even though a patterned sapphire substrate (PSS) has been used for the growth of a high-quality epilayer because of its many advantages, it has not been successfully used to grow an AlN epilayer for ultraviolet (UV) light-emitting diodes (LEDs) on a PSS up to now. We report the growth of a high-quality AlN epilayer on a PSS, as a substrate for the manufacture of UV LEDs, by hydride vapor phase epitaxy (HVPE). The X-ray diffraction (XRD) peaks for the AlN epilayer grown on the PSS indicate that crystalline AlN with a wurtzite structure was grown successfully on the PSS. Furthermore, HVPE combining both in situ HVPE technology and liquid-phase epitaxy (LPE) using a mixed source is proposed as a novel method for the growth of a flat AlN epilayer on a PSS.

  3. Development of biomedical publications on ametropia research in PubMed from 1845 to 2010: a bibliometric analysis

    PubMed Central

    Xu, Chang-Tai; Li, Shan-Qu; Lü, Yong-Gang; Pan, Bo-Rong

    2011-01-01

    AIM We have carried out a bibliometric analysis on the development of ametropia literature to determine its growth rule and tendency, and to provide the basis for the problems related to ametropia research. METHODS Literatures that contained the descriptors of ametropia in title or paper published before Nov. 10, 2010 in PubMed databases (www.ncbi.nlm.nih.gov/Pubmed) were selected. As bibliometric indicators of ametropia, biomedical journals referring to ophthalmology by ISSN were calculated. The principal bibliometric indicators: Price's and Bradford's laws were applied on the increase or dispersion of scientific literature, the participation index of languages and the journals. By means of manual coding, literatures were classified according to documents study and statistical analysis. RESULTS The literatures cited in ametropia, astigmatism, myopia and hypermetropia had accumulated to 26475, which consists of Review (n=1560), Randomized Controlled Trial (n=776), Practice Guideline (n=10), Meta-Analysis (n=23), Letter (n=1222), Editorial (n=328), Clinical Trial (n=1726) and Others (n=20830), and Humans (n=23073), Animals(n=1434) and others (n=1968). 1136 literatures were included in PubMed Central, 22384 in MEDLINE and 2955 in others. The ametropia literatures rose every 5 years which of the ametropia-year cumulated amount of the literatures had three periods: before 1900, slowly increasing from 1901 to 1950, rapidly rising from 1951 to 2010 (increased approximate exponentiation exponent). Sixty kinds of languages listed in PubMed databases, of which English is dominant for aborting to ametropia research documents before 2010 (77.32%, 20471/26475). The document languages of top eight account for 95.58% (English, German, French, Japanese, Russian, Italian, Spanish, Chinese), and others for 4.42% (1171/26475). The SCI database includes 48 ophthalmologic journals and the impact factor of 39 journals is ≥1 on Thomson-Reuters in 2010. Of 48 ophthalmologic journals

  4. Dynamic Tumor Growth Patterns in a Novel Murine Model of Colorectal Cancer

    PubMed Central

    Olson, Terrah J. Paul; Hadac, Jamie N.; Sievers, Chelsie K.; Leystra, Alyssa A.; Deming, Dustin A.; Zahm, Christopher D.; Albrecht, Dawn M.; Nomura, Alice; Nettekoven, Laura A.; Plesh, Lauren K.; Clipson, Linda; Sullivan, Ruth; Newton, Michael A.; Schelman, William R.; Halberg, Richard B.

    2014-01-01

    Colorectal cancer (CRC) often arises from adenomatous colonic polyps. Polyps can grow and progress to cancer, but may also remain static in size, regress, or resolve. Predicting which progress and which remain benign is difficult. We developed a novel long-lived murine model of CRC with tumors that can be followed by colonoscopy. Our aim was to assess whether these tumors have similar growth patterns and histologic fates to human colorectal polyps to identify features to aid in risk-stratification of colonic tumors. Long-lived ApcMin/+ mice were treated with dextran sodium sulfate to promote colonic tumorigenesis. Tumor growth patterns were characterized by serial colonoscopy with biopsies obtained for immunohistochemistry and gene expression profiling. Tumors grew, remained static, regressed, or resolved over time with different relative frequencies. Newly developed tumors demonstrated higher rates of growth and resolution than more established tumors that tended to remain static in size. Colonic tumors were hyperplastic lesions (3%), adenomas (73%), intramucosal carcinomas (20%), or adenocarcinomas (3%). Interestingly, the level of β-catenin was higher in adenomas that became intratumoral carcinomas as compared to those that failed to progress. In addition, differentially expressed genes between adenomas and intramucosal carcinomas were identified. This novel murine model of intestinal tumorigenesis develops colonic tumors that can be monitored by serial colonoscopy, mirror growth patterns seen in human colorectal polyps, and progress to CRC. Further characterization of cellular and molecular features are needed to determine which features can be used to risk-stratify polyps for progression to CRC and potentially guide prevention strategies. PMID:24196829

  5. The study of craniofacial growth patterns using 3D laser scanning and geometric morphometrics

    NASA Astrophysics Data System (ADS)

    Friess, Martin

    2006-02-01

    Throughout childhood, braincase and face grow at different rates and therefore exhibit variable proportions and positions relative to each other. Our understanding of the direction and magnitude of these growth patterns is crucial for many ergonomic applications and can be improved by advanced 3D morphometrics. The purpose of this study is to investigate this known growth allometry using 3D imaging techniques. The geometry of the head and face of 840 children, aged 2 to 19, was captured with a laser surface scanner and analyzed statistically. From each scan, 18 landmarks were extracted and registered using General Procrustes Analysis (GPA). GPA eliminates unwanted variation due to position, orientation and scale by applying a least-squares superimposition algorithm to individual landmark configurations. This approach provides the necessary normalization for the study of differences in size, shape, and their interaction (allometry). The results show that throughout adolescence, boys and girls follow a different growth trajectory, leading to marked differences not only in size but also in shape, most notably in relative proportions of the braincase. These differences can be observed during early childhood, but become most noticeable after the age of 13 years, when craniofacial growth in girls slows down significantly, whereas growth in boys continues for at least 3 more years.

  6. The impact of arbuscular mycorrhizal fungi on plant growth following herbivory: A search for pattern

    NASA Astrophysics Data System (ADS)

    Borowicz, Victoria A.

    2013-10-01

    Arbuscular mycorrhizal (AM) fungi can facilitate nutrient uptake and increase host plant growth but also place constraints on the host's carbon budget. When plants are stressed by herbivory the net effect of the symbiosis may be altered tolerance. Individual experiments manipulating AM fungi and herbivory have demonstrated increased, decreased, and no effect on tolerance but patterns with respect to plant, herbivore, or fungus characteristics have not emerged. Meta-analysis of published results from factorial experiments was used to describe the size of the effects of herbivory and of AM fungi on host growth when factors such as cause of damage, inoculum, and host characteristics are considered, and to determine whether AM fungi alter the effects of herbivory. Also, the correlation between the effect of AM fungi on tolerance and resistance was tested with data from studies that examined insect performance. Herbivory strongly and consistently reduced shoot and root growth, especially in perennial plants and crops. AM fungi increased shoot growth of perennials but not annuals, and when insects caused damage but not when artificial defoliation was applied. Root growth was consistently greater with AM fungi. The interaction of AM fungi and herbivory, which indicates whether AM fungi alter the effects of herbivory, was variable and never significant overall but homogeneity tests indicated underlying structure. In experiments that used single species inoculum, Glomus intraradices increased, whereas Glomus mosseae reduced, effects of herbivory on shoot growth. Multispecies inocula magnified effects of herbivory on root growth whereas single species inocula ameliorated effects. The impact of AM fungi on resistance to herbivory was positively correlated with the impact on tolerance; however AM fungi reduced both tolerance and resistance in many cases. Review of these results with respect to the types of systems studied suggests directions for future investigation.

  7. Mojokerto revisited: evidence for an intermediate pattern of brain growth in Homo erectus.

    PubMed

    O'Connell, Caitlin A; DeSilva, Jeremy M

    2013-08-01

    Brain development in Homo erectus is a subject of great interest, and the infant calvaria from Mojokerto, Indonesia, has featured prominently in these debates. Some researchers have suggested that the pattern of brain development in H. erectus resembled that of non-human apes, while others argue for a more human-like growth pattern. In this study, we retested hypotheses regarding brain ontogeny in H. erectus using new methods (resampling), and data from additional H. erectus crania. Our results reveal that humans achieve 62% (±10%) and chimpanzees 80% (±9%) of their adult endocranial volume by 0.5-1.5 years of age. Using brain mass data, humans achieve on average 65% and chimpanzees 81% of adult size by 0.5-1.5 years. When compared with adult H. erectus crania (n = 9) from Indonesian sites greater than 1.2 million years old, Mojokerto had reached ∼70% of its adult cranial capacity. Mojokerto thus falls almost directly between the average growth in humans and chimpanzees, and well within the range of both. We therefore suggest that brain development in H. erectus cannot be dichotomized as either ape-like or human-like; it was H. erectus-like. These data indicate that H. erectus may have had a unique developmental pattern that should be considered as an important step along the continuum of brain ontogeny between apes and humans. PMID:23815827

  8. A preliminary investigation of cell growth after irradiation using a modulated x-ray intensity pattern

    NASA Astrophysics Data System (ADS)

    Bromley, Regina; Davey, Ross; Oliver, Lyn; Harvie, Rozelle; Baldock, Clive

    2006-08-01

    In this study we have investigated a spatial distribution of cell growth after their irradiation using a modulated x-ray intensity pattern. An A549 human non-small cell lung cancer cell line was grown in a 6-well culture. Two of the wells were the unirradiated control wells, whilst another two wells were irradiated with a modulated x-ray intensity pattern and the third two wells were uniformly irradiated. A number of plates were incubated for various times after irradiation and stained with crystal violet. The spatial distribution of the stained cells within each well was determined by measurement of the crystal violet optical density at multiple positions in the plate using a microplate photospectrometer. The crystal violet optical density for a range of cell densities was measured for the unirradiated well and this correlated with cell viability as determined by the MTT cell viability assay. An exponential dose response curve was measured for A549 cells from the average crystal violet optical density in the uniformly irradiated well up to a dose of 30 Gy. By measuring the crystal violet optical density distribution within a well the spatial distribution of cell growth after irradiation with a modulated x-ray intensity pattern can be plotted. This method can be used for in vitro investigation into the changes in radiation response associated with treatment using intensity modulated radiation therapy (IMRT).

  9. Controlled Patterning and Growth of Single Wall and Multi-wall Carbon Nanotubes

    NASA Technical Reports Server (NTRS)

    Delzeit, Lance D. (Inventor)

    2005-01-01

    Method and system for producing a selected pattern or array of at least one of a single wall nanotube and/or a multi-wall nanotube containing primarily carbon. A substrate is coated with a first layer (optional) of a first selected metal (e.g., Al and/or Ir) and with a second layer of a catalyst (e.g., Fe, Co, Ni and/or Mo), having selected first and second layer thicknesses provided by ion sputtering, arc discharge, laser ablation, evaporation or CVD. The first layer and/or the second layer may be formed in a desired non-uniform pattern, using a mask with suitable aperture(s), to promote growth of carbon nanotubes in a corresponding pattern. A selected heated feed gas (primarily CH4 or C2Hn with n=2 and/or 4) is passed over the coated substrate and forms primarily single wall nanotubes or multiple wall nanotubes, depending upon the selected feed gas and its temperature. Nanofibers, as well as single wall and multi-wall nanotubes, are produced using plasma-aided growth from the second (catalyst) layer. An overcoating of a selected metal or alloy can be deposited, over the second layer, to provide a coating for the carbon nanotubes grown in this manner.

  10. Growth of indium oxide nanowalls on patterned conducting substrates: towards direct fabrication of gas sensors.

    PubMed

    Chen, Changlong; Wei, Yuling; Sun, Guoxin; Shao, Baiqi

    2012-05-01

    Nanowall materials are ideal two-dimensional structures with high surface-to-volume ratios and open edge geometries. We first report on the growth and characterization of indium oxide nanowalls on transparent and conducting indium tin oxide substrates. The nanosheets that compose the nanowalls are single-crystalline and are approximately 8 nm in thickness. The density and the lateral dimensions of the nanosheets on the substrate can be controlled by the growth time. Adopting a bridgework-like strategy, we directly construct indium oxide nanowall gas sensors on the patterned indium tin oxide substrates. The pattern lines on the substrates are etched using transparent plastic adhesive tape as shadow mask, which is both simple and cheap in comparison with the conventional photolithography technique. The sensors exhibit fast response/recovery behavior and good reproducibility to NO(2) gas under mild testing conditions, such as room temperature, ambient pressure, dry air background, and 1.5 V dc bias, and can achieve a detection limit as low as 50 ppb. We propose an assumption that the gas adsorption is composed of deep adsorption and probe adsorption to explain the interesting gas-sensing behavior of the indium oxide nanowalls. We suggest that the work reported herein, including the facile growth of indium oxide nanowalls, the bridgework-like strategy to directly construct electronic devices, and the high gas-sensing performance of the indium oxide nanowalls sensors, is a significant step towards the real applications of novel semiconductor nanostructures. PMID:22328146

  11. Quantitative spectral light scattering polarimetry for monitoring fractal growth pattern of Bacillus thuringiensis bacterial colonies

    NASA Astrophysics Data System (ADS)

    Banerjee, Paromita; Soni, Jalpa; Ghosh, Nirmalya; Sengupta, Tapas K.

    2013-02-01

    It is of considerable current interest to develop various methods which help to understand and quantify the cellular association in growing bacterial colonies and is also important in terms of detection and identification of a bacterial species. A novel approach is used here to probe the morphological structural changes occurring during the growth of the bacterial colony of Bacillus thuringiensis under different environmental conditions (in normal nutrient agar, in presence of glucose - acting as additional nutrient and additional 3mM arsenate as additional toxic material). This approach combines the quantitative Mueller matrix polarimetry to extract intrinsic polarization properties and inverse analysis of the polarization preserving part of the light scattering spectra to determine the fractal parameter H (Hurst exponent) using Born approximation. Interesting differences are observed in the intrinsic polarization parameters and also in the Hurst exponent, which is a measurement of the fractality of a pattern formed by bacteria while growing as a colony. These findings are further confirmed with optical microscopic studies of the same sample and the results indicate a very strong and distinct dependence on the environmental conditions during growth, which can be exploited to quantify different bacterial species and their growth patterns.

  12. Does prenatal restraint stress change the craniofacial growth pattern of rat offspring?

    PubMed

    Aminabadi, Naser A; Behroozian, Ahmad; Talatahari, Elham; Samiei, Mohammad; Sadigh-Eteghad, Saeed; Shirazi, Sajjad

    2016-02-01

    A major and frequently encountered condition underlying the long-term programming effects of the intrauterine environment is exposure to stress. Gestational stress is an environmental factor that induces physical and behavioral alterations in offspring. Seventy female virgin Wistar rats were mated with one male rat for a maximum of four times, after which 52 pregnant rats were divided into two groups. In the experimental group the rats were exposed to restraint stress during pregnancy, whereas the control group did not receive the stress protocol. One male litter was randomly chosen from the offspring of each rat with 8-13 pups. A total of 40 male rat offspring were available for analysis. Thirty-one linear and angular measurements were analyzed in both study groups to investigate whether prenatal restraint stress changes the craniofacial growth pattern of rat offspring. In the prenatally stressed group, anterior cranial base length and viscerocranium measures were significantly increased compared with the control group, whereas cranial width, mandibular dimensions, and posterior cranial height and length remained unchanged. Furthermore, the prenatally stressed group showed backward rotation of the midface and decreased flattening of the cranial vault. It was concluded that prenatal chronic stress can induce alterations in the craniofacial growth pattern by promoting endochondral growth in the cranial base and nasal septum. PMID:26620628

  13. Field Heterogeneity Patterns as a Crucial Factor for Improving Crop Growth Simulations

    NASA Astrophysics Data System (ADS)

    Stadler, A.; Kupisch, M.; Langensiepen, M.; Ewert, F.

    2012-12-01

    Agricultural ecosystems depend on environmental factors, especially the weather and the soil characteristics. Heterogeneous conditions within a field cause spatial variations of biomass, leaf area index and yield. The effects of varying spatial conditions on crop growth are generally examined on different spatial scales, but just few studies address spatial heterogeneity at the field level. Since crop growth models try to represent an image of reality, they should consider variations in field conditions, especially regarding small-scale simulations and precision agriculture. Some studies already described that the tested models are able to represent spatial heterogeneity at regional scale, if parameters of environmental conditions are adapted. Therefore, we hypothesize that taking into account the effects of soil heterogeneity on plant water and nutrient uptake also improves the accuracy of crop growth models at field scale. A crop growth model was applied using information from winter wheat and sugar beet field trials carried out near Jülich, located in the central western part of Germany. These fields are all characterized by strong spatial variability in soil conditions and managed according to standard agronomic practice. The crop growth model was calibrated separately for each winter wheat and sugar beet cultivar grown on these fields by adjusting the respective parameters with the help of crop physiological measurements at point level. The soil model was parameterized for different field sample points with electromagnetic induction measurements to account for the spatial heterogeneity in soil conditions within each field. After that, the crop growth model was tested whether it could reproduce the observed spatial patterns of crop growth in the selected fields (2010 - 2012) by considering the spatial variability in soil properties. The analysis of our measurements on heterogeneous winter wheat fields showed a distribution of soil properties whose patterns are

  14. Growth Mode and Threading Dislocation Behavior of GaN Films Grown on Patterned Sapphire Substrate with Radial Stripe Pattern

    NASA Astrophysics Data System (ADS)

    Okuno, Koji; Oshio, Takahide; Shibata, Naoki; Honda, Yoshio; Yamaguchi, Masahito; Amano, Hiroshi

    2013-08-01

    A sapphire substrate with a grooved stripe pattern along different radial directions was prepared to investigate the effects of stripe direction on the growth mode and threading dislocation (TD) behavior of GaN films. When the stripe direction is oriented parallel to [10bar 10]sapphire, the GaN films have a triangular structure that is formed by the GaN{10bar 11} facets. As the stripe direction rotates from [10bar 10]sapphire, nanosteps with a step height of around 80 nm are formed on the GaN{10bar 11} facets and then the coalescence of GaN on the ridges and grooves advances. GaN films with a smooth surface and a TD density as low as 2.0×108 cm-2 were achieved when the stripe direction was rotated 3° from [10bar 10]sapphire. Our result indicates that the surface roughness and TD density of GaN films can be controlled by precisely adjusting the angle of the stripe direction from [10bar 10]sapphire.

  15. Risk Factors for Bladder Cancer: Challenges of Conducting a Literature Search Using PubMed

    PubMed Central

    Joshi, Ashish; Preslan, Elicia

    2011-01-01

    The objective of this study was to assess the risk factors for bladder cancer using PubMed articles from January 2000 to December 2009. The study also aimed to describe the challenges encountered in the methodology of a literature search for bladder cancer risk factors using PubMed. Twenty-six categories of risk factors for bladder cancer were identified using the National Cancer Institute Web site and the Medical Subject Headings (MeSH) Web site. A total of 1,338 PubMed searches were run using the term “urinary bladder cancer” and a risk factor term (e.g., “cigarette smoking”) and were screened to identify 260 articles for final analysis. The search strategy had an overall precision of 3.42 percent, relative recall of 12.64 percent, and an F -measure of 5.39 percent. Although search terms derived from MeSH had the highest overall precision and recall, the differences did not reach significance, which indicates that for generalized, free-text searches of the PubMed database, the searchers' own terms are generally as effective as MeSH terms. PMID:21464862

  16. Multi-lingual search engine to access PubMed monolingual subsets: a feasibility study.

    PubMed

    Darmoni, Stéfan J; Soualmia, Lina F; Griffon, Nicolas; Grosjean, Julien; Kerdelhué, Gaétan; Kergourlay, Ivan; Dahamna, Badisse

    2013-01-01

    PubMed contains many articles in languages other than English but it is difficult to find them using the English version of the Medical Subject Headings (MeSH) Thesaurus. The aim of this work is to propose a tool allowing access to a PubMed subset in one language, and to evaluate its performance. Translations of MeSH were enriched and gathered in the information system. PubMed subsets in main European languages were also added in our database, using a dedicated parser. The CISMeF generic semantic search engine was evaluated on the response time for simple queries. MeSH descriptors are currently available in 11 languages in the information system. All the 654,000 PubMed citations in French were integrated into CISMeF database. None of the response times exceed the threshold defined for usability (2 seconds). It is now possible to freely access biomedical literature in French using a tool in French; health professionals and lay people with a low English language may find it useful. It will be expended to several European languages: German, Spanish, Norwegian and Portuguese. PMID:23920740

  17. Mentoring programs for medical students - a review of the PubMed literature 2000 - 2008

    PubMed Central

    2010-01-01

    Background Although mentoring is acknowledged as a key to successful and satisfying careers in medicine, formal mentoring programs for medical students are lacking in most countries. Within the framework of planning a mentoring program for medical students at Zurich University, an investigation was carried out into what types of programs exist, what the objectives pursued by such programs are, and what effects are reported. Methods A PubMed literature search was conducted for 2000 - 2008 using the following keywords or their combinations: mentoring, mentoring program, medical student, mentor, mentee, protégé, mentorship. Although a total of 438 publications were identified, only 25 papers met the selection criteria for structured programs and student mentoring surveys. Results The mentoring programs reported in 14 papers aim to provide career counseling, develop professionalism, increase students' interest in research, and support them in their personal growth. There are both one-to-one and group mentorships, established in the first two years of medical school and continuing through graduation. The personal student-faculty relationship is important in that it helps students to feel that they are benefiting from individual advice and encourages them to give more thought to their career choices. Other benefits are an increase in research productivity and improved medical school performance in general. Mentored students also rate their overall well-being as higher. - The 11 surveys address the requirements for being an effective mentor as well as a successful mentee. A mentor should empower and encourage the mentee, be a role model, build a professional network, and assist in the mentee's personal development. A mentee should set agendas, follow through, accept criticism, and be able to assess performance and the benefits derived from the mentoring relationship. Conclusion Mentoring is obviously an important career advancement tool for medical students. In Europe

  18. Patterned Growth of Organic Semiconductors: Selective Nucleation of Perylene on Self-Assembled Monolayers.

    PubMed

    Pick, André; Witte, Gregor

    2016-08-16

    Organic semiconductors (OSC) have received a large amount of attention because they afford the fabrication of flexible electronic devices. However, the limited resistance to radiation and etching of such materials does not permit their patterning by photolithography, which has been a driving force for the development of integrated circuits and therefore requires alternative structuring techniques. One approach is based on precoating the substrate with self-assembled monolayers (SAMs) to control the nucleation of subsequently deposited OSC layers, but the underlying mechanism is barely understood. Here, we used alkanethiols with different chemical terminations to prepare SAMs on gold substrates serving as model systems to identify the mechanism of selective nucleation for the case of the OSC perylene. Using atomic force microscopy and fluorescence microscopy, we demonstrate that the chemical functionalization of the SAMs determines the adhesion forces for the OSC that are smallest for CF3-terminated and largest for OH-terminated SAMs, hence yielding distinctly different sticking probabilities upon perylene deposition at room temperature. Microcontact printing and immersion were employed to prepare SAM patterns that enable the selective growth of polycrystalline perylene films. A quite different situation is found upon printing long-chain thiols with low vapor pressure, which leads to the transfer of multilayers and favors the growth of perylene single crystallites. In a more abstract scenario, patterns of silicone oil droplets were printed on a gold substrate, which was previously covered with a repelling fluorinated SAM. Such droplets provide nucleation centers for liquid-mediated growth, often yielding platelet-shaped perylene single crystallites without unwanted perylene nucleation on the remaining surface. PMID:27441921

  19. Simulation of Epitaxial Growth of DNA-nanoparticle Superlattices on Pre-patterned Substrates

    NASA Astrophysics Data System (ADS)

    Pan, Saijie; Li, Ting; Olvera de La Cruz, Monica

    2015-03-01

    DNA self-assembly is a well-developed approach towards the construction of a great variety of nanoarchitectures. E-beam lithography is widely used for high-resolution nanoscale patterning. Recently, a new technique combining the two methods was developed to epitaxially grow DNA-mediated nanoparticle superlattices on a pre-patterned surface. Here we use multi-scale simulations to study and predict the formation and defects of the absorbed superlattice monolayer. We demonstrate that the epitaxial growth is enthalpy driven and show that the anisotropy of the DNA-mediated substrates leads to structure defects. We develop design rules to dramatically reduce defects of the attached layer. Ultimately, with the assist of our simulation, this technique will open the door for the construction of well-ordered, three-dimensional novel metamaterials. This work was supported by the the Air Force Office of Scientific Research (AFOSR) Multidisciplinary University Research Initiative (MURI) FA9550-11-1-0275.

  20. Synthesis of carbon nanotube bridges on patterned silicon wafers by selective lateral growth

    NASA Astrophysics Data System (ADS)

    Han, Young-Soo; Shin, Jin-Koog; Kim, Sung-Tae

    2001-12-01

    Floated carbon nanotube bridges were synthesized on a patterned silicon wafer by thermal chemical vapor deposition of acetylene. A conventional photolithography was used to define the catalytic nickel line patterns. The carbon nanotubes grow laterally from the side face to side face of the nickel catalyst by a SiO2 vertical growth barrier deposited on the nickel layer. The typical diameter of carbon nanotube bridges is 10-30 nm and it depends on the thickness of the catalytic nickel layer. Our laterally grown carbon nanotubes have a bamboo structure in which the spacing of compartment layers increases with an increase in temperature. We can control the length, linearity, and density of the carbon nanotube bridges by adjusting various synthetic process parameters and find they may possibly be applied to nanoelectronic devices.

  1. Patterning nanofibrils through the templated growth of multiple modified amyloid peptides.

    PubMed

    Sakai, Hiroki; Watanabe, Ken; Kudoh, Fuki; Kamada, Rui; Chuman, Yoshiro; Sakaguchi, Kazuyasu

    2016-01-01

    There has been considerable interest in the patterning of functionalized nanowires because of the potential applications of these materials to the construction of nanodevices. A variety of biomolecular building blocks containing amyloid peptides have been used to functionalize nanowires. However, the patterning of self-assembled nanowires can be challenging because of the difficulties associated with controlling the self-assembly of these functionalized building blocks. Herein, we present a versatile approach for the patterning of nanowires based on the combination of templated fibril growth with a versatile functionalization method using our structure-controllable amyloid peptides (SCAPs). Using this approach, we have succeeded in the formation of multi-type nanowires with tandem domain structures in high yields. Given that the mixing-SCAP method can lead to the formation of tandem fibrils, it is noteworthy that our method allowed us to control the initiation of fibril formation from the gold nanoparticles, which were attached to a short fibril as initiation points. This approach could be used to prepare a wide variety of fibril patterns, and therefore holds great potential for the development of novel self-assembled nanodevices. PMID:27559011

  2. Patterning nanofibrils through the templated growth of multiple modified amyloid peptides

    PubMed Central

    Sakai, Hiroki; Watanabe, Ken; Kudoh, Fuki; Kamada, Rui; Chuman, Yoshiro; Sakaguchi, Kazuyasu

    2016-01-01

    There has been considerable interest in the patterning of functionalized nanowires because of the potential applications of these materials to the construction of nanodevices. A variety of biomolecular building blocks containing amyloid peptides have been used to functionalize nanowires. However, the patterning of self-assembled nanowires can be challenging because of the difficulties associated with controlling the self-assembly of these functionalized building blocks. Herein, we present a versatile approach for the patterning of nanowires based on the combination of templated fibril growth with a versatile functionalization method using our structure-controllable amyloid peptides (SCAPs). Using this approach, we have succeeded in the formation of multi-type nanowires with tandem domain structures in high yields. Given that the mixing-SCAP method can lead to the formation of tandem fibrils, it is noteworthy that our method allowed us to control the initiation of fibril formation from the gold nanoparticles, which were attached to a short fibril as initiation points. This approach could be used to prepare a wide variety of fibril patterns, and therefore holds great potential for the development of novel self-assembled nanodevices. PMID:27559011

  3. Monitoring of Water Spectral Pattern Reveals Differences in Probiotics Growth When Used for Rapid Bacteria Selection.

    PubMed

    Slavchev, Aleksandar; Kovacs, Zoltan; Koshiba, Haruki; Nagai, Airi; Bázár, György; Krastanov, Albert; Kubota, Yousuke; Tsenkova, Roumiana

    2015-01-01

    Development of efficient screening method coupled with cell functionality evaluation is highly needed in contemporary microbiology. The presented novel concept and fast non-destructive method brings in to play the water spectral pattern of the solution as a molecular fingerprint of the cell culture system. To elucidate the concept, NIR spectroscopy with Aquaphotomics were applied to monitor the growth of sixteen Lactobacillus bulgaricus one Lactobacillus pentosus and one Lactobacillus gasseri bacteria strains. Their growth rate, maximal optical density, low pH and bile tolerances were measured and further used as a reference data for analysis of the simultaneously acquired spectral data. The acquired spectral data in the region of 1100-1850nm was subjected to various multivariate data analyses - PCA, OPLS-DA, PLSR. The results showed high accuracy of bacteria strains classification according to their probiotic strength. Most informative spectral fingerprints covered the first overtone of water, emphasizing the relation of water molecular system to cell functionality. PMID:26133176

  4. Patterns of dynamic urban population growth in Russia, 1989-1996: a research report.

    PubMed

    Rowland, R H

    1997-01-01

    "The purpose of this paper is to investigate locations in which rapid urban growth occurred in Russia over the period 1989 to 1996....Particular emphasis will be given to the geographical patterns, economic functions, and population size of rapidly growing towns. In addition, the discussion of trends for 1989-1996 also will be briefly preceded by and compared to those of 1979-1989, although the paper will emphasize trends during the 1990s. Furthermore, the topic of ¿new towns', which themselves often are rapidly growing centers, will be addressed as well." PMID:12292848

  5. Urban vegetation and thermal patterns following city growth in different socio-economic contexts

    NASA Astrophysics Data System (ADS)

    Dronova, I.; Clinton, N.; Yang, J.; Radke, J.; Marx, S. S.; Gong, P.

    2015-12-01

    Urban expansion accompanied by losses of vegetated spaces and their ecological services raises significant concerns about the future of humans in metropolitan "habitats". Despite recent growth of urban studies globally, it is still not well understood how environmental effects of urbanization vary with the rate and socioeconomic context of development. Our study hypothesized that with urban development, spatial patterns of surface thermal properties and green plant cover would shift towards higher occurrence of relatively warmer and less vegetated spaces such as built-up areas, followed by losses of greener and cooler areas such as urban forests, and that these shifts would be more pronounced with higher rate of economic and/or population growth. To test these ideas, we compared 1992-2011 changes in remotely sensed patterns of green vegetation and surface temperature in three example cities that experienced peripheral growth under contrasting socio-economic context - Dallas, TX, USA, Beijing, China and Kyiv, Ukraine. To assess their transformation, we proposed a metric of thermal-vegetation angle (TVA) estimated from per-pixel proxies of vegetation greenness and surface temperature from Landsat satellite data and examined changes in TVA distributions within each city's core and two decadal zones of peripheral sprawl delineated from nighttime satellite data. We found that higher economic and population growth were coupled with more pronounced changes in TVA distributions, and more urbanized zones often exhibited higher frequencies of warmer, less green than average TVA values with novel patterns such as "cooler" clusters of building shadows. Although greener and cooler spaces generally diminished with development, they remained relatively prevalent in low-density residential areas of Dallas and peripheral zones of Kyiv with exurban subsistence farming. Overall, results indicate that the effects of modified green space and thermal patterns within growing cities

  6. The pattern of histogenesis and growth of tooth plates in larval stages of extant lungfish.

    PubMed Central

    Smith, M M

    1985-01-01

    Comparison of new data obtained in this study on Protopterus aethiopicus with that published on Protopterus aethiopicus and Neoceratodus forsteri has confirmed the suggestion that the pattern of histogenesis of tooth plates in the early larval stages is very similar in the two genera. These similarities are more apparent both when a common terminology is adopted, based on a topogenic classification, and when the fundamental assumption is made that a single morphogenetic system operates for all odontodes. The model to explain the structure of all vertebrate dentitions with separate teeth in single or multiple tooth rows has been found to apply to dipnoan dentitions with fused teeth in a composite tooth plate. In this model, the epithelial invagination surrounding the margins of the tooth plate represents the dental lamina and, where this is in contact with mesenchymal cells, cell clusters (protogerms) arise. From these protogerms new odontodes (teeth) may develop if factors to inhibit differentiation are not present. Sites for initiation of odontodes become restricted to the labial margins of existing ridges on the tooth plate. Experimental studies on mammalian tooth germs are discussed and a model proposed for control of odontogenesis and histogenesis in dipnoan dentitions. Patterns of growth of hypermineralised petrodentine have been analysed and shown to depend initially on the arrangement of odontodes, and subsequently upon the ability of special cells in the pulp to generate new and wider layers of petrodentine. The initial pattern of petrodentine depends upon the position of odontodes in the forming ridges of the tooth plate. Subsequent patterns of petrodentine depend upon the extent of replacement growth beneath the tritural surface. Specialised cells, petroblasts, secrete the petrodentine within a shell of dentine. These cells differentiate from cells of the dental papilla after odontoblasts have begun to form dentine. They are regarded as a unique type of

  7. The pattern of histogenesis and growth of tooth plates in larval stages of extant lungfish.

    PubMed

    Smith, M M

    1985-06-01

    Comparison of new data obtained in this study on Protopterus aethiopicus with that published on Protopterus aethiopicus and Neoceratodus forsteri has confirmed the suggestion that the pattern of histogenesis of tooth plates in the early larval stages is very similar in the two genera. These similarities are more apparent both when a common terminology is adopted, based on a topogenic classification, and when the fundamental assumption is made that a single morphogenetic system operates for all odontodes. The model to explain the structure of all vertebrate dentitions with separate teeth in single or multiple tooth rows has been found to apply to dipnoan dentitions with fused teeth in a composite tooth plate. In this model, the epithelial invagination surrounding the margins of the tooth plate represents the dental lamina and, where this is in contact with mesenchymal cells, cell clusters (protogerms) arise. From these protogerms new odontodes (teeth) may develop if factors to inhibit differentiation are not present. Sites for initiation of odontodes become restricted to the labial margins of existing ridges on the tooth plate. Experimental studies on mammalian tooth germs are discussed and a model proposed for control of odontogenesis and histogenesis in dipnoan dentitions. Patterns of growth of hypermineralised petrodentine have been analysed and shown to depend initially on the arrangement of odontodes, and subsequently upon the ability of special cells in the pulp to generate new and wider layers of petrodentine. The initial pattern of petrodentine depends upon the position of odontodes in the forming ridges of the tooth plate. Subsequent patterns of petrodentine depend upon the extent of replacement growth beneath the tritural surface. Specialised cells, petroblasts, secrete the petrodentine within a shell of dentine. These cells differentiate from cells of the dental papilla after odontoblasts have begun to form dentine. They are regarded as a unique type of

  8. Digital Transfer Growth of Patterned 2D Metal Chalcogenides by Confined Nanoparticle Evaporation

    DOE PAGESBeta

    Mahjouri-Samani, Masoud; Tian, Mengkun; Wang, Kai; Boulesbaa, Abdelaziz; Rouleau, Christopher M.; Puretzky, Alexander A.; McGuire, Michael A.; Srijanto, Bernadeta R.; Xiao, Kai; Eres, Gyula; et al

    2014-10-19

    Developing methods for the facile synthesis of two-dimensional (2D) metal chalcogenides and other layered materials is crucial for emerging applications in functional devices. Controlling the stoichiometry, number of the layers, crystallite size, growth location, and areal uniformity is challenging in conventional vapor phase synthesis. Here, we demonstrate a new route to control these parameters in the growth of metal chalcogenide (GaSe) and dichalcogenide (MoSe2) 2D crystals by precisely defining the mass and location of the source materials in a confined transfer growth system. A uniform and precise amount of stoichiometric nanoparticles are first synthesized and deposited onto a substrate bymore » pulsed laser deposition (PLD) at room temperature. This source substrate is then covered with a receiver substrate to form a confined vapor transport growth (VTG) system. By simply heating the source substrate in an inert background gas, a natural temperature gradient is formed that evaporates the confined nanoparticles to grow large, crystalline 2D nanosheets on the cooler receiver substrate, the temperature of which is controlled by the background gas pressure. Large monolayer crystalline domains (~ 100 m lateral sizes) of GaSe and MoSe2 are demonstrated, as well as continuous monolayer films through the deposition of additional precursor materials. This novel PLD-VTG synthesis and processing method offers a unique approach for the controlled growth of large-area, metal chalcogenides with a controlled number of layers in patterned growth locations for optoelectronics and energy related applications.« less

  9. Volume Changes After Stereotactic LINAC Radiotherapy in Vestibular Schwannoma: Control Rate and Growth Patterns

    SciTech Connect

    Langenberg, Rick van de; Dohmen, Amy J.C.; Bondt, Bert J. de; Nelemans, Patty J.; Baumert, Brigitta G.; Stokroos, Robert J.

    2012-10-01

    Purpose: The purpose of this study was to evaluate the control rate of vestibular schwannomas (VS) after treatment with linear accelerator (LINAC)-based stereotactic radiosurgery (SRS) or radiotherapy (SRT) by using a validated volumetric measuring tool. Volume-based studies on prognosis after LINAC-based SRS or SRT for VS are reported scarcely. In addition, growth patterns and risk factors predicting treatment failure were analyzed. Materials and Methods: Retrospectively, 37 VS patients treated with LINAC based SRS or SRT were analyzed. Baseline and follow-up magnetic resonance imaging scans were analyzed with volume measurements on contrast enhanced T1-weighted magnetic resonance imaging. Absence of intervention after radiotherapy was defined as 'no additional intervention group, ' absence of radiological growth was defined as 'radiological control group. ' Significant growth was defined as a volume change of 19.7% or more, as calculated in a previous study. Results: The cumulative 4-year probability of no additional intervention was 96.4% {+-} 0.03; the 4-year radiological control probability was 85.4% {+-} 0.1). The median follow-up was 40 months. Overall, shrinkage was seen in 65%, stable VS in 22%, and growth in 13%. In 54% of all patients, transient swelling was observed. No prognostic factors were found regarding VS growth. Previous treatment and SRS were associated with transient swelling significantly. Conclusions: Good control rates are reported for LINAC based SRS or SRT in VS, in which the lower rate of radiological growth control is attributed to the use of the more sensitive volume measurements. Transient swelling after radiosurgery is a common phenomenon and should not be mistaken for treatment failure. Previous treatment and SRS were significantly associated with transient swelling.

  10. Growth patterns of Chromolaena odorata in varied ecosystems at Kodayar in the Western Ghats, India

    NASA Astrophysics Data System (ADS)

    Chandrasekaran, Sivagnanam; Swamy, P. S.

    2010-07-01

    The growth and allocation patterns of biomass and nutrients (nitrogen, phosphorus and potassium) were studied in Chromolaena odorata populations grown in different human modified ecosystems including an Albizia plantation, a rubber plantation, community land and a naturally regenerating forest. The greater shoot length of C. odorata in the regenerating forest could be attributed to the competitive and shady environment created by the mature vegetation here. High relative growth rate, net assimilation rate and reproductive potential of C. odorata populations growing on the community land and in the rubber plantation may be due to the open habitat and frequent disturbances to these sites. In general, allocation of biomass and nutrients to the leaf and reproductive components was low in the regenerating forest. On the other hand, greater allocation to the root component in the regenerating forest may be a strategy for survival and regeneration after the disturbance. Low nutrient uptake and greater resource use efficiency in the regenerating forest could be a response to limited resource availability under the competitive micro-environment created by the fast growing tree species. C. odorata has an exploitative growth strategy and will persist in regenerating open habitats whereas it showed suppressed growth in the light - limited shaded environment.

  11. Cell-Type Dependent Effect of Surface-Patterned Microdot Arrays on Neuronal Growth

    PubMed Central

    Jang, Min Jee; Kim, Woon Ryoung; Joo, Sunghoon; Ryu, Jae Ryun; Lee, Eunsoo; Nam, Yoonkey; Sun, Woong

    2016-01-01

    Surface micropatterns have been widely used as chemical cues to control the microenvironment of cultured neurons, particularly for neurobiological assays and neurochip designs. However, the cell-type dependency on the interactions between neurons and underlying micropatterns has been rarely investigated despite the inherent differences in the morphology of neuronal types. In this study, we used surface-printed microdot arrays to investigate the effect of the same micropatterns on the growth of mouse spinal interneuron, mouse hippocampal neurons, and rat hippocampal neurons. While mouse hippocampal neurons showed no significantly different growth on control and patterned substrates, we found the microdot arrays had different effects on early neuronal growth depending on the cell type; spinal interneurons tended to grow faster in length, whereas hippocampal neurons tended to form more axon collateral branches in response to the microdot arrays. Although there was a similar trend in the neurite length and branch number of both neurons changed across the microdot arrays with the expanded range of size and spacing, the dominant responses of each neuron, neurite elongation of mouse spinal interneurons and branching augmentation of rat hippocampal neurons were still preserved. Therefore, our results demonstrate that the same design of micropatterns could cause different neuronal growth results, raising an intriguing issue of considering cell types in neural interface designs. PMID:27242421

  12. Cell-Type Dependent Effect of Surface-Patterned Microdot Arrays on Neuronal Growth.

    PubMed

    Jang, Min Jee; Kim, Woon Ryoung; Joo, Sunghoon; Ryu, Jae Ryun; Lee, Eunsoo; Nam, Yoonkey; Sun, Woong

    2016-01-01

    Surface micropatterns have been widely used as chemical cues to control the microenvironment of cultured neurons, particularly for neurobiological assays and neurochip designs. However, the cell-type dependency on the interactions between neurons and underlying micropatterns has been rarely investigated despite the inherent differences in the morphology of neuronal types. In this study, we used surface-printed microdot arrays to investigate the effect of the same micropatterns on the growth of mouse spinal interneuron, mouse hippocampal neurons, and rat hippocampal neurons. While mouse hippocampal neurons showed no significantly different growth on control and patterned substrates, we found the microdot arrays had different effects on early neuronal growth depending on the cell type; spinal interneurons tended to grow faster in length, whereas hippocampal neurons tended to form more axon collateral branches in response to the microdot arrays. Although there was a similar trend in the neurite length and branch number of both neurons changed across the microdot arrays with the expanded range of size and spacing, the dominant responses of each neuron, neurite elongation of mouse spinal interneurons and branching augmentation of rat hippocampal neurons were still preserved. Therefore, our results demonstrate that the same design of micropatterns could cause different neuronal growth results, raising an intriguing issue of considering cell types in neural interface designs. PMID:27242421

  13. Modeling Microbial Growth Dynamics, Patterns, and Coexistence on Partially Saturated Rough Surfaces

    NASA Astrophysics Data System (ADS)

    Long, T.; Or, D.

    2005-12-01

    A new modeling tool was developed to study the impact of variations in matric potential on aquatic pathways and substrate diffusion, and on microbial growth and movement on unsaturated rough surfaces. The modeling domain is composed of prescribed distributions of conical pits (sites) connected by prismatic channels (bonds) representing rough surfaces of soils or rocks. The well-defined geometry facilitates exact description of aqueous phase distribution within the roughness for a given matric potential. Microbial growth within the resulting highly variable diffusion network architectures (vary with matric potential) and interactions with nutrient diffusion patterns are simulated by coupling Reaction-Diffusion Method (RDM) and the Active Walker Method (AWM). Simulation results show direct impact of wetness conditions (matric potential values) on microbial growth rates and expansion patters for the same surface roughness. In addition to modification of mean diffusion rates for drier or wetter conditions, the network connectivity may induce significant changes in spatial patters of microbial growth. Impact of these changes on coexistence of two competing microbial species will be discussed.

  14. Response to long-term growth hormone therapy in patients affected by RASopathies and growth hormone deficiency: Patterns of growth, puberty and final height data.

    PubMed

    Tamburrino, Federica; Gibertoni, Dino; Rossi, Cesare; Scarano, Emanuela; Perri, Annamaria; Montanari, Francesca; Fantini, Maria Pia; Pession, Andrea; Tartaglia, Marco; Mazzanti, Laura

    2015-11-01

    RASopathies are developmental disorders caused by heterozygous germline mutations in genes encoding proteins in the RAS-MAPK signaling pathway. Reduced growth is a common feature. Several studies generated data on growth, final height (FH), and height velocity (HV) after growth hormone (GH) treatment in patients with these disorders, particularly in Noonan syndrome, the most common RASopathy. These studies, however, refer to heterogeneous cohorts in terms of molecular information, GH status, age at start and length of therapy, and GH dosage. This work reports growth data in 88 patients affected by RASopathies with molecularly confirmed diagnosis, together with statistics on body proportions, pubertal pattern, and FH in 33, including 16 treated with GH therapy for proven GH deficiency. Thirty-three patients showed GH deficiency after pharmacological tests, and were GH-treated for an average period of 6.8 ± 4.8 years. Before starting therapy, HV was -2.6 ± 1.3 SDS, and mean basal IGF1 levels were -2.0 ± 1.1 SDS. Long-term GH therapy, starting early during childhood, resulted in a positive height response compared with untreated patients (1.3 SDS in terms of height-gain), normalizing FH for Ranke standards but not for general population and Target Height. Pubertal timing negatively affected pubertal growth spurt and FH, with IGF1 standardized score increased from -2.43 to -0.27 SDS. During GH treatment, no significant change in bone age velocity, body proportions, or cardiovascular function was observed. PMID:26227443

  15. Craniofacial divergence by distinct prenatal growth patterns in Fgfr2 mutant mice

    PubMed Central

    2014-01-01

    Background Differences in cranial morphology arise due to changes in fundamental cell processes like migration, proliferation, differentiation and cell death driven by genetic programs. Signaling between fibroblast growth factors (FGFs) and their receptors (FGFRs) affect these processes during head development and mutations in FGFRs result in congenital diseases including FGFR-related craniosynostosis syndromes. Current research in model organisms focuses primarily on how these mutations change cell function local to sutures under the hypothesis that prematurely closing cranial sutures contribute to skull dysmorphogenesis. Though these studies have provided fundamentally important information contributing to the understanding of craniosynostosis conditions, knowledge of changes in cell function local to the sutures leave change in overall three-dimensional cranial morphology largely unexplained. Here we investigate growth of the skull in two inbred mouse models each carrying one of two gain-of-function mutations in FGFR2 on neighboring amino acids (S252W and P253R) that in humans cause Apert syndrome, one of the most severe FGFR-related craniosynostosis syndromes. We examine late embryonic skull development and suture patency in Fgfr2 Apert syndrome mice between embryonic day 17.5 and birth and quantify the effects of these mutations on 3D skull morphology, suture patency and growth. Results We show in mice what studies in humans can only infer: specific cranial growth deviations occur prenatally and worsen with time in organisms carrying these FGFR2 mutations. We demonstrate that: 1) distinct skull morphologies of each mutation group are established by E17.5; 2) cranial suture patency patterns differ between mice carrying these mutations and their unaffected littermates; 3) the prenatal skull grows differently in each mutation group; and 4) unique Fgfr2-related cranial morphologies are exacerbated by late embryonic growth patterns. Conclusions Our analysis of

  16. Maternal Dietary Patterns and Fetal Growth: A Large Prospective Cohort Study in China

    PubMed Central

    Lu, Min-Shan; Chen, Qiao-Zhu; He, Jian-Rong; Wei, Xue-Ling; Lu, Jin-Hua; Li, Sheng-Hui; Wen, Xing-Xuan; Chan, Fan-Fan; Chen, Nian-Nian; Qiu, Lan; Mai, Wei-Bi; Zhang, Rui-Fang; Hu, Cui-Yue; Xia, Hui-Min; Qiu, Xiu

    2016-01-01

    There was limited evidence revealing the association of Chinese maternal dietary patterns with fetal growth. We aimed to examine the relationship of maternal dietary patterns during pregnancy to neonatal birth weight and birth weight for gestational age in a Chinese population. A total of 6954 mother-child pairs were included from the Born in Guangzhou Cohort Study. Maternal diet during pregnancy was assessed using a self-administered food frequency questionnaire. Cluster analysis was used to identify dietary patterns. The following six dietary patterns were identified: “Cereals, eggs, and Cantonese soups” (n 1026, 14.8%), “Dairy” (n 1020, 14.7%), “Fruits, nuts, and Cantonese desserts” (n 799, 11.5%), “Meats” (n 1066, 15.3%), “Vegetables” (n 1383, 19.9%), and “Varied” (n 1224, 17.6%). The mean neonatal birth weight Z scores of women in the above patterns were 0.02, 0.07, 0.20, 0.01, 0.06, and 0.14, respectively. Women in the “Fruits, nuts, and Cantonese desserts” and “Varied” groups had significantly heavier infants compared with those in the “Cereals, eggs, and Cantonese soups” group. Compared with women in the “Cereals, eggs, and Cantonese soups” group, those in the “Varied” group had marginally significantly lower odds of having a small-for-gestational age (SGA) infant after adjustment for other confounders (OR 0.77, 95% CI 0.57, 1.04, p = 0.08). These findings suggest that compared to a traditional Cantonese diet high in cereals, eggs, and Cantonese soups, a diet high in fruits, nuts, and Cantonese desserts might be associated with a higher birth weight, while a varied diet might be associated with a greater birth weight and also a decreased risk of having a SGA baby. PMID:27136584

  17. Maternal Dietary Patterns and Fetal Growth: A Large Prospective Cohort Study in China.

    PubMed

    Lu, Min-Shan; Chen, Qiao-Zhu; He, Jian-Rong; Wei, Xue-Ling; Lu, Jin-Hua; Li, Sheng-Hui; Wen, Xing-Xuan; Chan, Fan-Fan; Chen, Nian-Nian; Qiu, Lan; Mai, Wei-Bi; Zhang, Rui-Fang; Hu, Cui-Yue; Xia, Hui-Min; Qiu, Xiu

    2016-01-01

    There was limited evidence revealing the association of Chinese maternal dietary patterns with fetal growth. We aimed to examine the relationship of maternal dietary patterns during pregnancy to neonatal birth weight and birth weight for gestational age in a Chinese population. A total of 6954 mother-child pairs were included from the Born in Guangzhou Cohort Study. Maternal diet during pregnancy was assessed using a self-administered food frequency questionnaire. Cluster analysis was used to identify dietary patterns. The following six dietary patterns were identified: "Cereals, eggs, and Cantonese soups" (n 1026, 14.8%), "Dairy" (n 1020, 14.7%), "Fruits, nuts, and Cantonese desserts" (n 799, 11.5%), "Meats" (n 1066, 15.3%), "Vegetables" (n 1383, 19.9%), and "Varied" (n 1224, 17.6%). The mean neonatal birth weight Z scores of women in the above patterns were 0.02, 0.07, 0.20, 0.01, 0.06, and 0.14, respectively. Women in the "Fruits, nuts, and Cantonese desserts" and "Varied" groups had significantly heavier infants compared with those in the "Cereals, eggs, and Cantonese soups" group. Compared with women in the "Cereals, eggs, and Cantonese soups" group, those in the "Varied" group had marginally significantly lower odds of having a small-for-gestational age (SGA) infant after adjustment for other confounders (OR 0.77, 95% CI 0.57, 1.04, p = 0.08). These findings suggest that compared to a traditional Cantonese diet high in cereals, eggs, and Cantonese soups, a diet high in fruits, nuts, and Cantonese desserts might be associated with a higher birth weight, while a varied diet might be associated with a greater birth weight and also a decreased risk of having a SGA baby. PMID:27136584

  18. Regeneration patterns of northern white cedar, an old-growth forest dominant

    USGS Publications Warehouse

    Scott, Michael L.; Murphy, Peter G.

    1987-01-01

    Regeneration of Thuja occidentalis L. was examined in an old-growth dune forest on South Manitou Island, Michigan. To estimate the current status of cedar regeneration, we determined size structure of seedlings and stems and analyzed present patterns of establishment and persistence relative to substrate type. There has been a shift in the pattern of cedar establishment from soil to log substrates. While 97% of all stems ≥15 cm dbh are associated with a soil substrate, 81% of stems ≥2.5cm-25 cm tall. There was no significant relationship between the state of log decay and the density of seedlings >25 cm in height, indicating that long-term survival is not dependent on the degree of log decomposition. However, survival on logs is associated with canopy openings. Seedlings >25 cm tall were associated with gaps, and 78% of cedar stems (≥2.5 cm dbh) on logs were associated with a single windthrow gap. Thus, current cedar regeneration in this old-growth forest depends on logs and the canopy openings associated with them.

  19. Zebra pattern in rocks as a function of grain growth affected by second-phase particles

    NASA Astrophysics Data System (ADS)

    Kelka, Ulrich; Koehn, Daniel; Beaudoin, Nicolas

    2015-09-01

    In this communication we present a simple microdynamic model which can explain the beginning of the zebra pattern formation in rocks. The two dimensional model consists of two main processes, mineral replacement along a reaction front, and grain boundary migration affected by impurities. In the numerical model we assume that an initial distribution of second-phase particles is present due to sedimentary layering. The reaction front percolates the model and redistributes second-phase particles by shifting them until the front is saturated and drops the particles again. This produces and enhances initial layering. Grain growth is hindered in layers with high second-phase particle concentrations whereas layers with low concentrations coarsen. Due to the grain growth activity in layers with low second-phase particle concentrations these impurities are collected at grain boundaries and the crystals become very clean. Therefore the white layers in the pattern contain large grains with low concentration of second-phase particles, whereas the dark layers contain small grains with a large second-phase particle concentration.

  20. Academic Subenvironments and Differential Patterns of Self-Perceived Growth During College: A Test of Holland's Theory.

    ERIC Educational Resources Information Center

    Smart, John C.

    1997-01-01

    Examines differential patterns of college students' self-perceived growth within the framework of a theory of vocational choice/personality. Findings support the theory's premise that distinctive subenvironments encourage, reinforce, and reward distinctive attitudinal and behavioral patterns. Implications of the theory's potential to promote…

  1. The 2000 Census and Growth Patterns in Rural America. The Main Street Economist: Commentary on the Rural Economy.

    ERIC Educational Resources Information Center

    Sheaff, Katharine

    The 2000 Census reveals four patterns of change in rural America. Rural areas in states such as Florida and Arizona are gaining population due to high retiree growth. These areas will experience growth in service sector jobs that have low pay and low educational requirements. Florida and Arizona trail the nation in high school and college…

  2. Spatial patterns of tree-growth anomalies in the United States and southeastern Canada

    SciTech Connect

    Meko, D.; Stockton, C.W.; Hughes, M.K. ); Cook, E.R. ); Stahle, D.W. )

    1993-09-01

    A network of 248 tree-ring chronologies in the conterminous United States is assembled and analyzed by rotated principal components analysis (RPCA) to delineate [open quotes]regions[close quotes] of common tree-growth variation during the period 1705-1979. Spatial continuity of the tree-ring data is summarized by variogram analysis, and tree-ring data are gridded before RPCA to reduce effects of site clustering. Principal component drought information is evaluated by comparing PC scores and primary pattern coefficients with Palmer Drought Severity Index (PDSI) data from instrumental records. High PC pattern coefficients group geographically into regions coinciding roughly with nine drought regions delineated by RPCA of PDSI by other researchers. The drought signal as measured by the correlation between tree-ring PC scores and July PDSI, 1929-79, is strongest in the South and the interior West (r>0.7), and weakest in the Northeast and Pacific Northwest (r<0.16). A count of years with large negative PC scores in multiple regions marks the 1950s as the extreme in widespread drought across the southern United States to 1705. Tree-growth regions are sensitive to whether tree-ring data are gridded before RPCA. Principal components on ungridded tree-ring data to center on dense clusters of sites. The importance of site density is most noticeable in the RPCA results for the southeast, where the gridded data yield a PC centered on a group of climate-sensitive but widely spaced bald cypress chronologies. Cross-validation indicates that gridding of tree-ring anomalies over different species for drought reconstruction is more appropriate in the semiarid southwest than in cooler, moisture regions-especially the northeast and the Pacific Northwest. Our results endorse the large-scale chronology network as a long-term proxy for the spatial and temporal patterns of past drought across the United States. 41 refs., 12 figs., 2 tabs.

  3. The effect of butterfly-scale inspired patterning on leading-edge vortex growth

    NASA Astrophysics Data System (ADS)

    Wilroy, Jacob; Lang, Amy; Wahidi, Redha

    2014-11-01

    Leading edge vortices (LEVs) are important for generating thrust and lift in flapping flight, and the surface patterning (scales) on butterfly wings is hypothesized to play a role in the vortex formation of the LEV. To simplify this complex flow problem, we designed an experiment to focus on the alteration of 2-D vortex development with a variation in surface patterning. Specifically we are interested in the secondary vorticity generated by the LEV interacting at the patterned surface and how this can affect the growth rate of the circulation in the LEV. For this experiment we used rapid-prototyped longitudinal and transverse square grooves attached to a flat plate and compared the vortex formation as the plate moved vertically. The plate is impulsively started in quiescent water and flow fields at Re = 1500, 3000, and 6000 are examined using Digital Particle Image Velocimetry (DPIV). The vortex formation time is 0.6 and is based on the flat plate travel length and chord length. Support for this research came from NSF REU Grant 1358991 and CBET 1335848.

  4. The effect of butterfly-scale inspired patterning on leading-edge vortex growth

    NASA Astrophysics Data System (ADS)

    Wilroy, Jacob; Lang, Amy

    2015-11-01

    Leading edge vortices (LEVs) are important for generating thrust and lift in flapping flight, and the surface patterning (scales) on butterfly wings is hypothesized to play a role in the vortex formation of the LEV. To simplify this complex flow problem, an experiment was designed to focus on the alteration of 2-D vortex development with a variation in surface patterning. Specifically, the secondary vorticity generated by the LEV interacting at the patterned surface was studied and the subsequent affect on the growth rate of the circulation in the LEV. For this experiment we used butterfly inspired grooves attached to a flat plate and compared the vortex formation to a smooth plate case as the plate moved vertically. The plate is impulsively started in quiescent water and flow fields at Re = 1500, 3000, and 6000 are examined using Digital Particle Image Velocimetry (DPIV). The vortex formation time is 3.0 and is based on the flat plate travel length and chord length. We would like to thank the National Science Foundation REU Site Award 1358991 for funding this research.

  5. Origin of craniopharyngiomas: implications for growth pattern, clinical characteristics, and outcomes of tumor recurrence.

    PubMed

    Bao, Yun; Pan, Jun; Qi, Song-Tao; Lu, Yun-Tao; Peng, Jun-Xiang

    2016-07-01

    OBJECT Craniopharyngiomas are associated with a high rate of recurrence. The surgical management of recurrent lesions has been among the most challenging neurosurgical procedures because of the craniopharyngioma's complex topographical relationship with surrounding structures. The aim of this study was to define the determinative role of the site of origin on the growth pattern and clinical features of recurrent craniopharyngiomas. METHODS The authors performed a retrospective analysis of 52 patients who had undergone uniform treatment by a single surgeon. For each patient, data concerning symptoms and signs, imaging features, hypothalamic-pituitary function, and recurrence-free survival rate were collected. RESULTS For children, delayed puberty was more frequent in the group with Type I (infradiaphragmatic) craniopharyngioma than in the group with Type TS (tuberoinfundibular and suprasellar extraventricular) lesions (p < 0.05). For adults, blindness was more frequent in the Type I group than in the Type TS group (p < 0.05). Nausea or vomiting, delayed puberty, and growth retardation were more frequent in children than in adults (p < 0.05). Overall clinical outcome was good in 48.07% of the patients and poor in 51.92%. Patients with Type TS recurrent tumors had significantly worse functional outcomes and hypothalamic function than patients with the Type I recurrent tumors but better pituitary function especially in children. CONCLUSIONS The origin of recurrent craniopharyngiomas significantly affected the symptoms, signs, functional outcomes, and hypothalamic-pituitary functions of patients undergoing repeated surgery. Differences in tumor growth patterns and site of origin should be considered when one is comparing outcomes and survival across treatment paradigms in patients with recurrent craniopharyngiomas. PMID:26654183

  6. Multidisciplinary characterization of the long-bone cortex growth patterns through sheep's ontogeny.

    PubMed

    Cambra-Moo, Oscar; Nacarino-Meneses, Carmen; Díaz-Güemes, Idoia; Enciso, Silvia; García Gil, Orosia; Llorente Rodríguez, Laura; Rodríguez Barbero, Miguel Ángel; de Aza, Antonio H; González Martín, Armando

    2015-07-01

    Bone researches have studied extant and extinct taxa extensively trying to disclose a complete view of the complex structural and chemical transformations that model and remodel the macro and microstructure of bone during growth. However, to approach bone growth variations is not an easy task, and many aspects related with histological transformations during ontogeny remain unresolved. In the present study, we conduct a holistic approach using different techniques (polarized microscopy, Raman spectroscopy and X-ray diffraction) to examine the histomorphological and histochemical variations in the cortical bone of sheep specimens from intrauterine to adult stages, using environmentally controlled specimens from the same species. Our results suggest that during sheep bone development, the most important morphological (shape and size) and chemical transformations in the cortical bone occur during the first weeks of life; synchronized but dissimilar variations are established in the forelimb and hind limb cortical bone; and the patterns of bone tissue maturation in both extremities are differentiated in the adult stage. All of these results indicate that standardized histological models are useful not only for evaluating many aspects of normal bone growth but also to understand other important influences on the bones, such as pathologies that remain unknown. PMID:26091739

  7. A comparison of craniofacial Class I and Class II growth patterns.

    PubMed

    Riesmeijer, Arnold M; Prahl-Andersen, Birte; Mascarenhas, Anna K; Joo, Bert H; Vig, Katherine W L

    2004-04-01

    Longitudinal craniofacial databases, including the Fels Longitudinal Study, the Michigan Growth Study, and the Nijmegen (The Netherlands) Growth Study, were compared for a set of 12 craniofacial measurements on lateral skull cephalograms. The age ranges of the subjects were 7-14 years for females and 9-14 years for males. When we compared the normally distributed databases using multiple comparisons, a small sample test statistic t for differences between means of the databases showed few statistical differences. The databases were therefore pooled, and sex-specific Class I (ANB < 4 degrees), and Class II (ANB > or = 4 degrees) subsamples were analyzed with the same t test. The sizes of these subsamples ranged from 39 to 122 at the different ages. The findings showed that the Class II samples had greater SNA and SN-GoMe angles. Compared with the Class I group, shorter mandibles were found in the younger age groups of the Class II samples. No differences were found in mandibular length (Ar-Gn) and mandibular body length (Go-Gn) in the older Class II groups compared with the Class I groups. These findings indicate that the greater mandibular lengthening in the Class II groups might have contributed to successful Class II treatment in studies in which a Class I group was the control. Because of individual biological variability, the average Class I or Class II growth pattern might not be a realistic assumption or have clinical relevance for individual patients. PMID:15067263

  8. The global pattern of urbanization and economic growth: evidence from the last three decades.

    PubMed

    Chen, Mingxing; Zhang, Hua; Liu, Weidong; Zhang, Wenzhong

    2014-01-01

    The relationship between urbanization and economic growth has been perplexing. In this paper, we identify the pattern of global change and the correlation of urbanization and economic growth, using cross-sectional, panel estimation and geographic information systems (GIS) methods. The analysis has been carried out on a global geographical scale, while the timescale of the study spans the last 30 years. The data shows that urbanization levels have changed substantially during these three decades. Empirical findings from cross-sectional data and panel data support the general notion of close links between urbanization levels and GDP per capita. However, we also present significant evidence that there is no correlation between urbanization speed and economic growth rate at the global level. Hence, we conclude that a given country cannot obtain the expected economic benefits from accelerated urbanization, especially if it takes the form of government-led urbanization. In addition, only when all facets are taken into consideration can we fully assess the urbanization process. PMID:25099392

  9. The Global Pattern of Urbanization and Economic Growth: Evidence from the Last Three Decades

    PubMed Central

    Chen, Mingxing; Zhang, Hua; Liu, Weidong; Zhang, Wenzhong

    2014-01-01

    The relationship between urbanization and economic growth has been perplexing. In this paper, we identify the pattern of global change and the correlation of urbanization and economic growth, using cross-sectional, panel estimation and geographic information systems (GIS) methods. The analysis has been carried out on a global geographical scale, while the timescale of the study spans the last 30 years. The data shows that urbanization levels have changed substantially during these three decades. Empirical findings from cross-sectional data and panel data support the general notion of close links between urbanization levels and GDP per capita. However, we also present significant evidence that there is no correlation between urbanization speed and economic growth rate at the global level. Hence, we conclude that a given country cannot obtain the expected economic benefits from accelerated urbanization, especially if it takes the form of government-led urbanization. In addition, only when all facets are taken into consideration can we fully assess the urbanization process. PMID:25099392

  10. Teaching PubMed in cyberspace: the development of a self-learning package.

    PubMed

    King, Samuel; Kaplan, Richard; MacDonald, Kathleen

    2008-01-01

    This article discusses the development of a series of online modules for learning the PubMed version of MEDLINE. Funded by a National Library of Medicine grant and targeted initially to physician assistants practicing in New Hampshire, the project is approved for CE credit nationally by the American Association of Physician Assistants. The development of the project is described, the tutorial modules are reviewed, and issues encountered with technology and human factors are discussed and evaluated. PMID:19042708

  11. An analysis of gene/protein associations at PubMed scale

    PubMed Central

    2011-01-01

    Background Event extraction following the GENIA Event corpus and BioNLP shared task models has been a considerable focus of recent work in biomedical information extraction. This work includes efforts applying event extraction methods to the entire PubMed literature database, far beyond the narrow subdomains of biomedicine for which annotated resources for extraction method development are available. Results In the present study, our aim is to estimate the coverage of all statements of gene/protein associations in PubMed that existing resources for event extraction can provide. We base our analysis on a recently released corpus automatically annotated for gene/protein entities and syntactic analyses covering the entire PubMed, and use named entity co-occurrence, shortest dependency paths and an unlexicalized classifier to identify likely statements of gene/protein associations. A set of high-frequency/high-likelihood association statements are then manually analyzed with reference to the GENIA ontology. Conclusions We present a first estimate of the overall coverage of gene/protein associations provided by existing resources for event extraction. Our results suggest that for event-type associations this coverage may be over 90%. We also identify several biologically significant associations of genes and proteins that are not addressed by these resources, suggesting directions for further extension of extraction coverage. PMID:22166173

  12. Canine splenic haemangiosarcoma: influence of metastases, chemotherapy and growth pattern on post-splenectomy survival and expression of angiogenic factors.

    PubMed

    Göritz, M; Müller, K; Krastel, D; Staudacher, G; Schmidt, P; Kühn, M; Nickel, R; Schoon, H-A

    2013-07-01

    Splenic haemangiosarcomas (HSAs) from 122 dogs were characterized and classified according to their patterns of growth, survival time post splenectomy, metastases and chemotherapy. The most common pattern of growth was a mixture of cavernous, capillary and solid tumour tissue. Survival time post splenectomy was independent of the growth pattern; however, it was influenced by chemotherapy and metastases. Immunohistochemical assessment of the expression of angiogenic factors (fetal liver kinase-1, angiopoietin-2, angiopoietin receptor-2 and vascular endothelial growth factor A) and conventional endothelial markers (CD31, factor VIII-related antigen) revealed variable expression, particularly in undifferentiated HSAs. Therefore, a combination of endothelial markers should be used to confirm the endothelial origin of splenic tumours. PMID:23276383

  13. Looking for age-related growth decline in natural forests: unexpected biomass patterns from tree rings and simulated mortality

    USGS Publications Warehouse

    Foster, Jane R.; D'Amato, Anthony W.; Bradford, John B.

    2014-01-01

    Forest biomass growth is almost universally assumed to peak early in stand development, near canopy closure, after which it will plateau or decline. The chronosequence and plot remeasurement approaches used to establish the decline pattern suffer from limitations and coarse temporal detail. We combined annual tree ring measurements and mortality models to address two questions: first, how do assumptions about tree growth and mortality influence reconstructions of biomass growth? Second, under what circumstances does biomass production follow the model that peaks early, then declines? We integrated three stochastic mortality models with a census tree-ring data set from eight temperate forest types to reconstruct stand-level biomass increments (in Minnesota, USA). We compared growth patterns among mortality models, forest types and stands. Timing of peak biomass growth varied significantly among mortality models, peaking 20–30 years earlier when mortality was random with respect to tree growth and size, than when mortality favored slow-growing individuals. Random or u-shaped mortality (highest in small or large trees) produced peak growth 25–30 % higher than the surviving tree sample alone. Growth trends for even-aged, monospecific Pinus banksiana or Acer saccharum forests were similar to the early peak and decline expectation. However, we observed continually increasing biomass growth in older, low-productivity forests of Quercus rubra, Fraxinus nigra, and Thuja occidentalis. Tree-ring reconstructions estimated annual changes in live biomass growth and identified more diverse development patterns than previous methods. These detailed, long-term patterns of biomass development are crucial for detecting recent growth responses to global change and modeling future forest dynamics.

  14. NEMO: Extraction and normalization of organization names from PubMed affiliation strings

    PubMed Central

    Jonnalagadda, Siddhartha; Topham, Philip

    2010-01-01

    Background. We are witnessing an exponential increase in biomedical research citations in PubMed. However, translating biomedical discoveries into practical treatments is estimated to take around 17 years, according to the 2000 Yearbook of Medical Informatics, and much information is lost during this transition. Pharmaceutical companies spend huge sums to identify opinion leaders and centers of excellence. Conventional methods such as literature search, survey, observation, self-identification, expert opinion, and sociometry not only need much human effort, but are also noncomprehensive. Such huge delays and costs can be reduced by “connecting those who produce the knowledge with those who apply it”. A humble step in this direction is large scale discovery of persons and organizations involved in specific areas of research. This can be achieved by automatically extracting and disambiguating author names and affiliation strings retrieved through Medical Subject Heading (MeSH) terms and other keywords associated with articles in PubMed. In this study, we propose NEMO (Normalization Engine for Matching Organizations), a system for extracting organization names from the affiliation strings provided in PubMed abstracts, building a thesaurus (list of synonyms) of organization names, and subsequently normalizing them to a canonical organization name using the thesaurus. Results: We used a parsing process that involves multi-layered rule matching with multiple dictionaries. The normalization process involves clustering based on weighted local sequence alignment metrics to address synonymy at word level, and local learning based on finding connected components to address synonymy. The graphical user interface and java client library of NEMO are available at http://lnxnemo.sourceforge.net . Conclusion: NEMO is developed to associate each biomedical paper and its authors with a unique organization name and the geopolitical location of that organization. This system

  15. Reduction of Nodular Growth Pattern of Metastatic Uveal Melanoma after Radioembolization of Hepatic Metastases

    PubMed Central

    Halenda, Kevin M.; Kudchadkar, Ragini R.; Lawson, David H.; Kies, Darren D.; Zhelnin, Kristen E.; Krasinskas, Alyssa M.; Grossniklaus, Hans E.

    2016-01-01

    Aim The aim of this study was to report a case of metastatic uveal melanoma in which radioembolized nodular liver metastases decreased in size while infiltrative sinusoidal metastases progressed, leading to jaundice without obstruction of the biliary ducts. Methods The relevant clinical features, imaging, and histopathologic findings of this case are reviewed. Results A 61-year-old Caucasian male with a history of uveal melanoma of the left eye status post plaque brachytherapy developed numerous liver metastases. After progression on systemic therapies, he underwent palliative radioembolization. Despite some radiographic improvement in the liver metastases, he developed hyperbilirubinemia without biliary tract obstruction or signs of liver failure. A biopsy of radiographically normal liver demonstrated extensive sinusoidal infiltration with melanoma. Conclusions Distinct angiographic and histopathologic growth patterns of metastatic uveal melanoma differ in their amenability to radioembolization. Sinusoidal infiltration may lead to hyperbilirubinemia in the absence of overt obstruction or liver failure. PMID:27239458

  16. Differentiation of bacterial colonies and temporal growth patterns using hyperspectral imaging

    NASA Astrophysics Data System (ADS)

    Mehrübeoglu, Mehrube; Buck, Gregory W.; Livingston, Daniel W.

    2014-09-01

    Detection and identification of bacteria are important for health and safety. Hyperspectral imaging offers the potential to capture unique spectral patterns and spatial information from bacteria which can then be used to detect and differentiate bacterial species. Here, hyperspectral imaging has been used to characterize different bacterial colonies and investigate their growth over time. Six bacterial species (Pseudomonas fluorescens, Escherichia coli, Serratia marcescens, Salmonella enterica, Staphylococcus aureus, Enterobacter aerogenes) were grown on tryptic soy agar plates. Hyperspectral data were acquired immediately after, 24 hours after, and 96 hours after incubation. Spectral signatures from bacterial colonies demonstrated repeatable measurements for five out of six species. Spatial variations as well as changes in spectral signatures were observed across temporal measurements within and among species at multiple wavelengths due to strengthening or weakening reflectance signals from growing bacterial colonies based on their pigmentation. Between-class differences and within-class similarities were the most prominent in hyperspectral data collected 96 hours after incubation.

  17. Universal Patterns of Equilibrium Cluster Growth in Aqueous Sugars Observed by Dynamic Light Scattering

    PubMed Central

    Sidebottom, D. L.; Tran, Tri D.

    2010-01-01

    Dynamic light scattering performed on aqueous solutions of three sugars (glucose, maltose and sucrose) reveal a common pattern of sugar cluster formation with a narrow cluster size distribution. In each case, equilibrium clusters form whose size increases with increasing sugar content in an identical power law manner in advance of a common, critical-like, percolation threshold near 83 wt% sugar. The critical exponent of the power law divergence of the cluster size varies with temperature, increasing with decreasing temperature, due to changes in the strength of the intermolecular hydrogen bond and appears to vanish for temperatures in excess of 90 °C. Detailed analysis of the cluster growth process suggests a two-stage process: an initial cluster phase formed at low volume fractions, φ, consisting of non-interacting, monodisperse sugar clusters whose size increases φ1/3 followed by an aggregation stage, active at concentrations above about φ = 40%, where cluster-cluster contact first occurs. PMID:21243043

  18. Growth and alignment of thin film organic single crystals from dewetting patterns.

    PubMed

    Tisserant, Jean-Nicolas; Wicht, Gaëtan; Göbel, Ole F; Bocek, Eva; Bona, Gian-Luca; Geiger, Thomas; Hany, Roland; Mezzenga, Raffaele; Partel, Stefan; Schmid, Peter; Schweizer, Wolfhard Bernd; Heier, Jakob

    2013-06-25

    Studying and understanding the conditions under which organic semiconductors can be engineered to form aligned single crystals in thin films is of primary importance owing to their unique orientation-dependent optoelectronic properties. Efforts to reach this goal by self-assembly from solution-processed films have been rewarded only with limited success. In this article we present a new method to grow single crystalline thin films via solvent annealing. We identify solvate crystal growth in combination with a specific film dewetting morphology as key to successful fabrication of single crystals. Furthermore, these 2D single crystals can align on chemically patterned substrates to minimize their interfacial energy. We explore in situ the conditions for crystal formation and alignment. PMID:23706086

  19. RNA interference silencing of CHS greatly alters the growth pattern of apple (Malus x domestica).

    PubMed

    Dare, Andrew P; Hellens, Roger P

    2013-08-01

    Plants produce a vast array of phenolic compounds which are essential for their survival on land. One major class of polyphenols are the flavonoids and their formation is dependent on the enzyme chalcone synthase (CHS). In a recent study we silenced the CHS genes of apple (Malus × domestica Borkh.) and observed a loss of pigmentation in the fruit skin, flowers and stems. More surprisingly, highly silenced lines were significantly reduced in size, with small leaves and shortened internode lengths. Chemical analysis also revealed that the transgenic shoots contained greatly reduced concentrations of flavonoids which are known to modulate auxin flow. An auxin transport study verified this, with an increased auxin transport in the CHS-silenced lines. Overall, these findings suggest that auxin transport in apple has adapted to take place in the presence of high endogenous concentrations of flavonoids. Removal of these compounds therefore results in abnormal auxin movement and a highly disrupted growth pattern. PMID:23733058

  20. Expression Patterns of CREBs in Oocyte Growth and Maturation of Fish.

    PubMed

    Senthilkumaran, Balasubramanian; Sreenivasulu, Gunti; Wang, De-Shou; Sudhakumari, Cheni-Chery; Kobayashi, Tohru; Nagahama, Yoshitaka

    2015-01-01

    In fish, oocyte meiotic maturation is regulated by 17α, 20β-dihydroxy-progesterone through cAMP. To study the role of cAMP response element binding protein (CREB) in meiotic maturation, we cloned and characterized the expression pattern of CREBs from two fish models, the Nile tilapia and catfish. In the Nile tilapia three different CREBs were identified where in CREB1 was found in many tissues including gonads with abundant expression in testis. CREB2, few amino acids shorter than CREB1, was expressed in several tissues with abundant expression in ovary. In addition, a 3'UTR variant form, CREB3 was exclusively found in ovary. During natural 14-day ovarian cycle of the Nile tilapia, CREB1 expression was stable throughout vitellogenesis with a sharp decrease on the day of spawning. In contrast, CREB2 remain unchanged throughout the ovarian cycle, however elevated in 11-day full-grown immature ovarian follicle and after hCG-induction. Interestingly, CREB3 expression was induced three folds on the day of spawning as well as during hCG-induced oocyte maturation. Based on the synergistic expression pattern, CREB1 is likely to control oocyte growth, whereas CREB 2 and 3 contribute to oocyte maturation in tilapia and the latter seems to be critical. In catfish, a single form of CREB showed a maximum expression during spawning phase and hCG-induced maturation both in vivo and in vitro augmented CREB expression. These results suggest that spatial and temporal expression of CREBs seems to be important for final oocyte maturation and may also regulate oocyte growth in fish. PMID:26700177

  1. Expression Patterns of CREBs in Oocyte Growth and Maturation of Fish

    PubMed Central

    Wang, De-Shou; Sudhakumari, Cheni-Chery; Kobayashi, Tohru; Nagahama, Yoshitaka

    2015-01-01

    In fish, oocyte meiotic maturation is regulated by 17α, 20β-dihydroxy-progesterone through cAMP. To study the role of cAMP response element binding protein (CREB) in meiotic maturation, we cloned and characterized the expression pattern of CREBs from two fish models, the Nile tilapia and catfish. In the Nile tilapia three different CREBs were identified where in CREB1 was found in many tissues including gonads with abundant expression in testis. CREB2, few amino acids shorter than CREB1, was expressed in several tissues with abundant expression in ovary. In addition, a 3’UTR variant form, CREB3 was exclusively found in ovary. During natural 14-day ovarian cycle of the Nile tilapia, CREB1 expression was stable throughout vitellogenesis with a sharp decrease on the day of spawning. In contrast, CREB2 remain unchanged throughout the ovarian cycle, however elevated in 11-day full-grown immature ovarian follicle and after hCG-induction. Interestingly, CREB3 expression was induced three folds on the day of spawning as well as during hCG-induced oocyte maturation. Based on the synergistic expression pattern, CREB1 is likely to control oocyte growth, whereas CREB 2 and 3 contribute to oocyte maturation in tilapia and the latter seems to be critical. In catfish, a single form of CREB showed a maximum expression during spawning phase and hCG-induced maturation both in vivo and in vitro augmented CREB expression. These results suggest that spatial and temporal expression of CREBs seems to be important for final oocyte maturation and may also regulate oocyte growth in fish. PMID:26700177

  2. A new perspective on the growth pattern of the Wandering Albatross (Diomedea exulans) through DEB theory

    NASA Astrophysics Data System (ADS)

    Teixeira, Carlos M. G. L.; Sousa, Tânia; Marques, Gonçalo M.; Domingos, Tiago; Kooijman, Sebastiaan A. L. M.

    2014-11-01

    The Wandering Albatross (Diomedea exulans) and other seabirds exhibit a growing pattern that includes a period of body mass decrease before fledging. Several hypotheses have been suggested to explain it without success. We hypothesized that: 1) chicks and adults have similar metabolic traits regulating assimilation, growth and maturation; 2) there is a difference in locomotion effort between chicks and adults, and 3) chicks are exposed to a decline in food availability before fledging. This set of hypotheses allows for an energy surplus to be available and stored in reserve during the first months of development, explaining the mass recession that starts before fledging and the fact that adults keep a lower weight than fledglings, throughout the rest of their life span. To test this set of hypotheses we applied the Dynamic Energy Budget (DEB) theory. Using a small set of life-history traits and growth curves we parameterized the DEB standard model. We confirmed this set of hypotheses and estimated the pattern of decline in food availability that explains mass recession. An assessment of the daily energy intake was also performed. The implications related to that energy flux and diet composition are discussed based on current knowledge. The DEB model for the Wandering Albatross also provided estimates for the adult daily food ingested by adults (464.06 kJ kg- 1 d- 1), fasting capacity (25 d), Field Metabolic Rate (4.29 W kg- 1) and resting metabolic rate (2.87 W kg- 1). These values are consistent with the averages obtained in the field, suggesting that DEB may be useful to provide good estimations on a broader scale.

  3. Simulating Spatial Growth Patterns in Developing Countries: A Case of Shama in the Western Region of Ghana.

    NASA Astrophysics Data System (ADS)

    Inkoom, J. N.; Nyarko, B. K.

    2014-12-01

    The integration of geographic information systems (GIS) and agent-based modelling (ABM) can be an efficient tool to improve spatial planning practices. This paper utilizes GIS and ABM approaches to simulate spatial growth patterns of settlement structures in Shama. A preliminary household survey on residential location decision-making choice served as the behavioural rule for household agents in the model. Physical environment properties of the model were extracted from a 2005 image implemented in NetLogo. The resulting growth pattern model was compared with empirical growth patterns to ascertain the model's accuracy. The paper establishes that the development of unplanned structures and its evolving structural pattern are a function of land price, proximity to economic centres, household economic status and location decision-making patterns. The application of the proposed model underlines its potential for integration into urban planning policies and practices, and for understanding residential decision-making processes in emerging cities in developing countries. Key Words: GIS; Agent-based modelling; Growth patterns; NetLogo; Location decision making; Computational Intelligence.

  4. Hydraulic redistribution of soil water in two old-growth coniferous forests: quantifying patterns and controls.

    PubMed

    Warren, Jeffrey M; Meinzer, Frederick C; Brooks, J Renée; Domec, Jean-Christophe; Coulombe, Rob

    2007-01-01

    Although hydraulic redistribution of soil water (HR) by roots is a widespread phenomenon, the processes governing spatial and temporal patterns of HR are not well understood. We incorporated soil/plant biophysical properties into a simple model based on Darcy's law to predict seasonal trajectories of HR. We investigated the spatial and temporal variability of HR across multiple years in two old-growth coniferous forest ecosystems with contrasting species and moisture regimes by measurement of soil water content (theta) and water potential (Psi) throughout the upper soil profile, root distribution and conductivity, and relevant climate variables. Large HR variability within sites (0-0.5 mm d(-1)) was attributed to spatial patterns of roots, soil moisture and depletion. HR accounted for 3-9% of estimated total site water depletion seasonally, peaking at 0.16 mm d(-1) (ponderosa pine; Pinus ponderosa) or 0.30 mm d(-1) (Douglas-fir; Pseudotsuga menziesii), then declining as modeled pathway conductance dropped with increasing root cavitation. While HR can vary tremendously within a site, among years and among ecosystems, this variability can be explained by natural variability in Psi gradients and seasonal courses of root conductivity. PMID:17286824

  5. Classes of Individual Growth Trajectories of Religious Coping in Older Adulthood: Patterns and Predictors.

    PubMed

    Hayward, R David; Krause, Neal

    2016-07-01

    For many individuals, religion provides important cognitive resources for coping with stressors, especially in older adulthood. Although older adults are thought to make more use of these coping strategies than those at younger ages, less is known about how patterns of use change during the span of older adulthood. In a largely Christian sample of U.S. older adults, positive and negative religious coping were measured between 2 and 5 times over a period of 11 years (N = 1,075). Growth mixture modeling extracted latent classes of growth. The optimal solution for positive coping indicated a five-class structure (high, stable; high, declining moderately; high, declining rapidly; low, increasing; and low, stable) and the optimal negative coping solution had three classes (low, declining; low, increasing; and high, declining). Nominal logistic regression examined the relationship of individual characteristics with latent class. Education, religious commitment, religious attendance, and religious doubt were related to positive coping trajectory class. Only religious doubt was related to negative coping class. PMID:26187618

  6. Polystyrene-microsphere-assisted patterning of ZnO nanostructures: growth and characterization.

    PubMed

    Dong, J J; Zhang, X W; Zhang, S G; Tan, H R; Yin, Z G; Gao, Y; Wang, J X

    2013-02-01

    In this work, periodic arrays of various ZnO nanostructures were fabricated on both Si and GaN substrates via a facile hydrothermal process. To realize the site-specific growth, two kinds of masks were introduced. The polystyrene (PS) microsphere self-assembled monolayer (SAM) was employed as the mask to create a patterned seed layer to guide the growth of ZnO nanostructures. However, the resulting ZnO nanostructures are non-equidistant, and the diameter of the ZnO nanostructures is uncontrollable. As an alternative, TiO2 sol was used to replicate the PS microsphere SAM, and the inverted SAM (ISAM) mask was obtained by extracting the PS microspheres with toluene. By using the ISAM mask, the hexagonal periodic array of ZnO nanostructures with high uniformity were readily produced. Furthermore, the effect of the underlying substrates on the morphology of ZnO nanostructures has been investigated. It is found that the highly ordered and vertically aligned ZnO nanorods epitaxially grow on the GaN substrate, while the ZnO nanoflowers on Si substrates are random oriented. PMID:23646580

  7. Seed storage conditions change the germination pattern of clonal growth plants in Mediterranean salt marshes.

    PubMed

    Espinar, José L; García, Luis V; Clemente, Luis

    2005-07-01

    The effect of salinity level and extended exposure to different salinity and flooding conditions on germination patterns of three salt-marsh clonal growth plants (Juncus subulatus, Scirpus litoralis, and S. maritimus) was studied. Seed exposure to extended flooding and saline conditions significantly affected the outcome of the germination process in a different, though predictable, way for each species, after favorable conditions for germination were restored. Tolerance of the germination process was related to the average salinity level measured during the growth/germination season at sites where established individuals of each species dominated the species cover. No relationship was found between salinity tolerance of the germination process and seed response to extended exposure to flooding and salinity conditions. The salinity response was significantly related to the conditions prevailing in the habitats of the respective species during the unfavorable (nongrowth/nongermination) season. Our results indicate that changes in salinity and hydrology while seeds are dormant affect the outcome of the seed-bank response, even when conditions at germination are identical. Because these environmental-history-dependent responses differentially affect seed germination, seedling density, and probably sexual recruitment in the studied and related species, these influences should be considered for wetland restoration and management. PMID:21646131

  8. Seed storage conditions change the germination pattern of clonal growth plants in Mediterranean salt marshes

    USGS Publications Warehouse

    Espinar, J.L.; Garcia, L.V.; Clemente, L.

    2005-01-01

    The effect of salinity level and extended exposure to different salinity and flooding conditions on germination patterns of three saltmarsh clonal growth plants (Juncus subulatus, Scirpus litoralis, and S. maritimus) was studied. Seed exposure to extended flooding and saline conditions significantly affected the outcome of the germination process in a different, though predictable, way for each species, after favorable conditions for germination were restored. Tolerance of the germination process was related to the average salinity level measured during the growth/germination season at sites where established individuals of each species dominated the species cover. No relationship was found between salinity tolerance of the germination process and seed response to extended exposure to flooding and salinity conditions. The salinity response was significantly related to the conditions prevailing in the habitats of the respective species during the unfavorable (nongrowth/nongermination) season. Our results indicate that changes in salinity and hydrology while seeds are dormant affect the outcome of the seed-bank response, even when conditions at germination are identical. Because these environmental-history-dependent responses differentially affect seed germination, seedling density, and probably sexual recruitment in the studied and related species, these influences should be considered for wetland restoration and management.

  9. Landscape analysis of urban growth patterns in Seremban, Malaysia, using spatio-temporal data

    NASA Astrophysics Data System (ADS)

    Aburas, Maher M.; Abdullah, Sabrina H.; Ramli, Mohammad F.; As'shari, Zulfa H.

    2016-06-01

    Urban growth is one of the major issues that have played a significant role in destroying the ecosystem in recent years. Landscape analysis is an important technique widely used to evaluate urban growth patterns. In this study, four land-use maps from 1984, 1990, 2000, and 2010 have been used to analyze an urban landscape. The values of a built-up area were initially computed using a geographic information system environment based on the spatial gradient approach. Mathematical matrices were then used to determine the amount of change in urban patches in each direction. Results of the number of patches, landscape shape index, aggregation index, and total edges confirmed that the urban patches in Seremban, Malaysia, have become more dispersed from 2000 to 2010. The urban patches have also become more continuous, especially in the north-western part of Seremban as a result of the urban development in the Nilai District. These results indicate the necessity to create new policies in the city to protect the sustainability of the land use of Seremban.

  10. Monitoring of Water Spectral Pattern Reveals Differences in Probiotics Growth When Used for Rapid Bacteria Selection

    PubMed Central

    Slavchev, Aleksandar; Kovacs, Zoltan; Koshiba, Haruki; Nagai, Airi; Bázár, György; Krastanov, Albert; Kubota, Yousuke; Tsenkova, Roumiana

    2015-01-01

    Development of efficient screening method coupled with cell functionality evaluation is highly needed in contemporary microbiology. The presented novel concept and fast non-destructive method brings in to play the water spectral pattern of the solution as a molecular fingerprint of the cell culture system. To elucidate the concept, NIR spectroscopy with Aquaphotomics were applied to monitor the growth of sixteen Lactobacillus bulgaricus one Lactobacillus pentosus and one Lactobacillus gasseri bacteria strains. Their growth rate, maximal optical density, low pH and bile tolerances were measured and further used as a reference data for analysis of the simultaneously acquired spectral data. The acquired spectral data in the region of 1100-1850nm was subjected to various multivariate data analyses – PCA, OPLS-DA, PLSR. The results showed high accuracy of bacteria strains classification according to their probiotic strength. Most informative spectral fingerprints covered the first overtone of water, emphasizing the relation of water molecular system to cell functionality. PMID:26133176

  11. Long Bone Histology and Growth Patterns in Ankylosaurs: Implications for Life History and Evolution

    PubMed Central

    Stein, Martina; Hayashi, Shoji; Sander, P. Martin

    2013-01-01

    The ankylosaurs are one of the major dinosaur groups and are characterized by unique body armor. Previous studies on other dinosaur taxa have revealed growth patterns, life history and evolutionary mechanisms based on their long bone histology. However, to date nothing is known about long bone histology in the Ankylosauria. This study is the first description of ankylosaurian long bone histology based on several limb elements, which were sampled from different individuals from the Ankylosauridae and Nodosauridae. The histology is compared to that of other dinosaur groups, including other Thyreophora and Sauropodomorpha. Ankylosaur long bone histology is characterized by a fibrolamellar bone architecture. The bone matrix type in ankylosaurs is closest to that of Stegosaurus. A distinctive mixture of woven and parallel-fibered bone together with overall poor vascularization indicates slow growth rates compared to other dinosaurian taxa. Another peculiar characteristic of ankylosaur bone histology is the extensive remodeling in derived North American taxa. In contrast to other taxa, ankylosaurs substitute large amounts of their primary tissue early in ontogeny. This anomaly may be linked to the late ossification of the ankylosaurian body armor. Metabolically driven remodeling processes must have liberated calcium to ossify the protective osteodermal structures in juveniles to subadult stages, which led to further remodeling due to increased mechanical loading. Abundant structural fibers observed in the primary bone and even in remodeled bone may have improved the mechanical properties of the Haversian bone. PMID:23894321

  12. Technical development of PubMed Interact: an improved interface for MEDLINE/PubMed searches

    PubMed Central

    Muin, Michael; Fontelo, Paul

    2006-01-01

    Background The project aims to create an alternative search interface for MEDLINE/PubMed that may provide assistance to the novice user and added convenience to the advanced user. An earlier version of the project was the 'Slider Interface for MEDLINE/PubMed searches' (SLIM) which provided JavaScript slider bars to control search parameters. In this new version, recent developments in Web-based technologies were implemented. These changes may prove to be even more valuable in enhancing user interactivity through client-side manipulation and management of results. Results PubMed Interact is a Web-based MEDLINE/PubMed search application built with HTML, JavaScript and PHP. It is implemented on a Windows Server 2003 with Apache 2.0.52, PHP 4.4.1 and MySQL 4.1.18. PHP scripts provide the backend engine that connects with E-Utilities and parses XML files. JavaScript manages client-side functionalities and converts Web pages into interactive platforms using dynamic HTML (DHTML), Document Object Model (DOM) tree manipulation and Ajax methods. With PubMed Interact, users can limit searches with JavaScript slider bars, preview result counts, delete citations from the list, display and add related articles and create relevance lists. Many interactive features occur at client-side, which allow instant feedback without reloading or refreshing the page resulting in a more efficient user experience. Conclusion PubMed Interact is a highly interactive Web-based search application for MEDLINE/PubMed that explores recent trends in Web technologies like DOM tree manipulation and Ajax. It may become a valuable technical development for online medical search applications. PMID:17083729

  13. PubMed, The New York Times and The Chicago Tribune as Tools for Teaching Genetics

    PubMed Central

    Strauss, Bernard S.

    2005-01-01

    An elementary course in human heredity for students not planning to major in the sciences can be based on current scientific literature and on the popular media. Examinations are constructed from questions on recent abstracts obtained from PubMed. The course is designed to promote writing skills in the sciences, and students write two papers in the course of a quarter. In the first paper, students trace the primary source of media reports on genetics and attempt to evaluate the reporter's translation. In a second paper, students write popular articles on the basis of current primary sources. PMID:16143615

  14. Beyond PubMed: Searching the "Grey Literature" for Clinical Trial Results.

    PubMed

    Citrome, Leslie

    2014-07-01

    Clinical trial results have been traditionally communicated through the publication of scholarly reports and reviews in biomedical journals. However, this dissemination of information can be delayed or incomplete, making it difficult to appraise new treatments, or in the case of missing data, evaluate older interventions. Going beyond the routine search of PubMed, it is possible to discover additional information in the "grey literature." Examples of the grey literature include clinical trial registries, patent databases, company and industrywide repositories, regulatory agency digital archives, abstracts of paper and poster presentations on meeting/congress websites, industry investor reports and press releases, and institutional and personal websites. PMID:25337445

  15. Beyond PubMed: Searching the “Grey Literature” for Clinical Trial Results

    PubMed Central

    2014-01-01

    Clinical trial results have been traditionally communicated through the publication of scholarly reports and reviews in biomedical journals. However, this dissemination of information can be delayed or incomplete, making it difficult to appraise new treatments, or in the case of missing data, evaluate older interventions. Going beyond the routine search of PubMed, it is possible to discover additional information in the “grey literature.” Examples of the grey literature include clinical trial registries, patent databases, company and industrywide repositories, regulatory agency digital archives, abstracts of paper and poster presentations on meeting/congress websites, industry investor reports and press releases, and institutional and personal websites. PMID:25337445

  16. Micro-patterning of Mammalian Cells on Suspended MEMS Resonant Sensors for Long-Term Growth Measurements

    PubMed Central

    Corbin, Elise A.; Dorvel, Brian R.; Millet, Larry J.; King, William P.; Bashir, Rashid

    2014-01-01

    MEMS resonant mass sensors can measure the mass of individual cells, though long-term growth measurements are limited by the movement of cells off the sensor area. Micro-patterning techniques are a powerful approach to control the placement of individual cells in an arrayed format. In this work we present a method for micro-patterning cells on fully suspended resonant sensors through select functionalization and passivation of the chip surface. This method combines high-resolution photolithography with a blanket transfer technique for applying photoresist to avoid damaging the sensors. Cells are constrained to the patterned collagen area on the sensor by pluronic acting as a cell adhesion blocker. This micro-patterning method enables long-term growth measurements, which is demonstrated by a measurement of the change in mass of a human breast cancer cell over 18 h. PMID:24535001

  17. Analysis of changes in relative elemental growth rate patterns in the elongation zone of Arabidopsis roots upon gravistimulation

    NASA Technical Reports Server (NTRS)

    Mullen, J. L.; Ishikawa, H.; Evans, M. L.

    1998-01-01

    Although Arabidopsis is an important system for studying root physiology, the localized growth patterns of its roots have not been well defined, particularly during tropic responses. In order to characterize growth rate profiles along the apex of primary roots of Arabidopsis thaliana (L.) Heynh (ecotype Columbia) we applied small charcoal particles to the root surface and analyzed their displacement during growth using an automated video digitizer system with custom software for tracking the markers. When growing vertically, the maximum elongation rate occurred 481 +/- 50 microns back from the extreme tip of the root (tip of root cap), and the elongation zone extended back to 912 +/- 137 microns. The distal elongation zone (DEZ) has previously been described as the apical region of the elongation zone in which the relative elemental growth rate (REGR) is < or = 30% of the peak rate in the central elongation zone. By this definition, our data indicate that the basal limit of the DEZ was located 248 +/- 30 microns from the root tip. However, after gravistimulation, the growth patterns of the root changed. Within the first hour of graviresponse, the basal limit of the DEZ and the position of peak REGR shifted apically on the upper flank of the root. This was due to a combination of increased growth in the DEZ and growth inhibition in the central elongation zone. On the lower flank, the basal limit of the DEZ shifted basipetally as the REGR decreased. These factors set up the gradient of growth rate across the root, which drives curvature.

  18. Geography of Africa biomedical publications: An analysis of 1996–2005 PubMed papers

    PubMed Central

    Uthman, Olalekan A; Uthman, Mubashir B

    2007-01-01

    Background Scientific publications play an important role in scientific process providing a key linkage between knowledge production and use. Scientific publishing activity worldwide over the past decades shows that most countries in Africa have low levels of publication. We sought to examine trends and contribution of different Africa subregions and individual countries as represented by the articles indexed by PubMed between 1996 and 2005. Results Research production in Africa is highly skewed; South Africa, Egypt, and Nigeria make up a striking 60% of the total number of articles indexed by PubMed between 1996 and 2005. When adjusted for population size smaller countries, such as The Gambia, Gabon and Botswana, were more productive than Nigeria and Kenya. The Gambia and Eritrea had better records when total production was adjusted for gross domestic product. The contribution of Africa to global research production was persistently low through the period studied. Conclusion In this study, we found that most populous and rich countries (such as South Africa, Egypt, and Nigeria) have correspondingly higher research production; but smaller countries can be productive. We noted continuous increases and reassuring trends in the production of research articles from all African subregions during the period 1996 – 2005. However, contribution of Africa to global research production was limited. PMID:17927837

  19. Improving efficacy of PubMed Clinical Queries for retrieving scientifically strong studies on treatment.

    PubMed

    Corrao, Salvatore; Colomba, Daniela; Arnone, Sabrina; Argano, Christiano; Di Chiara, Tiziana; Scaglione, Rosario; Licata, Giuseppe

    2006-01-01

    The authors evaluated the retrieval power of PubMed "Clinical Queries," narrow search string, about therapy in comparison with a modified search string to avoid possible retrieval bias. PubMed search strategy was compared to a slightly modified string that included the Britannic English term "randomised." The authors tested the two strings joined onto each of four terms concerning topics of broad interest: hypertension, hepatitis, diabetes, and heart failure. In particular, precision was computed for not-indexed citations. The added word "randomised" improved total citation retrieval in any case. Total retrieval gain for not-indexed citations ranged from 11.1% to 21.4%. A significant number of Randomized Controlled Trial(s) (RCT)s (9.1-18.2%) was retrieved for each of the selected topics. They were often recently published RCTs. The authors think that correction of the Clinical Queries filter (when they focus on therapy and use narrow searches) is necessary to avoid biased search results with loss of relevant and up-to-date scientifically sound information. PMID:16799123

  20. A comparison of postnatal arterial patterns in a growth series of giraffe (Artiodactyla: Giraffa camelopardalis)

    PubMed Central

    Gignac, Paul M.; Hieronymus, Tobin L.; Witmer, Lawrence M.

    2016-01-01

    Nearly all living artiodactyls (even-toed ungulates) possess a derived cranial arterial pattern that is highly distinctive from most other mammals. Foremost among a suite of atypical arterial configurations is the functional and anatomical replacement of the internal carotid artery with an extensive, subdural arterial meshwork called the carotid rete. This interdigitating network branches from the maxillary artery and is housed within the cavernous venous sinus. As the cavernous sinus receives cooled blood draining from the nasal mucosa, heat rapidly dissipates across the high surface area of the rete to be carried away from the brain by the venous system. This combination yields one of the most effective mechanisms of selective brain cooling. Although arterial development begins from the same embryonic scaffolding typical of mammals, possession of a rete is typically accompanied by obliteration of the internal carotid artery. Among taxa with available ontogenetic data, the point at which the internal carotid obliterates is variable throughout development. In small-bodied artiodactyls, the internal carotid typically obliterates prior to parturition, but in larger species, the vessel may remain patent for several years. In this study, we use digital anatomical data collection methods to describe the cranial arterial patterns for a growth series of giraffe (Giraffa camelopardalis), from parturition to senescence. Giraffes, in particular, have unique cardiovascular demands and adaptations owing to their exceptional body form and may not adhere to previously documented stages of cranial arterial development. We find the carotid arterial system to be conserved between developmental stages and that obliteration of the giraffe internal carotid artery occurs prior to parturition. PMID:26925324

  1. A comparison of postnatal arterial patterns in a growth series of giraffe (Artiodactyla: Giraffa camelopardalis).

    PubMed

    O'Brien, Haley D; Gignac, Paul M; Hieronymus, Tobin L; Witmer, Lawrence M

    2016-01-01

    Nearly all living artiodactyls (even-toed ungulates) possess a derived cranial arterial pattern that is highly distinctive from most other mammals. Foremost among a suite of atypical arterial configurations is the functional and anatomical replacement of the internal carotid artery with an extensive, subdural arterial meshwork called the carotid rete. This interdigitating network branches from the maxillary artery and is housed within the cavernous venous sinus. As the cavernous sinus receives cooled blood draining from the nasal mucosa, heat rapidly dissipates across the high surface area of the rete to be carried away from the brain by the venous system. This combination yields one of the most effective mechanisms of selective brain cooling. Although arterial development begins from the same embryonic scaffolding typical of mammals, possession of a rete is typically accompanied by obliteration of the internal carotid artery. Among taxa with available ontogenetic data, the point at which the internal carotid obliterates is variable throughout development. In small-bodied artiodactyls, the internal carotid typically obliterates prior to parturition, but in larger species, the vessel may remain patent for several years. In this study, we use digital anatomical data collection methods to describe the cranial arterial patterns for a growth series of giraffe (Giraffa camelopardalis), from parturition to senescence. Giraffes, in particular, have unique cardiovascular demands and adaptations owing to their exceptional body form and may not adhere to previously documented stages of cranial arterial development. We find the carotid arterial system to be conserved between developmental stages and that obliteration of the giraffe internal carotid artery occurs prior to parturition. PMID:26925324

  2. Impact of Fertilizing Pattern on the Biodiversity of a Weed Community and Wheat Growth

    PubMed Central

    Tang, Leilei; Cheng, Chuanpeng; Wan, Kaiyuan; Li, Ruhai; Wang, Daozhong; Tao, Yong; Pan, Junfeng; Xie, Juan; Chen, Fang

    2014-01-01

    Weeding and fertilization are important farming practices. Integrated weed management should protect or improve the biodiversity of farmland weed communities for a better ecological environment with not only increased crop yield, but also reduced use of herbicides. This study hypothesized that appropriate fertilization would benefit both crop growth and the biodiversity of farmland weed communities. To study the effects of different fertilizing patterns on the biodiversity of a farmland weed community and their adaptive mechanisms, indices of species diversity and responses of weed species and wheat were investigated in a 17-year field trial with a winter wheat-soybean rotation. This long term field trial includes six fertilizing treatments with different N, P and K application rates. The results indicated that wheat and the four prevalent weed species (Galium aparine, Vicia sativa, Veronica persica and Geranium carolinianum) showed different responses to fertilizer treatment in terms of density, plant height, shoot biomass, and nutrient accumulations. Each individual weed population exhibited its own adaptive mechanisms, such as increased internode length for growth advantages and increased light interception. The PK treatment had higher density, shoot biomass, Shannon-Wiener and Pielou Indices of weed community than N plus P fertilizer treatments. The N1/2PK treatment showed the same weed species number as the PK treatment. It also showed higher Shannon-Wiener and Pielou Indices of the weed community, although it had a lower wheat yield than the NPK treatment. The negative effects of the N1/2PK treatment on wheat yield could be balanced by the simultaneous positive effects on weed communities, which are intermediate in terms of the effects on wheat and weeds. PMID:24416223

  3. Impact of fertilizing pattern on the biodiversity of a weed community and wheat growth.

    PubMed

    Tang, Leilei; Cheng, Chuanpeng; Wan, Kaiyuan; Li, Ruhai; Wang, Daozhong; Tao, Yong; Pan, Junfeng; Xie, Juan; Chen, Fang

    2014-01-01

    Weeding and fertilization are important farming practices. Integrated weed management should protect or improve the biodiversity of farmland weed communities for a better ecological environment with not only increased crop yield, but also reduced use of herbicides. This study hypothesized that appropriate fertilization would benefit both crop growth and the biodiversity of farmland weed communities. To study the effects of different fertilizing patterns on the biodiversity of a farmland weed community and their adaptive mechanisms, indices of species diversity and responses of weed species and wheat were investigated in a 17-year field trial with a winter wheat-soybean rotation. This long term field trial includes six fertilizing treatments with different N, P and K application rates. The results indicated that wheat and the four prevalent weed species (Galium aparine, Vicia sativa, Veronica persica and Geranium carolinianum) showed different responses to fertilizer treatment in terms of density, plant height, shoot biomass, and nutrient accumulations. Each individual weed population exhibited its own adaptive mechanisms, such as increased internode length for growth advantages and increased light interception. The PK treatment had higher density, shoot biomass, Shannon-Wiener and Pielou Indices of weed community than N plus P fertilizer treatments. The N1/2PK treatment showed the same weed species number as the PK treatment. It also showed higher Shannon-Wiener and Pielou Indices of the weed community, although it had a lower wheat yield than the NPK treatment. The negative effects of the N1/2PK treatment on wheat yield could be balanced by the simultaneous positive effects on weed communities, which are intermediate in terms of the effects on wheat and weeds. PMID:24416223

  4. The influence of infant feeding patterns on growth of children in American Samoa.

    PubMed

    Bindon, J R

    1985-01-01

    This paper examines the trends in infant feeding practices in American Samoa and analyzes the relationship between infant feeding and growth among children born in American Samoa from 1976 to 1982. The study population is composed of the Polynesian inhabitants of the islands comprising the Territory of American Samoa. The sample is drawn from the records of the Well Baby Clinic in American Samoa. Feeding habit information and health of the infant was solicited by the nurses and doctor during clinic visits. The mothers were questioned about the child's diet. About 40% of the infants were exclusively breastfed; 13% had bottle supplements; 6% were classified as milk drinkers; and 40% were formula-fed. Frequently more than 1 feeding pattern was noted for a given child. Feeding influences were found to be significant on weight up to age 4, and height up to age 3. The timing of the introduction of solids was found to have a significant relationship with length through age 2. There appears to be a complex set of interactions between socioeconomic, growth and health factors. Mothers wean children early to return of work. This results from the availability of infant formula in Samoan stores, more jobs for women and the desire to improve socioeconomic status. Bottlefed infants of working mothers are more likely to have gastrointestinal problems than other infants. As a group, however, bottlefed infants are likely to have higher weights. The most significant contributing factor to morbidity and mortality among adults in American Samoa is the high prevalence of obesity. Extended breastfeeding of the infant can promote health in infancy and in later years. PMID:3836322

  5. Age, growth, and recruitment patterns of juvenile ladyfish (Elops sp) from the east coast of Florida (USA)

    PubMed Central

    2015-01-01

    Ladyfish (Elops sp) are a common and economically valuable coastal nearshore species found along coastal beaches, bays, and estuaries of the southeastern United States, and subtropical and tropical regions worldwide. Previously, ladyfish were a substantial bycatch in Florida’s commercial fisheries, but changes in regulations significantly reduced commercial landings. Today, ladyfish are still taken in commercial fisheries in Florida, but many are also taken by recreational anglers. Life-history information and research interest in ladyfish is almost non-existent, especially information on age and growth. Thus, the overarching purpose of this study was to expand our understanding of ladyfish age and growth characteristics. The specific objectives were to describe, for the first time, age, growth, and recruitment patterns of juvenile ladyfish from the east coast of Florida (USA). In the Indian River Lagoon (IRL), annual monthly length-frequency distributions were confounded because a few small individuals recruited throughout the year; monthly length-frequency data generally demonstrated a cyclical pattern. The smallest were collected in September and the largest in May. Post-hoc analysis showed no significant difference in length between August and May, or among the other months. In Volusia County (VC), annual monthly length-frequency distribution demonstrated growth generally occurred from late-winter and spring to summer. The smallest ladyfish were collected in February and the largest in August. On average, the absolute growth rate in the IRL was 36.3 mm in 60 days or 0.605 mm day−1. Cohort-specific daily growth rates, elevations, and coincidentals were similar among sampling years. Cohort-specific growth rates ranged from 1.807 in 1993 to 1.811 mm day−1 in 1994. Overall, growth was best (i.e., goodness of fit) described by exponential regression. On average, the absolute growth rate in VC was 28 mm in 150 days or 0.1866 mm day−1. Cohort-specific daily

  6. Control of patterning, growth, and differentiation by floral organ identity genes.

    PubMed

    Sablowski, Robert

    2015-02-01

    In spite of the different morphologies of sepals, petals, stamens, and carpels, all these floral organs are believed to be modified versions of a ground-state organ similar to the leaf. Modifications of the ground-state developmental programme are orchestrated by different combinations of MADS-domain transcription factors encoded by floral organ identity genes. In recent years, much has been revealed about the gene regulatory networks controlled by the floral organ identity genes and about the genetic pathways that control leaf development. This review examines how floral organ identity is connected with the control of morphogenesis and differentiation of shoot organs, focusing on the model species Arabidopsis thaliana. Direct links have emerged between floral organ identity genes and genes involved in abaxial-adaxial patterning, organ boundary formation, tissue growth, and cell differentiation. In parallel, predictive models have been developed to explain how the activity of regulatory genes can be coordinated by intercellular signalling and constrained by tissue mechanics. When combined, these advances provide a unique opportunity for revealing exactly how leaf-like organs have been 'metamorphosed' into floral organs during evolution and showing crucial regulatory points in the generation of plant form. PMID:25609826

  7. Growth of interleaved masking patterns for cochlear implant listeners at different stimulation rates

    NASA Astrophysics Data System (ADS)

    Kwon, Bom Jun; van den Honert, Chris; Parkinson, Wendy

    2003-04-01

    This study investigates the pattern of growth of masking (GOM) for interleaved masking with Nucleus cochlear implant users. For an interleaved masking paradigm, where the masker and probe overlap in a same time window, the masker may have contrasting effects: it may increase the threshold (as a masker normally does) or decrease it due to a neural summation effect, facilitating detection of the probe. Several stimulation rates and masker levels were tested to examine under what conditions what phenomenon would occur. The results indicated that, in most of the conditions, the amount of masking was positive, i.e., the facilitating effect was not consistently observed. However, the slope of the GOM appears to be dependent upon the stimulation rate: the higher the stimulation rate, the lower the slope, implying that the facilitating effect might be always present and make a bigger impact on overall masking as the stimulation rate becomes high. The amount of masking was also often nonzero (positive) even when the masker was below the threshold level. Overall, the present findings indicate that interleaved masking should be handled with care to understand cochlear implant users speech perception and improve speech coding, as it contains some nontraditional aspects of masking.

  8. Interfacial growth of controllable morphology of silver patterns on plastic substrates.

    PubMed

    Cui, Guanghui; Qi, Shengli; Wang, Xiaodong; Tian, Guofeng; Sun, Guang; Liu, Wei; Yan, Xiaona; Wu, Dezhen; Wu, Zhanpeng; Zhang, Li

    2012-10-11

    Controllable growth of newly born silver nanoparticles to fractal, cauliflower-like, microscale disks and continuous silver layers with high conductivity and reflectivity on plastic substrates has been developed via solid-liquid interfacial reduction and growing of ion-doped polymeric films. Such approaches involve polyimide (PI) films as substrates, its corresponding silver-ion-doped precursors as solid oxidants, and facile immersion of ion-doped polymeric films in aqueous reducing solution. The solution reducing process belongs to liquid-solid interfacial reduction processes, during which silver ions doped in polymeric matrix transformed to newly born silver nanoparticles which further aggregated and migrated along the liquid-solid interface to form dendrite, cauliflower-like and lamella disk-like architecture and/or severely compact continuous silver nanolayers with highly reflective and conductive properties. Time-dependent morphology evolutions of silver particles were traced by scanning electron microscopy (SEM), atomic force microscopy (AFM), and transmission electron microscopy (TEM). This strategy can also extend to synthesis of many other metals on polymeric films while maintaining outstanding metal-polymer adhesion based on incorporation of various metal ions, and may offer an opportunity to fabricate large scale, high-output, cost-effective processes for metal patterns on flexible polymeric substrates. PMID:23016702

  9. The pathology of urinary bladder lesions with an inverted growth pattern.

    PubMed

    Guo, Aitao; Liu, Aijun; Teng, Xiaodong

    2016-02-01

    Inverted lesions in the urinary bladder have been the source of some difficulty in urological pathology. The two common ones are von Brunn's nests and cystitis cystic/cystitis glandularis, which are considered normal variants of urothelium. Apart from them, a number of other rare urothelial lesions with inverted growth pattern occur in the urinary bladder. Some of them are only reactive conditions, just as pseudocarcinomatous hyperplasia. Some are benign tumors, namely inverted papilloma. Whereas others are malignant neoplasms, including inverted papillary urothelial neoplasm of low malignant potential (PUNLMP), non-invasive inverted papillary urothelial carcinoma (low-grade and high-grade), and invasive urothelial carcinoma (inverted, nested and big nested variants). Because of the overlapping morphological features of all the inverted lesions mentioned above, even between high-grade invasive carcinoma and pseudocarcinomatous hyperplasia which are only a kind of reactive conditions, it is very important for the surgical pathologist to recognize and be familiar with these inverted lesions in urinary bladder. In this article, we review these spectrums of inverted lesions of the urinary bladder. Emphasis is placed on histogenesis, morphology, differential diagnosis of these lesions, and the pathologic grading of the non-invasive inverted neoplasms, such as inverted papilloma, inverted PUNLMP, non-invasive inverted papillary urothelial carcinoma with low-grade, and non-invasive inverted papillary urothelial carcinoma with high-grade. PMID:27041933

  10. Scaling up the shape: A novel growth pattern of gallium clusters

    SciTech Connect

    Kaware, Vaibhav; Joshi, Kavita E-mail: kavita.p.joshi@gmail.com

    2014-08-07

    Putative global minima for Ga{sub N}{sup +} clusters with size “N” ranging from 49 to 70 are found by employing the Kohn-Sham formulation of the density functional theory, and their evolution is described and discussed in detail. We have discovered a unique growth pattern in these clusters, all of which are hollow core-shell structures. They evolve with size from one spherical core-shell to the next spherical core-shell structure mediated by prolate geometries, with an increase in overall diameter of the core, as well as the shell, without putting on new layers of atoms. We also present a complete picture of bonding in gallium clusters by critically analyzing the molecular orbitals, the electron localization function, and Bader charges. Bonding in these clusters is a mixture of metallic and covalent type that leans towards covalency, accompanied by marginal charge transfer from the surface to the core. Most molecular orbitals of Ga clusters are non-jellium type. Covalency of bonding is supported by a wide localization window of electron localization function, and joining of its basins along the bonds.

  11. Process for selectively patterning epitaxial film growth on a semiconductor substrate

    DOEpatents

    Sheldon, Peter; Hayes, Russell E.

    1986-01-01

    A process is disclosed for selectively patterning epitaxial film growth on a semiconductor substrate. The process includes forming a masking member on the surface of the substrate, the masking member having at least two layers including a first layer disposed on the substrate and the second layer covering the first layer. A window is then opened in a selected portion of the second layer by removing that portion to expose the first layer thereunder. The first layer is then subjected to an etchant introduced through the window to dissolve a sufficient amount of the first layer to expose the substrate surface directly beneath the window, the first layer being adapted to preferentially dissolve at a substantially greater rate than the second layer so as to create an overhanging ledge portion with the second layer by undercutting the edges thereof adjacent to the window. The epitaxial film is then deposited on the exposed substrate surface directly beneath the window. Finally, an etchant is introduced through the window to dissolve the remainder of the first layer so as to lift-off the second layer and materials deposited thereon to fully expose the balance of the substrate surface.

  12. Process for selectively patterning epitaxial film growth on a semiconductor substrate

    DOEpatents

    Sheldon, P.; Hayes, R.E.

    1984-12-04

    Disclosed is a process for selectively patterning epitaxial film growth on a semiconductor substrate. The process includes forming a masking member on the surface of the substrate, the masking member having at least two layers including a first layer disposed on the substrate and the second layer covering the first layer. A window is then opened in a selected portion of the second layer by removing that portion to expose the first layer thereunder. The first layer is then subjected to an etchant introduced through the window to dissolve the first layer a sufficient amount to expose the substrate surface directly beneath the window, the first layer being adapted to preferentially dissolve at a substantially greater rate than the second layer so as to create an overhanging ledge portion with the second layer by undercutting the edges thereof adjacent the window. The epitaxial film is then deposited on the exposed substrate surface directly beneath the window. Finally, an etchant is introduced through the window to dissolve the remainder of the first layer so as to lift-off the second layer and materials deposited thereon to fully expose the balance of the substrate surface.

  13. Controlling the Growth Modes of Femtoliter Sessile Droplets Nucleating on Chemically Patterned Surfaces.

    PubMed

    Bao, Lei; Werbiuk, Zenon; Lohse, Detlef; Zhang, Xuehua

    2016-03-17

    Femtoliter droplet arrays on immersed substrates are essential elements in a broad range of advanced droplet-based technologies, such as light manipulation, sensing, and high throughput diagnosis. Solvent exchange is a bottom-up approach for producing those droplets from a pulse of oil oversaturation when a good solvent of the droplet liquid is displaced by a poor solvent. The position and arrangement of the droplets are regulated by chemical micropatterns on the substrate. Here we show experimentally and theoretically that the growth modes of droplets confined in planar micropatterns on the surface can be manipulated through the laminar flow of the solvent exchange. The control parameters are the area size of the micropatterns and the flow rate, and the observables are the contact angle and the final droplet volume. For a given pattern size, the Peclet number of the flow determines whether the growing droplets switch from an initial constant contact angle mode to a subsequent constant contact radius mode. Good agreement is achieved between the experimental results and our theoretical model that describes the dependence of the final droplet size on Pe. PMID:26938312

  14. The pathology of urinary bladder lesions with an inverted growth pattern

    PubMed Central

    Liu, Aijun; Teng, Xiaodong

    2016-01-01

    Inverted lesions in the urinary bladder have been the source of some difficulty in urological pathology. The two common ones are von Brunn’s nests and cystitis cystic/cystitis glandularis, which are considered normal variants of urothelium. Apart from them, a number of other rare urothelial lesions with inverted growth pattern occur in the urinary bladder. Some of them are only reactive conditions, just as pseudocarcinomatous hyperplasia. Some are benign tumors, namely inverted papilloma. Whereas others are malignant neoplasms, including inverted papillary urothelial neoplasm of low malignant potential (PUNLMP), non-invasive inverted papillary urothelial carcinoma (low-grade and high-grade), and invasive urothelial carcinoma (inverted, nested and big nested variants). Because of the overlapping morphological features of all the inverted lesions mentioned above, even between high-grade invasive carcinoma and pseudocarcinomatous hyperplasia which are only a kind of reactive conditions, it is very important for the surgical pathologist to recognize and be familiar with these inverted lesions in urinary bladder. In this article, we review these spectrums of inverted lesions of the urinary bladder. Emphasis is placed on histogenesis, morphology, differential diagnosis of these lesions, and the pathologic grading of the non-invasive inverted neoplasms, such as inverted papilloma, inverted PUNLMP, non-invasive inverted papillary urothelial carcinoma with low-grade, and non-invasive inverted papillary urothelial carcinoma with high-grade. PMID:27041933

  15. Self-Esteem Trajectories among Ethnic Minority Adolescents: A Growth Curve Analysis of the Patterns and Predictors of Change

    ERIC Educational Resources Information Center

    Greene, Melissa L.; Way, Niobe

    2005-01-01

    The current study presents a growth curve analysis of self-esteem among Black, Latino, and Asian American high school students. A series of hierarchical linear models were used to examine patterns and predictors of change in self-esteem over time. Results revealed an average increase in self-esteem with age. Although boys and girls experienced…

  16. Spiral and target patterns in bivalve nacre manifest a natural excitable medium from layer growth of a biological liquid crystal

    PubMed Central

    Cartwright, Julyan H. E.; Checa, Antonio G.; Escribano, Bruno; Sainz-Díaz, C. Ignacio

    2009-01-01

    Nacre is an exquisitely structured biocomposite of the calcium carbonate mineral aragonite with small amounts of proteins and the polysaccharide chitin. For many years, it has been the subject of research, not just because of its beauty, but also to discover how nature can produce such a superior product with excellent mechanical properties from such relatively weak raw materials. Four decades ago, Wada [Wada K (1966) Spiral growth of nacre. Nature 211:1427] proposed that the spiral patterns in nacre could be explained by using the theory Frank [Frank F (1949) The influence of dislocations on crystal growth. Discuss Faraday Soc 5:48–54] had put forward of the growth of crystals by means of screw dislocations. Frank's mechanism of crystal growth has been amply confirmed by experimental observations of screw dislocations in crystals, but it is a growth mechanism for a single crystal, with growth fronts of molecules. However, the growth fronts composed of many tablets of crystalline aragonite visible in micrographs of nacre are not a molecular-scale but a mesoscale phenomenon, so it has not been evident how the Frank mechanism might be of relevance. Here, we demonstrate that nacre growth is organized around a liquid-crystal core of chitin crystallites, a skeleton that the other components of nacre subsequently flesh out in a process of hierarchical self-assembly. We establish that spiral and target patterns can arise in a liquid crystal formed layer by layer through the Burton–Cabrera–Frank [Burton W, Cabrera N, Frank F (1951) The growth of crystals and the equilibrium structure of their surfaces. Philos Trans R Soc London Ser A 243:299–358] dynamics, and furthermore that this layer growth mechanism is an instance of an important class of physical systems termed excitable media. Artificial liquid crystals grown in this way may have many technological applications. PMID:19528636

  17. Spiral and target patterns in bivalve nacre manifest a natural excitable medium from layer growth of a biological liquid crystal.

    PubMed

    Cartwright, Julyan H E; Checa, Antonio G; Escribano, Bruno; Sainz-Díaz, C Ignacio

    2009-06-30

    Nacre is an exquisitely structured biocomposite of the calcium carbonate mineral aragonite with small amounts of proteins and the polysaccharide chitin. For many years, it has been the subject of research, not just because of its beauty, but also to discover how nature can produce such a superior product with excellent mechanical properties from such relatively weak raw materials. Four decades ago, Wada [Wada K (1966) Spiral growth of nacre. Nature 211:1427] proposed that the spiral patterns in nacre could be explained by using the theory Frank [Frank F (1949) The influence of dislocations on crystal growth. Discuss Faraday Soc 5:48-54] had put forward of the growth of crystals by means of screw dislocations. Frank's mechanism of crystal growth has been amply confirmed by experimental observations of screw dislocations in crystals, but it is a growth mechanism for a single crystal, with growth fronts of molecules. However, the growth fronts composed of many tablets of crystalline aragonite visible in micrographs of nacre are not a molecular-scale but a mesoscale phenomenon, so it has not been evident how the Frank mechanism might be of relevance. Here, we demonstrate that nacre growth is organized around a liquid-crystal core of chitin crystallites, a skeleton that the other components of nacre subsequently flesh out in a process of hierarchical self-assembly. We establish that spiral and target patterns can arise in a liquid crystal formed layer by layer through the Burton-Cabrera-Frank [Burton W, Cabrera N, Frank F (1951) The growth of crystals and the equilibrium structure of their surfaces. Philos Trans R Soc London Ser A 243:299-358] dynamics, and furthermore that this layer growth mechanism is an instance of an important class of physical systems termed excitable media. Artificial liquid crystals grown in this way may have many technological applications. PMID:19528636

  18. Growth and characterization of semi-polar (11-22) GaN on patterned (113) Si substrates

    NASA Astrophysics Data System (ADS)

    Bai, J.; Yu, X.; Gong, Y.; Hou, Y. N.; Zhang, Y.; Wang, T.

    2015-06-01

    Patterned (113) Si substrates have been fabricated for the growth of (11-22) semi-polar GaN, which completely eliminates one of the great issues in the growth of semi-polar GaN on silicon substrates, ‘Ga melting-back’. Furthermore, unlike any other mask patterning approaches which normally lead to parallel grooves along a particular orientation, our approach is to form periodic square window patterns. As a result, crack-free semi-polar (11-22) GaN with a significant improvement in crystal quality has been achieved, in particular, basal stacking faults (BSFs) have been significantly reduced. The mechanism for the defect suppression has been investigated based on detailed transmission electron microscopy measurements. It has been found that the BSFs can be impeded effectively at an early growth stage due to the priority growth along the <0001> direction. The additional <1-100> lateral growth above the masks results in a further reduction in dislocation density. The significant reduction in BSFs has been confirmed by low temperature photoluminescence measurements.

  19. Automated Determination of Publications Related to Adverse Drug Reactions in PubMed

    PubMed Central

    Adams, Hayden; Friedman, Carol; Finkelstein, Joseph

    2015-01-01

    Timely dissemination of up-to-date information concerning adverse drug reactions (ADRs) at the point of care can significantly improve medication safety and prevent ADRs. Automated methods for finding relevant articles in MEDLINE which discuss ADRs for specific medications can facilitate decision making at the point of care. Previous work has focused on other types of clinical queries and on retrieval for specific ADRs or drug-ADR pairs, but little work has been published on finding ADR articles for a specific medication. We have developed a method to generate a PubMED query based on MESH, supplementary concepts, and textual terms for a particular medication. Evaluation was performed on a limited sample, resulting in a sensitivity of 90% and precision of 93%. Results demonstrated that this method is highly effective. Future work will integrate this method within an interface aimed at facilitating access to ADR information for specified drugs at the point of care. PMID:26306227

  20. Seedless Pattern Growth of Quasi-Aligned ZnO Nanorod Arrays on Cover Glass Substrates in Solution

    NASA Astrophysics Data System (ADS)

    Ahsanulhaq, Q.; Kim, Jin Hwan; Kim, Jeong Hyun; Hahn, Y. B.

    2010-03-01

    A hybrid technique for the selective growth of ZnO nanorod arrays on wanted areas of thin cover glass substrates was developed without the use of seed layer of ZnO. This method utilizes electron-beam lithography for pattern transfer on seedless substrate, followed by solution method for the bottom-up growth of ZnO nanorod arrays on the patterned substrates. The arrays of highly crystalline ZnO nanorods having diameter of 60 ± 10 nm and length of 750 ± 50 nm were selectively grown on different shape patterns and exhibited a remarkable uniformity in terms of diameter, length, and density. The room temperature cathodluminescence measurements showed a strong ultraviolet emission at 381 nm and broad visible emission at 585-610 nm were observed in the spectrum.

  1. Water temperature and fish growth: otoliths predict growth patterns of a marine fish in a changing climate.

    PubMed

    Rountrey, Adam N; Coulson, Peter G; Meeuwig, Jessica J; Meekan, Mark

    2014-08-01

    Ecological modeling shows that even small, gradual changes in body size in a fish population can have large effects on natural mortality, biomass, and catch. However, efforts to model the impact of climate change on fish growth have been hampered by a lack of long-term (multidecadal) data needed to understand the effects of temperature on growth rates in natural environments. We used a combination of dendrochronology techniques and additive mixed-effects modeling to examine the sensitivity of growth in a long-lived (up to 70 years), endemic marine fish, the western blue groper (Achoerodus gouldii), to changes in water temperature. A multi-decadal biochronology (1952-2003) of growth was constructed from the otoliths of 56 fish collected off the southwestern coast of Western Australia, and we tested for correlations between the mean index chronology and a range of potential environmental drivers. The chronology was significantly correlated with sea surface temperature in the region, but common variance among individuals was low. This suggests that this species has been relatively insensitive to past variations in climate. Growth increment and age data were also used in an additive mixed model to predict otolith growth and body size later this century. Although growth was relatively insensitive to changes in temperature, the model results suggested that a fish aged 20 in 2099 would have an otolith about 10% larger and a body size about 5% larger than a fish aged 20 in 1977. Our study shows that species or populations regarded as relatively insensitive to climate change could still undergo significant changes in growth rate and body size that are likely to have important effects on the productivity and yield of fisheries. PMID:24862838

  2. A Bibliometric Analysis of PubMed Literature on Middle East Respiratory Syndrome

    PubMed Central

    Wang, Zhengting; Chen, Yongdi; Cai, Gaofeng; Jiang, Zhenggang; Liu, Kui; Chen, Bin; Jiang, Jianmin; Gu, Hua

    2016-01-01

    Middle East Respiratory Syndrome (MERS), a pandemic threat to human beings, has aroused huge concern worldwide, but no bibliometric studies have been conducted on MERS research. The aim of this study was to map research productivity on the disease based on the articles indexed in PubMed. The articles related to MERS dated from 2012 to 2015 were retrieved from PubMed. The articles were classified into three categories according to their focus. Publication outputs were assessed and frequently used terms were mapped using the VOS viewer software. A total of 443 articles were included for analysis. They were published in 162 journals, with Journal of Virology being the most productive (44 articles; 9.9%) and by six types of organizations, with universities being the most productive (276 articles; 62.4%).The largest proportion of the articles focused on basic medical sciences and clinical studies (47.2%) and those on prevention and control ranked third (26.2%), with those on other focuses coming in between (26.6%). The articles on prevention and control had the highest mean rank for impact factor (IF) (226.34), followed by those on basic medical sciences and clinical studies (180.23) and those on other focuses (168.03). The mean rank differences were statistically significant (p = 0.000). Besides, “conronavirus”, “case”, “transmission” and “detection” were found to be the most frequently used terms. The findings of this first bibliometric study on MERS suggest that the prevention and control of the disease has become a big concern and related research should be strengthened. PMID:27304963

  3. A Bibliometric Analysis of PubMed Literature on Middle East Respiratory Syndrome.

    PubMed

    Wang, Zhengting; Chen, Yongdi; Cai, Gaofeng; Jiang, Zhenggang; Liu, Kui; Chen, Bin; Jiang, Jianmin; Gu, Hua

    2016-01-01

    Middle East Respiratory Syndrome (MERS), a pandemic threat to human beings, has aroused huge concern worldwide, but no bibliometric studies have been conducted on MERS research. The aim of this study was to map research productivity on the disease based on the articles indexed in PubMed. The articles related to MERS dated from 2012 to 2015 were retrieved from PubMed. The articles were classified into three categories according to their focus. Publication outputs were assessed and frequently used terms were mapped using the VOS viewer software. A total of 443 articles were included for analysis. They were published in 162 journals, with Journal of Virology being the most productive (44 articles; 9.9%) and by six types of organizations, with universities being the most productive (276 articles; 62.4%).The largest proportion of the articles focused on basic medical sciences and clinical studies (47.2%) and those on prevention and control ranked third (26.2%), with those on other focuses coming in between (26.6%). The articles on prevention and control had the highest mean rank for impact factor (IF) (226.34), followed by those on basic medical sciences and clinical studies (180.23) and those on other focuses (168.03). The mean rank differences were statistically significant (p = 0.000). Besides, "conronavirus", "case", "transmission" and "detection" were found to be the most frequently used terms. The findings of this first bibliometric study on MERS suggest that the prevention and control of the disease has become a big concern and related research should be strengthened. PMID:27304963

  4. Scaling in the growth of geographically subdivided populations: invariant patterns from a continent-wide biological survey.

    PubMed

    Keitt, Timothy H; Amaral, Luis A N; Buldyrev, Sergey V; Stanley, H Eugene

    2002-05-29

    We consider statistical patterns of variation in growth rates for over 400 species of breeding birds across North America surveyed from 1966 to 1998. We report two results. First, the standard deviation of population growth rates decays as a power-law function of total population size with an exponent beta = 0.36 +/- 0.02. Second, the number of subpopulations, measured as the number of survey locations with non-zero counts, scales to the 3/4 power of total number of birds counted in a given species. We show how these patterns may be related, and discuss a simple stochastic growth model for a geographically subdivided population that formalizes the relationship. We also examine reasons that may explain why some species deviate from these scaling laws. PMID:12079524

  5. PubMed vs. HighWire Press: a head-to-head comparison of two medical literature search engines.

    PubMed

    Vanhecke, Thomas E; Barnes, Michael A; Zimmerman, Janet; Shoichet, Sandor

    2007-09-01

    PubMed and HighWire Press are both useful medical literature search engines available for free to anyone on the internet. We measured retrieval accuracy, number of results generated, retrieval speed, features and search tools on HighWire Press and PubMed using the quick search features of each. We found that using HighWire Press resulted in a higher likelihood of retrieving the desired article and higher number of search results than the same search on PubMed. PubMed was faster than HighWire Press in delivering search results regardless of search settings. There are considerable differences in search features between these two search engines. PMID:17184763

  6. PubMed Informer: Monitoring MEDLINE/PubMed through E-mail Alerts, SMS, PDA downloads and RSS feeds

    PubMed Central

    Muin, Michael; Fontelo, Paul; Ackerman, Michael

    2005-01-01

    Summary PubMed Informer is a Web-based monitoring tool for topics of interest from MEDLINE/PubMed primarily designed for healthcare professionals. Five tracking methods are available: Web access, e-mail, Short Message Service (SMS), PDA downloads and RSS feeds. PubMed Informer delivers focused search updates and specific information to users with varying information-seeking practices. PMID:16779344

  7. Growth patterns in mesophotic octocorals: Timing the branching process in the highly-valuable Mediterranean Corallium rubrum

    NASA Astrophysics Data System (ADS)

    Benedetti, Maria Carla; Priori, Cristina; Erra, Fabrizio; Santangelo, Giovanni

    2016-03-01

    This study examined colony growth in the long-lived red coral Corallium rubrum, a slow growing octocoral endemic to the Mediterranean Sea and neighboring Atlantic areas and one of the most valuable of all marine species. Age and growth rate were determined on 165 sections of colony bases and branches by means of a validated age dating method in populations living between 50 and 130 m in the NW Mediterranean. The ratio between minimum and maximum diameter remained constant, indicating proportional growth of colony bases. No significant difference was found between the growth rate of bases and branches. A significantly different branching pattern (colony height/number of branches) and average growth rate were found between the colonies of the different geographic areas. As growth rate decreases with age, this was due to the different age structure of the two samples. The maximum lifespan was found to be 106 years, a value not determined previously for C. rubrum colonies, and the average age of colonies at first branching was about 10 years. Linear growth varied widely between colonies as well as between branches in the same colony, confirming the lack of any strict relation between height and age. The study illustrates the growth of a mesophotic, heavily exploited Corallidae.

  8. Hybridization between Yellowstone Cutthroat Trout and Rainbow Trout Alters the Expression of Muscle Growth-Related Genes and Their Relationships with Growth Patterns

    PubMed Central

    Ostberg, Carl O.; Chase, Dorothy M.; Hauser, Lorenz

    2015-01-01

    Hybridization creates novel gene combinations that may generate important evolutionary novelty, but may also reduce existing adaptation by interrupting inherent biological processes, such as genotype-environment interactions. Hybridization often causes substantial change in patterns of gene expression, which, in turn, may cause phenotypic change. Rainbow trout (Oncorhynchus mykiss) and cutthroat trout (O. clarkii) produce viable hybrids in the wild, and introgressive hybridization with introduced rainbow trout is a major conservation concern for native cutthroat trout. The two species differ in body shape, which is likely an evolutionary adaptation to their native environments, and their hybrids tend to show intermediate morphology. The characterization of gene expression patterns may provide insights on the genetic basis of hybrid and parental morphologies, as well as on the ecological performance of hybrids in the wild. Here, we evaluated the expression of eight growth-related genes (MSTN-1a, MSTN-1b, MyoD1a, MyoD1b, MRF-4, IGF-1, IGF-2, and CAST-L) and the relationship of these genes with growth traits (length, weight, and condition factor) in six line crosses: both parental species, both reciprocal F1 hybrids, and both first-generation backcrosses (F1 x rainbow trout and F1 x cutthroat trout). Four of these genes were differentially expressed among rainbow, cutthroat, and their hybrids. Transcript abundance was significantly correlated with growth traits across the parent species, but not across hybrids. Our findings suggest that rainbow and cutthroat trout exhibit differences in muscle growth regulation, that transcriptional networks may be modified by hybridization, and that hybridization disrupts intrinsic relationships between gene expression and growth patterns that may be functionally important for phenotypic adaptations. PMID:26485525

  9. Hybridization between Yellowstone Cutthroat Trout and Rainbow Trout Alters the Expression of Muscle Growth-Related Genes and Their Relationships with Growth Patterns.

    PubMed

    Ostberg, Carl O; Chase, Dorothy M; Hauser, Lorenz

    2015-01-01

    Hybridization creates novel gene combinations that may generate important evolutionary novelty, but may also reduce existing adaptation by interrupting inherent biological processes, such as genotype-environment interactions. Hybridization often causes substantial change in patterns of gene expression, which, in turn, may cause phenotypic change. Rainbow trout (Oncorhynchus mykiss) and cutthroat trout (O. clarkii) produce viable hybrids in the wild, and introgressive hybridization with introduced rainbow trout is a major conservation concern for native cutthroat trout. The two species differ in body shape, which is likely an evolutionary adaptation to their native environments, and their hybrids tend to show intermediate morphology. The characterization of gene expression patterns may provide insights on the genetic basis of hybrid and parental morphologies, as well as on the ecological performance of hybrids in the wild. Here, we evaluated the expression of eight growth-related genes (MSTN-1a, MSTN-1b, MyoD1a, MyoD1b, MRF-4, IGF-1, IGF-2, and CAST-L) and the relationship of these genes with growth traits (length, weight, and condition factor) in six line crosses: both parental species, both reciprocal F1 hybrids, and both first-generation backcrosses (F1 x rainbow trout and F1 x cutthroat trout). Four of these genes were differentially expressed among rainbow, cutthroat, and their hybrids. Transcript abundance was significantly correlated with growth traits across the parent species, but not across hybrids. Our findings suggest that rainbow and cutthroat trout exhibit differences in muscle growth regulation, that transcriptional networks may be modified by hybridization, and that hybridization disrupts intrinsic relationships between gene expression and growth patterns that may be functionally important for phenotypic adaptations. PMID:26485525

  10. Hybridization between Yellowstone cutthroat trout and rainbow trout alters the expression of muscle growth-related genes and their relationships with growth patterns

    USGS Publications Warehouse

    Ostberg, Carl O.; Chase, Dorothy M.; Hauser, Lorenz

    2015-01-01

    Hybridization creates novel gene combinations that may generate important evolutionary novelty, but may also reduce existing adaptation by interrupting inherent biological processes, such as genotype-environment interactions. Hybridization often causes substantial change in patterns of gene expression, which, in turn, may cause phenotypic change. Rainbow trout (Oncorhynchus mykiss) and cutthroat trout (O. clarkii) produce viable hybrids in the wild, and introgressive hybridization with introduced rainbow trout is a major conservation concern for native cutthroat trout. The two species differ in body shape, which is likely an evolutionary adaptation to their native environments, and their hybrids tend to show intermediate morphology. The characterization of gene expression patterns may provide insights on the genetic basis of hybrid and parental morphologies, as well as on the ecological performance of hybrids in the wild. Here, we evaluated the expression of eight growth-related genes (MSTN-1a, MSTN-1b, MyoD1a, MyoD1b, MRF-4, IGF-1, IGF-2, and CAST-L) and the relationship of these genes with growth traits (length, weight, and condition factor) in six line crosses: both parental species, both reciprocal F1 hybrids, and both first-generation backcrosses (F1 x rainbow trout and F1 x cutthroat trout). Four of these genes were differentially expressed among rainbow, cutthroat, and their hybrids. Transcript abundance was significantly correlated with growth traits across the parent species, but not across hybrids. Our findings suggest that rainbow and cutthroat trout exhibit differences in muscle growth regulation, that transcriptional networks may be modified by hybridization, and that hybridization disrupts intrinsic relationships between gene expression and growth patterns that may be functionally important for phenotypic adaptations.

  11. Leaf growth pattern in evergreen and deciduous species of the Central Himalaya, India

    NASA Astrophysics Data System (ADS)

    Negi, G. C. S.; Singh, S. P.

    1992-12-01

    Leaf growth patterns were investigated in 11 evergreen (with leaf life-spans of just more than 1 year) and 15 deciduous species, occurring along an elevational gradient of 600-2200 m elevation in the Central Himalaya. Records were made of the leaf initiation period, leaf population dynamics, leaf expansion, leaf mass changes, leaf longevity and related parameters. Species of both groups produced leaves at similar rates during March to April, the driest period of the year. Species of both groups had approximately fully developed foliage during the warm, wet period (mid-June to mid-September) of the monsoon. However, significant differences were found at group level in other characters: shoot length (19.5 cm per shoot for deciduous and 11.7 cm for evergreen species); leaf population per 10 cm shoot length (4.7 vs 15.0); leaf area (107.9 vs 41.4 cm2/ leaf); specific leaf mass (106.9 vs 191.3 g/m2); and leaf mass loss after the monsoon period, being rapid and higher (31.6%) in deciduous species and slow and limited in the evergreens (26.2%). However, species of the two groups showed considerable overlaps in the values of above characters. The evergreen species of the Central Himalaya resembled the deciduous species of the region more than the multi-year leaves of clearly evergreen species. The evergreens bear leaves throughout the year, but like deciduous species bear the cost of annual replacement of old leaves by new leaves. They seem to outcompete deciduous species by producing annually a greater mass of leaves of low-carbon cost (per unit leaf mass), which is capable of conducting photosynthesis all year round. A situation of less marked contrast between favourable and nonfavourable periods, with respect to temperature, seems to favour the leaf characters of the evergreens.

  12. Maternal dietary patterns in pregnancy and fetal growth in Japan: the Osaka Maternal and Child Health Study.

    PubMed

    Okubo, Hitomi; Miyake, Yoshihiro; Sasaki, Satoshi; Tanaka, Keiko; Murakami, Kentaro; Hirota, Yoshio; Kanzaki, Hideharu; Kitada, Mitsuyoshi; Horikoshi, Yorihiko; Ishiko, Osamu; Nakai, Yuichiro; Nishio, Junko; Yamamasu, Seiichi; Yasuda, Jinsuke; Kawai, Seigo; Yanagihara, Kazumi; Wakuda, Koji; Kawashima, Tokio; Narimoto, Katsuhiko; Iwasa, Yoshihiko; Orino, Katsuhiko; Tsunetoh, Itsuo; Yoshida, Junichi; Iito, Junichi; Kaneko, Takuzi; Kamiya, Takao; Kuribayashi, Hiroyuki; Taniguchi, Takeshi; Takemura, Hideo; Morimoto, Yasuhiko; Matsunaga, Ichiro; Oda, Hajime; Ohya, Yukihiro

    2012-05-01

    Maternal nutritional status during pregnancy is an important determinant of fetal growth. Although the effects of several nutrients and foods have been well examined, little is known about the relationship of overall maternal diet in pregnancy to fetal growth, particularly in non-Western populations. We prospectively examined the relationship of maternal dietary patterns in pregnancy to neonatal anthropometric measurements at birth and risk of small-for-gestational-age (SGA) birth among 803 Japanese women with live-born, singleton, term deliveries. Maternal diet in pregnancy was assessed using a validated, self-administered diet history questionnaire. Dietary patterns from thirty-three predefined food groups (g/4184 kJ) were extracted by cluster analysis. The following three dietary patterns were identified: the 'meat and eggs' (n 326), 'wheat products', with a relatively high intake of bread, confectioneries and soft drinks (n 303), and 'rice, fish and vegetables' (n 174) patterns. After adjustment for potential confounders, women in the 'wheat products' pattern had infants with the significantly lowest birth weight (P = 0·045) and head circumference (P = 0·036) among those in the three dietary patterns. Compared with women in the 'rice, fish and vegetables' pattern, women in the 'wheat products' pattern had higher odds of having a SGA infant for weight (multivariate OR 5·2, 95 % CI 1·1, 24·4), but this was not the case for birth length or head circumference. These results suggest that a diet high in bread, confectioneries, and soft drinks and low in fish and vegetables during pregnancy might be associated with a small birth weight and an increased risk of having a SGA infant. PMID:21929833

  13. Population Growth in the 1990s: Patterns within the United States.

    ERIC Educational Resources Information Center

    Perry, Marc

    2002-01-01

    Examines population growth during the 1990s for a variety of geographic levels including regions, divisions, states, metropolitan areas, counties, and large cities. Compares growth rates for the 1990s with earlier decades to provide an historical context for present-day trends in population growth and decline. Discusses how differential population…

  14. Lithography-free plasma-induced patterned growth of MoS2 and its heterojunction with graphene.

    PubMed

    Chen, Xiang; Park, Yong Ju; Das, Tanmoy; Jang, Houk; Lee, Jae-Bok; Ahn, Jong-Hyun

    2016-08-18

    Application-oriented patterned growth of transition metal dichalcogenides (TMDCs) and their heterojunctions is of critical importance for sophisticated, customized two-dimensional (2D) electronic and optoelectronic devices; however, it is still difficult to fabricate these patterns in a simple, clean, and high controllability manner without using optical lithography. Here, we report the direct synthesis of patterned MoS2 and graphene-MoS2 heterojunctions via selective plasma treatment of a SiO2/Si substrate and chemical vapor deposition of MoS2. This method has multiple merits, such as simple steps, a short operating time, easily isolated MoS2 layers with clean surfaces and controllable locations, shapes, sizes and thicknesses, which enable their integration into the device structure without using a photoresist. In addition, we demonstrate the direct growth of patterned graphene-MoS2 heterojunctions for the fabrication of transistor. This study reveals a novel method to fabricate and use patterned MoS2 and graphene-MoS2 heterojunctions, which could be generalized to the rational design of other 2D materials, heterojunctions and devices in the future. PMID:27432242

  15. GLAD4U: deriving and prioritizing gene lists from PubMed literature

    PubMed Central

    2012-01-01

    Background Answering questions such as "Which genes are related to breast cancer?" usually requires retrieving relevant publications through the PubMed search engine, reading these publications, and creating gene lists. This process is not only time-consuming, but also prone to errors. Results We report GLAD4U (Gene List Automatically Derived For You), a new, free web-based gene retrieval and prioritization tool. GLAD4U takes advantage of existing resources of the NCBI to ensure computational efficiency. The quality of gene lists created by GLAD4U for three Gene Ontology (GO) terms and three disease terms was assessed using corresponding "gold standard" lists curated in public databases. For all queries, GLAD4U gene lists showed very high recall but low precision, leading to low F-measure. As a comparison, EBIMed's recall was consistently lower than GLAD4U, but its precision was higher. To present the most relevant genes at the top of a list, we studied two prioritization methods based on publication count and the hypergeometric test, and compared the ranked lists and those generated by EBIMed to the gold standards. Both GLAD4U methods outperformed EBIMed for all queries based on a variety of quality metrics. Moreover, the hypergeometric method allowed for a better performance by thresholding genes with low scores. In addition, manual examination suggests that many false-positives could be explained by the incompleteness of the gold standards. The GLAD4U user interface accepts any valid queries for PubMed, and its output page displays the ranked gene list and information associated with each gene, chronologically-ordered supporting publications, along with a summary of the run and links for file export and functional enrichment and protein interaction network analysis. Conclusions GLAD4U has a high overall recall. Although precision is generally low, the prioritization methods successfully rank truly relevant genes at the top of the lists to facilitate efficient

  16. Selective growth and field emission of vertically well-aligned carbon nanotubes on hole-patterned silicon substrates

    NASA Astrophysics Data System (ADS)

    Huh, Y.; Lee, J. Y.; Lee, J. H.; Lee, T. J.; Lyu, S. C.; Lee, C. J.

    2003-07-01

    We have achieved selective growth of high-purity carbon nanotubes (CNTs) on iron-deposited hole-patterns by thermal chemical vapor deposition (CVD) of acetylene gas. The vertically well-aligned CNTs were uniformly synthesized with good selectivity on hole-patterned silicon substrates. The CNTs indicated multiwalled and bamboo-like structure. The turn-on gate voltage at the CNT-based triode structure was about 55 V and emission current density was 2.0 μA at the applied gate voltage of 100 V.

  17. A Search Engine to Access PubMed Monolingual Subsets: Proof of Concept and Evaluation in French

    PubMed Central

    Schuers, Matthieu; Soualmia, Lina Fatima; Grosjean, Julien; Kerdelhué, Gaétan; Kergourlay, Ivan; Dahamna, Badisse; Darmoni, Stéfan Jacques

    2014-01-01

    Background PubMed contains numerous articles in languages other than English. However, existing solutions to access these articles in the language in which they were written remain unconvincing. Objective The aim of this study was to propose a practical search engine, called Multilingual PubMed, which will permit access to a PubMed subset in 1 language and to evaluate the precision and coverage for the French version (Multilingual PubMed-French). Methods To create this tool, translations of MeSH were enriched (eg, adding synonyms and translations in French) and integrated into a terminology portal. PubMed subsets in several European languages were also added to our database using a dedicated parser. The response time for the generic semantic search engine was evaluated for simple queries. BabelMeSH, Multilingual PubMed-French, and 3 different PubMed strategies were compared by searching for literature in French. Precision and coverage were measured for 20 randomly selected queries. The results were evaluated as relevant to title and abstract, the evaluator being blind to search strategy. Results More than 650,000 PubMed citations in French were integrated into the Multilingual PubMed-French information system. The response times were all below the threshold defined for usability (2 seconds). Two search strategies (Multilingual PubMed-French and 1 PubMed strategy) showed high precision (0.93 and 0.97, respectively), but coverage was 4 times higher for Multilingual PubMed-French. Conclusions It is now possible to freely access biomedical literature using a practical search tool in French. This tool will be of particular interest for health professionals and other end users who do not read or query sufficiently in English. The information system is theoretically well suited to expand the approach to other European languages, such as German, Spanish, Norwegian, and Portuguese. PMID:25448528

  18. Convection patterns and temperature fields of ammonothermal GaN bulk crystal growth process

    NASA Astrophysics Data System (ADS)

    Masuda, Yoshio; Sato, Osamu; Tomida, Daisuke; Yokoyama, Chiaki

    2016-05-01

    The natural convection heat transfer in an ammonothermal process for growing GaN bulk single crystals has been examined numerically. We consider only one crystal to simplify the calculation and discuss the relationship between convection patterns and temperature fields. Two types of convection patterns are observed owing to the difference in the crystal radius. When the convection pattern is transformed, the crystal surface temperature decreases as the crystal radius increases.

  19. The influence of growth patterns on sexual size monomorphism in lemurs.

    PubMed

    Tennenhouse, E M

    2015-09-01

    The lack of sexual size dimorphism among lemurs is puzzling given the high degree of polygyny in this clade. It has been proposed that the unique ecological conditions of Madagascar favour rapid completion of growth, limiting the opportunities for bimaturism and sexual size dimorphism in lemurs. Using recently compiled large data sets on many species across the lemur clade, I examined the prevalence of sexual size monomorphism of body mass among lemurs and tested the hypothesis that limited growth durations constrain sexual size dimorphism. I used segmented regression analyses to accurately model growth in each species. The majority of species analysed exhibited a period of rapid growth followed by a distinct period of slow growth prior to attainment of adult body mass. Whereas the first period of growth was constrained by the need to attain the majority of adult body mass prior to the onset of the infant's first dry season, the subsequent period of slow growth was unconstrained and sufficiently long to promote sexual bimaturism. Sex differences in the duration and rate of growth during this second growth phase appeared to account for the sexual size dimorphism exhibited by three lemur species. Therefore, constraints on growth processes do not limit sexual size dimorphism in lemurs, and other explanations for the prevalence of sexual size monomorphism in this clade should be examined. The importance of considering ontogeny in future investigations of sexual size monomorphism in lemurs is highlighted. PMID:26134876

  20. PubMed related articles: a probabilistic topic-based model for content similarity

    PubMed Central

    Lin, Jimmy; Wilbur, W John

    2007-01-01

    Background We present a probabilistic topic-based model for content similarity called pmra that underlies the related article search feature in PubMed. Whether or not a document is about a particular topic is computed from term frequencies, modeled as Poisson distributions. Unlike previous probabilistic retrieval models, we do not attempt to estimate relevance–but rather our focus is "relatedness", the probability that a user would want to examine a particular document given known interest in another. We also describe a novel technique for estimating parameters that does not require human relevance judgments; instead, the process is based on the existence of MeSH ® in MEDLINE ®. Results The pmra retrieval model was compared against bm25, a competitive probabilistic model that shares theoretical similarities. Experiments using the test collection from the TREC 2005 genomics track shows a small but statistically significant improvement of pmra over bm25 in terms of precision. Conclusion Our experiments suggest that the pmra model provides an effective ranking algorithm for related article search. PMID:17971238

  1. Homo and heteroepitaxial growth and study of orientation-patterned GaP for nonlinear frequency conversion devices

    NASA Astrophysics Data System (ADS)

    Tassev, V. L.; Vangala, S.; Peterson, R.; Kimani, M.; Snure, M.; Markov, I.

    2016-03-01

    Frequency conversion in orientation-patterned quasi-phase matched materials is a leading approach for generating tunable mid- and long-wave coherent IR radiation for a wide variety of applications. A number of nonlinear optical materials are currently under intensive investigation. Due to their unique properties, chiefly wide IR transparency and high nonlinear susceptibility, GaAs and GaP are among the most promising. Compared to GaAs, GaP has the advantage of having higher thermal conductivity and significantly lower 2PA in the convenient pumping range of 1- 1.7 μm. HVPE growth of OPGaP, however, has encountered certain challenges: low quality and high price of commercially available GaP wafers; and strong parasitic nucleation during HVPE growth that reduces growth rate and aggravates layer quality, often leading to pattern overgrowth. Lessons learned from growing OPGaAs were not entirely helpful, leaving us to alternative solutions for both homoepitaxial growth and template preparation. We report repeatable one-step HVPE growth of up to 400 μm thick OPGaP with excellent domain fidelity deposited for first time on OPGaAs templates. The templates were prepared by wafer fusion bonding or MBE assisted polarity inversion technique. A close to equilibrium growth at such a large lattice mismatch (-3.6%) is itself noteworthy, especially when previously reported attempts (growth of OPZnSe on OPGaAs templates) at much smaller mismatch (+0.3%) have produced limited results. Combining the advantages of the two most promising materials, GaAs and GaP, is a solution that will accelerate the development of high power, tunable laser sources for the mid- and long-wave IR, and THz region.

  2. Differential radial growth patterns between beech (Fagus sylvatica L.) and oak (Quercus robur L.) on periodically waterlogged soils.

    PubMed

    Scharnweber, Tobias; Manthey, Michael; Wilmking, Martin

    2013-04-01

    Climate scenarios for northern Central Europe project rising temperatures and increasing frequency and intensity of droughts but also a shift in precipitation pattern with more humid winters. This in turn may result in soil waterlogging during the following spring, leading to increasing stress for trees growing on hydric sites. The influence of waterlogging on growth of common beech and pedunculate oak has been studied intensively on seedlings under experimental conditions. However, the question remains whether results of these studies can be transferred to mature trees growing under natural conditions. To test this, we investigated general growth patterns and climate-growth relationships in four mature stands of beech and oak growing on hydromorphic soils (Stagnosols) in northeast Germany using dendrochronological methods. Our results confirmed the expected tolerance of oak to strong water-level fluctuations. Neither extremely wet conditions during spring nor summer droughts significantly affected its radial growth. Oak growth responded positively to warmer temperatures during previous year October and March of the current year of ring formation. Contrary to our expectations, also beech showed relatively low sensitivity to periods of high soil water saturation. Instead, summer drought turned out to be the main climatic factor influencing ring width of beech even under the specific periodically wet soil conditions of our study. This became evident from general climate-growth correlations over the last century as well as from discontinuous (pointer year) analysis with summer drought being significantly correlated to the occurrence of growth depressions. As ring width of the two species is affected by differing climate parameters, species-specific chronologies show no coherence in high-frequency variations even for trees growing in close proximity. We assume differences in rooting depth as the main reason for the differing growth patterns and climate correlations of

  3. Mistletoe effects on Scots pine decline following drought events: insights from within-tree spatial patterns, growth and carbohydrates.

    PubMed

    Sangüesa-Barreda, Gabriel; Linares, Juan Carlos; Camarero, J Julio

    2012-05-01

    Forest decline has been attributed to the interaction of several stressors including biotic factors such as mistletoes and climate-induced drought stress. However, few data exist on how mistletoes are spatially arranged within trees and how this spatial pattern is related to changes in radial growth, responses to drought stress and carbon use. We used dendrochronology to quantify how mistletoe (Viscum album L.) infestation and drought stress affected long-term growth patterns in Pinus sylvestris L. at different heights. Basal area increment (BAI) trends and comparisons between trees of three different infestation degrees (without mistletoe, ID1; moderately infested trees, ID2; and severely infested trees, ID3) were performed using linear mixed-effects models. To identify the main climatic drivers of tree growth tree-ring widths were converted into indexed chronologies and related to climate data using correlation functions. We performed spatial analyses of the 3D distribution of mistletoe individuals and their ages within the crowns of three severely infested pines to describe their patterns. Lastly, we quantified carbohydrate and nitrogen concentrations in needles and sapwood of branches from severely infested trees and from trees without mistletoe. Mistletoe individuals formed strongly clustered groups of similar age within tree crowns and their age increased towards the crown apex. Mistletoe infestation negatively impacted growth but this effect was stronger near the tree apex than in the rest of sampled heights, causing an average loss of 64% in BAI (loss of BAI was ∼51% at 1.3 m or near the tree base). We found that BAI of severely infested trees and moderately or non-infested trees diverged since 2001 and such divergence was magnified by drought. Infested trees had lower concentrations of soluble sugars in their needles than non-infested ones. We conclude that mistletoe infestation causes growth decline and increases the sensitivity of trees to drought

  4. Increased water use efficiency but contrasting tree growth patterns in Fitzroya cupressoides forests of southern Chile during recent decades

    NASA Astrophysics Data System (ADS)

    Urrutia-Jalabert, Rocío.; Malhi, Yadvinder; Barichivich, Jonathan; Lara, Antonio; Delgado-Huertas, Antonio; Rodríguez, Carmen Gloria; Cuq, Emilio

    2015-12-01

    Little is known about how old-growth and massive forests are responding to environmental change. We investigated tree-ring growth and carbon isotopes of the long-lived and high biomass Fitzroya cupressoides in two stands growing in contrasting environmental conditions in the Coastal Range (~300 years old) and Andean Cordilleras (>1500 years old) of southern Chile. The interannual variability in δ13C was assessed for the period 1800-2010, and changes in discrimination and intrinsic water use efficiency (iWUE) were evaluated in relation to changes in climate and tree-ring growth during the last century. 13C discrimination has significantly decreased, and iWUE has increased since the 1900s in both sites. However, these trends in isotopic composition have been accompanied by different growth patterns: decreasing growth rates in the Coastal Range since the 1970s and increasing growth rates in the Andes since the 1900s. Trees growing in the Coastal Range have become more efficient in their use of water, probably due to reduced stomatal conductance caused by increases in CO2 and warming. Trees growing in the Andes have also become more water use efficient, but this has been likely due to increased photosynthetic rates. Fitzroya forests, including particularly old-growth stands, are responding to recent environmental changes, and their response has been site dependent. The growth of forests under a more Mediterranean climate influence and restrictive soil conditions in the Coastal Range has been more negatively affected by current warming and drying; while the growth of old stands in the wet Andes has been positively affected by changes in climate (decreasing cloudiness) and increasing CO2. Permanent monitoring of these endangered forests under ongoing environmental changes is needed in order to reassure the long-term preservation of this millennial-aged species.

  5. Public accessibility of biomedical articles from PubMed Central reduces journal readership—retrospective cohort analysis

    PubMed Central

    Davis, Philip M.

    2013-01-01

    Does PubMed Central—a government-run digital archive of biomedical articles—compete with scientific society journals? A longitudinal, retrospective cohort analysis of 13,223 articles (5999 treatment, 7224 control) published in 14 society-run biomedical research journals in nutrition, experimental biology, physiology, and radiology between February 2008 and January 2011 reveals a 21.4% reduction in full-text hypertext markup language (HTML) article downloads and a 13.8% reduction in portable document format (PDF) article downloads from the journals' websites when U.S. National Institutes of Health-sponsored articles (treatment) become freely available from the PubMed Central repository. In addition, the effect of PubMed Central on reducing PDF article downloads is increasing over time, growing at a rate of 1.6% per year. There was no longitudinal effect for full-text HTML downloads. While PubMed Central may be providing complementary access to readers traditionally underserved by scientific journals, the loss of article readership from the journal website may weaken the ability of the journal to build communities of interest around research papers, impede the communication of news and events to scientific society members and journal readers, and reduce the perceived value of the journal to institutional subscribers.—Davis, P. M. Public accessibility of biomedical articles from PubMed Central reduces journal readership—retrospective cohort analysis. PMID:23554455

  6. Growth patterns of the slime mold Physarum on a nonuniform substrate

    NASA Astrophysics Data System (ADS)

    Halvorsrud, Ragnhild; Wagner, Geri

    1998-01-01

    The Myxomycete Physarum polycephalum has been grown on nonuniform substrates, where the nutrients were confined in separated drops of agar medium. Spatial and temporal aspects of the resulting growth structures were studied by time-lapse video techniques and analyzed using image processing software. The growth process on a linear substrate of drops can be described in terms of a searching phase alternating with a feeding phase. On a linear array of drops, the Physarum advanced uniformly after an initial lag phase. On a two-dimensional drop substrate two different growth regimes could be distinguished: branched growth was observed on substrates with small drop diameters and compact growth, similar to growth on uniform substrates, was observed on substrates with larger drop diameters. The drop size is a crucial parameter that mediates characteristic plasmodial morphologies. A crossover from branched to compact growth was observed in some of the experiments. A spatial correlation function was used that could quantitatively distinguish between the different growth regimes.

  7. Use of positive and negative words in scientific PubMed abstracts between 1974 and 2014: retrospective analysis

    PubMed Central

    Tijdink, Joeri K; Otte, Willem M

    2015-01-01

    Objective To investigate whether language used in science abstracts can skew towards the use of strikingly positive and negative words over time. Design Retrospective analysis of all scientific abstracts in PubMed between 1974 and 2014. Methods The yearly frequencies of positive, negative, and neutral words (25 preselected words in each category), plus 100 randomly selected words were normalised for the total number of abstracts. Subanalyses included pattern quantification of individual words, specificity for selected high impact journals, and comparison between author affiliations within or outside countries with English as the official majority language. Frequency patterns were compared with 4% of all books ever printed and digitised by use of Google Books Ngram Viewer. Main outcome measures Frequencies of positive and negative words in abstracts compared with frequencies of words with a neutral and random connotation, expressed as relative change since 1980. Results The absolute frequency of positive words increased from 2.0% (1974-80) to 17.5% (2014), a relative increase of 880% over four decades. All 25 individual positive words contributed to the increase, particularly the words “robust,” “novel,” “innovative,” and “unprecedented,” which increased in relative frequency up to 15 000%. Comparable but less pronounced results were obtained when restricting the analysis to selected journals with high impact factors. Authors affiliated to an institute in a non-English speaking country used significantly more positive words. Negative word frequencies increased from 1.3% (1974-80) to 3.2% (2014), a relative increase of 257%. Over the same time period, no apparent increase was found in neutral or random word use, or in the frequency of positive word use in published books. Conclusions Our lexicographic analysis indicates that scientific abstracts are currently written with more positive and negative words, and provides an insight into the

  8. Maternal constraint on fetal growth patterns in the rhesus monkey (Macaca mulatta): the intergenerational link between mothers and daughters.

    PubMed

    Price, K C; Coe, C L

    2000-02-01

    The gestational experience of a mother can influence the intrauterine environment she provides her own offspring, allowing prenatal events to affect pregnancy outcomes across several generations. Using a multigenerational database, we determined the reproductive consequences for rhesus monkeys descended from small-for-date and large-for-date birth weight matrilines. Both the maternal half-brothers and -sisters of large-for-date infants exhibited enhanced fetal growth, but for small-for-date probands, only the maternal half-sisters experienced significant intrauterine growth constraint. In addition, the growth-restricted females were at higher risk of poor reproductive outcomes in adulthood, and they perpetuated the matrilineal birth weight pattern by selectively constraining the fetal development of their daughters. Collectively, these findings suggest a mechanism for the intergenerational persistence of suboptimal pregnancy outcomes. PMID:10655322

  9. Site-specific growth of ZnO nanowires from patterned Zn via compatible semiconductor processing

    NASA Astrophysics Data System (ADS)

    Law, J. B. K.; Boothroyd, C. B.; Thong, J. T. L.

    2008-05-01

    An alternative method for site-selective growth of ZnO nanowires without the use of an Au catalyst or a ZnO thin-film seed layer is presented. Using conventional lithography and metallization semiconductor processing steps, regions for selective nanowire growth are defined using Zn, which acts as a self-catalyst for subsequent ZnO nanowire growth via a simple thermal oxidation process. Scanning electron microscopy, transmission electron microscopy and X-ray diffraction reveal that the nanowires grown by this technique are single-crystalline wurtzite ZnO. Room temperature photoluminescence exhibits strong ultraviolet emission from these nanowires, indicating good optical properties. A series of experiments was conducted to elucidate the unique growth behavior of these nanowires directly from the Zn grains and a growth model is proposed.

  10. Mining locus tags in PubMed Central to improve microbial gene annotation

    PubMed Central

    2014-01-01

    Background The scientific literature contains millions of microbial gene identifiers within the full text and tables, but these annotations rarely get incorporated into public sequence databases. We propose to utilize the Open Access (OA) subset of PubMed Central (PMC) as a gene annotation database and have developed an R package called pmcXML to automatically mine and extract locus tags from full text, tables and supplements. Results We mined locus tags from 1835 OA publications in ten microbial genomes and extracted tags mentioned in 30,891 sentences in main text and 20,489 rows in tables. We identified locus tag pairs marking the start and end of a region such as an operon or genomic island and expanded these ranges to add another 13,043 tags. We also searched for locus tags in supplementary tables and publications outside the OA subset in Burkholderia pseudomallei K96243 for comparison. There were 168 publications containing 48,470 locus tags and 83% of mentions were from supplementary materials and 9% from publications outside the OA subset. Conclusions B. pseudomallei locus tags within the full text and tables of OA publications represent only a small fraction of the total mentions in the literature. For microbial genomes with very few functionally characterized proteins, the locus tags mentioned in supplementary tables and within ranges like genomic islands contain the majority of locus tags. Significantly, the functions in the R package provide access to additional resources in the OA subset that are not currently indexed or returned by searching PMC. PMID:24499370

  11. Microtask crowdsourcing for disease mention annotation in PubMed abstracts.

    PubMed

    Good, Benjamin M; Nanis, Max; Wu, Chunlei; Su, Andrew I

    2015-01-01

    Identifying concepts and relationships in biomedical text enables knowledge to be applied in computational analyses. Many biological natural language processing (BioNLP) projects attempt to address this challenge, but the state of the art still leaves much room for improvement. Progress in BioNLP research depends on large, annotated corpora for evaluating information extraction systems and training machine learning models. Traditionally, such corpora are created by small numbers of expert annotators often working over extended periods of time. Recent studies have shown that workers on microtask crowdsourcing platforms such as Amazon's Mechanical Turk (AMT) can, in aggregate, generate high-quality annotations of biomedical text. Here, we investigated the use of the AMT in capturing disease mentions in PubMed abstracts. We used the NCBI Disease corpus as a gold standard for refining and benchmarking our crowdsourcing protocol. After several iterations, we arrived at a protocol that reproduced the annotations of the 593 documents in the 'training set' of this gold standard with an overall F measure of 0.872 (precision 0.862, recall 0.883). The output can also be tuned to optimize for precision (max = 0.984 when recall = 0.269) or recall (max = 0.980 when precision = 0.436). Each document was completed by 15 workers, and their annotations were merged based on a simple voting method. In total 145 workers combined to complete all 593 documents in the span of 9 days at a cost of $.066 per abstract per worker. The quality of the annotations, as judged with the F measure, increases with the number of workers assigned to each task; however minimal performance gains were observed beyond 8 workers per task. These results add further evidence that microtask crowdsourcing can be a valuable tool for generating well-annotated corpora in BioNLP. Data produced for this analysis are available at http://figshare.com/articles/Disease_Mention_Annotation_with_Mechanical_Turk/1126402

  12. Trends and topics in eye disease research in PubMed from 2010 to 2014

    PubMed Central

    Denion, Eric; Mortemousque, Bruno; Mouriaux, Fréderic

    2016-01-01

    Background: The purpose of this study is to provide a report on scientific production during the period 2010–2014 in order to identify the major topics as well as the predominant actors (journals, countries, continents) involved in the field of eye disease. Methods: A PubMed search was carried out to extract articles related to eye diseases during the period 2010–2014. Data were downloaded and processed through developed PHP scripts for further analysis. Results: A total of 62,123 articles were retrieved. A total of 3,368 different journals were found, and 19 journals were identified as “core journals” according to Braford’s law. English was by far the predominant language. A total of 853,182 MeSH terms were found, representing an average of 13.73 (SD = 4.98) MeSH terms per article. Among these 853,182 MeSH terms, 14,689 different MeSH terms were identified. Vision Disorders, Glaucoma, Diabetic Retinopathy, Macular Degeneration, and Cataract were the most frequent five MeSH terms related to eye diseases. The analysis of the total number of publications showed that Europe and Asia were the most productive continents, and the USA and China the most productive countries. Interestingly, using the mean Five-Year Impact Factor, the two most productive continents were North America and Oceania. After adjustment for population, the overall ranking positions changed in favor of smaller countries (i.e. Iceland, Switzerland, Denmark, and New Zealand), while after adjustment for Gross Domestic Product (GDP), the overall ranking positions changed in favor of some developing countries (Malawi, Guatemala, Singapore). Conclusions: Due to the large number of articles included and the numerous parameters analyzed, this study provides a wide view of scientific productivity related to eye diseases during the period 2010–2014 and allows us to better understand this field. PMID:26819840

  13. Retrieval comparison of EndNote to search MEDLINE (Ovid and PubMed) versus searching them directly.

    PubMed

    Gall, Carole; Brahmi, Frances A

    2004-01-01

    Using EndNote version 7.0, the authors tested the search capabilities of the EndNote search engine for retrieving citations from MEDLINE for importation into EndNote, a citation management software package. Ovid MEDLINE and PubMed were selected for the comparison. Several searches were performed on Ovid MEDLINE and PubMed using EndNote as the search engine, and the same searches were run on both Ovid and PubMed directly. Findings indicate that it is preferable to search MEDLINE directly rather than using EndNote. The publishers of EndNote do warn its users about the limitations of their product as a search engine when searching external databases. In this article, the limitations of EndNote as a search engine for searching MEDLINE were explored as related to MeSH, non-MeSH, citation verification, and author searching. PMID:15364649

  14. Long-term patterns in estuarine fish growth across two climatically divergent regions.

    PubMed

    Doubleday, Zoë A; Izzo, Christopher; Haddy, James A; Lyle, Jeremy M; Ye, Qifeng; Gillanders, Bronwyn M

    2015-12-01

    Long-term ecological datasets are vital for investigating how species respond to changes in their environment, yet there is a critical lack of such datasets from aquatic systems. We developed otolith growth 'chronologies' to reconstruct the growth history of a temperate estuarine fish species, black bream (Acanthopagrus butcheri). Chronologies represented two regions in south-east Australia: South Australia, characterised by a relatively warm, dry climate, and Tasmania, characterised by a relatively cool, wet climate. Using a mixed modelling approach, we related inter-annual growth variation to air temperature, rainfall, freshwater inflow (South Australia only), and El Niño-Southern Oscillation events. Otolith chronologies provided a continuous record of growth over a 13- and 21-year period for fish from South Australia and Tasmania, respectively. Even though fish from Tasmania were sourced across multiple estuaries, they showed higher levels of growth synchronicity across years, and greater year-to-year growth variation, than fish from South Australia, which were sourced from a single, large estuary. Growth in Tasmanian fish declined markedly over the time period studied and was negatively correlated to temperature. In contrast, growth in South Australian fish was positively correlated to both temperature and rainfall. The stark contrast between the two regions suggests that Tasmanian black bream populations are more responsive to regional scale environmental variation and may be more vulnerable to global warming. This study highlights the importance of examining species response to climate change at the intra-specific level and further validates the emerging use of growth chronologies for generating long-term ecological data in aquatic systems. PMID:26245148

  15. Direct growth and patterning of multilayer graphene onto a targeted substrate without an external carbon source.

    PubMed

    Kang, Dongseok; Kim, Won-Jun; Lim, Jung Ah; Song, Yong-Won

    2012-07-25

    Using only a simple tube furnace, we demonstrate the synthesis of patterned graphene directly on a designed substrate without the need for an external carbon source. Carbon atoms are absorbed onto Ni evaporator sources as impurities, and incorporated into catalyst layers during the deposition. Heat treatment conditions were optimized so that the atoms diffused out along the grain boundaries to form nanocrystals at the catalyst-substrate interfaces. Graphene patterns were obtained under patterned catalysts, which restricted graphene formation to within patterned areas. The resultant multilayer graphene was characterized by Raman spectroscopy and transmission electron microscopy to verify the high crystallinity and two-dimensional nanomorphology. Finally, a metal-semiconductor diode with a catalyst-graphene contact structure were fabricated and characterized to assess the semiconducting properties of the graphene sheets with respect to the display of asymmetric current-voltage behavior. PMID:22709270

  16. Sequence of morphological transitions in two-dimensional pattern growth from aqueous ascorbic Acid solutions.

    PubMed

    Paranjpe, A S

    2002-08-12

    A sequence of morphological transitions in two-dimensional dehydration patterns of aqueous solutions of ascorbic acid is observed with humidity as a control parameter. Change in morphology occurs due to humidity induced variation in the concentration of the metastable supersaturated solution phase formed after initial solvent evaporation. As percent humidity is varied from 40 to 80, patterns change from compact circular --> radial --> density modulated radial (a new morphology) --> density modulated circular --> density modulated dendritic (a new morphology) --> dense branching. PMID:12190528

  17. Seasonal and spatial patterns of growth of rainbow trout in the Colorado River in Grand Canyon, AZ

    USGS Publications Warehouse

    Yard, Micheal D.; Korman, Josh; Walters, Carl J.; Kennedy, T.A.

    2016-01-01

    Rainbow trout (Oncorhynchus mykiss) have been purposely introduced in many regulated rivers, with inadvertent consequences on native fishes. We describe how trout growth rates and condition could be influencing trout population dynamics in a 130 km section of the Colorado River below Glen Canyon Dam based on a large-scale mark–recapture program where ∼8000 rainbow trout were recaptured over a 3-year period (2012–2014). There were strong temporal and spatial variations in growth in both length and weight as predicted from von Bertalanffy and bioenergetic models, respectively. There was more evidence for seasonal variation in the growth coefficient and annual variation in the asymptotic length. Bioenergetic models showed more variability for growth in weight across seasons and years than across reaches. These patterns were consistent with strong seasonal variation in invertebrate drift and effects of turbidity on foraging efficiency. Highest growth rates and relative condition occurred in downstream reaches with lower trout densities. Results indicate that reduction in rainbow trout abundance in Glen Canyon will likely increase trout size in the tailwater fishery and may reduce downstream dispersal into Grand Canyon.

  18. Find Duplicates among the PubMed, EMBASE, and Cochrane Library Databases in Systematic Review

    PubMed Central

    Wang, Juan; Han, Guohong; Fan, Daiming

    2013-01-01

    Background Finding duplicates is an important phase of systematic review. However, no consensus regarding the methods to find duplicates has been provided. This study aims to describe a pragmatic strategy of combining auto- and hand-searching duplicates in systematic review and to evaluate the prevalence and characteristics of duplicates. Methods and Findings Literatures regarding portal vein thrombosis (PVT) and Budd-Chiari syndrome (BCS) were searched by the PubMed, EMBASE, and Cochrane library databases. Duplicates included one index paper and one or more redundant papers. They were divided into type-I (duplicates among different databases) and type-II (duplicate publications in different journals/issues) duplicates. For type-I duplicates, reference items were further compared between index and redundant papers. Of 10936 papers regarding PVT, 2399 and 1307 were identified as auto- and hand-searched duplicates, respectively. The prevalence of auto- and hand-searched redundant papers was 11.0% (1201/10936) and 6.1% (665/10936), respectively. They included 3431 type-I and 275 type-II duplicates. Of 11403 papers regarding BCS, 3275 and 2064 were identified as auto- and hand-searched duplicates, respectively. The prevalence of auto- and hand-searched redundant papers was 14.4% (1640/11403) and 9.1% (1039/11403), respectively. They included 5053 type-I and 286 type-II duplicates. Most of type-I duplicates were identified by auto-searching method (69.5%, 2385/3431 in PVT literatures; 64.6%, 3263/5053 in BCS literatures). Nearly all type-II duplicates were identified by hand-searching method (94.9%, 261/275 in PVT literatures; 95.8%, 274/286 in BCS literatures). Compared with those identified by auto-searching method, type-I duplicates identified by hand-searching method had a significantly higher prevalence of wrong items (47/2385 versus 498/1046, p<0.0001 in PVT literatures; 30/3263 versus 778/1790, p<0.0001 in BCS literatures). Most of wrong items originated from

  19. A Gain-of-Function Screen Identifying Genes Required for Growth and Pattern Formation of the Drosophila melanogaster Wing

    PubMed Central

    Cruz, Cristina; Glavic, Alvaro; Casado, Mar; de Celis, Jose F.

    2009-01-01

    The Drosophila melanogaster wing is a model system for analyzing the genetic control of organ size, shape, and pattern formation. The formation of the wing involves a variety of processes, such as cell growth, proliferation, pattern formation, and differentiation. These developmental processes are under genetic control, and many genes participating in specific aspects of wing development have already being characterized. In this work, we aim to identify novel genes regulating wing growth and patterning. To this end, we have carried out a gain-of-function screen generating novel P-UAS (upstream activating sequences) insertions allowing forced gene expression. We produced 3340 novel P-UAS insertions and isolated 300 that cause a variety of wing phenotypes in combination with a Gal4 driver expressed exclusively in the central domain of the presumptive wing blade. The mapping of these P-UAS insertion sites allowed us to identify the gene that causes the gain-of-function phenotypes. We show that a fraction of these phenotypes are related to the induction of cell death in the domain of ectopic gene expression. Finally, we present a preliminary characterization of a gene identified in the screen, the function of which is required for the development of the L5 longitudinal vein. PMID:19737745

  20. E-cadherin-negative acinar cell carcinoma of the pancreas: report of a case showing a solid pseudopapillary growth pattern.

    PubMed

    Tajima, Shogo; Waki, Michihiko; Azuma, Masaki; Koda, Kenji; Ohata, Akihiko

    2016-09-01

    E-cadherin expression patterns in acinar cell carcinomas (ACCs) of the pancreas have not been well documented. Herein, we present a hitherto undescribed case of E-cadherin-negative ACC with a solid pseudopapillary growth pattern in a 65-year-old man. We used an antibody against the extracellular domain of E-cadherin. As a further unusual status in ACC, faint β-catenin expression was observed in the cytoplasm of carcinoma cells. Morphological distinction from a solid pseudopapillary neoplasm (SPN) of the pancreas might be problematic in such a case, because of their similarities concerned with the growth pattern and E-cadherin negativity. Without nuclear accumulation of β-catenin, a diagnosis of SPN was almost excluded. Immunoreactivity for trypsin and BCL10 made an accurate diagnosis of ACC to this case. The tumor recurred 10 months post-surgery as rapidly enlarging masses in the liver, presumably indicating the aggressiveness of the E-cadherin-negative phenotype among ACCs. PMID:25600280

  1. Growth Pattern Responses to Photoperiod across Latitudes in a Northern Damselfly

    PubMed Central

    Śniegula, Szymon; Nilsson-Örtman, Viktor; Johansson, Frank

    2012-01-01

    Background Latitudinal clines in temperature and seasonality impose strong seasonal constraints on ectotherms. Studies of population differentiation in phenotypic plasticity of life history traits along latitudinal gradients are important for understanding how organisms have adapted to seasonal environments and predict how they respond to climate changes. Such studies have been scarce for species with a northern distribution. Methodology/Principle Finding Larvae of the northern damselfly Coenagrion johanssoni originating from semivoltine central, partivoltine northern, and partivoltine northernmost Swedish populations were reared in the laboratory. To investigate whether larvae use photoperiodic cues to induce compensatory growth along this latitudinal gradient, larvae were reared under two different photoperiods corresponding to a northern and southern latitude. In addition, field adult size was assessed to test the strength of possible compensatory growth mechanisms under natural conditions and hatchling size was measured to test for maternal effects. We hypothesized that populations originating from lower latitudes would be more time constrained than high-latitude populations because they have a shorter life cycle. The results showed that low-latitude populations had higher growth rates in summer/fall. In general northern photoperiods induced higher growth rates, but this plastic response to photoperiod was strongest in the southernmost populations and negligible in the northernmost population. During spring, central populations grew faster under the southern rather than the northern photoperiod. On the other hand, northern and northernmost populations did not differ between each other and grew faster in the northern rather than in the southern photoperiod. Field sampled adults did not differ in size across the studied regions. Conclusion/Significance We found a significant differentiation in growth rate across latitudes and latitudinal difference in growth rate

  2. Preferential growth orientation of laser-patterned LiNbO{sub 3} crystals in lithium niobium silicate glass

    SciTech Connect

    Komatsu, T.; Koshiba, K.; Honma, T.

    2011-02-15

    Dots and lines consisting of LiNbO{sub 3} crystals are patterned on the surface of 1CuO-40Li{sub 2}O-32Nb{sub 2}O{sub 5}-28SiO{sub 2} (mole ratio) glass by irradiations of continuous-wave Nd:YAG laser (wavelength: {lambda}=1064 nm), diode laser ({lambda}=795 nm), and Yb:YVO{sub 4} fiber laser ({lambda}=1080 nm), and the feature of laser-patterned LiNbO{sub 3} crystal growth is examined from linearly polarized micro-Raman scattering spectrum measurements. LiNbO{sub 3} crystals with the c-axis orientation are formed at the edge parts of the surface and cross-section of dots. The growth direction of an LiNbO{sub 3} along the laser scanning direction is the c-axis. It is proposed that the profile of the temperature distribution in the laser-irradiated region and its change along laser scanning would be one of the most important conditions for the patterning of crystals with a preferential growth orientation. Laser irradiation giving a narrow width is also proposed to be one of the important factors for the patterning of LiNbO{sub 3} crystal lines with homogeneous surface morphologies. -- Graphical abstract: Polarized optical microscope observations for the surface and cross-section of the dot obtained by LD laser ({lambda}=795 nm) irradiations of P=1.4 W and t=20 s in Cu-LNS glass. Schematic model for the orientation of LiNbO{sub 3} crystals at the edge parts of the surface and cross-section of the dot is also shown. Display Omitted Research highlights: > Dots and lines with LiNbO{sub 3} crystals are patterned on the glass surface by laser irradiations. > LiNbO{sub 3} crystals with the c-axis orientation are formed at the edge parts of the surface and cross-section of dots. > The profile of the temperature distribution in the laser-irradiated region is one of the most important conditions for the patterning of highly oriented crystals.

  3. Observations of pore-scale growth patterns of carbon dioxide hydrate using X-ray computed microtomography

    NASA Astrophysics Data System (ADS)

    Ta, Xuan Hien; Yun, Tae Sup; Muhunthan, Balasingam; Kwon, Tae-Hyuk

    2015-03-01

    Natural and artificial gas hydrates with internal pores of nano to centimeters and weak grain-cementation have been widely reported, while the detailed formation process of grain-cementing hydrates remains poorly identified. Pore-scale morphology of carbon dioxide (CO2) hydrate formed in a partially brine-saturated porous medium was investigated via X-ray computed microtomography (X-ray CMT). Emphasis is placed on the pore-scale growth patterns of gas hydrate, including the growth of dendritic hydrate crystals on preformed hydrate and water-wetted grains, porous nature of the hydrate phase, volume expansion of more than 200% during the water-to-hydrate phase transformation, preference of unfrozen water wetting hydrophilic minerals, and the relevance to a weak cementation effect on macroscale physical properties. The presented pore-scale morphology and growth patterns of gas hydrate are expected in natural sediment settings where free gas is available for hydrate formation, such as active gas vents, gas seeps, mud volcanoes, permafrost gas hydrate provinces, and CO2 injected formation for the sake of geologic carbon storage; and in laboratory hydrate samples synthesized from partially brine-saturated sediments or formed from water-gas interfaces.

  4. Investigation of Growth Patterns due to Environmental Factors on the Surface of Bivalve shells with LIBS and Raman Spectroscopy

    NASA Astrophysics Data System (ADS)

    Palmer, Andria; Mays, Joseph; Amos, James; Dynka, Tom; Ujj, Laszlo

    Environmental disturbances (such as temperature or chemical disturbances) can cause bivalve mollusk shells to grow faster or slower and cause changes in color and surface ring pattern. We have selected a few shells from our local habitat in Pensacola Beach, FL to analyze without sample treatment to determine what factors may have come into play during growth and use this as a way to analyze our marine environment. Laser Induced Breakdown Spectroscopy (LIBS) uses high energy laser pulses (355 and 532nm) to ablate the sample and create a micro-plasma from which emission spectra can be recorded. Based upon the analysis of intensities, wavelengths, and band patterns of spectral emission bands, the spatial qualitative elemental composition of the shell samples can be determined. Raman spectra were also recorded and correlated to molecules in the sample. By analyzing these measurements using LIBS-Raman spectroscopic techniques, we will be able to see how the local environment is effecting growth, with the largest chemical disturbance in the area being the BP Oil Spill in the Gulf in 2010. Therefore if samples are selected from this period of time it may be possible to identify the effects on shell growth. UWF NIH MARC U-STAR 1T34GM110517-01, UWF Office of Undergraduate Research.

  5. Understanding the growth rate patterns of ion Bernstein instabilities driven by ring-like proton velocity distributions

    NASA Astrophysics Data System (ADS)

    Min, Kyungguk; Liu, Kaijun

    2016-04-01

    Fast magnetosonic waves in Earth's inner magnetosphere, which have as their source ion Bernstein instabilities, are driven by hot proton velocity distributions (fp) with ∂fp(v⊥)/∂v⊥>0. Two typical types of distributions with such features are ring and shell velocity distributions. Both have been used in studies of ion Bernstein instabilities and fast magnetosonic waves, but the differences between instabilities driven by the two types of distributions have not been thoroughly addressed. The present study uses linear kinetic theory to examine and understand these differences. It is found that the growth rate pattern is primarily determined by the cyclotron resonance condition and the structure of the velocity distribution in gyroaveraged velocity space. For ring-driven Bernstein instabilities, as the parallel wave number (k∥) increases, the discrete unstable modes approximately follow the corresponding proton cyclotron harmonic frequencies while they become broader in frequency space. At sufficiently large k∥, the neighboring discrete modes merge into a continuum. In contrast, for shell-driven Bernstein instabilities, the curved geometry of the shell velocity distribution in gyroaveraged velocity space results in a complex alternating pattern of growth and damping rates in frequency and wave number space and confines the unstable Bernstein modes to relatively small k∥. In addition, when k∥ increases, the unstable modes are no longer limited to the proton cyclotron harmonic frequencies. The local growth rate peak near an exact harmonic at small k∥ bifurcates into two local peaks on both sides of the harmonic when k∥ becomes large.

  6. Superhydrophobic surfaces using selected zinc oxide microrod growth on ink-jetted patterns.

    PubMed

    Myint, Myo Tay Zar; Kitsomboonloha, Rungrot; Baruah, Sunandan; Dutta, Joydeep

    2011-02-15

    The synthesis and properties of superhydrophobic surfaces based on binary surface topography made of zinc oxide (ZnO) microrod-decorated micropatterns are reported. ZnO is intrinsically hydrophilic but can be utilized to create hydrophobic surfaces by creating artificial roughness via microstructuring. Micron scale patterns consisting of nanocrystalline ZnO seed particles were applied to glass substrates with a modified ink-jet printer. Microrods were then grown on the patterns by a hydrothermal process without any further chemical modification. Water contact angle (WCA)(1) up to 153° was achieved. Different micro array patterned surfaces with varying response of static contact angle or sessile droplet analysis are reported. PMID:21109250

  7. Plant development. Integration of growth and patterning during vascular tissue formation in Arabidopsis.

    PubMed

    De Rybel, Bert; Adibi, Milad; Breda, Alice S; Wendrich, Jos R; Smit, Margot E; Novák, Ondřej; Yamaguchi, Nobutoshi; Yoshida, Saiko; Van Isterdael, Gert; Palovaara, Joakim; Nijsse, Bart; Boekschoten, Mark V; Hooiveld, Guido; Beeckman, Tom; Wagner, Doris; Ljung, Karin; Fleck, Christian; Weijers, Dolf

    2014-08-01

    Coordination of cell division and pattern formation is central to tissue and organ development, particularly in plants where walls prevent cell migration. Auxin and cytokinin are both critical for division and patterning, but it is unknown how these hormones converge upon tissue development. We identify a genetic network that reinforces an early embryonic bias in auxin distribution to create a local, nonresponding cytokinin source within the root vascular tissue. Experimental and theoretical evidence shows that these cells act as a tissue organizer by positioning the domain of oriented cell divisions. We further demonstrate that the auxin-cytokinin interaction acts as a spatial incoherent feed-forward loop, which is essential to generate distinct hormonal response zones, thus establishing a stable pattern within a growing vascular tissue. PMID:25104393

  8. Early development and allometric growth patterns of the grumatã (Prochilodus vimboides Kner, 1859).

    PubMed

    Souza, Guilherme; Melo, Edésio J T; Caramaschi, Erica P; Andrade, Dalcio R; Monteiro, Leandro R

    2016-06-01

    The objective of this study was to characterize the early development and allometric growth of the grumatã (Prochilodus vimboides). We describe a sample of 266 eggs and larvae obtained through induced spawning. The eggs were spherical (mean 3.7 mm diameter), exhibited a yellow yolk and were non-adhesive and pelagic after fertilization and hydration. The time elapsed between the early cleavage and post-flexion stages was considered short (328 hours, 8054 hour-degrees) in regard to the development times of other Neotropical rheophilic species, but time to hatching was considerably longer than in other Prochilodus species. The most notable anatomical changes were observed between the end of the yolk larval stage and the beginning of the pre-flexion stage, when the larvae displayed directed swimming and the digestive system became functional, enabling the transition from endogenous to exogenous feeding. After hatching, the larvae grew from 6.04 to 15.15 mm in total length average. Two growth phases were observed at this stage: a non-linear asymptotic curve in yolk-sac larvae, and a linear constant-rate growth phase after exogenous feeding started. Allometric growth related to standard length was positive for head length, negative for eye diameter, and switched between phases from negative to positive in body depth and head height. Morphological development and allometric growth in different larval phases impose drastic anatomical and physiological changes that are synchronic with habitat changes and the flood cycles during the reproductive period. PMID:26199146

  9. Strain-induced growth instability and nanoscale surface patterning in perovskite thin films

    PubMed Central

    Pandya, Shishir; Damodaran, Anoop R.; Xu, Ruijuan; Hsu, Shang-Lin; Agar, Joshua C.; Martin, Lane W.

    2016-01-01

    Despite extensive studies on the effects of epitaxial strain on the evolution of the lattice and properties of materials, considerably less work has explored the impact of strain on growth dynamics. In this work, we demonstrate a growth-mode transition from 2D-step flow to self-organized, nanoscale 3D-island formation in PbZr0.2Ti0.8O3/SrRuO3/SrTiO3 (001) heterostructures as the kinetics of the growth process respond to the evolution of strain. With increasing heterostructure thickness and misfit dislocation formation at the buried interface, a periodic, modulated strain field is generated that alters the adatom binding energy and, in turn, leads to a kinetic instability that drives a transition from 2D growth to ordered, 3D-island formation. The results suggest that the periodically varying binding energy can lead to inhomogeneous adsorption kinetics causing preferential growth at certain sites. This, in conjunction with the presence of an Ehrlich-Schwoebel barrier, gives rise to long-range, periodically-ordered arrays of so-called “wedding cake” 3D nanostructures which self-assemble along the [100] and [010]. PMID:27194595

  10. Patterns of proteoglycan degradation by a neutral protease from human growth-plate epiphyseal cartilage

    SciTech Connect

    Ehrlich, M.G.; Armstrong, A.L.; Neuman, R.G.; Davis, M.W.; Mankin, H.J.

    1982-12-01

    The hypothesis is widely held that proteolytic degradation of proteoglycans in the lower hypertrophic zone of the growth plate may be involved in the initiation of mineralization in the zone of provisional calcification. However, a neutral protease that is responsible for the degradation of proteoglycans in the growth plate has not been identified, isolated, and characterized. In the work reported here, neutral protease activity in the growth plate is demonstrated for the first time, and some of the properties of the enzyme are described. Proteoglycans subunits were prepared from bovine nasal cartilage and calf costal cartilage by equilibrium density-gradient centrifugation under dissociative conditions. The proteoglycan subunits were labeled with /sup 14/C-formaldehyde. Homogenates from human growth plates were examined for neutral protease activity using the proteoglycan subunits as substrates. Following incubation of the proteoglycan subunits with growth-plate homogenates at pH 5.3 and at pH 7.5 in the presence and absence of ten-millimolar magnesium chloride and calcium chloride, the digestion products were examined by gel chromatography on Sepharose-2B and 6B columns. Column eluants containing proteoglycan-subunit degradation products were monitored for uronic acid, hexose, and radio-activity. Maximum extensive degradation of proteoglycan subunits occurred at pH 7.5 in the presence of ten-millimolar magnesium chloride and calcium chloride.

  11. Strain-induced growth instability and nanoscale surface patterning in perovskite thin films.

    PubMed

    Pandya, Shishir; Damodaran, Anoop R; Xu, Ruijuan; Hsu, Shang-Lin; Agar, Joshua C; Martin, Lane W

    2016-01-01

    Despite extensive studies on the effects of epitaxial strain on the evolution of the lattice and properties of materials, considerably less work has explored the impact of strain on growth dynamics. In this work, we demonstrate a growth-mode transition from 2D-step flow to self-organized, nanoscale 3D-island formation in PbZr0.2Ti0.8O3/SrRuO3/SrTiO3 (001) heterostructures as the kinetics of the growth process respond to the evolution of strain. With increasing heterostructure thickness and misfit dislocation formation at the buried interface, a periodic, modulated strain field is generated that alters the adatom binding energy and, in turn, leads to a kinetic instability that drives a transition from 2D growth to ordered, 3D-island formation. The results suggest that the periodically varying binding energy can lead to inhomogeneous adsorption kinetics causing preferential growth at certain sites. This, in conjunction with the presence of an Ehrlich-Schwoebel barrier, gives rise to long-range, periodically-ordered arrays of so-called "wedding cake" 3D nanostructures which self-assemble along the [100] and [010]. PMID:27194595

  12. Strain-induced growth instability and nanoscale surface patterning in perovskite thin films

    NASA Astrophysics Data System (ADS)

    Pandya, Shishir; Damodaran, Anoop R.; Xu, Ruijuan; Hsu, Shang-Lin; Agar, Joshua C.; Martin, Lane W.

    2016-05-01

    Despite extensive studies on the effects of epitaxial strain on the evolution of the lattice and properties of materials, considerably less work has explored the impact of strain on growth dynamics. In this work, we demonstrate a growth-mode transition from 2D-step flow to self-organized, nanoscale 3D-island formation in PbZr0.2Ti0.8O3/SrRuO3/SrTiO3 (001) heterostructures as the kinetics of the growth process respond to the evolution of strain. With increasing heterostructure thickness and misfit dislocation formation at the buried interface, a periodic, modulated strain field is generated that alters the adatom binding energy and, in turn, leads to a kinetic instability that drives a transition from 2D growth to ordered, 3D-island formation. The results suggest that the periodically varying binding energy can lead to inhomogeneous adsorption kinetics causing preferential growth at certain sites. This, in conjunction with the presence of an Ehrlich-Schwoebel barrier, gives rise to long-range, periodically-ordered arrays of so-called “wedding cake” 3D nanostructures which self-assemble along the [100] and [010].

  13. Patterns of leaf and flower removal: Their effect on fruit growth in Chamaenerion angustifolium (fireweed)

    SciTech Connect

    Shea, M.M.; Watson, M.A. )

    1989-06-01

    The response of Chamaenerion angustifolium (fireweed) plants of different patterns of artificial leaf and flower herbivory was examined to determine if the effects of localized herbivory were confined within vertical sectors of the plant. The effect of leaf and flower removal on fruit development was compared for removals within sectors and distributed among sectors. Fruit development did not differ in plants subjected to different patterns of leaf and flower removal. These results suggest that in disturbed plants carbohydrate movement is not confined within vertical sectors.

  14. Shifting Sands: Science Researchers on Google Scholar, Web of Science, and PubMed, with Implications for Library Collections Budgets

    ERIC Educational Resources Information Center

    Hightower, Christy; Caldwell, Christy

    2010-01-01

    Science researchers at the University of California Santa Cruz were surveyed about their article database use and preferences in order to inform collection budget choices. Web of Science was the single most used database, selected by 41.6%. Statistically there was no difference between PubMed (21.5%) and Google Scholar (18.7%) as the second most…

  15. Public accessibility of biomedical articles from PubMed Central reduces journal readership--retrospective cohort analysis.

    PubMed

    Davis, Philip M

    2013-07-01

    Does PubMed Central--a government-run digital archive of biomedical articles--compete with scientific society journals? A longitudinal, retrospective cohort analysis of 13,223 articles (5999 treatment, 7224 control) published in 14 society-run biomedical research journals in nutrition, experimental biology, physiology, and radiology between February 2008 and January 2011 reveals a 21.4% reduction in full-text hypertext markup language (HTML) article downloads and a 13.8% reduction in portable document format (PDF) article downloads from the journals' websites when U.S. National Institutes of Health-sponsored articles (treatment) become freely available from the PubMed Central repository. In addition, the effect of PubMed Central on reducing PDF article downloads is increasing over time, growing at a rate of 1.6% per year. There was no longitudinal effect for full-text HTML downloads. While PubMed Central may be providing complementary access to readers traditionally underserved by scientific journals, the loss of article readership from the journal website may weaken the ability of the journal to build communities of interest around research papers, impede the communication of news and events to scientific society members and journal readers, and reduce the perceived value of the journal to institutional subscribers. PMID:23554455

  16. Using patterned H-resist for controlled three-dimensional growth of nanostructures

    NASA Astrophysics Data System (ADS)

    Goh, K. E. J.; Chen, S.; Xu, H.; Ballard, J.; Randall, J. N.; Von Ehr, J. R.

    2011-04-01

    We present a study addressing the effectiveness of a monolayer of hydrogen as the lithographic resist for controlled three-dimensional (3D) growth of nanostructures on the Si(100) surface. Nanoscale regions on the H-terminated Si(100) were defined by H-desorption lithography via the biased tip of a scanning tunneling microscope (STM) to create well-defined regions of surface "dangling bonds," and the growth of 3D nanostructures within these regions was achieved using a simultaneous disilane deposition and STM H-desorption technique. We demonstrate that 3D growth is strongly confined within STM depassivated regions while unpatterned H:Si(100) regions are robust against adsorption of the precursor molecules.

  17. Global observation of nitrous oxide: changes in growth rate and spatial patterns

    NASA Astrophysics Data System (ADS)

    Hall, B. D.; Dlugokencky, E. J.; Dutton, G. S.; Nance, J. D.; Crotwell, A. M.; Mondeel, D. J.; Elkins, J. W.

    2015-12-01

    Nitrous oxide (N2O) currently exerts the third largest climate forcing of the long-lived greenhouse gases, after CO2 and CH4. N2O is also involved in the destruction of stratospheric ozone. It is produced by microbial activity in soils and oceans, and also by industry. The atmospheric burden of N2O has increased more than 20% from its preindustrial level of ~270 nmol mol-1 (ppb). Much of this increase is related to the application of nitrogen-containing fertilizers, including manure. The NOAA Global Monitoring Division has measured the atmospheric mole fraction of N2O at Earth's surface in air samples collected around the globe (since the late 1970s) and at in situ sites mostly in the Western Hemisphere (since 1998). ). Measurements of the global burden and growth rate constrain global emissions, e.g. 18.2 ± 2.7 Tg N yr-1 in 2013, where most of the uncertainty is related to uncertainty in the global lifetime. The average growth rate of N2O from 1990 to 2010 was ~0.75 ppb yr-1. Since 2004, however, the growth rate has been increasing, and is now about 25% higher than the 1990-2010 average. Between 2010 and 2013 the growth rate averaged ~0.95 ppb yr-1. As the growth rate increased from 2004-2013, gradients derived from surface, zonal-mean N2O mole fraction, such the mean pole-to-pole difference, and the difference between NH temperate latitudes and the southern polar region, decreased. This suggests a change in the distribution of N2O emissions over this period. We will present our N2O data and examine trends, gradients, and other features that could shed light on recent changes in the growth rate. We will also compare N2O gradients to those of other trace gases, such as SF6.

  18. Living bacteria rheology: Population growth, aggregation patterns, and collective behavior under different shear flows

    NASA Astrophysics Data System (ADS)

    Patrício, P.; Almeida, P. L.; Portela, R.; Sobral, R. G.; Grilo, I. R.; Cidade, T.; Leal, C. R.

    2014-08-01

    The activity of growing living bacteria was investigated using real-time and in situ rheology—in stationary and oscillatory shear. Two different strains of the human pathogen Staphylococcus aureus—strain COL and its isogenic cell wall autolysis mutant, RUSAL9—were considered in this work. For low bacteria density, strain COL forms small clusters, while the mutant, presenting deficient cell separation, forms irregular larger aggregates. In the early stages of growth, when subjected to a stationary shear, the viscosity of the cultures of both strains increases with the population of cells. As the bacteria reach the exponential phase of growth, the viscosity of the cultures of the two strains follows different and rich behaviors, with no counterpart in the optical density or in the population's colony-forming units measurements. While the viscosity of strain COL culture keeps increasing during the exponential phase and returns close to its initial value for the late phase of growth, where the population stabilizes, the viscosity of the mutant strain culture decreases steeply, still in the exponential phase, remains constant for some time, and increases again, reaching a constant plateau at a maximum value for the late phase of growth. These complex viscoelastic behaviors, which were observed to be shear-stress-dependent, are a consequence of two coupled effects: the cell density continuous increase and its changing interacting properties. The viscous and elastic moduli of strain COL culture, obtained with oscillatory shear, exhibit power-law behaviors whose exponents are dependent on the bacteria growth stage. The viscous and elastic moduli of the mutant culture have complex behaviors, emerging from the different relaxation times that are associated with the large molecules of the medium and the self-organized structures of bacteria. Nevertheless, these behaviors reflect the bacteria growth stage.

  19. An Evaluation of Upper and Lower Pharyngeal Airway Width, Tongue Posture and Hyoid Bone Position in Subjects with Different Growth Patterns

    PubMed Central

    Tarkar, Jaipal Singh; Parashar, Sandeep; Gupta, Garima; Bhardwaj, Preeti; Singh, Atul; Singh, Parul

    2016-01-01

    Introduction It is important to evaluate the position of the hyoid bone in relation to the tongue at the beginning of orthodontic treatment so that during the treatment, its position may be directed hence overall impact on airway could be assessed. Aim The aim of this study was to evaluate the upper and lower pharyngeal airway dimensions, posture of tongue and hyoid bone position in young adults with different growth patterns. Materials and Methods Sample size of the study included 90 post-adolescent subjects, within the age range of 18-32 years. Based on the different growth pattern of the face, subjects were divided into Group I (n=30; average growth pattern), Group II (n=30; horizontal growth pattern) and Group III (n=30; vertical growth pattern). Lateral cephalogram were traced and analysed manually by the same investigator for evaluation of upper and lower pharyngeal airway, tongue posture and hyoid bone position. The intergroup comparison of upper and lower pharyngeal airway dimensions, posture of tongue and hyoid bone was performed with one-way ANOVA test. Results The results showed that upper oropharyngeal widths were significantly different in different facial skeletal patterns (p=0.00). Subjects with vertical skeletal pattern have significantly narrower upper airways than those with horizontal skeletal pattern (p= 0.025). There was significantly higher difference in position of dorsum of the tongue in vertical growth pattern group (p=0.00). The hyoid bone was positioned farther from the mandibular symphysis in brachyfacial subjects, reflected by the larger H-RGN (Hyoid- retrognathion) values compared with the dolichofacial and normal subjects (p=0.044). Conclusion The upper oropharyngeal width was found to be narrower in subjects with vertical growth pattern. The dorsum of the tongue is seen to be placed higher in subjects with vertical growth pattern. The hyoid bone was more inferiorly and posteriorly positioned in subjects with horizontal growth pattern

  20. HYDRAULIC REDISTRIBUTION OF SOIL WATER IN TWO OLD-GROWTH CONIFEROUS FORESTS: QUANTIFYING PATTERNS AND CONTROLS

    EPA Science Inventory

    Although hydraulic redistribution of soil water (HR) by roots is a widespread phenomenon, the processes governing spatial and temporal patterns of HR are not well understood. We incorporated soil/plant biophysical properties into a simple model based on Darcy's law to predict sea...

  1. Algal morphogenesis: modelling interspecific variation in Micrasterias with reaction--diffusion patterned catalysis of cell surface growth

    PubMed Central

    Holloway, D. M.

    1999-01-01

    Semi-cell morphogenesis in unicellular desmid algae of the genus Micrasterias generates a stellar shape by repeated dichotomous branching of growing tips of the cell surface. The numerous species of the genus display variations of the branching pattern that differ markedly in number of branchings, lobe width and lobe length. We have modelled this morphogenesis, following previous work by D. M. Harrison and M. Kolar (1988), on the assumptions that patterning occurs by chemical reaction-diffusion activity within the plasma membrane, leading to morphological expression by patterned catalysis of the extension of the cell surface. The latter has been simulated in simplified form by two-dimensional computations. Our results indicate that for generation of repeated branchings and for the control of diverse species-specific shapes, the loss of patterning activity and of rapid growth in regions separating the active growing tips is an essential feature. We believe this conclusion to be much more general than the specific details of our model. We discuss the limitations of the model especially in terms of what extra features might be addressed in three-dimensional computation.

  2. A cortical folding model incorporating stress-dependent growth explains gyral wavelengths and stress patterns in the developing brain

    PubMed Central

    Bayly, PV; Okamoto, RJ; Xu, G.; Shi, Y; Taber, LA

    2013-01-01

    In humans and many other mammals, the cortex (the outer layer of the brain) folds during development. The mechanics of folding are not well understood; leading explanations are either incomplete or at odds with physical measurements. We propose a mathematical model in which (i) folding is driven by tangential expansion of the cortex and (ii) deeper layers grow in response to the resulting stress. In this model the wavelength of cortical folds depends predictably on the rate of cortical growth relative to the rate of stress-induced growth. We show analytically and in simulations that faster cortical expansion leads to shorter gyral wavelengths; slower cortical expansion leads to long wavelengths or even smooth (lissencephalic) surfaces. No inner or outer (skull) constraint is needed to produce folding, but initial shape and mechanical heterogeneity influence the final shape. The proposed model predicts patterns of stress in the tissue that are consistent with experimental observations. PMID:23357794

  3. Observation of different reflected high-energy electron diffraction patterns during atomic layer epitaxy growth of CdTe epilayers

    NASA Astrophysics Data System (ADS)

    Faschinger, W.; Juza, P.; Sitter, H.

    1991-12-01

    We present the first RHEED observations during atomic layer epitaxy growth of CdTe on GaAs substrates. The evolution of the RHEED pattern shows that, despite the large lattice mismatch, growth becomes two-dimensional after the deposition of a few monolayers. We observe intensity variations of two RHEED spots under surface resonance conditions and show that this new approach is superior to the observation of the specular spot for the measurement of surface coverages and adsorption kinetics. From the variation of the spot intensities with substrate temperature, we deduce that the Cd and Te surface coverages drop to 0.5 at substrate temperatures higher than 315°C.

  4. Direct Growth and Controlled Coalescence of Thick AlN Template on Micro-circle Patterned Si Substrate

    PubMed Central

    Tran, Binh Tinh; Hirayama, Hideki; Maeda, Noritoshi; Jo, Masafumi; Toyoda, Shiro; Kamata, Norihiko

    2015-01-01

    High-density micro-circle patterned Si substrates were successfully fabricated for the direct overgrowth of thick AlN templates by using NH3 pulsed-flow multilayer AlN growth and epitaxial lateral overgrowth techniques. The experimental results show that an 8-μm-thick AlN template was grown at a very high growth rate on the substrates. The AlN template had full widths at half maximum of 0.23° and 0.37° for the (002) and (102) reflection planes in X-ray diffraction rocking curves. Atomic force microscopy and transmission electron microscopy confirmed that the roughness of the surface was low (3.5 nm) and the dislocation density was very low (1.5 × 108 cm−2 (screw), 3.7 × 108 (edge) cm−2). PMID:26439169

  5. Bayesian model selection framework for identifying growth patterns in filamentous fungi.

    PubMed

    Lin, Xiao; Terejanu, Gabriel; Shrestha, Sajan; Banerjee, Sourav; Chanda, Anindya

    2016-06-01

    This paper describes a rigorous methodology for quantification of model errors in fungal growth models. This is essential to choose the model that best describes the data and guide modeling efforts. Mathematical modeling of growth of filamentous fungi is necessary in fungal biology for gaining systems level understanding on hyphal and colony behaviors in different environments. A critical challenge in the development of these mathematical models arises from the indeterminate nature of their colony architecture, which is a result of processing diverse intracellular signals induced in response to a heterogeneous set of physical and nutritional factors. There exists a practical gap in connecting fungal growth models with measurement data. Here, we address this gap by introducing the first unified computational framework based on Bayesian inference that can quantify individual model errors and rank the statistical models based on their descriptive power against data. We show that this Bayesian model comparison is just a natural formalization of Occam׳s razor. The application of this framework is discussed in comparing three models in the context of synthetic data generated from a known true fungal growth model. This framework of model comparison achieves a trade-off between data fitness and model complexity and the quantified model error not only helps in calibrating and comparing the models, but also in making better predictions and guiding model refinements. PMID:27000772

  6. Patterns of Growth in Adaptive Social Abilities among Children with Autism Spectrum Disorders

    ERIC Educational Resources Information Center

    Anderson, Deborah K.; Oti, Rosalind S.; Lord, Catherine; Welch, Kathleen

    2009-01-01

    Adaptive social skills were assessed longitudinally at approximately ages 2, 3, 5, 9, and 13 years in a sample of 192 children with a clinical diagnosis of autism (n = 93), PDD-NOS (n = 51), or nonspectrum developmental disabilities (n = 46) at age 2. Growth curve analyses with SAS proc mixed were used to analyze social trajectories over time.…

  7. How do snow and winter changes influence alpine plant growth, vegetation patterns and phenology?

    NASA Astrophysics Data System (ADS)

    Rixen, C.

    2012-12-01

    Alpine shrub- and grasslands are shaped by extreme climatic conditions such as a long-lasting snow cover and a short vegetation period. Such ecosystems are expected to be highly sensitive to global environmental change. Prolonged growing seasons and shifts in temperature and precipitation are likely to affect plant phenology and growth. In this talk I will report on long-term and large-scale experiments in the Swiss Alps on alpine plants, treelines and snow cover. In one study, we used data from a network of snow and climate measuring stations in Switzerland to analyse relationships between snow cover, plant phenology and productivity. Regression analyses revealed highly significant correlations between mean air temperature in May/June and snow melt out, onset of plant growth, and plant height. These correlations were used to project plant growth phenology for future climate conditions based on the gridded output of a set of regional climate models runs. Melt out and onset of growth were projected to occur on average 17 days earlier by the end of the century than in the control period from 1971-2000 under the future climate conditions of the low resolution climate model ensemble. Plant height and biomass production were expected to increase by 77% and 45%, respectively. The earlier melt out and onset of growth will probably cause a considerable shift towards higher growing plants and thus increased biomass production. Our results represent the first quantitative and spatially explicit estimates of climate change impacts on future growing season length and the respective productivity of alpine plant communities in the Swiss Alps.

  8. The growth and characterization of GaN films on cone-shaped patterned sapphire by MOCVD

    NASA Astrophysics Data System (ADS)

    Liang, Jing; Hongling, Xiao; Xiaoliang, Wang; Cuimei, Wang; Qingwen, Deng; Zhidong, Li; Jieqin, Ding; Zhanguo, Wang; Xun, Hou

    2013-11-01

    GaN films are grown on cone-shaped patterned sapphire substrates (CPSSs) by metal-organic chemical vapor deposition, and the influence of the temperature during the middle stage of GaN growth on the threading dislocation (TD) density of GaN is investigated. High-resolution X-ray diffraction (XRD) and cathode-luminescence (CL) were used to characterize the GaN films. The XRD results showed that the edge-type dislocation density of GaN grown on CPSS is remarkably reduced compared to that of GaN grown on conventional sapphire substrates (CSSs). Furthermore, when the growth temperature in the middle stage of GaN grown on CPSS decreases, the full width at half maximum of the asymmetry (102) plane of GaN is reduced. This reduction is attributed to the enhancement of vertical growth in the middle stage with a more triangular-like shape and the bending of TDs. The CL intensity spatial mapping results also showed the superior optical properties of GaN grown on CPSS to those of GaN on CSS, and that the density of dark spots of GaN grown on CPSS induced by nonradiative recombination is reduced when the growth temperature in the middle stage decreases.

  9. Longitudinal burnout-collaboration patterns in Japanese medical care workers at special needs schools: a latent class growth analysis.

    PubMed

    Kanayama, Mieko; Suzuki, Machiko; Yuma, Yoshikazu

    2016-01-01

    The present study aimed to identify and characterize potential burnout types and the relationship between burnout and collaboration over time. Latent class growth analysis and the growth mixture model were used to identify and characterize heterogeneous patterns of longitudinal stability and change in burnout, and the relationship between burnout and collaboration. We collected longitudinal data at three time points based on Japanese academic terms. The 396 study participants included academic teachers, yogo teachers, and registered nurses in Japanese special needs schools. The best model included four types of both burnout and collaboration in latent class growth analysis with intercept, slope, and quadratic terms. The four types of burnout were as follows: low stable, moderate unstable, high unstable, and high decreasing. They were identified as involving inverse collaboration function. The results indicated that there could be dynamic burnout types, namely moderate unstable, high unstable, and high decreasing, when focusing on growth trajectories in latent class analyses. The finding that collaboration was dynamic for dynamic burnout types and stable for stable burnout types is of great interest. This was probably related to the inverse relationship between the two constructs. PMID:27366107

  10. Longitudinal burnout-collaboration patterns in Japanese medical care workers at special needs schools: a latent class growth analysis

    PubMed Central

    Kanayama, Mieko; Suzuki, Machiko; Yuma, Yoshikazu

    2016-01-01

    The present study aimed to identify and characterize potential burnout types and the relationship between burnout and collaboration over time. Latent class growth analysis and the growth mixture model were used to identify and characterize heterogeneous patterns of longitudinal stability and change in burnout, and the relationship between burnout and collaboration. We collected longitudinal data at three time points based on Japanese academic terms. The 396 study participants included academic teachers, yogo teachers, and registered nurses in Japanese special needs schools. The best model included four types of both burnout and collaboration in latent class growth analysis with intercept, slope, and quadratic terms. The four types of burnout were as follows: low stable, moderate unstable, high unstable, and high decreasing. They were identified as involving inverse collaboration function. The results indicated that there could be dynamic burnout types, namely moderate unstable, high unstable, and high decreasing, when focusing on growth trajectories in latent class analyses. The finding that collaboration was dynamic for dynamic burnout types and stable for stable burnout types is of great interest. This was probably related to the inverse relationship between the two constructs. PMID:27366107

  11. Growth pattern switch of renal cells and expression of cell cycle related proteins at the early stage of diabetic nephropathy

    SciTech Connect

    Zhang Yanling; Shi Yonghong; Liu Yaling; Dong Hui; Liu, Maodong; Li Ying; Duan Huijun

    2007-11-09

    Renal hypertrophy, partly due to cell proliferation and hypertrophy, has been found correlated to renal function deterioration in diabetes mellitus. We screened the up-regulated cell cycle related genes to investigate cell growth and the expression of cell cycle regulating proteins at the early stage of diabetic nephropathy using STZ-induced diabetic rats. Cyclin E, CDK{sub 2} and P{sup 27} were found significantly up-regulated in diabetic kidney. Increased cell proliferation in the kidney was seen at day 3, peaked at day 5, and returned to normal level at day 30. Cyclin E and CDK{sub 2} expression also peeked at day 5 and P{sup 27} activity peaked at day 14. These findings indicate that a hyperplastic growth period of renal cells is followed by a hypertrophic growth period at the early stage of diabetes. The growth pattern switch may be regulated by cell cycle regulating proteins, Cyclin E, CDK{sub 2}, and P{sup 27}.

  12. Impact of growth patterns and early diet on obesity and cardiovascular risk factors in young children from developing countries.

    PubMed

    Corvalán, Camila; Kain, Juliana; Weisstaub, Gerardo; Uauy, Ricardo

    2009-08-01

    Non-communicable chronic diseases are now a worldwide epidemic. Diet and physical activity throughout life are among its main determinants. In countries undergoing the early stages of the nutrition transition weight gain from birth to 2 years of life is related to lean mass gain, while ponderal gain after age 2 years is related to adiposity and later diabetes and CVD risk. Evidence from developing countries undergoing the more advanced stages of the nutrition transition is limited. The early growth patterns of a cohort of Chilean children born in 2002 with normal birth weight who at 4 years had a high prevalence of obesity and CVD risk factors have been assessed. Results indicate that BMI gain in early life, particularly from 6 months to 24 months, is positively associated with adiposity and CVD risk status at 4 years. These results together with existing evidence suggest that actions to prevent obesity and nutrition-related chronic diseases in developing countries should start early in life, possibly after 6 months of age. This approach should consider assessing the effect of mode of feeding and the amount and type of energy fed, as well as the resulting growth patterns. The challenge for researchers addressing the nutrition transition is to define the optimal nutrition in early life, considering not only the short- and long-term health consequences but also taking into account the stage of the nutritional transition for the given population of interest. The latter will probably require redefining optimal postnatal growth based on the context of maternal size and fetal growth. PMID:19400973

  13. Unstrained and strained semiconductor nanostructure fabrication via molecular beam epitaxical growth on non-planar patterned gallium arsenide(001) substrates

    NASA Astrophysics Data System (ADS)

    Konkar, Atul Ashok

    1999-11-01

    This dissertation contributes to three areas in the emerging field of nanostructures: (i) fabrication of quantum wires (QWR) and quantum dots (QD) via molecular beam epitaxy (MBE) on non-planar patterned substrates (NPPS), (ii) nature of mesa profile evolution with MBE growth, and (iii) nature of highly strained epitaxy on nanoscale mesas. Using the approach of substrate-encoded size-reducing epitaxy (SESRE) we have successfully fabricated QWRs and QBs in the unstrained GaAs/AlGaAs system and QBs in the highly strained InAs/GaAs system on GaAs (001) mesas with edges oriented along the <100> directions. By controlling the InAs delivery just below that required for 3D island formation on planar GaAs (001) substrates and optimizing the growth conditions, we have been able to selectively position 3D InAs islands on stripe mesas with appropriate shape, size, and orientation. Studies of the effect of growth interruption on the mesa growth profile evolution reveal the dynamic nature of the NPPS surface at typical MBE growth conditions. In the case of [100] oriented stripe mesas, during growth adatom migration was seen from the {101}, sidewalls to the (001) mesa top, whereas during growth interruption adatom migration from the mesa top to the sidewalls was observed. These results have significant implications for the relative magnitudes of the energy barriers relevant to the crystal growth processes on different surfaces. Studies of growth profile evolution dependence on the orientation and the sidewall profile of mesas created via focused ion beam assisted chemical etching evidenced the mesa profiles suitable for nanostructure fabrication via SESRE. We observe a dramatic suppression of 3D island formation during InAs deposition on nanoscale square mesas due to the strain relief available at the free edges of the mesa and substantial strain accommodation in the underlying mesa. The interplay between the strain build-up and the interfacet migration kinetics causes reversal

  14. Pattern Formation in Keller-Segel Chemotaxis Models with Logistic Growth

    NASA Astrophysics Data System (ADS)

    Jin, Ling; Wang, Qi; Zhang, Zengyan

    In this paper, we investigate pattern formation in Keller-Segel chemotaxis models over a multidimensional bounded domain subject to homogeneous Neumann boundary conditions. It is shown that the positive homogeneous steady state loses its stability as chemoattraction rate χ increases. Then using Crandall-Rabinowitz local theory with χ being the bifurcation parameter, we obtain the existence of nonhomogeneous steady states of the system which bifurcate from this homogeneous steady state. Stability of the bifurcating solutions is also established through rigorous and detailed calculations. Our results provide a selection mechanism of stable wavemode which states that the only stable bifurcation branch must have a wavemode number that minimizes the bifurcation value. Finally, we perform extensive numerical simulations on the formation of stable steady states with striking structures such as boundary spikes, interior spikes, stripes, etc. These nontrivial patterns can model cellular aggregation that develop through chemotactic movements in biological systems.

  15. Influence of condition of growth of bacterial colonies on fractal dimension of bacterial speckle patterns

    NASA Astrophysics Data System (ADS)

    Ulyanov, Alexander S.; Lyapina, Anna M.; Ulianova, Onega V.; Feodorova, Valentina A.

    2010-10-01

    New field of application of fractal dimensions is proposed. A technique, based on the calculation of fractal dimension, was used for express-diagnostics and identification of bacteria of the vaccine strain Yersinia pestis EV line NIIEG. Purpose of this study was the experimental investigation of properties of speckle patterns, formed under laser illumination of a single colony of the strain that was grown on different agars.

  16. Influence of condition of growth of bacterial colonies on fractal dimension of bacterial speckle patterns

    NASA Astrophysics Data System (ADS)

    Ulyanov, Alexander S.; Lyapina, Anna M.; Ulianova, Onega V.; Feodorova, Valentina A.

    2011-03-01

    New field of application of fractal dimensions is proposed. A technique, based on the calculation of fractal dimension, was used for express-diagnostics and identification of bacteria of the vaccine strain Yersinia pestis EV line NIIEG. Purpose of this study was the experimental investigation of properties of speckle patterns, formed under laser illumination of a single colony of the strain that was grown on different agars.

  17. Electrical activity in cerebellar cultures determines Purkinje cell dendritic growth patterns.

    PubMed

    Schilling, K; Dickinson, M H; Connor, J A; Morgan, J I

    1991-12-01

    In primary dissociated cultures of mouse cerebellum a number of Purkinje cell-specific marker proteins and characteristic ionic currents appear at the appropriate developmental time. During the first week after plating, Purkinje cell dendrites elongate, but as electrical activity emerges the dendrites stop growing and branch. If endogenous electrical activity is inhibited by chronic tetrodotoxin or high magnesium treatment, dendrites continue to elongate, as if they were still immature. At the time that branching begins, intracellular calcium levels become sensitive to tetrodotoxin, suggesting that this cation may be involved in dendrite growth. Even apparently mature Purkinje cells alter their dendritic growth in response to changes in activity, suggesting long-term plasticity. PMID:1684902

  18. Shape-Controlled Synthesis of Ni-Based Nanoparticles and Patterning for Carbon Nanofiber Growth

    NASA Astrophysics Data System (ADS)

    Sarac, Mehmet Fahri

    This dissertation reviews a comprehensive set of research results comprised of three studies, which includes the synthesis of nickel (Ni) nanoparticles (NPs) and their conversion chemistry, methods for depositing them onto substrates, and catalysis of carbon nanofiber growth. The first part of the work is concerned with the synthesis of Ni NPs, dropcasting and growing them in alignment with carbon nanofibers along a silicon (Si) substrate. Following observed success of this step, Ni NPs were airbrushed across different substrates, attempting to observe differences while reporting the results of an extensive comparative analysis of the different substrates used. Here, it was observed that the Ni NPs had a tendency to have dendritic rather than spherical shapes, motivating an additional study of the cause of branching and how it can be controlled. All three portions of this study are presented and discussed in detail. In the first set of experiments, vertically aligned carbon nanofibers (VACNFs) were created through ligand-stabilized Ni nanoparticle (NP) catalysts and plasma enhanced chemical vapor deposition; these NPs were used to allow growth of VACNFs in dense arrays. In the pregrowth heating process, the ligands are converted into graphitic shells that prevent agglomeration and coalescence of the catalyst NPs, resulting in a monodisperse VACNF size distribution. Meanwhile, VACNFs were grown from Ni NPs that had been airbrushed onto various substrates (silicon (Si), aluminum (Al), copper (Cu), and titanium (Ti)). Si micropowder was also used as a precursor for Si coatings formed in situ on VACNFs, causing rigidity. Growth of VACNFs on metal foils will facilitate applications that require thermal or electrical contact to the VACNFs, such as anode materials for Li-ion batteries and thermal interface materials. A related study focused on the synthesis of Ni3C1-x NPs, the control of branching in dendritic Ni3C1-x NPs and the effect of branching on the conversion into

  19. [Kinetic patterns in the growth of transplantable mouse tumor RShM-1].

    PubMed

    Svinogeeva, T P; Konopliannikov, A G; Shtein, L V

    1976-01-01

    Under study was the kinetics of growth of cervical cancer (CCM-1) transplanted on mice CBA, also the mitotic cycle and diurnal activity of tumor cells division. The tumor growth can well be described with the Hompertz equation, the constants of acceleration and retardation being equal to 0.34 day-1 and 0.004 day-1 accordingly. A linear dependence between the size, weight and number of CCM-1 celos is shown. In the tumor under study a persistant diurnal rhythm of the cell division was found with the maximum at 7 and 19 hours and the minimum at 13. The basis parameters of the mitotic cycle of tumor cells were determined: Tc=17.8 hr., G2 approximately 40 min.; S=9 hr., M approximately 24 min., G1 approximately 18.4 hr. The time of tumor doubling was 48.7 hr. The cell loss factor is as much as 42.1 per cent. PMID:1034368

  20. Structure and Growth Pattern of Pseudoteeth in Pelagornis mauretanicus (Aves, Odontopterygiformes, Pelagornithidae)

    PubMed Central

    Louchart, Antoine; Sire, Jean-Yves; Mourer-Chauviré, Cécile; Geraads, Denis; Viriot, Laurent; de Buffrénil, Vivian

    2013-01-01

    The extinct Odontopterygiformes are the sole birds known to possess strong and sharp bony pseudoteeth, the shape and location of which are closely mimetic of real teeth. The structure of the pseudoteeth is investigated here in a late Pliocene/early Pleistocene species, Pelagornis mauretanicus, using X-ray microtomography and thin sections. The results are interpreted with regard to the pseudotooth mode of growth, and have implications concerning aspects of Pelagornis ecology. The larger pseudoteeth are hollow and approximately cone-shaped, and the smaller ones are rostro-caudally constricted. The walls of pseudoteeth are composed of bone tissue of the fibro-lamellar type, which is intensively remodeled by Haversian substitution. The jaw bones display the same structure as the pseudoteeth, but their vascular canals are oriented parallel to the long axis of the bones, whereas they are perpendicular to this direction in the pseudoteeth. There is no hiatus or evidence of a fusion between the pseudoteeth and the jaw bones. Two possible models for pseudotooth growth are derived from the histological data. The most plausible model is that pseudotooth growth began after the completion of jaw bone growth, as a simple local protraction of periosteal osteogenic activity. Pseudotooth development thus occurred relatively late during ontogeny. The highly vascularized structure and the relative abundance of parallel-fibered bone tissue in the pseudoteeth suggest poor mechanical capabilities. The pseudoteeth were most likely covered and protected by the hardened, keratinized rhamphotheca in the adult during life. The late development of the pseudoteeth would involve a similarly late and/or partial hardening of the rhamphotheca, as displayed by extant Anseriformes, Apterygiformes and some Charadriiformes. This would add support to the hypothesis of a close phylogenetic relationship between Odontopterygiformes and Anseriformes. The late maturation of the Pelagornis feeding apparatus

  1. Nanoscale growth factor patterns by immobilization on a heparin-mimicking polymer.

    PubMed

    Christman, Karen L; Vázquez-Dorbatt, Vimary; Schopf, Eric; Kolodziej, Christopher M; Li, Ronald C; Broyer, Rebecca M; Chen, Yong; Maynard, Heather D

    2008-12-10

    In this study, electrostatic interactions between sulfonate groups of an immobilized polymer and the heparin binding domains of growth factors important in cell signaling were exploited to nanopattern the proteins. Poly(sodium 4-styrenesulfonate-co-poly(ethylene glycol) methacrylate) (pSS-co-pPEGMA) was synthesized by reversible addition-fragmentation chain transfer (RAFT) polymerization using ethyl S-thiobenzoyl-2-thiopropionate as a chain transfer agent and 2,2'-azoisobutyronitrile (AIBN) as the initiator. The resulting polymer (1) was characterized by 1H NMR, GPC, FT-IR, and UV-vis and had a number average molecular weight (Mn) of 24,000 and a polydispersity index (PDI) of 1.17. The dithioester end group of 1 was reduced to the thiol, and the polymer was subsequently immobilized on a gold substrate. Binding of basic fibroblast growth factor (bFGF) and vascular endothelial growth factor (VEGF) to the polymer via the heparin binding domains was then confirmed by surface plasmon resonance (SPR). The interactions were stable at physiological salt concentrations. Polymer 1 was cross-linked onto silicon wafers using an electron beam writer forming micro- and nanopatterns. Resolutions of 100 nm and arbitrary nanoscale features such as concentric circles and contiguous squares and triangles were achieved. Fluorescence microscopy confirmed that bFGF and VEGF were subsequently immobilized to the polymer micro- and nanopatterns. PMID:19554729

  2. Growth patterns of the Cambrian microbialite: Phototropism and speciation of Epiphyton

    NASA Astrophysics Data System (ADS)

    Woo, J.; Chough, S. K.

    2010-07-01

    Microbes started constructing shallow marine stromatolitic bioherms in the Archean, but they transferred their role as a major buildup maker to metazoans in Phanerozoic. Microbial buildups often recovered their predominance in the carbonate platform when reefal metazoan communities collapsed. Epiphyton, an extinct taxon of calcified microbe that possessed branching filamentous trichomes, was an important reef builder in the shallow marine carbonate platform during Middle Cambrian, aftermath of an extinction of archaeocyath sponges which were major reef-building sessile organisms in the Early Cambrian. Here we present direct evidence of phototropism of Epiphyton, found from fossilized behavior in micro- and macro-structures of meter-scale microbial bioherms of the Zhangxia Formation (Middle Cambrian), North China Platform, Shandong Province, China. The bioherms consist of stacked growth layers with the inner and outer divisions divided by distinct boundary. The inner division of growth layers of the Epiphyton bioherm is dominated by dense uniform bush-shaped Epiphyton thalli, whereas the curved outer division has layered texture normal to the surface, comprised of elongated and chambered thalli. It suggests that photosynthetic Epiphyton reacted actively to the spatial changes in intensity of sunlight, controlled by angle of illumination on the curved growth surface of the bioherm. The inner and the outer divisions comprise different morpho-types of Epiphyton. The spatial distributions of different morpho-types in variously illuminated divisions of Epiphyton might have caused further speciation of Epiphyton.

  3. Postnatal Growth Patterns in a Chilean Cohort: The Role of SES and Family Environment

    PubMed Central

    Kang Sim, D. E.; Cappiello, M.; Castillo, M.; Lozoff, B.; Martinez, S.; Blanco, E.; Gahagan, S.

    2012-01-01

    Objective. This study examined how family environmental characteristics served as mediators in the relationship between socioeconomic conditions and infant growth in a cohort of Chilean infants. Methods. We studied 999 infants, born between 1991 and 1996, from a longitudinal cohort which began as an iron deficiency anemia preventive trial. SES (Graffar Index), the Life Experiences Survey, and the Home Observation for Measurement of the Environment (HOME) were assessed in infancy. Using path analysis, we assessed the relationships between the social factors, home environment, and infant growth. Results. During the first year, weight and length gain averaged 540 grams/month and 6.5 cm/month, respectively. In the path analysis model for weight gain, higher SES and a better physical environment were positively related to higher maternal warmth, which in turn was associated with higher average weight gain. Higher SES was directly related to higher average length gain. Conclusions. In our cohort, a direct relationship between SES and length gain developed during infancy. Higher SES was indirectly related to infant weight gain through the home environment and maternal warmth. As the fastest growing infants are at risk for later obesity, new strategies are needed to encourage optimal rather than maximal growth. PMID:22666275

  4. Temperature-controlled coalescence during the growth of Ge crystals on deeply patterned Si substrates

    NASA Astrophysics Data System (ADS)

    Bergamaschini, Roberto; Salvalaglio, Marco; Scaccabarozzi, Andrea; Isa, Fabio; Falub, Claudiu V.; Isella, Giovanni; von Känel, Hans; Montalenti, Francesco; Miglio, Leo

    2016-04-01

    A method for growing suspended Ge films on micron-sized Si pillars in Si(001) is discussed. In [C.V. Falub et al., Science 335 (2012) 1330] vertically aligned three-dimensional Ge crystals, separated by a few tens of nanometers, were obtained by depositing several micrometers of Ge using Low-Energy Plasma-Enhanced Chemical Vapor Deposition. Here a different regime of high growth temperature is exploited in order to induce the merging of the crystals into a connected structure eventually forming a continuous, two-dimensional film. The mechanisms leading to such a behavior are discussed with the aid of an effective model of crystal growth. Both the effects of deposition and curvature-driven surface diffusion are considered to reproduce the main features of coalescence. The key enabling role of high temperature is identified with the activation of the diffusion process on a time scale competitive with the deposition rate. We demonstrate the versatility of the deposition process, which allows to switch between the formation of individual crystals and a continuous suspended film simply by tuning the growth temperature.

  5. Interannual variations in the hatching pattern, larval growth and otolith size of a sand-dwelling fish from central Chile

    NASA Astrophysics Data System (ADS)

    Rodríguez-Valentino, Camilo; Landaeta, Mauricio F.; Castillo-Hidalgo, Gissella; Bustos, Claudia A.; Plaza, Guido; Ojeda, F. Patricio

    2015-09-01

    The interannual variation (2010-2013) of larval abundance, growth and hatching patterns of the Chilean sand stargazer Sindoscopus australis (Pisces: Dactyloscopidae) was investigated through otolith microstructure analysis from samples collected nearshore (<500 m from shore) during austral late winter-early spring off El Quisco bay, central Chile. In the studied period, the abundance of larval stages in the plankton samples varied from 2.2 to 259.3 ind. 1000 m-3; larval abundance was similar between 2010 and 2011, and between 2012 and 2013, but increased significantly from 2011 to 2012. The estimated growth rates increased twice, from 0.09 to 0.21 mm day-1, between 2011 and 2013. Additionally, otolith size (radius, perimeter and area), related to body length of larvae, significantly decreased from 2010 to 2012, but increases significantly in 2013. Although the mean values of microincrement widths of sagitta otoliths were similar between 2010 and 2011 (around 0.6-0.7 μm), the interindividual variability increases in 2011 and 2013, suggesting large environmental variability experienced by larvae during these years. Finally, the hatching pattern of S. australis changed significantly from semi-lunar to lunar cycle after 2012.

  6. Mechanisms of growth and patterns of gene expression in oxygen-deprived rice coleoptiles.

    PubMed

    Narsai, Reena; Edwards, Joshua M; Roberts, Thomas H; Whelan, James; Joss, Gregory H; Atwell, Brian J

    2015-04-01

    Coleoptiles of rice (Oryza sativa) seedlings grown under water commonly elongate by up to 1 mm h(-1) to reach the atmosphere. We initially analysed this highly specialized phenomenon by measuring epidermal cell lengths along the coleoptile axis to determine elongation rates. This revealed a cohort of cells in the basal zone that elongated rapidly following emergence from the embryo, reaching 200 μm within 12 h. After filming coleoptiles in vivo for a day, kinematic analysis was applied. Eight time-sliced 'segments' were defined by their emergence from the embryo at four-hourly intervals, revealing a mathematically simple growth model. Each segment entering the coleoptile from the embryo elongated at a constant velocity, resulting in accelerating growth for the entire organ. Consistent with the epidermal cell lengths, relative rates of elongation (mm mm(-1) h(-1)) were tenfold greater in the small, newly emerged basal segments than the older distal tip segments. This steep axial gradient defined two contrasting growth zones (bases versus tips) in which we measured ATP production and protein, RNA and DNA content, and analysed the global transcriptome under steady-state normoxia, hypoxia (3% O2) and anoxia. Determination of the transcriptome revealed tip-specific induction of genes encoding TCP [Teosinte Branched1 (Tb1) of maize, Cycloidea (Cyc), and Proliferating Cell Factor (Pcf)] transcription factors, RNA helicases, ribosomal proteins and proteins involved in protein folding, whilst expression of F-box domain-containing proteins in the ubiquitin E3-SCF complex (Skp, Cullin, F-box containing complex) was induced specifically in bases under low oxygen conditions. We ascribed the sustained elongation under hypoxia to hypoxia-specific responses such as controlled suppression of photosystem components and induction of RNA binding/splicing functions, indicating preferential allocation of energy to cell extension. PMID:25650041

  7. Cultural variation in early feeding pattern and maternal perceptions of infant growth.

    PubMed

    van Eijsden, Manon; Meijers, Claire M C; Jansen, Jessica E; de Kroon, Marlou L A; Vrijkotte, Tanja G M

    2015-08-14

    The perception of healthy growth and weight may differ between cultures, which could influence feeding practises and consequently affect the development of overweight. The present study examined ethnic variation in maternal perceptions of growth and their influence on feeding practises among Turkish and Dutch infants aged 0-6 months. Data were obtained from the mothers of 143 Turkish and 143 Dutch healthy, singleton, term infants with birth weights appropriate for gestational age, using structured interviews at 1, 4 and 6 months after birth. Compared with Dutch mothers, mothers of Turkish descent perceived a chubby infant more often as pretty (43 v. 22%), and were more often worried about their infant's growth (13 v. 4%). Turkish mothers were more likely to give full breast-feeding (BF) until at least 6 months (adjusted OR (aOR) 2.1, 95% CI 1.0, 4.3) and to start introducing complementary feeding, including rice flour porridge, at the age of 6 months (aOR 2.4, 95% CI 1.1, 4.9). Infants of Turkish descent were fed on average one milk feeding more during the day and, if introduced to complementary foods before 6 months, were more often given uncommon types of foods (e.g., yogurt and cookies) (aOR 2.1, 95% CI 1.1, 4.3). The differences in perceptions affected differences in feeding practises only to a small extent. Preventive advice offered to Turkish mothers in Child Health Care should include discussing choices of complementary foods and frequency of feeding from an early age onwards. In Dutch mothers, support for the continuation of BF remains an important issue. PMID:26166487

  8. Increased erythrocyte protoporphyrins and blood lead - a pilot study of childhood growth patterns

    SciTech Connect

    Angle, C.R.; Kuntzelman, D.R. )

    1989-01-01

    The National Health and Nutrition Survey 1976-1980 demonstrated the inverse association of blood lead 8-35 {mu}g/dl (0.4-1.7 {mu}M) with height and weight in 2680 children 1-7 yr old. Growth has not been examined. A retrospective pilot study was made of growth, 0-42 mo, for 54 children found to have erythrocyte protoporphyrins >35 {mu}g/dl (0.6 mM) at 12-23 mo. For 24/54, all blood leads were <30 {mu}g/dl (1.2 {mu}M), with a peak annual mean of 18.5 {mu}g/dl (0.9 {mu}M); for 30/54, mean blood lead was 46.7 {mu}/dl (2.2 {mu}M) at 12-23 mo with all subsequent blood leads {ge}30 {mu}g/dl (1.2 {mu}M). In both groups the mean height and weight at birth were at the 25th percentile. The high-lead children had increased weight velocity at 15 mo of age and were heavier at 24 mo. Weight gain related to total caloric intake, supporting food consumption, and hand-to-mouth behavior as significant factors in an increased blood lead ages 9-24 mo. The monthly directional change of height and weight percentiles after 24 mo, however, showed a decreased frequency of upward shifts when blood lead was {ge}30 {mu}g/dl. Although an early high food intake appears to contribute to high blood lead by increasing the intake of lead from food and mouthing, persistent increases in the high blood lead and erythrocyte protoporphyrins were associated with subsequent growth retardation.

  9. Neighborhood matters: Patterns and controls on wood distribution in old-growth forest streams of the Colorado Front Range, USA

    NASA Astrophysics Data System (ADS)

    Wohl, Ellen; Cadol, Daniel

    2011-01-01

    We surveyed wood characteristics along four headwater channel segments of the Colorado Front Range with drainage areas of 8-82 km 2. Stream lengths surveyed range from 3025 to 8980 m and together include a total of 15,706 pieces of wood. Time since last disturbance in the form of a stand-killing fire varied from 31 to > 500 years. Individual pieces of wood were highly aggregated at length scales of 1 to 150 m. Trends among jams were more weakly developed, but jams tended to be more segregated at lengths < 10 m, slightly more aggregated at lengths ~ 100-300 m, and to have diverging patterns at lengths > 300 m, with jams along individual channels being aggregated, segregated, or random. Multiple linear regressions failed to produce highly predictive models to explain the response variables of wood load, piece dimensions, or characteristics of jams other than jam volume (which correlated with drainage area and wood load); but examination of downstream patterns suggests that local valley and channel geometry (valley-bottom width, gradient, and sequence of longitudinal channel changes) exert a stronger influence on patterns of wood distribution than either time since last forest disturbance or progressive downstream trends associated with increasing drainage area. The longitudinal sequences of wood recruitment sources, forest stand age, and channel geometry together exert an important control on reach-scale wood load and aggregation. Wood loads in streams draining old-growth (> 250 years) forests of the Colorado Front Range are low compared to old-growth sites in other regions of the world, which we interpret to reflect decreased retention of wood recruited to the streams.

  10. [Spatial distribution pattern and allometric growth of three common species on moving sand dunes in Horqin Sandy Land, China].

    PubMed

    Jia, Mei-yu; Li, Xue-hua; Oh, Choong-hyeon; Park, Hong-chul; Miao, Chun-ping; Han, Xu

    2015-10-01

    Research on fine scale pattern and characteristics of allometric growth could contribute to better understanding plants' adaptation in moving sandy dunes. The abundance, height and biomass of 3 species Agriophilum aquarrosum, Corispermum candelabrum and Setaria viridis in twenty-eight 1 m x 1 m quadrats of Horqin Sandy Land were identified, mapped and described. The nearest neighbor method and O-ring O(r) function analysis were applied to analyze the spatial patterns. The results showed that the individual spatial pattern was mainly aggregated in 1 m x 1 m quadrat at community level but mainly random at population level. At 0-50 cm individual distance scale, both intraspecific and interspecific relationship were facilitation and aggregated distribution occurred at some scales and varied with increasing plant abundance in 1 m x 1 m quadrat. In 0-40 cm, the aggregated distribution of S. viridis and A. aquarrosum increased obviously; in 10-20 cm, both intraspecific and interspecific aggregation increased; in 10-30 cm, the occurrence possibility of positive correlations between S. viridis and A. aquarrosum, S. viridis and C. candelabrum all increased; in 40-50 cm, the possibility of positive correlations between A. squarrosum and S. viridis, A. squarrosum and C. candelabrum all increased. Research on the three species components indicated that the growth rate of above-ground was faster than that of underground. S. viridis had the highest ratio of under-ground biomass to above-ground biomass but its nutritional organs' biomass ratio was medium. C. candelabrum allocated more biomass to propagative organs and stem, but A. squarrosum allocated more biomass to nutritional organs. Based on the spatial distribution and allometric characteristics, the three common species in moving sand dunes preferred r strategy in their life history. PMID:26995902

  11. Growth of solid and hollow gold particles through the thermal annealing of nanoscale patterned thin films

    SciTech Connect

    Lin, Junhao; He, Weidong; Vilayur Ganapathy, Subramanian; Peppernick, Samuel J.; Wang, Bin; Palepu, Sandeep; Remec, Miroslav; Hess, Wayne P.; Hmelo, Anthony B.; Pantelides, Sokrates T.; Dickerson, James

    2013-11-27

    Through thermally annealing well-arrayed, circular, nanoscale thin films of gold, deposited onto [111] silicon/silicon dioxide substrates, both solid and hollow gold particles of different morphologies with controllable sizes were obtained. The thin film could form individual particle or clusters of particles by tuning the diameter of it. Hollow gold particles were featured by their large size whose diameter was larger than 500 nm and confirmed by a cross-section view. Hollow gold particles show greater plasmonic field enhancement under photoemission electron microscopy. Potential growth mechanisms for these structures are explored

  12. A rabbit model of human familial, nonsyndromic unicoronal suture synostosis. I. Synostotic onset, pathology, and sutural growth patterns.

    PubMed

    Mooney, M P; Siegel, M I; Burrows, A M; Smith, T D; Losken, H W; Dechant, J; Cooper, G; Kapucu, M R

    1998-06-01

    Poswillo has stated, "The more severe anomalies of the calvaria, such as plagiocephaly, Crouzon [syndrome], and Apert syndrome still defy explanation, in the absence of an appropriate animal system to study" (p. 207). This two-part study reviews data from a recently developed colony of New Zealand white rabbits with familial, nonsyndromic unilateral coronal suture synostosis. Part 1 presents pathological findings and compensatory sutural growth data from 109 normal rabbits and 82 craniosynostotic rabbits from this colony. Synostotic foci, onset, and progression were described in the calvariae from 102 staged (fetal days 21, 25, 27, 33; term = 30 days) fetuses (39 normal, 63 synostosed). Calvarial suture growth patterns from 10 to 126 days of age were assessed from serial radiographs obtained from 89 rabbits (70 normal rabbits and 19 rabbits with unicoronal suture synostosis) with amalgam bone marker implants. Perinatal results revealed that by fetal day 25 the synostotic focal point in synostotic rabbits consistently originated from the endocortical surface of the calvaria in the middle of the coronal suture at a presumed high-tension, interdigitating zone. Histological analysis revealed hyperostotic osteogenic fronts on the affected side compared with the unaffected side. Postnatal sutural growth data revealed a predictable pattern of plagiocephaly (contralateral coronal sutures growing more than ipsilateral sutures and ipsilateral frontonasal and anterior lambdoidal sutures growing more than contralateral sutures), which resulted in early cranial vault deformities and a double "S" shape torquing towards the affected side. The advantages and disadvantages of these rabbits as a model for human familial, nonsyndromic unicoronal suture synostosis are discussed, especially in light of recent cytokine and genetic findings from human craniosynostotic studies. PMID:9694335

  13. Effects of biological and methodological factors on volatile organic compound patterns during cultural growth of Mycobacterium avium ssp. paratuberculosis.

    PubMed

    Küntzel, Anne; Fischer, Sina; Bergmann, Andreas; Oertel, Peter; Steffens, Markus; Trefz, Phillip; Miekisch, Wolfram; Schubert, Jochen K; Reinhold, Petra; Köhler, Heike

    2016-01-01

    Mycobacterium avium ssp. paratuberculosis (MAP) causes chronic granulomatous enteritis in ruminants. Bacterial growth is still the diagnostic 'gold standard', but is very time consuming. MAP-specific volatile organic compounds (VOCs) above media could accelerate cultural diagnosis. The aim of this project was to assess the kinetics of a VOC profile linked to the growth of MAP in vitro. The following sources of variability were taken into account: five different culture media, three different MAP strains, inoculation with different bacterial counts, and different periods of incubation. Needle-trap microextraction was employed for pre-concentration of VOCs, and gas chromatography-mass spectrometry for subsequent analysis. All volatiles were identified and calibrated by analysing pure references at different concentration levels. More than 100 VOCs were measured in headspaces above MAP-inoculated and control slants. Results confirmed different VOC profiles above different culture media. Emissions could be assigned to either egg-containing media or synthetic ingredients. 43 VOCs were identified as potential biomarkers of MAP growth on Herrold's Egg Yolk Medium without significant differences between the tree MAP strains. Substances belonged to the classes of alcohols, aldehydes, esters, ketones, aliphatic and aromatic hydrocarbons. With increasing bacterial density the VOC concentrations above MAP expressed different patterns: the majority of substances increased (although a few decreased after reaching a peak), but nine VOCs clearly decreased. Data support the hypotheses that (i) bacteria emit different metabolites on different culture media; (ii) different MAP strains show uniform VOC patterns; and (iii) cultural diagnosis can be accelerated by taking specific VOC profiles into account. PMID:27604146

  14. Pathogen associated molecular pattern (PAMP)-triggered immunity is compromised under C-limited growth.

    PubMed

    Park, Hyeong Cheol; Lee, Shinyoung; Park, Bokyung; Choi, Wonkyun; Kim, Chanmin; Lee, Sanghun; Chung, Woo Sik; Lee, Sang Yeol; Sabir, Jamal; Bressan, Ray A; Bohnert, Hans J; Mengiste, Tesfaye; Yun, Dae-Jin

    2015-01-31

    In the interaction between plants and pathogens, carbon (C) resources provide energy and C skeletons to maintain, among many functions, the plant immune system. However, variations in C availability on pathogen associated molecular pattern (PAMP) triggered immunity (PTI) have not been systematically examined. Here, three types of starch mutants with enhanced susceptibility to Pseudomonas syringae pv. tomato DC3000 hrcC were examined for PTI. In a dark period-dependent manner, the mutants showed compromised induction of a PTI marker, and callose accumulation in response to the bacterial PAMP flagellin, flg22. In combination with weakened PTI responses in wild type by inhibition of the TCA cycle, the experiments determined the necessity of C-derived energy in establishing PTI. Global gene expression analyses identified flg22 responsive genes displaying C supply-dependent patterns. Nutrient recycling-related genes were regulated similarly by C-limitation and flg22, indicating re-arrangements of expression programs to redirect resources that establish or strengthen PTI. Ethylene and NAC transcription factors appear to play roles in these processes. Under C-limitation, PTI appears compromised based on suppression of genes required for continued biosynthetic capacity and defenses through flg22. Our results provide a foundation for the intuitive perception of the interplay between plant nutrition status and pathogen defense. PMID:25387755

  15. Morphological transition between diffusion-limited and ballistic aggregation growth patterns.

    PubMed

    Ferreira, S C; Alves, S G; Brito, A Faissal; Moreira, J G

    2005-05-01

    In this work, the transition between diffusion-limited (DLA) and ballistic aggregation (BA) models was reconsidered using a model in which biased random walks simulate the particle trajectories. The bias is controlled by a parameter lambda, which assumes the value lambda=0 (1) for the ballistic (diffusion-limited) aggregation model. Patterns growing from a single seed were considered. In order to simulate large clusters, an efficient algorithm was developed. For lambda (not equal to) 0 , the patterns are fractal on small length scales, but homogeneous on large ones. We evaluated the mean density of particles (-)rho in the region defined by a circle of radius r centered at the initial seed. As a function of r, (-)rho reaches the asymptotic value rho(0)(lambda) following a power law (-)rho = rho(0) +Ar(-gamma) with a universal exponent gamma=0.46 (2) , independent of lambda . The asymptotic value has the behavior rho(0) approximately |1-lambda|(beta) , where beta=0.26 (1) . The characteristic crossover length that determines the transition from DLA- to BA-like scaling regimes is given by xi approximately |1-lambda|(-nu) , where nu=0.61 (1) , while the cluster mass at the crossover follows a power law M(xi) approximately |1-lambda(-alpha) , where alpha=0.97 (2) . We deduce the scaling relations beta=nugamma and beta=2nu-alpha between these exponents. PMID:16089530

  16. Study of defect management in the growth of semipolar (11-22) GaN on patterned sapphire

    NASA Astrophysics Data System (ADS)

    Vennéguès, P.; Tendille, F.; De Mierry, P.

    2015-08-01

    This work describes, using mainly transmission electron microscopy as an investigation tool, the nature and behaviour of the crystalline defects which are present in (11-22) semipolar GaN films grown epitaxially on patterned r-sapphire substrates using a 3 step growth process. The microstructure at these different growth stages is described. The independent 3D-crystallites nucleated on the substrate surface contain threading dislocations resulting from the epitaxy on c-sapphire facets and basal stacking faults (BSFs), mainly in the  -c-wings. These defects are concentrated in a few hundred nanometre wide stripe-like regions emerging on the top facet of the islands. By a careful choice of the growth conditions, these defective regions may be overgrown by defect-free material, blocking their propagation towards the coalesced surface. However, when the 3D crystals coalesce, new dislocations together with very few BSFs are created at the coalescence boundaries. These coalescence defects propagate to the surface of the films in (0001) planes. In summary, the control of the nucleation and propagation of the crystalline defects allows obtaining large area semipolar films with very low defect densities: 7   ×   107 cm-2 for TDs and 70 cm-1 for BSFs.

  17. Gender, season and habitat: Patterns of variation in photosynthetic activity, growth and fecundity in Thymelaea velutina

    NASA Astrophysics Data System (ADS)

    de la Bandera, Maria del Carmen; Traveset, Anna; Valladares, Fernando; Gulías, Javier

    2008-11-01

    Changes in the ecophysiological performance of a plant species due to different environmental conditions generally reflect adaptations to the habitat where the plant grows and are often related to its survival capacity in a particular place. We examined this with the dioecious shrub Thymelaea velutina, in two contrasting populations representing the extremes of the altitudinal gradient where the species lives (coastal dunes and mountain habitats over 1000 m). We measured net photosynthetic rates and stomatal conductance, estimated the level of plant stress by chlorophyll fluorescence, and assessed their correlations with growth rate, plant size, flower production and fruit set. We hypothesized that plants at high altitude were more photosynthetically stressed than at sea level and expected a gender × habitat interaction in performance as females need more resources than males. Plants in the mountain experienced chronic photoinhibition during winter and a reduced photosynthetic performance both in winter and spring compared to plants in coastal dunes. However, there was no association between any of the fluorescence variables and either plant growth or fecundity, suggesting that other factors are involved determining performance. Mountain plants showed also an apparent lower capacity of heat dissipation to excessive radiation than dune plants. In the dunes, the greater leaf area and mass can lead to a higher photosynthetic carbon gain by whole individuals compared to plants in the mountain. No effect of gender was detected on the ecophysiological performance of this species, which we partly attribute to the small size of fruits of the female plants.

  18. Demystifying the Search Button: A Comprehensive PubMed Search Strategy for Performing an Exhaustive Literature Review.

    PubMed

    McKeever, Liam; Nguyen, Van; Peterson, Sarah J; Gomez-Perez, Sandra; Braunschweig, Carol

    2015-08-01

    A thorough review of the literature is the basis of all research and evidence-based practice. A gold-standard efficient and exhaustive search strategy is needed to ensure all relevant citations have been captured and that the search performed is reproducible. The PubMed database comprises both the MEDLINE and non-MEDLINE databases. MEDLINE-based search strategies are robust but capture only 89% of the total available citations in PubMed. The remaining 11% include the most recent and possibly relevant citations but are only searchable through less efficient techniques. An effective search strategy must employ both the MEDLINE and the non-MEDLINE portion of PubMed to ensure all studies have been identified. The robust MEDLINE search strategies are used for the MEDLINE portion of the search. Usage of the less robust strategies is then efficiently confined to search only the remaining 11% of PubMed citations that have not been indexed for MEDLINE. The current article offers step-by-step instructions for building such a search exploring methods for the discovery of medical subject heading (MeSH) terms to search MEDLINE, text-based methods for exploring the non-MEDLINE database, information on the limitations of convenience algorithms such as the "related citations feature," the strengths and pitfalls associated with commonly used filters, the proper usage of Boolean operators to organize a master search strategy, and instructions for automating that search through "MyNCBI" to receive search query updates by email as new citations become available. PMID:26129895

  19. Publications in PubMed on Ebola and the 2014 outbreak.

    PubMed

    Ballabeni, Andrea; Boggio, Andrea

    2015-01-01

    In this research note we examine the biomedical publication output about Ebola in 2014. We show that the volume of publications has dramatically increased in the past year. In 2014 there have been over 888 publications with 'ebola' or 'ebolavirus' in the title, approximately 13 times the volume of publication of 2013. The rise reflects an impressive growth starting in the month of August, concomitant with or following the surge in infections, deaths and coverage in news and social media. Though non-research articles have been the major contributors to this growth, there has been a substantial increase in original research articles too, including many papers of basic science. The United States has been the country with the highest number of research articles, followed by Canada and the United Kingdom. We present a comprehensive set of charts and facts that, by describing the volumes and nature of publications in 2014, show how the scientific community has responded to the Ebola outbreak and how it might respond to future similar global threats and media events. This information will assist scholars and policymakers in their efforts to improve scientific research policies with the goal of maximizing both public health and knowledge advancement. PMID:26539291

  20. Using Clinical Data, Hypothesis Generation Tools and PubMed Trends to Discover the Association between Diabetic Retinopathy and Antihypertensive Drugs

    SciTech Connect

    Senter, Katherine G; Sukumar, Sreenivas R; Patton, Robert M; Chaum, Ed

    2015-01-01

    Diabetic retinopathy (DR) is a leading cause of blindness and common complication of diabetes. Many diabetic patients take antihypertensive drugs to prevent cardiovascular problems, but these drugs may have unintended consequences on eyesight. Six common classes of antihypertensive drug are angiotensin converting enzyme (ACE) inhibitors, alpha blockers, angiotensin receptor blockers (ARBs), -blockers, calcium channel blockers, and diuretics. Analysis of medical history data might indicate which of these drugs provide safe blood pressure control, and a literature review is often used to guide such analyses. Beyond manual reading of relevant publications, we sought to identify quantitative trends in literature from the biomedical database PubMed to compare with quantitative trends in the clinical data. By recording and analyzing PubMed search results, we found wide variation in the prevalence of each antihypertensive drug in DR literature. Drug classes developed more recently such as ACE inhibitors and ARBs were most prevalent. We also identified instances of change-over-time in publication patterns. We then compared these literature trends to a dataset of 500 diabetic patients from the UT Hamilton Eye Institute. Data for each patient included class of antihypertensive drug, presence and severity of DR. Graphical comparison revealed that older drug classes such as diuretics, calcium channel blockers, and -blockers were much more prevalent in the clinical data than in the DR and antihypertensive literature. Finally, quantitative analysis of the dataset revealed that patients taking -blockers were statistically more likely to have DR than patients taking other medications, controlling for presence of hypertension and year of diabetes onset. This finding was concerning given the prevalence of -blockers in the clinical data. We determined that clinical use of -blockers should be minimized in diabetic patients to prevent retinal damage.

  1. Patterns of children's growth in east-central Europe in the eighteenth century.

    PubMed

    Komlos, J

    1986-01-01

    Records in Vienna of the heights of (a) Military Academy youths born between 1730 and 1760, (b) orphanage children born between 1760 and 1780 and (c) military boarding-school children born between 1775 and 1815 have been retrieved and analysed. This constitutes the earliest extant set of measurements of the heights of a group of individuals. Stature was increasing in the late 1740s and decreasing after the 1770s. This evidence indicates a rise and subsequent fall in nutritional status and is consistent with the known pattern of European agricultural conditions in the eighteenth century. Shifts in the age of maximum increment support the notion of the secular changes in the nutritional status of these boys. The stature of the Habsburg boys was greater than the poorest boys of contemporary London but compared unfavourably with the height of the English gentry and American cadets of the nineteenth century and, of course, with the height of today's populations. PMID:3516059

  2. Analysis of directional root growth patterns from corn and soybean seeds germinated in space

    NASA Astrophysics Data System (ADS)

    Levine, H.; Tynes, G.; Norwood, K.

    The JOSE (JASON Outreach Seed Experiment) payload was the first plant experiment conducted on the International Space Station (ISS). It consisted of having an on-orbit watering of eight transparent seed pouches each of which contained 6 individual seeds of either soybean (Glycine max cv McCall) or corn ( Zea mays ). The seeds were glued to a germination paper substrate using a 1.2% guar glue solution. The payload was launched on the Orbiter Endeavour (STS-97; ISS Flight 4A) on 11/30/00 and transferred to the ISS on 12/8/00. The eight seed pouches were each watered with 12 mL of distilled water on 1/5/01. Two pouches containing corn plus two pouches containing soybean seeds were maintained in the light after watering. Two additional seed pouches of each species were maintained in the dark after watering. Digital photography was used to document the growth of the germinating seedlings in space. The images were down-linked to a world wide web site for dissemination to students. "Within" species differences (between the light and dark grown seedlings) as well as "between" species differences (comparing corn and soybean) were observed. By day 4 (post-imbibition) there was a clear phototropic effect in the light-grown corn seedlings, each, possessing a green shoot which grew upward towards the light source. In contrast, the dark-grown corn shoots were neither green (since chlorophyll synthesis had not been induced by light) nor were they growing in a uniform direction. For day 4 soybean seedlings, the only difference evident between those germinated under the light vs dark conditions was a slight greening up of the seeds maintained in the presence of light. For both the corn and soybean seedlings, roots grew in a random fashion, with some moving in an upward direction and others progressing downward, reflecting the lack of a gravitropic response which is the primary (earth-based) mechanism controlling the direction of root growth. By day 7 the initial 12 mL of water

  3. Lithography-free oxide patterns as templates for self-catalyzed growth of highly uniform GaAs nanowires on Si(111)

    NASA Astrophysics Data System (ADS)

    Hakkarainen, T. V.; Schramm, A.; Mäkelä, J.; Laukkanen, P.; Guina, M.

    2015-07-01

    We report self-catalyzed growth of GaAs nanowires (NWs) on Si/SiOx patterns fabricated by a lithography-free method. The patterns are defined using droplet epitaxy of GaAs nanocrystals, spontaneous oxidation, and thermal annealing. We investigate the influence of the size and density of the nucleation sites on the NW growth process and show that this approach enables the fabrication of highly uniform GaAs NWs with controllable density. The pattern fabrication and NW growth process are studied and discussed in relation to the surface morphology and chemical properties of the Si/SiOx patterns. Furthermore, the optical quality of the NWs is investigated by photoluminescence experiments performed for GaAs-AlGaAs core-shell NWs.

  4. Lithography-free oxide patterns as templates for self-catalyzed growth of highly uniform GaAs nanowires on Si(111).

    PubMed

    Hakkarainen, T V; Schramm, A; Mäkelä, J; Laukkanen, P; Guina, M

    2015-07-10

    We report self-catalyzed growth of GaAs nanowires (NWs) on Si/SiOx patterns fabricated by a lithography-free method. The patterns are defined using droplet epitaxy of GaAs nanocrystals, spontaneous oxidation, and thermal annealing. We investigate the influence of the size and density of the nucleation sites on the NW growth process and show that this approach enables the fabrication of highly uniform GaAs NWs with controllable density. The pattern fabrication and NW growth process are studied and discussed in relation to the surface morphology and chemical properties of the Si/SiOx patterns. Furthermore, the optical quality of the NWs is investigated by photoluminescence experiments performed for GaAs–AlGaAs core–shell NWs. PMID:26087248

  5. The Ocean's Carbon Factory: Ocean Composition. The Growth Patterns of Phytoplankton Species

    NASA Technical Reports Server (NTRS)

    Gregg, Watson

    2000-01-01

    According to biological data recorded by the Sea-Viewing Wide Field-of-View Sensor (SeaWiFS) satellite, the ocean contains nearly half of all the Earth's photosynthesis activity. Through photosynthesis, plant life forms use carbon from the atmosphere, and in return, plants produce the oxygen that life requires. In effect, ocean chlorophyll works like a factory, taking carbon and "manufacturing" the air we breathe. Most ocean-bound photosynthesis is performed by single-celled plants called phytoplankton. "These things are so small," according to Michael Behrenfeld, a researcher at NASA Goddard Space Flight Center, "that if you take hundreds of them and stack them end-to-end, the length of that stack is only the thickness of a penny". The humble phytoplankton species plays a vital role in balancing the amounts of oxygen and carbon dioxide in the atmosphere. Therefore, understanding exactly how phytoplankton growth works is important.

  6. PubMedMiner: Mining and Visualizing MeSH-based Associations in PubMed.

    PubMed

    Zhang, Yucan; Sarkar, Indra Neil; Chen, Elizabeth S

    2014-01-01

    The exponential growth of biomedical literature provides the opportunity to develop approaches for facilitating the identification of possible relationships between biomedical concepts. Indexing by Medical Subject Headings (MeSH) represent high-quality summaries of much of this literature that can be used to support hypothesis generation and knowledge discovery tasks using techniques such as association rule mining. Based on a survey of literature mining tools, a tool implemented using Ruby and R - PubMedMiner - was developed in this study for mining and visualizing MeSH-based associations for a set of MEDLINE articles. To demonstrate PubMedMiner's functionality, a case study was conducted that focused on identifying and comparing comorbidities for asthma in children and adults. Relative to the tools surveyed, the initial results suggest that PubMedMiner provides complementary functionality for summarizing and comparing topics as well as identifying potentially new knowledge. PMID:25954472

  7. PubMedMiner: Mining and Visualizing MeSH-based Associations in PubMed

    PubMed Central

    Zhang, Yucan; Sarkar, Indra Neil; Chen, Elizabeth S.

    2014-01-01

    The exponential growth of biomedical literature provides the opportunity to develop approaches for facilitating the identification of possible relationships between biomedical concepts. Indexing by Medical Subject Headings (MeSH) represent high-quality summaries of much of this literature that can be used to support hypothesis generation and knowledge discovery tasks using techniques such as association rule mining. Based on a survey of literature mining tools, a tool implemented using Ruby and R – PubMedMiner – was developed in this study for mining and visualizing MeSH-based associations for a set of MEDLINE articles. To demonstrate PubMedMiner’s functionality, a case study was conducted that focused on identifying and comparing comorbidities for asthma in children and adults. Relative to the tools surveyed, the initial results suggest that PubMedMiner provides complementary functionality for summarizing and comparing topics as well as identifying potentially new knowledge. PMID:25954472

  8. Experimental evolution alters the rate and temporal pattern of population growth in Batrachochytrium dendrobatidis, a lethal fungal pathogen of amphibians.

    PubMed

    Voyles, Jamie; Johnson, Leah R; Briggs, Cheryl J; Cashins, Scott D; Alford, Ross A; Berger, Lee; Skerratt, Lee F; Speare, Rick; Rosenblum, Erica Bree

    2014-09-01

    Virulence of infectious pathogens can be unstable and evolve rapidly depending on the evolutionary dynamics of the organism. Experimental evolution can be used to characterize pathogen evolution, often with the underlying objective of understanding evolution of virulence. We used experimental evolution techniques (serial transfer experiments) to investigate differential growth and virulence of Batrachochytrium dendrobatidis (Bd), a fungal pathogen that causes amphibian chytridiomycosis. We tested two lineages of Bd that were derived from a single cryo-archived isolate; one lineage (P10) was passaged 10 times, whereas the second lineage (P50) was passaged 50 times. We quantified time to zoospore release, maximum zoospore densities, and timing of zoospore activity and then modeled population growth rates. We also conducted exposure experiments with a susceptible amphibian species, the common green tree frog (Litoria caerulea) to test the differential pathogenicity. We found that the P50 lineage had shorter time to zoospore production (T min ), faster rate of sporangia death (d s ), and an overall greater intrinsic population growth rate (λ). These patterns of population growth in vitro corresponded with higher prevalence and intensities of infection in exposed Litoria caerulea, although the differences were not significant. Our results corroborate studies that suggest that Bd may be able to evolve relatively rapidly. Our findings also challenge the general assumption that pathogens will always attenuate in culture because shifts in Bd virulence may depend on laboratory culturing practices. These findings have practical implications for the laboratory maintenance of Bd isolates and underscore the importance of understanding the evolution of virulence in amphibian chytridiomycosis. PMID:25478154

  9. Experimental evolution alters the rate and temporal pattern of population growth in Batrachochytrium dendrobatidis, a lethal fungal pathogen of amphibians

    PubMed Central

    Voyles, Jamie; Johnson, Leah R; Briggs, Cheryl J; Cashins, Scott D; Alford, Ross A; Berger, Lee; Skerratt, Lee F; Speare, Rick; Rosenblum, Erica Bree

    2014-01-01

    Virulence of infectious pathogens can be unstable and evolve rapidly depending on the evolutionary dynamics of the organism. Experimental evolution can be used to characterize pathogen evolution, often with the underlying objective of understanding evolution of virulence. We used experimental evolution techniques (serial transfer experiments) to investigate differential growth and virulence of Batrachochytrium dendrobatidis (Bd), a fungal pathogen that causes amphibian chytridiomycosis. We tested two lineages of Bd that were derived from a single cryo-archived isolate; one lineage (P10) was passaged 10 times, whereas the second lineage (P50) was passaged 50 times. We quantified time to zoospore release, maximum zoospore densities, and timing of zoospore activity and then modeled population growth rates. We also conducted exposure experiments with a susceptible amphibian species, the common green tree frog (Litoria caerulea) to test the differential pathogenicity. We found that the P50 lineage had shorter time to zoospore production (Tmin), faster rate of sporangia death (ds), and an overall greater intrinsic population growth rate (λ). These patterns of population growth in vitro corresponded with higher prevalence and intensities of infection in exposed Litoria caerulea, although the differences were not significant. Our results corroborate studies that suggest that Bd may be able to evolve relatively rapidly. Our findings also challenge the general assumption that pathogens will always attenuate in culture because shifts in Bd virulence may depend on laboratory culturing practices. These findings have practical implications for the laboratory maintenance of Bd isolates and underscore the importance of understanding the evolution of virulence in amphibian chytridiomycosis. PMID:25478154

  10. Effects of growth patterns and dietary protein levels during rearing of broiler breeders on fertility, hatchability, embryonic mortality, and offspring performance.

    PubMed

    van Emous, R A; Kwakkel, R P; van Krimpen, M M; van den Brand, H; Hendriks, W H

    2015-04-01

    The objective of this study was to determine the effects of different growth patterns and dietary crude protein levels during rearing in broiler breeder females on fertility, hatchability, embryonic mortality, and offspring performance. A 2×3 factorial arrangement of treatments was used, with 2 growth patterns to reach a target body weight at 20 wk of age of 2,200 g (standard=standard growth pattern) or 2,400 g (high=high growth pattern), and 3 dietary protein levels (high=crude protein, high), (medium=crude protein, medium), and low=crude protein, low). Fresh egg composition and organ development in hatchlings were determined. Offspring of the different groups were reared until an age of 34 d and feed intake, body weight gain, mortality, and carcass composition were determined. In 29-wk-old high growth pattern breeders compared to standard growth pattern breeders, fertility and hatchability of set eggs were increased; embryonic mortality between d 1 and 9 was decreased whereas hatchability of fertile eggs was not affected. Breeders fed the medium crude protein diet showed a decreased hatchability of fertile eggs caused by an increased embryonic mortality between d 18 and 21 compared to breeders fed the high crude protein and low crude protein diets. Offspring of 29-wk-old high growth pattern breeders tended (P=0.059) to have a higher body weight at d 34 than offspring of standard growth pattern breeders, which was achieved by a tendency to a higher body weight gain (P=0.057). Offspring of breeders fed the medium and low crude protein diet showed a higher feed intake between d 18 and 27 and during the total growth period, as compared to offspring of high crude protein breeders. Male broilers of low crude protein breeders had higher breast meat yield than male broilers of high crude protein breeders, while breast meat yield of female broilers was not affected by dietary protein levels. This experiment showed that a higher growth pattern during the rearing period

  11. Using Noun Phrases for Navigating Biomedical Literature on Pubmed: How Many Updates Are We Losing Track of?

    PubMed Central

    Srikrishna, Devabhaktuni; Coram, Marc A.

    2011-01-01

    Author-supplied citations are a fraction of the related literature for a paper. The “related citations” on PubMed is typically dozens or hundreds of results long, and does not offer hints why these results are related. Using noun phrases derived from the sentences of the paper, we show it is possible to more transparently navigate to PubMed updates through search terms that can associate a paper with its citations. The algorithm to generate these search terms involved automatically extracting noun phrases from the paper using natural language processing tools, and ranking them by the number of occurrences in the paper compared to the number of occurrences on the web. We define search queries having at least one instance of overlap between the author-supplied citations of the paper and the top 20 search results as citation validated (CV). When the overlapping citations were written by same authors as the paper itself, we define it as CV-S and different authors is defined as CV-D. For a systematic sample of 883 papers on PubMed Central, at least one of the search terms for 86% of the papers is CV-D versus 65% for the top 20 PubMed “related citations.” We hypothesize these quantities computed for the 20 million papers on PubMed to differ within 5% of these percentages. Averaged across all 883 papers, 5 search terms are CV-D, and 10 search terms are CV-S, and 6 unique citations validate these searches. Potentially related literature uncovered by citation-validated searches (either CV-S or CV-D) are on the order of ten per paper – many more if the remaining searches that are not citation-validated are taken into account. The significance and relationship of each search result to the paper can only be vetted and explained by a researcher with knowledge of or interest in that paper. PMID:21935487

  12. Growth, patterning and alignment of organolead iodide perovskite nanowires for optoelectronic devices

    NASA Astrophysics Data System (ADS)

    Deng, Hui; Dong, Dongdong; Qiao, Keke; Bu, Lingling; Li, Bing; Yang, Dun; Wang, Hong-En; Cheng, Yibing; Zhao, Zhixin; Tang, Jiang; Song, Haisheng

    2015-02-01

    Organolead halide perovskites are becoming intriguing materials applied in optoelectronics. In the present work, organolead iodide perovskite (OIP) nanowires (NWs) have been fabricated by a one step self-assembly method. The controllable NW distributions were implemented by a series of facile techniques: monolayer and small diameter NWs were prepared by precursor concentration tuning; NW patterning was achieved via selected area treatment assisted by a mask; NW alignment was implemented by modified evaporation-induced self-assembly (EISA). The synthesized multifunctional NWs were further applied in photodetectors (PDs) and solar cells as application demos. The PD performances have reached 1.32 AW-1 for responsivity, 2.5 × 1012 Jones for detectivity and 0.3 ms for response speed, superior to OIP films and other typical inorganic NW based PD performances. An energy conversion efficiency of ~2.5% has been obtained for NW film based solar cells. The facile fabrication process, controllable distribution and optoelectronic applications make the OIP NWs promising building blocks for future optoelectronics, especially for low dimensional devices.Organolead halide perovskites are becoming intriguing materials applied in optoelectronics. In the present work, organolead iodide perovskite (OIP) nanowires (NWs) have been fabricated by a one step self-assembly method. The controllable NW distributions were implemented by a series of facile techniques: monolayer and small diameter NWs were prepared by precursor concentration tuning; NW patterning was achieved via selected area treatment assisted by a mask; NW alignment was implemented by modified evaporation-induced self-assembly (EISA). The synthesized multifunctional NWs were further applied in photodetectors (PDs) and solar cells as application demos. The PD performances have reached 1.32 AW-1 for responsivity, 2.5 × 1012 Jones for detectivity and 0.3 ms for response speed, superior to OIP films and other typical inorganic

  13. b-FGF Induces Corneal Blood and Lymphatic Growth in a Spatially Distinct Pattern

    PubMed Central

    Hajrasouliha, Amir R.; Sadrai, Zahra; Chauhan, Sunil K.; Dana, Reza

    2013-01-01

    Purpose To study the spatial variances in ligand expression and angiogenic effect in response to the inflammatory response induced by b-FGF. Methods b-FGF micropellets (80ng) were implanted in the temporal side of the cornea of Balbc/c mice. On days 1, 3, and 7 blood (heme) and lymph-angiogenesis were observed by immunofluorescence staining of corneal flat mounts with LYVE-1 and CD31 to identify lymphatic and blood vessels, respectively. A second group of corneas were harvested for quantitative RT-PCR. Each cornea was divided in two different area defines as (i) pre-pellet area and (ii) opposite-pellet area. Expression of VEGF ligands were evaluated using Real-time PCR in each respective zone. Results Blood vessels grew into the cornea from the pre-pellet area while corneal lymphatic vessels grew from the opposite-pellet area toward the center of the cornea. VEGF-A was upregulated in the pre-pellet while VEGF-D expression was mostly observed in the opposite-pellet area. VEGF-C level increased simultaneously in both areas. Conclusion A single inducing factor, i.e., b-FGF, may simultaneously provoke heme-and lymph-angiogenesis in different locations of the cornea through differential expression of VEGF ligands. This distinctive spatial pattern should be considered while evaluating the corneal predilection for inflammation beyond that which is directly visible by slit lamp examination. PMID:22467003

  14. The pattern of growth observed for Clostridium botulinum type A1 strain ATCC 19397 is influenced by nutritional status and quorum sensing: a modelling perspective

    PubMed Central

    Ihekwaba, Adaoha E. C.; Mura, Ivan; Peck, Michael W.; Barker, G. C.

    2015-01-01

    Botulinum neurotoxins (BoNTs) produced by the anaerobic bacterium Clostridium botulinum are the most poisonous substances known to mankind. However, toxin regulation and signals triggering synthesis as well as the regulatory network and actors controlling toxin production are unknown. Experiments show that the neurotoxin gene is growth phase dependent for C. botulinum type A1 strain ATCC 19397, and toxin production is influenced both by culture conditions and nutritional status of the medium. Building mathematical models to describe the genetic and molecular machinery that drives the synthesis and release of BoNT requires a simultaneous description of the growth of the bacterium in culture. Here, we show four plausible modelling options which could be considered when constructing models describing the pattern of growth observed in a botulinum growth medium. Commonly used bacterial growth models are unsuitable to fit the pattern of growth observed, since they only include monotonic growth behaviour. We find that a model that includes both the nutritional status and the ability of the cells to sense their surroundings in a quorum-sensing manner is most successful at explaining the pattern of growth obtained for C. botulinum type A1 strain ATCC 19397. PMID:26449712

  15. The pattern of growth observed for Clostridium botulinum type A1 strain ATCC 19397 is influenced by nutritional status and quorum sensing: a modelling perspective.

    PubMed

    Ihekwaba, Adaoha E C; Mura, Ivan; Peck, Michael W; Barker, G C

    2015-12-01

    Botulinum neurotoxins (BoNTs) produced by the anaerobic bacterium Clostridium botulinum are the most poisonous substances known to mankind. However, toxin regulation and signals triggering synthesis as well as the regulatory network and actors controlling toxin production are unknown. Experiments show that the neurotoxin gene is growth phase dependent for C. botulinum type A1 strain ATCC 19397, and toxin production is influenced both by culture conditions and nutritional status of the medium. Building mathematical models to describe the genetic and molecular machinery that drives the synthesis and release of BoNT requires a simultaneous description of the growth of the bacterium in culture. Here, we show four plausible modelling options which could be considered when constructing models describing the pattern of growth observed in a botulinum growth medium. Commonly used bacterial growth models are unsuitable to fit the pattern of growth observed, since they only include monotonic growth behaviour. We find that a model that includes both the nutritional status and the ability of the cells to sense their surroundings in a quorum-sensing manner is most successful at explaining the pattern of growth obtained for C. botulinum type A1 strain ATCC 19397. PMID:26449712

  16. Growth of primary motor neurons on horizontally aligned carbon nanotube thin films and striped patterns

    NASA Astrophysics Data System (ADS)

    Roberts, Megan J.; Leach, Michelle K.; Bedewy, Mostafa; Meshot, Eric R.; Copic, Davor; Corey, Joseph M.; Hart, A. John

    2014-06-01

    Objective. Carbon nanotubes (CNTs) are attractive for use in peripheral nerve interfaces because of their unique combination of strength, flexibility, electrical conductivity and nanoscale surface texture. Here we investigated the growth of motor neurons on thin films of horizontally aligned CNTs (HACNTs). Approach. We cultured primary embryonic rat motor neurons on HACNTs and performed statistical analysis of the length and orientation of neurites. We next presented motor neurons with substrates of alternating stripes of HACNTs and SiO2. Main results. The neurons survived on HACNT substrates for up to eight days, which was the full duration of our experiments. Statistical analysis of the length and orientation of neurites indicated that the longest neurites on HACNTs tended to align with the CNT direction, although the average neurite length was similar between HACNTs and glass control substrates. We observed that when motor neurons were presented with alternating stripes of HACNTs and SiO2, the proportion of neurons on HACNTs increases over time, suggesting that neurons selectively migrate toward and adhere to the HACNT surface. Significance. The behavior of motor neurons on CNTs has not been previously investigated, and we show that aligned CNTs could provide a viable interface material to motor neurons. Combined with emerging techniques to build complex hierarchical structures of CNTs, our results suggest that organised CNTs could be incorporated into nerve grafts that use physical and electrical cues to guide regenerating axons.

  17. Endothelial cells from bovine adrenal medulla develop capillary-like growth patterns in culture.

    PubMed Central

    Banerjee, D K; Ornberg, R L; Youdim, M B; Heldman, E; Pollard, H B

    1985-01-01

    The endocrine barrier between chromaffin cells and the blood stream in the adrenal medulla is made of capillary endothelial cells. We have now succeeded in isolating endothelial cells from adrenal medullary tissue, which are probably derived from this barrier. These cells grow on plastic surfaces in the absence of special growth factors or collagen overlays and differentiate into organized structures quite similar to true capillaries. The cells contain factor VIII:R, a marker for endothelial cells, and form intercellular junctions characteristic of capillary endothelial cells. They also synthesize and secrete basal lamina structures and engage in transcytosis, a characteristic ultrastructural and functional combination of exocytosis and endocytosis across the thin endothelial cell processes. These endothelial cells can take up and deaminate catecholamines by A-type monoamine oxidase, an enzyme functionally distinct from the B-type monoamine oxidase found in chromaffin cells. These data indicate that the chromaffin cell and its endothelial cell neighbor may constitute the functional unit of catecholamine metabolism in the adrenal medulla. Images PMID:3927288

  18. Universal scaling rules predict evolutionary patterns of myogenesis in species with indeterminate growth

    PubMed Central

    Johnston, Ian A.; Kristjánsson, Bjarni K.; Paxton, Charles G. P.; Vieira, Vera L. A.; Macqueen, Daniel J.; Bell, Michael A.

    2012-01-01

    Intraspecific phenotypic variation is ubiquitous and often associated with resource exploitation in emerging habitats. For example, reduced body size has evolved repeatedly in Arctic charr (Salvelinus alpinus L.) and threespine stickleback (Gasterosteus aculeatus L.) across post-glacial habitats of the Northern Hemisphere. Exploiting these models, we examined how body size and myogenesis evolve with respect to the ‘optimum fibre size hypothesis’, which predicts that selection acts to minimize energetic costs associated with ionic homeostasis by optimizing muscle fibre production during development. In eight dwarf Icelandic Arctic charr populations, the ultimate production of fast-twitch muscle fibres (FNmax) was only 39.5 and 15.5 per cent of that in large-bodied natural and aquaculture populations, respectively. Consequently, average fibre diameter (FD) scaled with a mass exponent of 0.19, paralleling the relaxation of diffusional constraints associated with mass-specific metabolic rate scaling. Similar reductions in FNmax were observed for stickleback, including a small-bodied Alaskan population derived from a larger-bodied oceanic stock over a decadal timescale. The results suggest that in species showing indeterminate growth, body size evolution is accompanied by strong selection for fibre size optimization, theoretically allowing resources saved from ionic homeostasis to be allocated to other traits affecting fitness, including reproduction. Gene flow between small- and large-bodied populations residing in sympatry may counteract the evolution of this trait. PMID:22237905

  19. [Simulation on the seasonal growth patterns of grassland plant communities in northern China].

    PubMed

    Zhang, Li; Zheng, Yuan-Run

    2008-10-01

    Soil moisture is the key factor limiting the productivity of grassland in northern China ranging from arid to subhumid arid regions. In this paper, the seasonal and annual growth, foliage projective cover (FPC), evaporative coefficient (k), and net primary productivity (NPP) of 7 types of grasslands in North China were simulated by using a simple model based on well established ecological processes of water balance and climatic data collected at 460 sites over 40 years. The observed NPPs were used to validate the model, and the simulated NPPs were in high agreement with the observed NPPs. The simulated k, NPP, and FPC deceased from east to west in temperate grasslands, and decreased from southeast to northwest in Qinghai-Tibet Plateau, reflecting the moisture gradient in northern China. Alpine meadow had the highest k, NPP, and FPC in the 7 types of grasslands, alpine steppe had the second highest FPC but with a NPP similar to that of temperate steppe, and the three simulated parameters of temperate desert were the smallest. The simulated results suggested that the livestock density should be lower than 5.2, 2.3, 3.6, 2.1, 1.0, 0.6, and 0.2 sheep unit x hm(-2), while the coverage of rehabilitated vegetation should be about 93%, 79%, 56%, 50%, 44%, 38%, and 37% in alpine meadow, alpine steppe, temperate meadow steppe, temperate steppe, temperate desert steppe, temperate steppe desert, and temperate desert, respectively. PMID:19123350

  20. Growth patterns and scaling laws governing AIDS epidemic in Brazilian cities.

    PubMed

    Antonio, Fernando Jose; de Picoli, Sergio; Teixeira, Jorge Juarez Vieira; Mendes, Renio dos Santos

    2014-01-01

    Brazil holds approximately 1/3 of population living infected with AIDS (acquired immunodeficiency syndrome) in Central and South Americas, and it was also the first developing country to implement a large-scale control and intervention program against AIDS epidemic. In this scenario, we investigate the temporal evolution and current status of the AIDS epidemic in Brazil. Specifically, we analyze records of annual absolute frequency of cases for more than 5000 cities for the first 33 years of the infection in Brazil. We found that (i) the annual absolute frequencies exhibit a logistic-type growth with an exponential regime in the first few years of the AIDS spreading; (ii) the actual reproduction number decaying as a power law; (iii) the distribution of the annual absolute frequencies among cities decays with a power law behavior; (iv) the annual absolute frequencies and the number of inhabitants have an allometric relationship; (v) the temporal evolution of the annual absolute frequencies have different profile depending on the average annual absolute frequencies in the cities. These findings yield a general quantitative description of the AIDS infection dynamics in Brazil since the beginning. They also provide clues about the effectiveness of treatment and control programs against the infection, that has had a different impact depending on the number of inhabitants of cities. In this framework, our results give insights into the overall dynamics of AIDS epidemic, which may contribute to select empirically accurate models. PMID:25340796

  1. Patterns in melanocytic lesions: impact of the geometry on growth and transport inside the epidermis

    PubMed Central

    Balois, Thibaut; Chatelain, Clément; Ben Amar, Martine

    2014-01-01

    In glabrous skin, nevi and melanomas exhibit pigmented stripes during clinical dermoscopic examination. They find their origin in the basal layer geometry which periodically exhibits ridges, alternatively large (limiting ridges) and thin (intermediate ridges). However, nevus and melanoma lesions differ by the localization of the pigmented stripes along furrows or ridges of the epidermis surface. Here, we propose a biomechanical model of avascular tumour growth which takes into account this specific geometry in the epidermis where both kinds of lesions first appear. Simulations show a periodic distribution of tumour cells inside the lesion, with a global contour stretched out along the ridges. In order to be as close as possible to clinical observations, we also consider the melanin transport by the keratinocytes. Our simulations show that reasonable assumptions on melanocytic cell repartition in the ridges favour the limiting ridges of the basal compared with the intermediate ones in agreement with nevus observations but not really with melanomas. It raises the question of cell aggregation and repartition of melanocytic cells in acral melanomas and requires further biological studies of these cells in situ. PMID:24872499

  2. Patterns and rates of enamel growth in the molar teeth of early hominids.

    PubMed

    Beynon, A D; Wood, B A

    A recent study of the surface manifestation of incremental lines associated with enamel formation suggested that the crowns of early hominid incisor teeth were formed more rapidly than those of modern humans. In the absence of comparative data, the authors were forced to assume that enamel increments in fossil teeth were similar to those in modern humans. We have used evidence from the fractured surfaces of molar teeth to deduce estimates for both long- and short-period incremental growth markers within enamel in east African 'robust' australopithecine and early Homo teeth. We conclude that in these early hominids, crown formation times in posterior teeth, particularly in the large thick enamelled molar teeth of the east African 'robust' australopithecines, were shorter than those of modern humans. This evidence, considered together with data on crown and root formation times in modern apes, suggests that the posterior teeth in these hominids both formed and erupted more rapidly than those of modern man. These results have implications for attempts to assess dental and skeletal maturity in hominids. PMID:3104794

  3. Linking sewage pollution and water quality to spatial patterns of Porites lobata growth anomalies in Puako, Hawaii.

    PubMed

    Yoshioka, Reyn M; Kim, Catherine J S; Tracy, Allison M; Most, Rebecca; Harvell, C Drew

    2016-03-15

    Sewage pollution threatens the health of coastal populations and ecosystems, including coral reefs. We investigated spatial patterns of sewage pollution in Puako, Hawaii using enterococci concentrations and δ(15)N Ulva fasciata macroalgal bioassays to assess relationships with the coral disease Porites lobata growth anomalies (PGAs). PGA severity and enterococci concentrations were high, spatially variable, and positively related. Bioassay algal δ(15)N showed low sewage pollution at the reef edge while high values of resident algae indicated sewage pollution nearshore. Neither δ(15)N metric predicted PGA measures, though bioassay δ(15)N was negatively related to coral cover. Furthermore, PGA prevalence was much higher than previously recorded in Hawaii and the greater Indo-Pacific, highlighting Puako as an area of concern. Although further work is needed to resolve the relationship between sewage pollution and coral cover and disease, these results implicate sewage pollution as a contributor to diminished reef health. PMID:26781454

  4. Changing exhumation patterns during Cenozoic growth and glaciation of the Alaska Range: Insights from detrital thermochronology and geochronology

    NASA Astrophysics Data System (ADS)

    Lease, Richard O.; Haeussler, Peter J.; O'Sullivan, Paul

    2016-04-01

    Cenozoic growth of the Alaska Range created the highest topography in North America, but the space-time pattern and drivers of exhumation are poorly constrained. We analyzed U/Pb and fission-track double dates of detrital zircon and apatite grains from 12 catchments that span a 450 km length of the Alaska Range to illuminate the timing and extent of exhumation during different periods. U/Pb ages indicate a dominant Late Cretaceous to Oligocene plutonic provenance for the detrital grains, with only a small percentage of grains recycled from the Mesozoic and Paleozoic sedimentary cover. Fission-track ages record exhumation during Alaska Range growth and incision and reveal three distinctive patterns. First, initial Oligocene exhumation was focused in the central Alaska Range at ~30 Ma and expanded outward along the entire length of the range until 18 Ma. Oligocene exhumation, coeval with initial Yakutat microplate collision >600 km to the southeast, suggests a far-field response to collision that was localized by the Denali Fault within a weak Mesozoic suture zone. Second, the variable timing of middle to late Miocene exhumation suggests independently evolving histories influenced by local structures. Time-transgressive cooling ages suggest successive rock uplift and erosion of Mounts Foraker (12 Ma) through Denali (6 Ma) as crust was advected through a restraining bend in the Denali Fault and indicate a long-term slip rate ~4 mm/yr. Third, Pliocene exhumation is synchronous (3.7-2.7 Ma) along the length of the Alaska Range but only occurs in high-relief, glacier-covered catchments. Pliocene exhumation may record an acceleration in glacial incision that was coincident with the onset of Northern Hemisphere glaciation.

  5. A high-transparency, micro-patternable chip for X-ray diffraction analysis of microcrystals under native growth conditions

    SciTech Connect

    Murray, Thomas D.; Lyubimov, Artem Y.; Ogata, Craig M.; Vo, Huy; Uervirojnangkoorn, Monarin; Brunger, Axel T.; Berger, James M.

    2015-09-26

    Microcrystals present a significant impediment to the determination of macromolecular structures by X-ray diffraction methods. Although microfocus synchrotron beamlines and X-ray free-electron lasers (XFELs) can enable the collection of interpretable diffraction data from microcrystals, there is a need for efficient methods of harvesting small volumes (<2µl) of microcrystals grown under common laboratory formats and delivering them to an X-ray beam source under native growth conditions. One approach that shows promise in overcoming the challenges intrinsic to microcrystal analysis is to pair so-called `fixed-target' sample-delivery devices with microbeam-based X-ray diffraction methods. However, to record weak diffraction patterns it is necessary to fabricate devices from X-ray-transparent materials that minimize background scattering. Presented here is the design of a new micro-diffraction device consisting of three layers fabricated from silicon nitride, photoresist and polyimide film. The chip features low X-ray scattering and X-ray absorption properties, and uses a customizable blend of hydrophobic and hydrophilic surface patterns to help localize microcrystals to defined regions. Microcrystals in their native growth conditions can be loaded into the chips with a standard pipette, allowing data collection at room temperature. Diffraction data collected from hen egg-white lysozyme microcrystals (10–15µm) loaded into the chips yielded a complete, high-resolution (<1.6Å) data set sufficient to determine a high-quality structure by molecular replacement. The features of the chip allow the rapid and user-friendly analysis of microcrystals grown under virtually any laboratory format at microfocus synchrotron beamlines and XFELs.

  6. A high-transparency, micro-patternable chip for X-ray diffraction analysis of microcrystals under native growth conditions.

    PubMed

    Murray, Thomas D; Lyubimov, Artem Y; Ogata, Craig M; Vo, Huy; Uervirojnangkoorn, Monarin; Brunger, Axel T; Berger, James M

    2015-10-01

    Microcrystals present a significant impediment to the determination of macromolecular structures by X-ray diffraction methods. Although microfocus synchrotron beamlines and X-ray free-electron lasers (XFELs) can enable the collection of interpretable diffraction data from microcrystals, there is a need for efficient methods of harvesting small volumes (<2 µl) of microcrystals grown under common laboratory formats and delivering them to an X-ray beam source under native growth conditions. One approach that shows promise in overcoming the challenges intrinsic to microcrystal analysis is to pair so-called `fixed-target' sample-delivery devices with microbeam-based X-ray diffraction methods. However, to record weak diffraction patterns it is necessary to fabricate devices from X-ray-transparent materials that minimize background scattering. Presented here is the design of a new micro-diffraction device consisting of three layers fabricated from silicon nitride, photoresist and polyimide film. The chip features low X-ray scattering and X-ray absorption properties, and uses a customizable blend of hydrophobic and hydrophilic surface patterns to help localize microcrystals to defined regions. Microcrystals in their native growth conditions can be loaded into the chips with a standard pipette, allowing data collection at room temperature. Diffraction data collected from hen egg-white lysozyme microcrystals (10-15 µm) loaded into the chips yielded a complete, high-resolution (<1.6 Å) data set sufficient to determine a high-quality structure by molecular replacement. The features of the chip allow the rapid and user-friendly analysis of microcrystals grown under virtually any laboratory format at microfocus synchrotron beamlines and XFELs. PMID:26457423

  7. A high-transparency, micro-patternable chip for X-ray diffraction analysis of microcrystals under native growth conditions

    DOE PAGESBeta

    Murray, Thomas D.; Lyubimov, Artem Y.; Ogata, Craig M.; Vo, Huy; Uervirojnangkoorn, Monarin; Brunger, Axel T.; Berger, James M.

    2015-08-11

    Microcrystals present a significant impediment to the determination of macromolecular structures by X-ray diffraction methods. Although microfocus synchrotron beamlines and X-ray free-electron lasers (XFELs) can enable the collection of interpretable diffraction data from microcrystals, there is a need for efficient methods of harvesting small volumes (<2 µl) of microcrystals grown under common laboratory formats and delivering them to an X-ray beam source under native growth conditions. One approach that shows promise in overcoming the challenges intrinsic to microcrystal analysis is to pair so-called `fixed-target' sample-delivery devices with microbeam-based X-ray diffraction methods. However, to record weak diffraction patterns it is necessarymore » to fabricate devices from X-ray-transparent materials that minimize background scattering. Presented here is the design of a new micro-diffraction device consisting of three layers fabricated from silicon nitride, photoresist and polyimide film. The chip features low X-ray scattering and X-ray absorption properties, and uses a customizable blend of hydrophobic and hydrophilic surface patterns to help localize microcrystals to defined regions. Microcrystals in their native growth conditions can be loaded into the chips with a standard pipette, allowing data collection at room temperature. Diffraction data collected from hen egg-white lysozyme microcrystals (10–15 µm) loaded into the chips yielded a complete, high-resolution (<1.6 Å) data set sufficient to determine a high-quality structure by molecular replacement. In addition, the features of the chip allow the rapid and user-friendly analysis of microcrystals grown under virtually any laboratory format at microfocus synchrotron beamlines and XFELs.« less

  8. Hapln1a Is Required for Connexin43-Dependent Growth and Patterning in the Regenerating Fin Skeleton

    PubMed Central

    Govindan, Jayalakshmi; Iovine, M. Kathryn

    2014-01-01

    Cell–cell communication, facilitating the exchange of small metabolites, ions and second messengers, takes place via aqueous proteinaceous channels called gap junctions. Connexins (cx) are the subunits of a gap junction channel. Mutations in zebrafish cx43 produces the short fin (sof b123) phenotype and is characterized by short fins due to reduced segment length of the bony fin rays and reduced cell proliferation. Previously established results from our lab demonstrate that Cx43 plays a dual role regulating both cell proliferation (growth) and joint formation (patterning) during the process of skeletal morphogenesis. In this study, we show that Hapln1a (Hyaluronan and Proteoglycan Link Protein 1a) functions downstream of cx43. Hapln1a belongs to the family of link proteins that play an important role in stabilizing the ECM by linking the aggregates of hyaluronan and proteoglycans. We validated that hapln1a is expressed downstream of cx43 by in situ hybridization and quantitative RT-PCR methods. Moreover, in situ hybridization at different time points revealed that hapln1a expression peaks at 3 days post amputation. Expression of hapln1a is located in the medial mesenchyme and the in the lateral skeletal precursor cells. Furthermore, morpholino mediated knock-down of hapln1a resulted in reduced fin regenerate length, reduced bony segment length and reduced cell proliferation, recapitulating all the phenotypes of cx43 knock-down. Moreover, Hyaluronic Acid (HA) levels are dramatically reduced in hapln1a knock-down fins, attesting the importance of Hapln1a in stabilizing the ECM. Attempts to place hapln1a in our previously defined cx43–sema3d pathway suggest that hapln1a functions in a parallel genetic pathway. Collectively, our data suggest that Cx43 mediates independent Sema3d and Hapln1a pathways in order to coordinate skeletal growth and patterning. PMID:24533114

  9. A high-transparency, micro-patternable chip for X-ray diffraction analysis of microcrystals under native growth conditions

    SciTech Connect

    Murray, Thomas D.; Lyubimov, Artem Y.; Ogata, Craig M.; Vo, Huy; Uervirojnangkoorn, Monarin; Brunger, Axel T.; Berger, James M.

    2015-09-26

    A highly X-ray-transparent, silicon nitride-based device has been designed and fabricated to harvest protein microcrystals for high-resolution X-ray diffraction data collection using microfocus beamlines and XFELs. Microcrystals present a significant impediment to the determination of macromolecular structures by X-ray diffraction methods. Although microfocus synchrotron beamlines and X-ray free-electron lasers (XFELs) can enable the collection of interpretable diffraction data from microcrystals, there is a need for efficient methods of harvesting small volumes (<2 µl) of microcrystals grown under common laboratory formats and delivering them to an X-ray beam source under native growth conditions. One approach that shows promise in overcoming the challenges intrinsic to microcrystal analysis is to pair so-called ‘fixed-target’ sample-delivery devices with microbeam-based X-ray diffraction methods. However, to record weak diffraction patterns it is necessary to fabricate devices from X-ray-transparent materials that minimize background scattering. Presented here is the design of a new micro-diffraction device consisting of three layers fabricated from silicon nitride, photoresist and polyimide film. The chip features low X-ray scattering and X-ray absorption properties, and uses a customizable blend of hydrophobic and hydrophilic surface patterns to help localize microcrystals to defined regions. Microcrystals in their native growth conditions can be loaded into the chips with a standard pipette, allowing data collection at room temperature. Diffraction data collected from hen egg-white lysozyme microcrystals (10–15 µm) loaded into the chips yielded a complete, high-resolution (<1.6 Å) data set sufficient to determine a high-quality structure by molecular replacement. The features of the chip allow the rapid and user-friendly analysis of microcrystals grown under virtually any laboratory format at microfocus synchrotron beamlines and XFELs.

  10. Insulin-like growth factor-1 content and pattern of expression correlates with histopathologic grade in diffusely infiltrating astrocytomas.

    PubMed Central

    Hirano, H.; Lopes, M. B.; Laws, E. R.; Asakura, T.; Goto, M.; Carpenter, J. E.; Karns, L. R.; VandenBerg, S. R.

    1999-01-01

    Studies of experimental tumorigenesis have strongly implicated signaling of the insulin-like growth factor 1 (IGF-1) as a key component in astrocytic neoplasia; however, its role in the growth of low-grade and malignant human tumors is not well understood. Correlative analyses of IGF-1, p53, and Ki-67 (MIB-1) immunohistochemistry and IGF-1 receptor (IGF-1R) mRNA expression were performed to examine the cellular pattern of IGF-1 signaling in 39 cases of astrocytoma (World Health Organization grades II-IV). Tumor cells expressing IGF-1 and IGF-1R were present in all tumor grades. The proportion of tumor cells that expressed IGF-1 correlated with both histopathologic grade and Ki-67 labeling indices, while expression of IGF-1R mRNA correlated with Ki-67 indices. In cases where stereotactic tissue sampling could be identified with a specific tumor area by neuroimaging features, the numbers of IGF-1 immunoreactive cells correlated with the tumor zones of highest cellularity and Ki-67 labeling. In glioblastomas, the localization of IGF-1 immunoreactivity was notable for several features: frequent accentuation in the perivascular tumor cells surrounding microvascular hyperplasia; increased levels in reactive astrocytes at the margins of tumor infiltration; and selective expression in microvascular cells exhibiting endothelial/pericytic hyperplasia. IGF-1R expression was particularly prominent in tumor cells adjacent to both microvascular hyperplasia and palisading necrosis. These data suggest that IGF-1 signaling occurs early in astroglial tumorigenesis in the setting of cell proliferation. The distinctive correlative patterns of IGF-1 and IGF-1R expression in glioblastomas also suggest that IGF-1 signaling has an association with the development of malignant phenotypes related to aberrant angiogenesis and invasive tumor interactions with reactive brain. PMID:11550306

  11. A high-transparency, micro-patternable chip for X-ray diffraction analysis of microcrystals under native growth conditions

    SciTech Connect

    Murray, Thomas D.; Lyubimov, Artem Y.; Ogata, Craig M.; Vo, Huy; Uervirojnangkoorn, Monarin; Brunger, Axel T.; Berger, James M.

    2015-08-11

    Microcrystals present a significant impediment to the determination of macromolecular structures by X-ray diffraction methods. Although microfocus synchrotron beamlines and X-ray free-electron lasers (XFELs) can enable the collection of interpretable diffraction data from microcrystals, there is a need for efficient methods of harvesting small volumes (<2 µl) of microcrystals grown under common laboratory formats and delivering them to an X-ray beam source under native growth conditions. One approach that shows promise in overcoming the challenges intrinsic to microcrystal analysis is to pair so-called `fixed-target' sample-delivery devices with microbeam-based X-ray diffraction methods. However, to record weak diffraction patterns it is necessary to fabricate devices from X-ray-transparent materials that minimize background scattering. Presented here is the design of a new micro-diffraction device consisting of three layers fabricated from silicon nitride, photoresist and polyimide film. The chip features low X-ray scattering and X-ray absorption properties, and uses a customizable blend of hydrophobic and hydrophilic surface patterns to help localize microcrystals to defined regions. Microcrystals in their native growth conditions can be loaded into the chips with a standard pipette, allowing data collection at room temperature. Diffraction data collected from hen egg-white lysozyme microcrystals (10–15 µm) loaded into the chips yielded a complete, high-resolution (<1.6 Å) data set sufficient to determine a high-quality structure by molecular replacement. In addition, the features of the chip allow the rapid and user-friendly analysis of microcrystals grown under virtually any laboratory format at microfocus synchrotron beamlines and XFELs.

  12. Self-assembly based nanometer-scale patterning for nanowire growth

    NASA Astrophysics Data System (ADS)

    Chandramohan, Abhishek; Sibirev, Nikolai; Dubrovskii, Vladimir G.; Mendis, Budhika; Petty, Mike C.; Gallant, Andrew J.; Zeze, Dagou A.

    2015-08-01

    Periodic nanostructure arrays have been ubiquitously exploited lately due to their properties and prospective applications in production of templates for self-induced and gold (Au)-catalysed nanowires (NWs), because this approach is relatively cheap, time-efficient and do not require electron beam lithography. The technique consists creating nanoholes in SiO2 to expose the silicon Si (111) beneath where self-induced NWs can nucleate, while nanodots deposited onto the Si (111) surface serve as catalyst seeds. For Au-catalysed NWs, a monolayer of self-assembled polystyrene nanospheres (PNS 300nm) was created on a 2 inch Si wafer by spin coating and later etched for a short time before a very thin Au-catalyst layer was deposited. In turn, for self-induced, PNS monolayer was created onto a SiO2-Si substrate. A longer etch was required to reduce PNS diameter significantly to leave relatively larger spacing where chromium is blanket deposited. PNS were lifted off by sonicating the samples in toluene produce the periodic arrays of nanodots and nanoholes, respectively. The underlying SiO2 was etched further through the nanoholes to uncover the Si below. 200 nm holes and 30-70 nm dots were demonstrated through the bespoke methods. The patterned substrates served as master templates, subsequently copied using polydimethylsiloxane (PDMS) to produce a flexible stamp for nanoimprint lithography. A bilayer resist lift off process was developed to print the replicated nanodots or nanoholes on large-area substrates onto which III-V NWs can be grown.

  13. Evolution of morphological novelty: a phylogenetic analysis of growth patterns in Streptocarpus (Gesneriaceae).

    PubMed

    Möller, M; Cronk, Q C

    2001-05-01

    Streptocarpus shows great variation in vegetative architecture. In some species a normal shoot apical meristem never forms and the entire vegetative plant body may consist of a single giant cotyledon, which may measure up to 0.75 m (the unifoliate type) or with further leaves arising from this structure (the rosulate type). A molecular phylogeny of 87 taxa (77 Streptocarpus species, seven related species, and three outgroup species) using the internal transcribed spacers and 5.8S region of nuclear ribosomal DNA suggests that Streptocarpus can be divided into two major clades. One of these broadly corresponds to the caulescent group (with conventional shoot architecture) classified as subgenus Streptocarpella, whereas the other is mainly composed of acaulescent species with unusual architecture (subgenus Streptocarpus). Some caulescent species (such as S. papangae) are anomalously placed with the acaulescent clade. Available cytological data are, however, completely congruent with the two major clades: the caulescent clade is x = 15 and the acaulescent clade (including the caulescent S. papangae) is x = 16 (or polyploid multiples of 16). The genera Linnaeopsis, Saintpaulia, and Schizoboea are nested within Streptocarpus. The sequenced region has evolved, on average, 2.44 times faster in the caulescent clade than in the acaulescent clade and this is associated with the more rapid life cycle of the caulescents. Morphological variation in plant architecture within the acaulescent clade is homoplastic and does not appear to have arisen by unique abrupt changes. Instead, rosulate and unifoliate growth forms have evolved several times, reversals have occurred, and intermediate architectures are found. An underlying developmental plasticity seems to be a characteristic of the acaulescent clade and is reflected in a great lability of form. PMID:11430652

  14. Architectural elements and growth patterns of submarine channels: Application to hydrocarbon exploration

    SciTech Connect

    Clark, J.D.; Pickering, K.T.

    1996-02-01

    Modern and ancient submarine channels show a wide range of architectural styles. Architectural element analysis is a useful descriptive means to characterize the type of channel fill, show the interconnectivity and lateral continuity of sand bodies, and interpret the causal sedimentary processes. This paper combines a review of the literature on submarine channels with new observations and analysis, and proposes architectural element models for submarine channels, in particular, demonstrating how these models can be applied to interpreting the sequential fill of ancient submarine channels. Data for the dimensions and degrees of lateral continuity and vertical connectivity of channel elements, such as those giving rise to reservoir heterogeneities in hydrocarbon exploration, are presented for a variety of examples of architectural elements, providing quantitative information for reservoir analog models. Sequence analysis; a development of these techniques, in particular their application to smaller scale features of turbidite systems, is described in Pickering et al.. A comparison of element analysis schemes for deep-water deposits. The characterization of outcrops of ancient deposits into their component elements at a variety of scales may help unravel complex depositional histories and help in understanding the development of the growth stages within turbidite systems. Studies of modern submarine channel data have shown that sinuosity and gradient are related, thereby permitting the identification of high- to low-sinuosity channel systems. It is important to attempt to link such observations to the different processes that may characterize, for example, low- vs. high-sinuosity deep-water channels, which will be particularly useful in evaluating the location and development of sand-prone hydrocarbon reservoirs within such systems.

  15. The use of substrate materials and topography to modify growth patterns and rates of differentiation of muscle cells.

    PubMed

    Murray, L M; Nock, V; Evans, J J; Alkaisi, M M

    2016-07-01

    Cells are cultured on platforms made of a variety of materials with selected topographies during studies of cell response and behavior. Understanding the effects of substrates is essential for such applications as developing effective interfaces between body cells and implanted materials and devices. In this study, the effects of substrate surface properties on cell differentiation and alignment on C2C12 myoblasts cultured on conventional or fabricated polymeric cell culture substrates were investigated. Comparisons were made between cells cultured on tissue culture grade polystyrene (TCPS), glass, Permanox, and cured polydimethylsiloxane (PDMS) substrates. Fluorescent immunohistochemistry of cell markers was used to analyse the extent of differentiation. Alignment and guidance of cell growth and spread were studied using patterned platforms. Gratings were made on polystyrene (PS) and PDMS and differentiation was facilitated after 5 days by media exchange. Differences in cell morphology were observed between cells cultured on TCPS and PDMS substrates. Fully differentiated myotubes were observed in highest numbers on TCPS substrates and were non-detectable on PDMS substrates in the time frame of 144 h. Muscle cell alignment and their differentiation followed along the grating patterns on PS and elongated along the pattern length. On the other hand, on PDMS cells formed sheets of tissue and peeled from the substrate. We have revealed the potential for the combinations of surface materials and topography on cell behavior to induce accelerated differentiation and coordinated alignment. The results demonstrate that culture environment can be designed or engineered to modify or regulate muscle cell functions. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 1638-1645, 2016. PMID:26916910

  16. The promoter methylomes of monochorionic twin placentas reveal intrauterine growth restriction-specific variations in the methylation patterns

    PubMed Central

    He, Zhiming; Lu, Hanlin; Luo, Huijuan; Gao, Fei; Wang, Tong; Gao, Yu; Fang, Qun; Wang, Junwen

    2016-01-01

    Intrauterine growth restriction (IUGR) affects the foetus and has a number of pathological consequences throughout life. Recent work has indicated that variations in DNA methylation might cause placental dysfunction, which may be associated with adverse pregnancy complications. Here, we investigated the promoter methylomes of placental shares from seven monochorionic (MC) twins with selective intrauterine growth restriction (sIUGR) using the healthy twin as an ideal control. Our work demonstrated that the IUGR placental shares harboured a distinct DNA hypomethylation pattern and that the methylation variations preferentially occurred in CpG island shores or non-CpG island promoters. The differentially methylated promoters could significantly separate the IUGR placental shares from the healthy ones. Ultra‐performance liquid chromatography/tandem mass spectrometry (UPLC‐MS/MS) further confirmed the genome‐wide DNA hypomethylation and the lower level of hydroxymethylation statuses in the IUGR placental shares. The methylation variations of the LRAT and SLC19A1 promoters, which are involved in vitamin A metabolism and folate transportation, respectively, and the EFS promoter were further validated in an additional 12 pairs of MC twins with sIUGR. Although the expressions of LRAT, SLC19A1 and EFS were not affected, we still speculated that DNA methylation and hydroxymethylation might serve a functional role during in utero foetal development. PMID:26830322

  17. The promoter methylomes of monochorionic twin placentas reveal intrauterine growth restriction-specific variations in the methylation patterns.

    PubMed

    He, Zhiming; Lu, Hanlin; Luo, Huijuan; Gao, Fei; Wang, Tong; Gao, Yu; Fang, Qun; Wang, Junwen

    2016-01-01

    Intrauterine growth restriction (IUGR) affects the foetus and has a number of pathological consequences throughout life. Recent work has indicated that variations in DNA methylation might cause placental dysfunction, which may be associated with adverse pregnancy complications. Here, we investigated the promoter methylomes of placental shares from seven monochorionic (MC) twins with selective intrauterine growth restriction (sIUGR) using the healthy twin as an ideal control. Our work demonstrated that the IUGR placental shares harboured a distinct DNA hypomethylation pattern and that the methylation variations preferentially occurred in CpG island shores or non-CpG island promoters. The differentially methylated promoters could significantly separate the IUGR placental shares from the healthy ones. Ultra-performance liquid chromatography/tandem mass spectrometry (UPLC-MS/MS) further confirmed the genome-wide DNA hypomethylation and the lower level of hydroxymethylation statuses in the IUGR placental shares. The methylation variations of the LRAT and SLC19A1 promoters, which are involved in vitamin A metabolism and folate transportation, respectively, and the EFS promoter were further validated in an additional 12 pairs of MC twins with sIUGR. Although the expressions of LRAT, SLC19A1 and EFS were not affected, we still speculated that DNA methylation and hydroxymethylation might serve a functional role during in utero foetal development. PMID:26830322

  18. Development of a PubMed Based Search Tool for Identifying Sex and Gender Specific Health Literature

    PubMed Central

    Song, Michael M.; Simonsen, Cheryl K.; Wilson, Joanna D.

    2016-01-01

    Abstract Background: An effective literature search strategy is critical to achieving the aims of Sex and Gender Specific Health (SGSH): to understand sex and gender differences through research and to effectively incorporate the new knowledge into the clinical decision making process to benefit both male and female patients. The goal of this project was to develop and validate an SGSH literature search tool that is readily and freely available to clinical researchers and practitioners. Methods: PubMed, a freely available search engine for the Medline database, was selected as the platform to build the SGSH literature search tool. Combinations of Medical Subject Heading terms, text words, and title words were evaluated for optimal specificity and sensitivity. The search tool was then validated against reference bases compiled for two disease states, diabetes and stroke. Results: Key sex and gender terms and limits were bundled to create a search tool to facilitate PubMed SGSH literature searches. During validation, the search tool retrieved 50 of 94 (53.2%) stroke and 62 of 95 (65.3%) diabetes reference articles selected for validation. A general keyword search of stroke or diabetes combined with sex difference retrieved 33 of 94 (35.1%) stroke and 22 of 95 (23.2%) diabetes reference base articles, with lower sensitivity and specificity for SGSH content. Conclusions: The Texas Tech University Health Sciences Center SGSH PubMed Search Tool provides higher sensitivity and specificity to sex and gender specific health literature. The tool will facilitate research, clinical decision-making, and guideline development relevant to SGSH. PMID:26555409

  19. Automated Patent Categorization and Guided Patent Search using IPC as Inspired by MeSH and PubMed

    PubMed Central

    2013-01-01

    Document search on PubMed, the pre-eminent database for biomedical literature, relies on the annotation of its documents with relevant terms from the Medical Subject Headings ontology (MeSH) for improving recall through query expansion. Patent documents are another important information source, though they are considerably less accessible. One option to expand patent search beyond pure keywords is the inclusion of classification information: Since every patent is assigned at least one class code, it should be possible for these assignments to be automatically used in a similar way as the MeSH annotations in PubMed. In order to develop a system for this task, it is necessary to have a good understanding of the properties of both classification systems. This report describes our comparative analysis of MeSH and the main patent classification system, the International Patent Classification (IPC). We investigate the hierarchical structures as well as the properties of the terms/classes respectively, and we compare the assignment of IPC codes to patents with the annotation of PubMed documents with MeSH terms. Our analysis shows a strong structural similarity of the hierarchies, but significant differences of terms and annotations. The low number of IPC class assignments and the lack of occurrences of class labels in patent texts imply that current patent search is severely limited. To overcome these limits, we evaluate a method for the automated assignment of additional classes to patent documents, and we propose a system for guided patent search based on the use of class co-occurrence information and external resources. PMID:23734562

  20. Summer global atmospheric patterns enhanced the Mediterranean East-West differences on tree growth at rear-edge temperate deciduous forests

    NASA Astrophysics Data System (ADS)

    Dorado Liñán, Isabel; Zorita, Eduardo; Gea-Izquierdo, Guillermo; Martínez-Sancho, Elisabet; Levanic, Tom; Zlatanov, Tzvetan; Di Filippo, Alfredo; Zang, Christian; Gutiérrez, Emilia; Menzel, Annette

    2016-04-01

    Overlaid to a general decrease on European beech and Sessile oak tree growth over the recent decades in the Mediterranean Basin, tree-ring records from western populations display a stronger growth decrease than eastern populations. We investigate here to what extent this spatial pattern of tree growth can be explained by the impact of sustained atmospheric circulation patterns in summertime. We use Canonical Correlation Analysis, a statistical method that identifies the patterns of two multivariate variables that are optimally correlated. A generalized change in growth trends, turning from a general increase during the period 1950-1981 to a generalized decrease in growth observed during the last three decades can be attributed to increasing summer temperatures, which exerts a dominant and negative influence on tree growth across sites. However, summer precipitation has gained in importance coinciding with the intensification of the geographical differences in tree sensitivity across the Mediterranean Basin. This intensification of the geographical differences in tree- growth during the last three decades can be traced back to an intensification of the Summer North Atlantic Oscillation that imparts an east-west dipole in summer precipitation. Under persistent positive SNAO, western populations are expected to face harsher summer conditions than central and eastern rear-edge populations, due to stronger decrease of precipitation in the west Mediterranean Basin. This increase in xericity will likely be negative for temperate deciduous broadleaf species at the rear-edge of their distribution in the Mediterranean Basin.

  1. Tuning the Growth Pattern in 2D Confinement Regime of Sm2O3 and the Emerging Room Temperature Unusual Superparamagnetism

    PubMed Central

    Guria, Amit K.; Dey, Koushik; Sarkar, Suresh; Patra, Biplab K.; Giri, Saurav; Pradhan, Narayan

    2014-01-01

    Programming the reaction chemistry for superseding the formation of Sm2O3 in a competitive process of formation and dissolution, the crystal growth patterns are varied and two different nanostructures of Sm2O3 in 2D confinement regime are designed. Among these, the regular and self-assembled square platelets nanostructures exhibit paramagnetic behavior analogous to the bulk Sm2O3. But, the other one, 2D flower like shaped nanostructure, formed by irregular crystal growth, shows superparamagnetism at room temperature which is unusual for bulk paramagnet. It has been noted that the variation in the crystal growth pattern is due to the difference in the binding ability of two organic ligands, oleylamine and oleic acid, used for the synthesis and the magnetic behavior of the nanostructures is related to the defects incorporated during the crystal growth. Herein, we inspect the formation chemistry and plausible origin of contrasting magnetism of these nanostructures of Sm2O3. PMID:25269458

  2. Mobile app versus Web app: a comparison using 2008-2012 "PubMed for Handhelds" server data.

    PubMed

    Fontelo, Paul; Liu, Fang

    2013-01-01

    Recent surveys show that mobile apps are more popular than Web apps. Apple's iTunes Store, now has about 800,000 apps and reported to have about 40 billion downloads. Android apps, although fewer, is available to the most number of smartphones today. About 40,000 apps are medical or health related. We developed a PubMed4Hh mobile app for iPhone/iPad users to search MEDLINE/PubMed with same features as our Web-based search tools, in use since 2002. Five-year (2008-2012) server data for PubMed4Hh and Web app were analyzed. Searches using the mobile app significantly increased compared to the same five-year time period. Month-by-month comparison showed a 3 to 5-fold increase in queries. The six-month total accesses comparison increased 280% from the previous four-year average. A review of 500 randomly selected queries revealed that the majority of queries were clinical questions ((97.8%) and 61% of these queries are searches related to therapy. PMID:24551349

  3. Patterned growth of single-crystal 3, 4, 9, 10-perylenetetracarboxylic dianhydride nanowire arrays for field-emission and optoelectronic devices

    NASA Astrophysics Data System (ADS)

    Pan, Huanhuan; Zhang, Xiujuan; Yang, Yang; Shao, Zhibin; Deng, Wei; Ding, Ke; Zhang, Yu; Jie, Jiansheng

    2015-07-01

    3, 4, 9, 10-perylenetetracarboxylic dianhydride (PTCDA) organic nanostructures possess extraordinary electronic and optoelectronic properties. However, it remains a challenge to achieve patterned growth of PTCDA nanowire (NW) arrays for integrated device applications. Here, we demonstrated the high-density, large-area, uniform, and cross-aligned growth of single-crystalline PTCDA NW arrays by using Au nanoparticles (NPs) as the growth templates. The high surface energy of Au NPs led to the cross-aligned growth of organic NWs, enabling the growth of PTCDA NW arrays with any desirable patterns by pre-patterning the Au films on a Si substrate. The PTCDA NW arrays as field emitters show good performance with a large emission current density and high emission stability. Furthermore, photodetectors based on PTCDA NW arrays were constructed via a simple in-situ growth approach, which exhibited high sensitivity to a wideband light ranging from 400-800 nm and surpassed the individual NW-based photodetectors in terms of higher photocurrent and faster response speed. Successful applications of PTCDA NW arrays in field emission and photodetectors show a great potential application of organic NW arrays in future efficient electronic and optoelectronic devices.

  4. Patterned growth of single-crystal 3, 4, 9, 10-perylenetetracarboxylic dianhydride nanowire arrays for field-emission and optoelectronic devices.

    PubMed

    Pan, Huanhuan; Zhang, Xiujuan; Yang, Yang; Shao, Zhibin; Deng, Wei; Ding, Ke; Zhang, Yu; Jie, Jiansheng

    2015-07-24

    3, 4, 9, 10-perylenetetracarboxylic dianhydride (PTCDA) organic nanostructures possess extraordinary electronic and optoelectronic properties. However, it remains a challenge to achieve patterned growth of PTCDA nanowire (NW) arrays for integrated device applications. Here, we demonstrated the high-density, large-area, uniform, and cross-aligned growth of single-crystalline PTCDA NW arrays by using Au nanoparticles (NPs) as the growth templates. The high surface energy of Au NPs led to the cross-aligned growth of organic NWs, enabling the growth of PTCDA NW arrays with any desirable patterns by pre-patterning the Au films on a Si substrate. The PTCDA NW arrays as field emitters show good performance with a large emission current density and high emission stability. Furthermore, photodetectors based on PTCDA NW arrays were constructed via a simple in-situ growth approach, which exhibited high sensitivity to a wideband light ranging from 400-800 nm and surpassed the individual NW-based photodetectors in terms of higher photocurrent and faster response speed. Successful applications of PTCDA NW arrays in field emission and photodetectors show a great potential application of organic NW arrays in future efficient electronic and optoelectronic devices. PMID:26135069

  5. Contrasting Spatial Patterns in Active-Fire and Fire-Suppressed Mediterranean Climate Old-Growth Mixed Conifer Forests

    PubMed Central

    Fry, Danny L.; Stephens, Scott L.; Collins, Brandon M.; North, Malcolm P.; Franco-Vizcaíno, Ernesto; Gill, Samantha J.

    2014-01-01

    In Mediterranean environments in western North America, historic fire regimes in frequent-fire conifer forests are highly variable both temporally and spatially. This complexity influenced forest structure and spatial patterns, but some of this diversity has been lost due to anthropogenic disruption of ecosystem processes, including fire. Information from reference forest sites can help management efforts to restore forests conditions that may be more resilient to future changes in disturbance regimes and climate. In this study, we characterize tree spatial patterns using four-ha stem maps from four old-growth, Jeffrey pine-mixed conifer forests, two with active-fire regimes in northwestern Mexico and two that experienced fire exclusion in the southern Sierra Nevada. Most of the trees were in patches, averaging six to 11 trees per patch at 0.007 to 0.014 ha−1, and occupied 27–46% of the study areas. Average canopy gap sizes (0.04 ha) covering 11–20% of the area were not significantly different among sites. The putative main effects of fire exclusion were higher densities of single trees in smaller size classes, larger proportion of trees (≥56%) in large patches (≥10 trees), and decreases in spatial complexity. While a homogenization of forest structure has been a typical result from fire exclusion, some similarities in patch, single tree, and gap attributes were maintained at these sites. These within-stand descriptions provide spatially relevant benchmarks from which to manage for structural heterogeneity in frequent-fire forest types. PMID:24586472

  6. Empowering a mesophilic inoculum for thermophilic nitrification: Growth mode and temperature pattern as critical proliferation factors for archaeal ammonia oxidizers.

    PubMed

    Courtens, Emilie N P; Vandekerckhove, Tom; Prat, Delphine; Vilchez-Vargas, Ramiro; Vital, Marius; Pieper, Dietmar H; Meerbergen, Ken; Lievens, Bart; Boon, Nico; Vlaeminck, Siegfried E

    2016-04-01

    Cost-efficient biological treatment of warm nitrogenous wastewaters requires the development of thermophilic nitrogen removal processes. Only one thermophilic nitrifying bioreactor was described so far, achieving 200 mg N L(-1) d(-1) after more than 300 days of enrichment from compost samples. From the practical point of view in which existing plants would be upgraded, however, a more time-efficient development strategy based on mesophilic nitrifying sludge is preferred. This study evaluated the adaptive capacities of mesophilic nitrifying sludge for two linear temperature increase patterns (non-oscillating vs. oscillating), two different slopes (0.25 vs. 0.08 °C d(-1)) and two different reactor types (floc vs. biofilm growth). The oscillating temperature pattern (0.25 °C d(-1)) and the moving bed biofilm reactor (0.08 °C d(-1)) could not reach nitrification at temperatures higher than 46 °C. However, nitrification rates up to 800 mg N L(-1) d(-1) and 150 mg N g(-1) volatile suspended solids d(-1) were achieved at a temperature as high as 49 °C by imposing the slowest linear temperature increase to floccular sludge. Microbial community analysis revealed that this successful transition was related with a shift in ammonium oxidizing archaea dominating ammonia oxidizing bacteria, while for nitrite oxidation Nitrospira spp. was constantly more abundant than Nitrobacter spp.. This observation was accompanied with an increase in observed sludge yield and a shift in maximal optimum temperature, determined with ex-situ temperature sensitivity measurements, predicting an upcoming reactor failure at higher temperature. Overall, this study achieved nitrification at 49 °C within 150 days by gradual adaptation of mesophilic sludge, and showed that ex-situ temperature sensitivity screening can be used to monitor and steer the transition process. PMID:26841233

  7. Growth pattern differences of captive born Antillean manatee (Trichechus manatus) calves and those rescued in the Brazilian northeastern coast.

    PubMed

    Borges, João Carlos Gomes; Freire, Augusto Carlos da Bôaviagem; Attademo, Fernanda Loffler Niemeyer; Serrano, Inês de Lima; Anzolin, Daiane Garcia; de Carvalho, Paulo Sérgio Martins; Vergara-Parente, Jociery Einhardt

    2012-09-01

    The aim of this work was to analyze whether there are differences between the development pattern of Antillean manatee (Trichechus manatus) calves born in captivity and those rescued and kept under rehabilitation. Biometrics data were collected from 1990 to 2010 from 38 calves, 29 of which still had the remnants of the umbilical cord and had been rescued from the Brazilian northeastern coastline (Group I), and nine individuals that were born in captivity and remained with their mothers (Group II). Among the measures obtained through biometry, the total length and weight of the animal were recorded. Given that the breastfeeding of calves occurs approximately until the age of 2 yr, data obtained until the 24th month of life of each individual were evaluated. An average increase in weight of 53.50 +/- 38.54 kg (mean +/- standard deviation [SD]) was detected in Group I and a gain of 106.87 +/- 47.21 kg (mean +/- SD) in Group II. From months 13 to 24, no significant difference in the weight increment was observed. A similar pattern occurred with regard to the increase in the overall length during the first year, where animals from Group I grew 34.81 +/- 17.94 cm (mean +/- SD) and from Group II grew 83.83 +/- 28.21 cm, a statistically significant difference. The growth was not significantly different from 13 to 24 mo. The results found in this study identified the need for a review of the nutritional diet offered to orphaned calves rescued and kept in captivity. The results also support the need for a better adequacy of facilities for these animals as a way to encourage the management strategies adopted for manatee calves maintained in captivity. PMID:23082512

  8. Phycoerythrin-containing picocyanobacteria in the Arabian Sea in February 1995:. diel patterns, spatial variability, and growth rates

    NASA Astrophysics Data System (ADS)

    Sherry, Nelson D.; Michelle Wood, A.

    The abundance of phycoerythrin-containing picocyanobacteria in the surface mixed layer was measured both along-shore and offshore between 8 and 23 February 1995 in the Northwestern Arabian Sea. Water samples from 3 m depth were taken at 2-h intervals and picocyanobacterial abundance and frequency of dividing cells were determined by epifluorescence microscopy. Cell counts showed an average diel change from a mid-day minimum of ˜50×10 3 cells ml -1 to an evening maximum of ˜180×10 3 cells ml -1. The diel change was greater than the differences observed between physically and spatially discrete water masses. By counting the frequency of dividing cells (FDC) and using a novel approach to estimating the length of time required to complete cell division, growth and loss rates were both estimated to be ˜2.9 d -1 with daily turnover being 140% of the mean standing stock. If differences in the intrinsic population growth rate ( μ) and the net rate of change in cell number ( r) are assumed to be due to grazing, then grazing occurred throughout the day at a relatively constant rate (reflecting phytoplankton loss rates of ˜0.12 h -1). Cell division rates peaked in the late afternoon and early evening. FDC decreased throughout the night, suggesting that dark-inhibition of cell division is weak or nonexistent in the picocyanobacteria we studied. While all cell types included in this study would be identified as Synechococcus by flow cytometry because they were small unicells with bright phycoerythrin fluorescence, morphological variability suggests that the community was actually taxonomically diverse and included cells other than Synechococcus, including Synechocystis. Despite this diversity, the strong diel patterns we observed persisted throughout the study region, suggesting that great care should be taken when interpreting picocyanobacterial survey data and experimental results that do not account for the effects of time-of-day.

  9. Fungal growth pattern, sources and factors of mould contamination in a dry-cured meat production facility.

    PubMed

    Asefa, Dereje T; Kure, Cathrine F; Gjerde, Ragnhild O; Omer, Mohamed K; Langsrud, Solveig; Nesbakken, Truls; Skaar, Ida

    2010-06-15

    The aims of this study were to investigate the patterns of fungal growth on dry-cured meat products, identify the important sources and factors of contamination and recommend intervention measures. The production processes of two smoked dry-cured hams and one unsmoked dry-cured leg of lamb were studied. A longitudinal observational study was performed to collect 642 samples from the meat, production materials, room installations and indoor and outdoor air of the production facility. Standard mycological isolation and identification procedures were followed. Totally, 901 fungal isolates were obtained; of which 57% were moulds while 43% were yeast. Yeasts were dominant on meat surfaces by covering 64% of the isolates. Mould growth was not observed until late in the dry-ripening stage. Yeasts and moulds were isolated from half of the environmental samples, of which moulds contributed by 80%. More than 39 mould species were isolated from the entire production process with a 77% contribution by the species of Penicillium. Penicillium nalgiovense dominated the species composition of moulds isolated from the products and the production environment. A preliminary bioassay analysis on bacterial colonies indicated that most of the P. nalgiovense isolates have the ability to produce penicillin. Such isolates might produce penicillin on the products and can become potential food safety hazards. Improper pressing at the salting process, the air quality in salting, brining and smoking rooms and activities in the sorting room were identified as important factors and sources of fungal contamination. Technical solutions and organized production activities that reduce crack formation, airborne spore concentration and improve air circulation in the facility are recommended as intervention measures. PMID:20442004

  10. Growth of In xGa 1- xAs layers with pyramidal morphology on (1 0 0)GaAs patterned substrates by liquid-phase epitaxy

    NASA Astrophysics Data System (ADS)

    Iida, S.; Balakrishnan, K.; Koyama, T.; Hayakawa, Y.; Kumagawa, M.

    2000-05-01

    Liquid-phase epitaxial growth of In xGa 1- xAs ( x=0.6) layers on various types of patterned (1 0 0)GaAs substrates was investigated. Non-planar InGaAs layer having filled tent-like structure was grown on non-patterned substrate. When the InGaAs was grown on circular-patterned substrate, a non-hollow pyramid structure was obtained. Perfect hollow pyramid structured InGaAs was found to be grown on trench substrates of (1 0 0)GaAs.

  11. How Twitter Is Studied in the Medical Professions: A Classification of Twitter Papers Indexed in PubMed

    PubMed Central

    2013-01-01

    Background Since their inception, Twitter and related microblogging systems have provided a rich source of information for researchers and have attracted interest in their affordances and use. Since 2009 PubMed has included 123 journal articles on medicine and Twitter, but no overview exists as to how the field uses Twitter in research. Objective This paper aims to identify published work relating to Twitter within the fields indexed by PubMed, and then to classify it. This classification will provide a framework in which future researchers will be able to position their work, and to provide an understanding of the current reach of research using Twitter in medical disciplines. Methods Papers on Twitter and related topics were identified and reviewed. The papers were then qualitatively classified based on the paper’s title and abstract to determine their focus. The work that was Twitter focused was studied in detail to determine what data, if any, it was based on, and from this a categorization of the data set size used in the studies was developed. Using open coded content analysis additional important categories were also identified, relating to the primary methodology, domain, and aspect. Results As of 2012, PubMed comprises more than 21 million citations from biomedical literature, and from these a corpus of 134 potentially Twitter related papers were identified, eleven of which were subsequently found not to be relevant. There were no papers prior to 2009 relating to microblogging, a term first used in 2006. Of the remaining 123 papers which mentioned Twitter, thirty were focused on Twitter (the others referring to it tangentially). The early Twitter focused papers introduced the topic and highlighted the potential, not carrying out any form of data analysis. The majority of published papers used analytic techniques to sort through thousands, if not millions, of individual tweets, often depending on automated tools to do so. Our analysis demonstrates that

  12. Patterns of growth and body condition in sea otters from the Aleutian archipelago before and after the recent population decline

    USGS Publications Warehouse

    Laidre, K.L.; Estes, J.A.; Tinker, M.T.; Bodkin, J.; Monson, D.; Schneider, K.

    2006-01-01

    3In addition to larger asymptotic values for mass and length, the rate of growth towards asymptotic values was more rapid in the 1990s than in the 1960s/70s: sea otters reached 95% of asymptotic body mass and body length 1–2 years earlier in the 1990s.4Body condition (as measured by the log mass/log length ratio) was significantly greater in males than in females. There was also an increasing trend from the 1960s/70s through 2004 despite much year-to-year variation.5Population age structures differed significantly between the 1960s/70s and the 1990s with the latter distribution skewed toward younger age classes (indicating an altered lxfunction) suggesting almost complete relaxation of age-dependent mortality patterns (i.e. those typical of food-limited populations).6This study spanned a period of time over which the population status of sea otters in the Aleutian archipelago declined precipitously from levels at or near equilibrium densities at some islands in the 1960s/70s to < 5% of estimated carrying capacity by the late 1990s. The results of this study indicate an improved overall health of sea otters over the period of decline and suggest that limited nutritional resources were not the cause of the observed reduced population abundance. Our findings are consistent with the hypothesis that the decline was caused by increased killer whale predation.

  13. Placental Expression Patterns of Galectin-1, Galectin-2, Galectin-3 and Galectin-13 in Cases of Intrauterine Growth Restriction (IUGR)

    PubMed Central

    Hutter, Stefan; Knabl, Julia; Andergassen, Ulrich; Hofmann, Simone; Kuhn, Christina; Mahner, Sven; Arck, Petra; Jeschke, Udo

    2016-01-01

    Galectins (gal) are members of the mammalian β-galactoside-binding proteins and recognize Galβ1-4GlcNAc and Galβ1-4GalNac (Thomsen-Friedenreich antigen (TF)) sequences of several cell surface oligosaccharides. In this study, gal-1, -2, -3 and -13 were investigated systematically in the trophoblast and decidua compartment of intrauterine growth restriction (IUGR) placentas and normal third trimester control placentas and stratified by fetal gender and gestational age. Within this study, 29 third trimester placentas after delivery were analyzed. Fetal gender was equally divided within both groups, and immunohistochemical staining was analyzed according to fetal gender and gestational age. Double immune-fluorescence with trophoblast-specific markers was used to identify galectin-expressing cells at the feto-maternal interface in the decidua. Gal-3 was significantly downregulated only in the extravillous trophoblast of IUGR placentas. In contrast, expressions of gal-2 and gal-13 were downregulated in both villous and extravillous trophoblast cells of IUGR placentas. In addition, gal-2 and gal-13 showed a highly correlated expression scheme in the placenta. There are significant gender-specific expression patterns for single prototype galectins with downregulation of gal-2 and gal-13 of male gender placentas in cases of IUGR. Gal-3 as the chimera type galectin shows only little gender-specific differences in expression, which disappear in IUGR cases. PMID:27070577

  14. From Plant Infectivity to Growth Patterns: The Role of Blue-Light Sensing in the Prokaryotic World.

    PubMed

    Losi, Aba; Mandalari, Carmen; Gärtner, Wolfgang

    2014-01-01

    Flavin-based photoreceptor proteins of the LOV (Light, Oxygen, and Voltage) and BLUF (Blue Light sensing Using Flavins) superfamilies are ubiquitous among the three life domains and are essential blue-light sensing systems, not only in plants and algae, but also in prokaryotes. Here we review their biological roles in the prokaryotic world and their evolution pathways. An unexpected large number of bacterial species possess flavin-based photosensors, amongst which are important human and plant pathogens. Still, few cases are reported where the activity of blue-light sensors could be correlated to infectivity and/or has been shown to be involved in the activation of specific genes, resulting in selective growth patterns. Metagenomics and bio-informatic analysis have only recently been initiated, but signatures are beginning to emerge that allow definition of a bona fide LOV or BLUF domain, aiming at better selection criteria for novel blue-light sensors. We also present here, for the first time, the phylogenetic tree for archaeal LOV domains that have reached a statistically significant number but have not at all been investigated thus far. PMID:27135492

  15. Placental Expression Patterns of Galectin-1, Galectin-2, Galectin-3 and Galectin-13 in Cases of Intrauterine Growth Restriction (IUGR).

    PubMed

    Hutter, Stefan; Knabl, Julia; Andergassen, Ulrich; Hofmann, Simone; Kuhn, Christina; Mahner, Sven; Arck, Petra; Jeschke, Udo

    2016-01-01

    Galectins (gal) are members of the mammalian β-galactoside-binding proteins and recognize Galβ1-4GlcNAc and Galβ1-4GalNac (Thomsen-Friedenreich antigen (TF)) sequences of several cell surface oligosaccharides. In this study, gal-1, -2, -3 and -13 were investigated systematically in the trophoblast and decidua compartment of intrauterine growth restriction (IUGR) placentas and normal third trimester control placentas and stratified by fetal gender and gestational age. Within this study, 29 third trimester placentas after delivery were analyzed. Fetal gender was equally divided within both groups, and immunohistochemical staining was analyzed according to fetal gender and gestational age. Double immune-fluorescence with trophoblast-specific markers was used to identify galectin-expressing cells at the feto-maternal interface in the decidua. Gal-3 was significantly downregulated only in the extravillous trophoblast of IUGR placentas. In contrast, expressions of gal-2 and gal-13 were downregulated in both villous and extravillous trophoblast cells of IUGR placentas. In addition, gal-2 and gal-13 showed a highly correlated expression scheme in the placenta. There are significant gender-specific expression patterns for single prototype galectins with downregulation of gal-2 and gal-13 of male gender placentas in cases of IUGR. Gal-3 as the chimera type galectin shows only little gender-specific differences in expression, which disappear in IUGR cases. PMID:27070577

  16. From Plant Infectivity to Growth Patterns: The Role of Blue-Light Sensing in the Prokaryotic World

    PubMed Central

    Losi, Aba; Mandalari, Carmen; Gärtner, Wolfgang

    2014-01-01

    Flavin-based photoreceptor proteins of the LOV (Light, Oxygen, and Voltage) and BLUF (Blue Light sensing Using Flavins) superfamilies are ubiquitous among the three life domains and are essential blue-light sensing systems, not only in plants and algae, but also in prokaryotes. Here we review their biological roles in the prokaryotic world and their evolution pathways. An unexpected large number of bacterial species possess flavin-based photosensors, amongst which are important human and plant pathogens. Still, few cases are reported where the activity of blue-light sensors could be correlated to infectivity and/or has been shown to be involved in the activation of specific genes, resulting in selective growth patterns. Metagenomics and bio-informatic analysis have only recently been initiated, but signatures are beginning to emerge that allow definition of a bona fide LOV or BLUF domain, aiming at better selection criteria for novel blue-light sensors. We also present here, for the first time, the phylogenetic tree for archaeal LOV domains that have reached a statistically significant number but have not at all been investigated thus far. PMID:27135492

  17. The Combined Effects of Response Time and Message Content on Growth Patterns of Discussion Threads in Computer-Supported Collaborative Argumentation

    ERIC Educational Resources Information Center

    Jeong, Allan

    2004-01-01

    This study examined the effects of response time and message content on the growth patterns of discussion threads in computer-supported collaborative argumentation. Event sequence analysis was used to measure response times between threaded messages and responses containing arguments, evidence, critiques, evaluations, and other comments from…

  18. Longitudinal Effects of a Universal Family-Focused Intervention on Growth Patterns of Adolescent Internalizing Symptoms and Polysubstance Use: Gender Comparisons

    ERIC Educational Resources Information Center

    Trudeau, Linda; Spoth, Richard; Randall, G. Kevin; Azevedo, Kari

    2007-01-01

    This study evaluated effects of the "Iowa Strengthening Families Program," a family-focused universal preventive intervention, on growth patterns of adolescent internalizing (anxiety and depressive symptoms) and monthly polysubstance use (alcohol, tobacco, marijuana, inhalants, and other illicit drugs), as well as the association between…

  19. Bibliometric Analysis of the Korean Journal of Parasitology: Measured from SCI, PubMed, Scopus, and Synapse Databases

    PubMed Central

    2009-01-01

    The Korean Journal of Parasitology (KJP) is the official journal of the Korean Society for Parasitology which is celebrating its 50th anniversary in 2009. To assess the contributions and achievements of the KJP, bibliometric analysis was conducted based on the citation data retrieved from 4 major databases; SCI, PubMed, Synapse, and Scopus. It was found that the KJP articles were constantly cited by the articles published in major international journals represented in these databases. More than 60% of 1,370 articles published in the KJP from 1963 to June 2009 were cited at least once by SCI articles. The overall average times cited by SCI articles are 2.6. The rate is almost 3 times higher for the articles published in the last 10 years compared to 1.0 for the articles of the 1960s. The SCI journal impact factor for 2008 is calculated as 0.871. It is increasing and it is expected to increase further with the introduction of the KJP in the database in 2008. The more realistic h-indixes were measured from the study data set covering all the citations to the KJP; 17 for SCI, 6 for PubMed, 19 for Synapse, and 17 for Scopus. Synapse extensively picked up the citations to the earlier papers not retrievable from the other 3 databases. It identified many papers published in the 1960s and in the 1980s which have been cited heavily, proving the central role of the KJP in the dissemination of the important research findings over the last 5 decades. PMID:19885331

  20. Wood growth patterns of Macrolobium acaciifolium (Benth.) Benth. (Fabaceae) in Amazonian black-water and white-water floodplain forests.

    PubMed

    Schöngart, Jochen; Piedade, Maria Teresa F; Wittmann, Florian; Junk, Wolfgang J; Worbes, Martin

    2005-09-01

    Macrolobium acaciifolium (Benth.) Benth. (Fabaceae) is a dominant legume tree species occurring at low elevations of nutrient-poor black-water (igapó) and nutrient-rich white-water floodplain forests (várzea) of Amazonia. As a consequence of the annual long-term flooding this species forms distinct annual tree rings allowing dendrochronological analyses. From both floodplain types in Central Amazonia we sampled cores from 20 large canopy trees growing at identical elevations with a flood-height up to 7 m. We determined tree age, wood density (WD) and mean radial increment (MRI) and synchronized ring-width patterns of single trees to construct tree-ring chronologies for every study site. Maximum tree age found in the igapó was more than 500 years, contrary to the várzea with ages not older than 200 years. MRI and WD were significantly lower in the igapó (MRI=1.52+/-0.38 mm year(-1), WD=0.39+/-0.05 g cm(-3)) than in the várzea (MRI=2.66+/-0.67 mm year(-1), WD=0.45+/-0.03 g cm(-3)). In both floodplain forests we developed tree-ring chronologies comprising the period 1857-2003 (n=7 trees) in the várzea and 1606-2003 (n=13 trees) in the igapó. The ring-width in both floodplain forests was significantly correlated with the length of the terrestrial phase (vegetation period) derived from the daily recorded water level in the port of Manaus since 1903. In both chronologies we found increased wood growth during El Niño events causing negative precipitation anomalies and a lower water discharge in Amazonian rivers, which leads to an extension of the terrestrial phase. The climate signal of La Niña was not evident in the dendroclimatic proxies. PMID:16025354

  1. Distinct developmental growth patterns account for the disproportionate expansion of the rostral and caudal isocortex in evolution

    PubMed Central

    Charvet, Christine J.

    2014-01-01

    In adulthood, the isocortex of several species is characterized by a gradient in neurons per unit of cortical surface area with fewer neurons per unit of cortical surface area in the rostral pole relative to the caudal pole. A gradient in neurogenesis timing predicts differences in neurons across the isocortex: neurons per unit of cortical surface area are fewer rostrally, where neurogenesis duration is short, and higher caudally where neurogenesis duration is longer. How species differences in neurogenesis duration impact cortical progenitor cells across its axis is not known. I estimated progenitor cells per unit of ventricular area across the rostro-caudal axis of the isocortex in cats (Felis catus) and in dogs (Canis familiaris) mostly before layers VI-II neurons are generated. I also estimated the ventricular length across the rostro-caudal axis at various stages of development in both species. These two species were chosen because neurogenesis duration in dogs is extended compared with cats. Caudally, cortical progenitors expand more tangentially and in numbers in dogs compared with cats. Rostrally, the cortical proliferative zone expands more tangentially in dogs compared with cats. However, the tangential expansion in the rostral cortical proliferative zone occurs without a concomitant increase in progenitor cell numbers. The tangential expansion of the ventricular surface in the rostral cortex is mediated by a reduction in cell density. These different developmental growth patterns account for the disproportionate expansion of the rostral (i.e., frontal cortex) and caudal cortex (e.g., primary visual cortex) when neurogenesis duration lengthens in evolution. PMID:24782736

  2. AND-34/BCAR3 Regulates Adhesion-Dependent p130Cas Serine Phosphorylation and Breast Cancer Cell Growth Pattern

    PubMed Central

    Makkinje, Anthony; Near, Richard I.; Infusini, Giuseppe; Borre, Pierre Vanden; Bloom, Alexander; Cai, Dongpo; Costello, Catherine E.; Lerner, Adam

    2009-01-01

    NSP protein family members associate with p130Cas, a focal adhesion adapter protein best known as a Src substrate that integrates adhesion-related signaling. Over-expression of AND-34/BCAR3/NSP2 (BCAR3), but not NSP1 or NSP3, induces anti-estrogen resistance in human breast cancer cell lines. BCAR3 over-expression in epithelial MCF-7 cells augments levels of a phosphorylated p130Cas species that migrates more slowly on SDS PAGE while NSP-1 and NSP3 induce modest or no phosphorylation, respectively. Conversely, reduction in BCAR3 expression in mesenchymal MDA-231 cells by inducible shRNA results in loss of such p130Cas phosphorylation. Replacement of NSP3's serine/proline-rich domain with that of AND-34/BCAR3 instills the ability to induce p130Cas phosphorylation. Phospho-amino acid analysis demonstrates that BCAR3 induces p130Cas serine phosphorylation. Mass spectrometry identified phosphorylation at p130Cas serines 139, 437 and 639. p130Cas serine phosphorylation accumulates for several hours after adhesion of MDA-231 cells to fibronectin and is dependent upon BCAR3 expression. BCAR3 knockdown alters p130Cas localization and converts MDA-231 growth to an epithelioid pattern characterized by striking cohesiveness and lack of cellular projections at colony borders. These studies demonstrate that BCAR3 regulates p130Cas serine phosphorylation that is adhesion-dependent, temporally distinct from previously well-characterized rapid Fak and Src kinase-mediated p130Cas tyrosine phosphorylation and that correlates with invasive phenotype. PMID:19454314

  3. Viral Vector Based Improvement of Optic Nerve Regeneration: Characterization of Individual Axons’ Growth Patterns and Synaptogenesis in a Visual Target

    PubMed Central

    Yungher, Benjamin J.; Luo, Xueting; Salgueiro, Yadira; Blackmore, Murray G.; Park, Kevin K.

    2015-01-01

    Lack of axon growth ability in the central nervous system poses a major barrier to achieving functional connectivity after injury. Thus, a non-transgenic regenerative approach to reinnervating targets has important implications in clinical and research settings. Previous studies using knockout (KO) mice have demonstrated long distance axon regeneration. Using an optic nerve injury model, here we evaluate the efficacy of viral, RNAi and pharmacological approaches that target the PTEN and STAT3 pathways to improve long distance axon regeneration in wild type (WT) mice. Our data show that adeno-associated virus (AAV) expressing short hairpin RNA (shRNA) against PTEN (shPTEN) enhances retinal ganglion cell axon regeneration after crush injury. However, compared to the previous data in PTEN KO mice, AAV-shRNA results in a lesser degree of regeneration, likely due to incomplete gene silencing inherent to RNAi. In comparison, an extensive enhancement in regeneration is seen when AAV-shPTEN is coupled to AAV encoding ciliary neurotrophic factor (CNTF) and to a cyclic adenosine monophosphate (cAMP) analogue, allowing axons to travel long distances and reach their target. We apply whole tissue imaging that facilitates three-dimensional visualization of single regenerating axons and document heterogeneous terminal patterns in the targets. This shows that some axonal populations generate extensive arbors and make synapses with the target neurons. Collectively, we show a combinatorial viral RNAi and pharmacological strategy that improves long distance regeneration in WT animals and provide single fiber projection data that indicates a degree of preservation of target recognition. PMID:26005861

  4. Growth

    NASA Astrophysics Data System (ADS)

    Waag, Andreas

    This chapter is devoted to the growth of ZnO. It starts with various techniques to grow bulk samples and presents in some detail the growth of epitaxial layers by metal organic chemical vapor deposition (MOCVD), molecular beam epitaxy (MBE), and pulsed laser deposition (PLD). The last section is devoted to the growth of nanorods. Some properties of the resulting samples are also presented. If a comparison between GaN and ZnO is made, very often the huge variety of different growth techniques available to fabricate ZnO is said to be an advantage of this material system. Indeed, growth techniques range from low cost wet chemical growth at almost room temperature to high quality MOCVD growth at temperatures above 1, 000∘C. In most cases, there is a very strong tendency of c-axis oriented growth, with a much higher growth rate in c-direction as compared to other crystal directions. This often leads to columnar structures, even at relatively low temperatures. However, it is, in general, not straight forward to fabricate smooth ZnO thin films with flat surfaces. Another advantage of a potential ZnO technology is said to be the possibility to grow thin films homoepitaxially on ZnO substrates. ZnO substrates are mostly fabricated by vapor phase transport (VPT) or hydrothermal growth. These techniques are enabling high volume manufacturing at reasonable cost, at least in principle. The availability of homoepitaxial substrates should be beneficial to the development of ZnO technology and devices and is in contrast to the situation of GaN. However, even though a number of companies are developing ZnO substrates, only recently good quality substrates have been demonstrated. However, these substrates are not yet widely available. Still, the situation concerning ZnO substrates seems to be far from low-cost, high-volume production. The fabrication of dense, single crystal thin films is, in general, surprisingly difficult, even when ZnO is grown on a ZnO substrate. However

  5. Lepidic and micropapillary growth pattern and expression of Napsin A can stratify patients of stage I lung adenocarcinoma into different prognostic subgroup

    PubMed Central

    Yang, Xin; Liu, Yu; Lian, Fang; Guo, Lei; Wen, Peng; Liu, Xiu-Yun; Lin, Dong-Mei

    2014-01-01

    Histologic categories and related growth pattern proposed by IASLC/ATS/ERS classification has been reported to be prognostically important in lung adenocarcinoma. Thyroid transcription factor-1 (TTF1) and Napsin A have been investigated as potential prognostic parameters with conflicting results. A total of 211 cases with stage I lung adenocarcinoma were analyzed according to the IASLC/ATS/ERS classification with slight modifications. Expression levels of TTF1 and Napsin A were evaluated by immunohistochemistry. In univariate analyses, we found female sex (p=0.009), lepidic growth pattern (P=0.011) and lack of micropapillary pattern (P=0.048) were favorable predictor significantly associated with disease-free survival (DFS). Lack of mitosis (P=0.044) and Napsin A expression (P=0.031) were favorable predictors for overall survival (OS). Tumors with a maximum diameter ≤2 cm had both longer DFS (P=0.008) and OS (P=0.020). Negative TTF1 expression indicated increased risk of death, but failure in statistical significance (P=0.215). After multivariate analysis, histologic subtype, tumor size and gender were identified as independent predictor for DFS (RR: 0.343, 3.697, 0.494; P=0.006, 0.029, 0.019), no feature was found as an independent predictor for overall survival (P>0.05). To conclude, lepidic growth pattern, female sex and tumor size ≤2 cm are independent favorable predictors for tumor recurrence, tumors with more than 5% percentage of lepidic growth pattern will have a better prognosis than absence, in early-stage lung adenocarcinoma. PMID:24817941

  6. The effect of reduced growth area by substrate patterning on misfit accommodation in molecular beam epitaxially grown InxGa1 - xAs/GaAs

    NASA Astrophysics Data System (ADS)

    Beam, E. A., III; Kao, Y. C.

    1991-04-01

    The effect of reduced growth area on the misfit accommodations of InxGa1-xAs/GaAs grown by molecular beam epitaxy has been studied with cross-sectional transmission electron microscopy (XTEM). Composition grading techniques as well as strained-layer superlattices were used for InxGa1-xAs compositions up to x=0.53 and growth areas which ranged from approximately 10 cm2 (blanket areas) to 4 μm2 squares. Results indicate that the use of step-composition grading and linear-composition grading are particularly effective when combined with reduced growth areas up to 30×30 μm and InxGa1-xAs compositions up to x=0.25. Dislocations which are generated for misfit accommodation during growth are effectively driven to the edges of the patterned growth areas with considerably fewer interactions than dislocations nucleated in blanket areas. XTEM samples prepared from blanket areas were generally found to contain randomly distributed threading dislocation-free regions on the order of 20-30 μm in width bounded by high density dislocation pile-ups. Higher InxGa1-xAs compositions resulted in large densities of threading dislocations with Burgers vectors perpendicular to the growth direction, particularly for step-composition graded layers. We attribute this behavior to roughening of the growth interface.

  7. Assessing the potential of amino acid 13C patterns as a carbon source tracer in marine sediments: effects of algal growth conditions and sedimentary diagenesis

    NASA Astrophysics Data System (ADS)

    Larsen, T.; Bach, L. T.; Salvatteci, R.; Wang, Y. V.; Andersen, N.; Ventura, M.; McCarthy, M. D.

    2015-08-01

    Burial of organic carbon in marine sediments has a profound influence in marine biogeochemical cycles and provides a sink for greenhouse gases such as CO2 and CH4. However, tracing organic carbon from primary production sources as well as its transformations in the sediment record remains challenging. Here we examine a novel but growing tool for tracing the biosynthetic origin of amino acid carbon skeletons, based on naturally occurring stable carbon isotope patterns in individual amino acids (δ13CAA). We focus on two important aspects for δ13CAA utility in sedimentary paleoarchives: first, the fidelity of source diagnostic of algal δ13CAA patterns across different oceanographic growth conditions, and second, the ability of δ13CAA patterns to record the degree of subsequent microbial amino acid synthesis after sedimentary burial. Using the marine diatom Thalassiosira weissflogii, we tested under controlled conditions how δ13CAA patterns respond to changing environmental conditions, including light, salinity, temperature, and pH. Our findings show that while differing oceanic growth conditions can change macromolecular cellular composition, δ13CAA isotopic patterns remain largely invariant. These results emphasize that δ13CAA patterns should accurately record biosynthetic sources across widely disparate oceanographic conditions. We also explored how δ13CAA patterns change as a function of age, total nitrogen and organic carbon content after burial, in a marine sediment core from a coastal upwelling area off Peru. Based on the four most informative amino acids for distinguishing between diatom and bacterial sources (i.e., isoleucine, lysine, leucine and tyrosine), bacterially derived amino acids ranged from 10 to 15 % in the sediment layers from the last 5000 years, and up to 35 % during the last glacial period. The greater bacterial contributions in older sediments indicate that bacterial activity and amino acid resynthesis progressed, approximately as a

  8. Biotea: RDFizing PubMed Central in support for the paper as an interface to the Web of Data

    PubMed Central

    2013-01-01

    Background The World Wide Web has become a dissemination platform for scientific and non-scientific publications. However, most of the information remains locked up in discrete documents that are not always interconnected or machine-readable. The connectivity tissue provided by RDF technology has not yet been widely used to support the generation of self-describing, machine-readable documents. Results In this paper, we present our approach to the generation of self-describing machine-readable scholarly documents. We understand the scientific document as an entry point and interface to the Web of Data. We have semantically processed the full-text, open-access subset of PubMed Central. Our RDF model and resulting dataset make extensive use of existing ontologies and semantic enrichment services. We expose our model, services, prototype, and datasets at http://biotea.idiginfo.org/ Conclusions The semantic processing of biomedical literature presented in this paper embeds documents within the Web of Data and facilitates the execution of concept-based queries against the entire digital library. Our approach delivers a flexible and adaptable set of tools for metadata enrichment and semantic processing of biomedical documents. Our model delivers a semantically rich and highly interconnected dataset with self-describing content so that software can make effective use of it. PMID:23734622

  9. A drug-adverse event extraction algorithm to support pharmacovigilance knowledge mining from PubMed citations.

    PubMed

    Wang, Wei; Haerian, Krystl; Salmasian, Hojjat; Harpaz, Rave; Chase, Herbert; Friedman, Carol

    2011-01-01

    Adverse drug events (ADEs) create a serious problem causing substantial harm to patients. An executable standardized knowledgebase of drug-ADE relations which is publicly available would be valuable so that it could be used for ADE detection. The literature is an important source that could be used to generate a knowledgebase of drug-ADE pairs. In this paper, we report on a method that automatically determines whether a specific adverse event (AE) is caused by a specific drug based on the content of PubMed citations. A drug-ADE classification method was initially developed to detect neutropenia based on a pre-selected set of drugs. This method was then applied to a different set of 76 drugs to determine if they caused neutropenia. For further proof of concept this method was applied to 48 drugs to determine whether they caused another AE, myocardial infarction. Results showed that AUROC was 0.93 and 0.86 respectively. PMID:22195210

  10. An experimental search strategy retrieves more precise results than PubMed and Google for questions about medical interventions

    PubMed Central

    Dylla, Daniel P.; Megison, Susan D.

    2015-01-01

    Objective. We compared the precision of a search strategy designed specifically to retrieve randomized controlled trials (RCTs) and systematic reviews of RCTs with search strategies designed for broader purposes. Methods. We designed an experimental search strategy that automatically revised searches up to five times by using increasingly restrictive queries as long at least 50 citations were retrieved. We compared the ability of the experimental and alternative strategies to retrieve studies relevant to 312 test questions. The primary outcome, search precision, was defined for each strategy as the proportion of relevant, high quality citations among the first 50 citations retrieved. Results. The experimental strategy had the highest median precision (5.5%; interquartile range [IQR]: 0%–12%) followed by the narrow strategy of the PubMed Clinical Queries (4.0%; IQR: 0%–10%). The experimental strategy found the most high quality citations (median 2; IQR: 0–6) and was the strategy most likely to find at least one high quality citation (73% of searches; 95% confidence interval 68%–78%). All comparisons were statistically significant. Conclusions. The experimental strategy performed the best in all outcomes although all strategies had low precision. PMID:25922798

  11. Growth patterns and nuclear distribution in white muscle fibers from black sea bass, Centropristis striata: evidence for the influence of diffusion

    PubMed Central

    Priester, Carolina; Morton, Lindsay C.; Kinsey, Stephen T.; Watanabe, Wade O.; Dillaman, Richard M.

    2011-01-01

    SUMMARY This study investigated the influence of fiber size on the distribution of nuclei and fiber growth patterns in white muscle of black sea bass, Centropristis striata, ranging in body mass from 0.45 to 4840 g. Nuclei were counted in 1 μm optical sections using confocal microscopy of DAPIand Acridine-Orange-stained muscle fibers. Mean fiber diameter increased from 36±0.87 μm in the 0.45 g fish to 280±5.47 μm in the 1885 g fish. Growth beyond 2000 g triggered the recruitment of smaller fibers, thus significantly reducing mean fiber diameter. Nuclei in the smaller fibers were exclusively subsarcolemmal (SS), whereas in larger fibers nuclei were more numerous and included intermyofibrillar (IM) nuclei. There was a significant effect of body mass on nuclear domain size (F=118.71, d.f.=3, P<0.0001), which increased to a maximum in fish of medium size (282–1885 g) and then decreased in large fish (>2000 g). Although an increase in the number of nuclei during fiber growth can help preserve the myonuclear domain, the appearance of IM nuclei during hypertrophic growth seems to be aimed at maintaining short effective diffusion distances for nuclear substrates and products. If only SS nuclei were present throughout growth, the diffusion distance would increase in proportion to the radius of the fibers. These observations are consistent with the hypothesis that changes in nuclear distribution and fiber growth patterns are mechanisms for avoiding diffusion limitation during animal growth. PMID:21430198

  12. Patterns of Cereal Yield Growth across China from 1980 to 2010 and Their Implications for Food Production and Food Security

    PubMed Central

    Li, Xiaoyun; Liu, Nianjie; You, Liangzhi; Ke, Xinli; Liu, Haijun; Huang, Malan; Waddington, Stephen R.

    2016-01-01

    After a remarkable 86% increase in cereal production from 1980 to 2005, recent crop yield growth in China has been slow. County level crop production data between 1980 and 2010 from eastern and middle China were used to analyze spatial and temporal patterns of rice, wheat and maize yield in five major farming systems that include around 90% of China's cereal production. Site-specific yield trends were assessed in areas where those crops have experienced increasing yield or where yields have stagnated or declined. We find that rice yields have continued to increase on over 12.3 million hectares (m. ha) or 41.8% of the rice area in China between 1980 and 2010. However, yields stagnated on 50% of the rice area (around 14.7 m. ha) over this time period. Wheat yields increased on 13.8 m. ha (58.2% of the total harvest area), but stagnated on around 3.8 m. ha (15.8% of the harvest area). Yields increased on a smaller proportion of the maize area (17.7% of harvest area, 5.3 m. ha), while yields have stagnated on over 54% (16.3 m. ha). Many parts of the lowland rice and upland intensive sub-tropical farming systems were more prone to stagnation with rice, the upland intensive sub-tropical system with wheat, and maize in the temperate mixed system. Large areas where wheat yield continues to rise were found in the lowland rice and temperate mixed systems. Land and water constraints, climate variability, and other environmental limitations undermine increased crop yield and agricultural productivity in these systems and threaten future food security. Technology and policy innovations must be implemented to promote crop yields and the sustainable use of agricultural resources to maintain food security in China. In many production regions it is possible to better match the crop with input resources to raise crop yields and benefits. Investments may be especially useful to intensify production in areas where yields continue to improve. For example, increased support to maize

  13. Patterns of Cereal Yield Growth across China from 1980 to 2010 and Their Implications for Food Production and Food Security.

    PubMed

    Li, Xiaoyun; Liu, Nianjie; You, Liangzhi; Ke, Xinli; Liu, Haijun; Huang, Malan; Waddington, Stephen R

    2016-01-01

    After a remarkable 86% increase in cereal production from 1980 to 2005, recent crop yield growth in China has been slow. County level crop production data between 1980 and 2010 from eastern and middle China were used to analyze spatial and temporal patterns of rice, wheat and maize yield in five major farming systems that include around 90% of China's cereal production. Site-specific yield trends were assessed in areas where those crops have experienced increasing yield or where yields have stagnated or declined. We find that rice yields have continued to increase on over 12.3 million hectares (m. ha) or 41.8% of the rice area in China between 1980 and 2010. However, yields stagnated on 50% of the rice area (around 14.7 m. ha) over this time period. Wheat yields increased on 13.8 m. ha (58.2% of the total harvest area), but stagnated on around 3.8 m. ha (15.8% of the harvest area). Yields increased on a smaller proportion of the maize area (17.7% of harvest area, 5.3 m. ha), while yields have stagnated on over 54% (16.3 m. ha). Many parts of the lowland rice and upland intensive sub-tropical farming systems were more prone to stagnation with rice, the upland intensive sub-tropical system with wheat, and maize in the temperate mixed system. Large areas where wheat yield continues to rise were found in the lowland rice and temperate mixed systems. Land and water constraints, climate variability, and other environmental limitations undermine increased crop yield and agricultural productivity in these systems and threaten future food security. Technology and policy innovations must be implemented to promote crop yields and the sustainable use of agricultural resources to maintain food security in China. In many production regions it is possible to better match the crop with input resources to raise crop yields and benefits. Investments may be especially useful to intensify production in areas where yields continue to improve. For example, increased support to maize

  14. ATP-competitive mTOR kinase inhibitors delay plant growth by triggering early differentiation of meristematic cells but no developmental patterning change

    PubMed Central

    Menand, Benoît

    2013-01-01

    The TOR (target of rapamycin) protein, a large phosphatidylinositol 3-kinase-like protein kinase (PIKK) that is conserved in eukaryotes and is a central regulator of growth and metabolism. The analysis of function of TOR in plant growth and development has been limited by the fact that plants are very poorly sensitive to rapamycin. As the kinase domain of TOR is highly conserved, this study analysed the dose-dependent effect of three sets of first- and second-generation ATP-competitive inhibitors (called asTORis for active-site TOR inhibitors) recently developed for the human TOR kinase on Arabidopsis thaliana growth. All six asTORis inhibited plant root growth in a dose-dependent manner, with 50% growth inhibitory doses (GI50) of <10 μM and <1 μM for the first- and second-generation inhibitors, respectively, similarly to the values in mammalian cells. A genetic approach further demonstrated that only asTORis inhibited root growth in an AtTOR gene-dosage-dependent manner. AsTORis decreased the length of: (i) the meristematic zone (MZ); (ii) the division zone in the MZ; (iii) epidermal cells in the elongation zone; and (iv) root hair cells. Whereas meristematic cells committed to early differentiation, the pattern of cell differentiation was not affected per se. AsTORis-induced root hair growth phenotype was shown to be specific by using other growth inhibitors blocking the cell cycle or translation. AsTORis dose-dependent inhibition of growth and root hairs was also observed in diverse groups of flowering plants, indicating that asTORis can be used to study the TOR pathway in other angiosperms, including crop plants. PMID:23963679

  15. Deconstructing the externalizing spectrum: Growth patterns of overt aggression, covert aggression, oppositional behavior, impulsivity/inattention, and emotion dysregulation between school entry and early adolescence

    PubMed Central

    Olson, Sheryl L.; Sameroff, Arnold J.; Lansford, Jennifer E.; Sexton, Holly; Davis-Kean, Pamela; Bates, John E.; Pettit, Gregory S.; Dodge, Kenneth A.

    2013-01-01

    The purpose of this study was to determine whether five subcomponents of children's externalizing behavior showed distinctive patterns of long-term growth and predictive correlates. We examined growth in teachers' ratings of overt aggression, covert aggression, oppositional defiance, impulsivity/inattention, and emotion dysregulation across three developmental periods spanning kindergarten through Grade 8 (ages 5–13 years). We also determined whether three salient background characteristics, family socioeconomic status, child ethnicity, and child gender, differentially predicted growth in discrete categories of child externalizing symptoms across development. Participants were 543 kindergarten-age children (52% male, 81% European American, 17% African American) whose problem behaviors were rated by teachers each successive year of development through Grade 8. Latent growth curve analyses were performed for each component scale, contrasting with overall externalizing, in a piecewise fashion encompassing three developmental periods: kindergarten–Grade 2, Grades 3–5, and Grades 6–8. We found that most subconstructs of externalizing behavior increased significantly across the early school age period relative to middle childhood and early adolescence. However, overt aggression did not show early positive growth, and emotion dysregulation significantly increased across middle childhood. Advantages of using subscales were most clear in relation to illustrating different growth functions between the discrete developmental periods. Moreover, growth in some discrete subcomponents was differentially associated with variations in family socioeconomic status and ethnicity. Our findings strongly affirmed the necessity of adopting a developmental approach to the analysis of growth in children's externalizing behavior and provided unique data concerning similarities and differences in growth between subconstructs of child and adolescent externalizing behavior. PMID

  16. Dependencies of the emission behavior and quantum well structure of a regularly-patterned, InGaN/GaN quantum-well nanorod array on growth condition.

    PubMed

    Liao, Che-Hao; Tu, Charng-Gan; Chang, Wen-Ming; Su, Chia-Ying; Shih, Pei-Ying; Chen, Hao-Tsung; Yao, Yu-Feng; Hsieh, Chieh; Chen, Horng-Shyang; Lin, Chun-Han; Yu, Chih-Kang; Kiang, Yean-Woei; Yang, C C

    2014-07-14

    To achieve green emission from the sidewall non-polar quantum wells (QWs) of a GaN nanorod (NR) light-emitting diode, regularly patterned InGaN/GaN QW NR arrays are grown under various growth conditions of indium supply rate, QW growth temperature, and QW growth time for comparing their emission wavelength variations of the top-face c-plane and sidewall m-plane QWs based on photoluminescence and cathodoluminescence (CL) measurements. Although the variation trends of QW emission wavelength by changing those growth conditions in the NR structure are similar to those in the planar structure, the emission wavelength range of the QWs on an NR is significantly shorter than that in a planar structure under the same growth conditions. Under the growth conditions for a longer NR QW emission wavelength, the difference of emission wavelength between the top-face and sidewall QWs is smaller. Also, the variation range of the emission wavelength from the sidewall QWs over different heights on the sidewall becomes larger. On the other hand, strain state analysis based on transmission electron microscopy is undertaken to calibrate the average QW widths and average indium contents in the two groups of QW of an NR. The variation trends of the calibrated QW widths and indium contents are consistent with those of the CL emission wavelengths from various portions of NR QWs. PMID:25090544

  17. The importance of seasonal temperature and moisture patterns on growth of Douglas-fir in western Oregon, USA

    EPA Science Inventory

    Douglas-fir growth in the Pacific Northwest is thought to be water limited. However, discerning the relative influence of air temperature and plant available soil water (W) on growth is difficult because they interact with each other, with other climate factors and with the inher...

  18. Microecology: Using Fast-Growing Filamentous Fungi to Study the Effects of Environmental Gradients on the Growth Patterns of Hyphae

    ERIC Educational Resources Information Center

    Delpech, Roger

    2004-01-01

    This paper describes some simple and rapid techniques for examining the growth responses of fungal hyphae cultivated on environmental gradients. The creation of such gradients using agar-based growth media in petri dishes is explained, along with recommendations for quantitative macroscopic and microscopic measurements. The intention is to provide…

  19. Analysis of growth patterns during gravitropic curvature in roots of Zea mays by use of a computer-based video digitizer

    NASA Technical Reports Server (NTRS)

    Nelson, A. J.; Evans, M. L.

    1986-01-01

    A computer-based video digitizer system is described which allows automated tracking of markers placed on a plant surface. The system uses customized software to calculate relative growth rates at selected positions along the plant surface and to determine rates of gravitropic curvature based on the changing pattern of distribution of the surface markers. The system was used to study the time course of gravitropic curvature and changes in relative growth rate along the upper and lower surface of horizontally-oriented roots of maize (Zea mays L.). The growing region of the root was found to extend from about 1 mm behind the tip to approximately 6 mm behind the tip. In vertically-oriented roots the relative growth rate was maximal at about 2.5 mm behind the tip and declined smoothly on either side of the maximum. Curvature was initiated approximately 30 min after horizontal orientation with maximal (50 degrees) curvature being attained in 3 h. Analysis of surface extension patterns during the response indicated that curvature results from a reduction in growth rate along both the upper and lower surfaces with stronger reduction along the lower surface.

  20. Photolithographic Patterning of C2C12 Myotubes using Vitronectin as Growth Substrate in Serum-Free Medium

    PubMed Central

    Molnar, Peter; Wang, Weishi; Natarajan, Anupama; Rumsey, John W.; Hickman, James J.

    2008-01-01

    The C2C12 cell line is frequently used as a model of skeletal muscle differentiation. In our serum-free defined culture system differentiation of C2C12 cells into myotubes required surface-bound signals such as substrate adsorbed vitronectin or laminin. Based on this substrate-requirement of myotube formation, we developed a photolithography-based method to pattern C2C12 myotubes, where myotubes formed exclusively on vitronectin surface patterns. We have determined that the optimal line width to form single myotubes is approximately 30 μm. In order to illustrate a possible application of this method, we patterned myotubes on the top of commercial substrate-embedded microelectrodes. In contrast to previous experiments where cell patterning was achieved by selective attachment of the cells to patterned surfaces in a medium that contained all the factors necessary for differentiation, this study illustrates that surface patterning of a signaling molecule, which is essential for skeletal muscle differentiation in a defined system, can result in the formation of aligned myotubes on the patterns. This technique is being developed for applications in cell biology, tissue engineering and robotics. PMID:17269697

  1. Building Disease-Specific Drug-Protein Connectivity Maps from Molecular Interaction Networks and PubMed Abstracts

    PubMed Central

    Li, Jiao; Zhu, Xiaoyan; Chen, Jake Yue

    2009-01-01

    The recently proposed concept of molecular connectivity maps enables researchers to integrate experimental measurements of genes, proteins, metabolites, and drug compounds under similar biological conditions. The study of these maps provides opportunities for future toxicogenomics and drug discovery applications. We developed a computational framework to build disease-specific drug-protein connectivity maps. We integrated gene/protein and drug connectivity information based on protein interaction networks and literature mining, without requiring gene expression profile information derived from drug perturbation experiments on disease samples. We described the development and application of this computational framework using Alzheimer's Disease (AD) as a primary example in three steps. First, molecular interaction networks were incorporated to reduce bias and improve relevance of AD seed proteins. Second, PubMed abstracts were used to retrieve enriched drug terms that are indirectly associated with AD through molecular mechanistic studies. Third and lastly, a comprehensive AD connectivity map was created by relating enriched drugs and related proteins in literature. We showed that this molecular connectivity map development approach outperformed both curated drug target databases and conventional information retrieval systems. Our initial explorations of the AD connectivity map yielded a new hypothesis that diltiazem and quinidine may be investigated as candidate drugs for AD treatment. Molecular connectivity maps derived computationally can help study molecular signature differences between different classes of drugs in specific disease contexts. To achieve overall good data coverage and quality, a series of statistical methods have been developed to overcome high levels of data noise in biological networks and literature mining results. Further development of computational molecular connectivity maps to cover major disease areas will likely set up a new model for

  2. Building disease-specific drug-protein connectivity maps from molecular interaction networks and PubMed abstracts.

    PubMed

    Li, Jiao; Zhu, Xiaoyan; Chen, Jake Yue

    2009-07-01

    The recently proposed concept of molecular connectivity maps enables researchers to integrate experimental measurements of genes, proteins, metabolites, and drug compounds under similar biological conditions. The study of these maps provides opportunities for future toxicogenomics and drug discovery applications. We developed a computational framework to build disease-specific drug-protein connectivity maps. We integrated gene/protein and drug connectivity information based on protein interaction networks and literature mining, without requiring gene expression profile information derived from drug perturbation experiments on disease samples. We described the development and application of this computational framework using Alzheimer's Disease (AD) as a primary example in three steps. First, molecular interaction networks were incorporated to reduce bias and improve relevance of AD seed proteins. Second, PubMed abstracts were used to retrieve enriched drug terms that are indirectly associated with AD through molecular mechanistic studies. Third and lastly, a comprehensive AD connectivity map was created by relating enriched drugs and related proteins in literature. We showed that this molecular connectivity map development approach outperformed both curated drug target databases and conventional information retrieval systems. Our initial explorations of the AD connectivity map yielded a new hypothesis that diltiazem and quinidine may be investigated as candidate drugs for AD treatment. Molecular connectivity maps derived computationally can help study molecular signature differences between different classes of drugs in specific disease contexts. To achieve overall good data coverage and quality, a series of statistical methods have been developed to overcome high levels of data noise in biological networks and literature mining results. Further development of computational molecular connectivity maps to cover major disease areas will likely set up a new model for

  3. Differential expression of mitotic regulators and tumor microenvironment influences the regional growth pattern of solid sarcoma along the cranio-caudal axis.

    PubMed

    Chattopadhyay, Sukalpa; Chaklader, Malay; Chatterjee, Ritam; Law, Aditya; Law, Sujata

    2016-01-01

    Soft tissue sarcomas are relatively rare, unusual, anatomically diverse group of malignancies. According to the recent literature and medical bulletins, tumor growth and aggressiveness immensely relies on its anatomical locations. However, it is unclear whether the cranio-caudal anatomical axis of the mammalian body can influence sarcoma development and the underlying molecular mechanisms are not yet deciphered. Here, we investigated the growth pattern of solid sarcoma implanted into the murine cranial and caudal anatomical locations and tried to explore the location specific expression pattern of crucial mammalian mitotic regulators such as Aurora kinase A, Histone H3 and c-Myc in the cranio-caudally originated solid tumors. In addition, the influence of local tumor microenvironment on regional sarcoma growth was also taken into consideration. We found that solid sarcoma developed differentially when implanted into two different anatomical locations and most notably, enhanced tumor growth was observed in case of cranially implanted sarcoma than the caudal sarcoma. Interestingly, Aurora kinase A and c-Myc expression and histone H3 phosphorylation level were comparatively higher in the cranial tumor than the caudal. In addition, variation of tumor stroma in a location specific manner also facilitated tumor growth. Cranial sarcoma microenvironment was well vascularized than the caudal one and consequently, a significantly higher microvessel density count was observed which was parallel with low hypoxic response with sign of local tumor inflammation in this region. Taken together, our findings suggest that differential gradient of mitotic regulators together with varied angiogenic response and local tumor microenvironment largely controls solid sarcoma growth along the cranio-caudal anatomical axis. PMID:26658517

  4. A DIRECTORY OF CLOSED-CIRCUIT INSTALLATIONS IN AMERICAN EDUCATION WITH A PATTERN OF GROWTH. STUDIES IN THE GROWTH OF INSTRUCTION TECHNOLOGY, II.

    ERIC Educational Resources Information Center

    CAMPION, LEE E.; AND OTHERS

    THE PURPOSE OF THIS STUDY WAS TO LOCATE CLOSED-CIRCUIT TELEVISION (CCTV) INSTALLATIONS IN EDUCATIONAL INSTITUTIONS ACROSS THE UNITED STATES, COMPILE A DIRECTORY OF THESE INSTITUTIONS, DESCRIBE THE EQUIPMENT AND FACILITIES IN USE, LOCATE PATTERNS OF UTILIZATION OF CCTV SYSTEMS, AND DESCRIBE THE DEVELOPMENTAL PROCESS OF THIS NEW FORM OF EDUCATIONAL…

  5. Application of a model to predict cyanobacterial growth patterns in response to climatic change at Farmoor reservoir, Oxfordshire, UK.

    PubMed

    Howard, Alan; Easthope, Mark P

    2002-01-23

    The cyanobacterial growth for the next 90 years at Farmoor Reservoir, Oxfordshire is predicted using the cyanobacterial growth model, CLAMM, with data obtained from HADCM2 climate change model. It is predicted that solar radiation at the water-body surface will decrease slightly due to increased cloud cover. Predictions of cyanobacterial growth indicate little change in total production although the main summer growing season may be extended. It is also suggested that increased wind velocities may affect the frequency of 'blooming incidents'. PMID:11846084

  6. ZnO nanowire array growth on precisely controlled patterns of inkjet-printed zinc acetate at low-temperatures

    NASA Astrophysics Data System (ADS)

    Tsangarides, Constantinos P.; Ma, Hanbin; Nathan, Arokia

    2016-06-01

    ZnO nanowires have been fabricated through the hydrothermal method on inkjet-printed patterns of zinc acetate dihydrate. The silicon substrate used was heated accordingly during the printing period in order to maintain good spatial uniformity of the zinc acetate nanoparticles, responsible for the pattern morphology. Printing more than one pass of precursor ink leads to an increase in seed layer thickness that subsequently alters the density and dimensions of nanowires. It has been demonstrated that with the right inkjet-printing parameters and substrate temperature, ZnO nanowires can be effortlessly fabricated in accordance with the desired pattern variations under low temperature and mild conditions that ensures promising applications in optoelectronic devices.ZnO nanowires have been fabricated through the hydrothermal method on inkjet-printed patterns of zinc acetate dihydrate. The silicon substrate used was heated accordingly during the printing period in order to maintain good spatial uniformity of the zinc acetate nanoparticles, responsible for the pattern morphology. Printing more than one pass of precursor ink leads to an increase in seed layer thickness that subsequently alters the density and dimensions of nanowires. It has been demonstrated that with the right inkjet-printing parameters and substrate temperature, ZnO nanowires can be effortlessly fabricated in accordance with the desired pattern variations under low temperature and mild conditions that ensures promising applications in optoelectronic devices. Electronic supplementary information (ESI) available: Printing parameters in detail and extra figures. See DOI: 10.1039/c6nr02962k

  7. Patterns in hydraulic architecture from roots to branches in six tropical tree species from cacao agroforestry and their relation to wood density and stem growth.

    PubMed

    Kotowska, Martyna M; Hertel, Dietrich; Rajab, Yasmin Abou; Barus, Henry; Schuldt, Bernhard

    2015-01-01

    For decades it has been assumed that the largest vessels are generally found in roots and that vessel size and corresponding sapwood area-specific hydraulic conductivity are acropetally decreasing toward the distal twigs. However, recent studies from the perhumid tropics revealed a hump-shaped vessel size distribution. Worldwide tropical perhumid forests are extensively replaced by agroforestry systems often using introduced species of various biogeographical and climatic origins. Nonetheless, it is unknown so far what kind of hydraulic architectural patterns are developed in those agroforestry tree species and which impact this exerts regarding important tree functional traits, such as stem growth, hydraulic efficiency and wood density (WD). We investigated wood anatomical and hydraulic properties of the root, stem and branch wood in Theobroma cacao and five common shade tree species in agroforestry systems on Sulawesi (Indonesia); three of these were strictly perhumid tree species, and the other three tree species are tolerating seasonal drought. The overall goal of our study was to relate these properties to stem growth and other tree functional traits such as foliar nitrogen content and sapwood to leaf area ratio. Our results confirmed a hump-shaped vessel size distribution in nearly all species. Drought-adapted species showed divergent patterns of hydraulic conductivity, vessel density, and relative vessel lumen area between root, stem and branch wood compared to wet forest species. Confirming findings from natural old-growth forests in the same region, WD showed no relationship to specific conductivity. Overall, aboveground growth performance was better predicted by specific hydraulic conductivity than by foliar traits and WD. Our study results suggest that future research on conceptual trade-offs of tree hydraulic architecture should consider biogeographical patterns underlining the importance of anatomical adaptation mechanisms to environment. PMID:25873922

  8. Patterns in hydraulic architecture from roots to branches in six tropical tree species from cacao agroforestry and their relation to wood density and stem growth

    PubMed Central

    Kotowska, Martyna M.; Hertel, Dietrich; Rajab, Yasmin Abou; Barus, Henry; Schuldt, Bernhard

    2015-01-01

    For decades it has been assumed that the largest vessels are generally found in roots and that vessel size and corresponding sapwood area-specific hydraulic conductivity are acropetally decreasing toward the distal twigs. However, recent studies from the perhumid tropics revealed a hump-shaped vessel size distribution. Worldwide tropical perhumid forests are extensively replaced by agroforestry systems often using introduced species of various biogeographical and climatic origins. Nonetheless, it is unknown so far what kind of hydraulic architectural patterns are developed in those agroforestry tree species and which impact this exerts regarding important tree functional traits, such as stem growth, hydraulic efficiency and wood density (WD). We investigated wood anatomical and hydraulic properties of the root, stem and branch wood in Theobroma cacao and five common shade tree species in agroforestry systems on Sulawesi (Indonesia); three of these were strictly perhumid tree species, and the other three tree species are tolerating seasonal drought. The overall goal of our study was to relate these properties to stem growth and other tree functional traits such as foliar nitrogen content and sapwood to leaf area ratio. Our results confirmed a hump-shaped vessel size distribution in nearly all species. Drought-adapted species showed divergent patterns of hydraulic conductivity, vessel density, and relative vessel lumen area between root, stem and branch wood compared to wet forest species. Confirming findings from natural old-growth forests in the same region, WD showed no relationship to specific conductivity. Overall, aboveground growth performance was better predicted by specific hydraulic conductivity than by foliar traits and WD. Our study results suggest that future research on conceptual trade-offs of tree hydraulic architecture should consider biogeographical patterns underlining the importance of anatomical adaptation mechanisms to environment. PMID:25873922

  9. Impact on offspring methylation patterns of maternal gestational diabetes mellitus and intrauterine growth restraint suggest common genes and pathways linked to subsequent type 2 diabetes risk.

    PubMed

    Quilter, Claire R; Cooper, Wendy N; Cliffe, Kerry M; Skinner, Benjamin M; Prentice, Philippa M; Nelson, LaTasha; Bauer, Julien; Ong, Ken K; Constância, Miguel; Lowe, William L; Affara, Nabeel A; Dunger, David B

    2014-11-01

    Size at birth, postnatal weight gain, and adult risk for type 2 diabetes may reflect environmental exposures during developmental plasticity and may be mediated by epigenetics. Both low birth weight (BW), as a marker of fetal growth restraint, and high birth weight (BW), especially after gestational diabetes mellitus (GDM), have been linked to increased risk of adult type 2 diabetes. We assessed DNA methylation patterns using a bead chip in cord blood samples from infants of mothers with GDM (group 1) and infants with prenatal growth restraint indicated by rapid postnatal catch-up growth (group 2), compared with infants with normal postnatal growth (group 3). Seventy-five CpG loci were differentially methylated in groups 1 and 2 compared with the controls (group 3), representing 72 genes, many relevant to growth and diabetes. In replication studies using similar methodology, many of these differentially methylated regions were associated with levels of maternal glucose exposure below that defined by GDM [the Hyperglycemia and Adverse Pregnancy Outcome (HAPO) study] or were identified as changes observed after randomized periconceptional nutritional supplementation in a Gambian cohort characterized by maternal deprivation. These studies provide support for the concept that similar epigenetic modifications may underpin different prenatal exposures and potentially increase long-term risk for diseases such as type 2 diabetes. PMID:25145626

  10. Assessing the potential of amino acid δ13C patterns as a carbon source tracer in marine sediments: effects of algal growth conditions and sedimentary diagenesis

    NASA Astrophysics Data System (ADS)

    Larsen, T.; Bach, L. T.; Salvatteci, R.; Wang, Y. V.; Andersen, N.; Ventura, M.; McCarthy, M. D.

    2015-01-01

    Burial of organic carbon in marine sediments has a profound influence in marine biogeochemical cycles, and provides a sink for greenhouse gases such as CO2 and CH4. However, tracing organic carbon from primary production sources as well as its transformations in the sediment record remains challenging. Here we examine a novel but growing tool for tracing biosynthetic origin of amino acid carbon skeletons, based on natural occurring stable carbon isotope patterns in individual amino acids (δ13CAA). We focus on two important aspects for δ13CAA utility in sedimentary paleoarchives: first, the fidelity of source diagnostic of algal δ13CAA patterns across different oceanographic growth conditions; and second, the ability of δ13CAA patterns to record the degree of subsequent microbial amino acid synthesis after sedimentary burial. Using the marine diatom Thalassiosira weissflogii, we tested under controlled conditions how δ13CAA patterns respond to changing environmental conditions, including light, salinity, temperature, and pH. Our findings show that while differing oceanic growth conditions can change macromolecular cellular composition, δ13CAA isotopic patterns remain largely invariant. These results underscore that δ13CAA patterns should accurately record biosynthetic sources across widely disparate oceanographic conditions. We also explored how δ13CAA patterns change as a function of age, total nitrogen and organic carbon content after burial, in a marine sediment core from a coastal upwelling area off Peru. Based on the four most informative amino acids for distinguishing between diatom and bacterial sources (i.e. isoleucine, lysine, leucine and tyrosine), bacterial derived amino acids ranged from 10-15% in the sediment layers from the last 5000 years to 35% during the last glacial period. The larger bacterial fractions in older sediments indicate that bacterial activity and amino acid resynthesis progressed, approximately as a function of sediment age, to

  11. Wnt Signaling Interacts with Bmp and Edn1 to Regulate Dorsal-Ventral Patterning and Growth of the Craniofacial Skeleton

    PubMed Central

    Alexander, Courtney; Piloto, Sarah; Le Pabic, Pierre; Schilling, Thomas F.

    2014-01-01

    Craniofacial development requires signals from epithelia to pattern skeletogenic neural crest (NC) cells, such as the subdivision of each pharyngeal arch into distinct dorsal (D) and ventral (V) elements. Wnt signaling has been implicated in many aspects of NC and craniofacial development, but its roles in D-V arch patterning remain unclear. To address this we blocked Wnt signaling in zebrafish embryos in a temporally-controlled manner, using transgenics to overexpress a dominant negative Tcf3, (dntcf3), (Tg(hsp70I:tcf3-GFP), or the canonical Wnt inhibitor dickkopf1 (dkk1), (Tg(hsp70i:dkk1-GFP) after NC migration. In dntcf3 transgenics, NC cells in the ventral arches of heat-shocked embryos show reduced proliferation, expression of ventral patterning genes (hand2, dlx3b, dlx5a, msxe), and ventral cartilage differentiation (e.g. lower jaws). These D-V patterning defects resemble the phenotypes of zebrafish embryos lacking Bmp or Edn1 signaling, and overexpression of dntcf3 dramatically reduces expression of a subset of Bmp receptors in the arches. Addition of ectopic BMP (or EDN1) protein partially rescues ventral development and expression of dlx3b, dlx5a, and msxe in Wnt signaling-deficient embryos, but surprisingly does not rescue hand2 expression. Thus Wnt signaling provides ventralizing patterning cues to arch NC cells, in part through regulation of Bmp and Edn1 signaling, but independently regulates hand2. Similarly, heat-shocked dkk1+ embryos exhibit ventral arch reductions, but also have mandibular clefts at the ventral midline not seen in dntcf3+ embryos. Dkk1 is expressed in pharyngeal endoderm, and cell transplantation experiments reveal that dntcf3 must be overexpressed in pharyngeal endoderm to disrupt D-V arch patterning, suggesting that distinct endodermal roles for Wnts and Wnt antagonists pattern the developing skeleton. PMID:25058015

  12. Numerical modeling of the effects of water flow, sediment transport and vegetation growth on the spatiotemporal patterning of the ridge and slough landscape of the Everglades wetland

    NASA Astrophysics Data System (ADS)

    Lago, Marcelo E.; Miralles-Wilhelm, Fernando; Mahmoudi, Mehrnoosh; Engel, Vic

    2010-10-01

    A numerical model has been developed to simulate the spatiotemporal patterning of the ridge and slough landscape in wetlands, characterized by crests (ridges) and valleys (sloughs) that are elongated parallel to the direction of water flow. The model formulation consists of governing equations for integrated surface water and groundwater flow, sediment transport, and soil accretion, as well as litter production by vegetation growth. The model simulations show how the spatial pattern self-organizes over time with the generation of ridges and sloughs through sediment deposition and erosion driven by the water flow field. The spatial and temporal distributions of the water depth, flow rates and sediment transport processes are caused by differential flow due to vegetation and topography heterogeneities. The model was parameterized with values that are representative of the Everglades wetland in the southern portion of the Florida peninsula in the USA. Model simulation sensitivity was tested with respect to numerical grid size, lateral vegetation growth and the rate of litter production. The characteristic wavelengths of the pattern in the directions along and perpendicular to flow that are simulated with this model develop over time into ridge and slough shapes that resemble field observations. Also, the simulated elevation differences between the ridges and sloughs are of the same order of those typically found in the field. The width of ridges and sloughs was found to be controlled by a lateral vegetation growth distance parameter in a simplified formulation of vegetation growth, which complements earlier modeling results in which a differential peat accretion mechanism alone did not reproduce observations of ridge and slough lateral wavelengths. The results of this work suggest that ridge and slough patterning occurs as a result of vegetation's ability to grow laterally, enhancing sediment deposition in ridge areas, balanced by increased sediment erosion in slough

  13. Surface modification for patterned cell growth on substrates with pronounced topographies using sacrificial photoresist and parylene-C peel-off

    NASA Astrophysics Data System (ADS)

    Larramendy, Florian; Yoshida, Shotaro; Jalabert, Laurent; Takeuchi, Shoji; Paul, Oliver

    2016-09-01

    A range of methods including soft lithography are available for patterning protein layers for cell adhesion on quasi-planar substrates. Suitably structured, these layers favor the geometrically constrained, controlled growth of cells and the development of cellular extensions on them. For this purpose, the ability to control the shape and dimension of cell-adhesive areas with high precision is crucial. For more advanced studies of cell interactions, the surface modification or functionalization of substrates with complex topographies is desirable. This paper describes a simple technique allowing to produce surface modification patterns using delicate molecules such as laminin on substrates exhibiting pronounced topographies with recessed and protruding microstructures. The technique is based on the combination of sacrificial photoresist structures with a connected parylene-C layer. This layer locally adheres to the substrate wherever the substrate needs to be protected against the surface modification. After surface modification, the parylene-C layer is peeled off. Patterns comprising arbitrary networks of modified and unmodified substrate areas can thus be realized. We demonstrate the technique with the guided growth of neuron-like PC12 cells on networks of laminin lines on substrates structured with micropillars and microwells.

  14. Characterization of Growth and Reproduction Performance, Transgene Integration, Expression, and Transmission Patterns in Transgenic Pigs Produced by piggyBac Transposition-Mediated Gene Transfer.

    PubMed

    Zeng, Fang; Li, Zicong; Cai, Gengyuan; Gao, Wenchao; Jiang, Gelong; Liu, Dewu; Urschitz, Johann; Moisyadi, Stefan; Wu, Zhenfang

    2016-10-01

    Previously we successfully produced a group of EGFP-expressing founder transgenic pigs by a newly developed efficient and simple pig transgenesis method based on cytoplasmic injection of piggyBac plasmids. In this study, we investigated the growth and reproduction performance and characterized the transgene insertion, transmission, and expression patterns in transgenic pigs generated by piggyBac transposition. Results showed that transgene has no injurious effect on the growth and reproduction of transgenic pigs. Multiple copies of monogenic EGFP transgene were inserted at noncoding sequences of host genome, and passed from founder transgenic pigs to their transgenic offspring in segregation or linkage manner. The EGFP transgene was ubiquitously expressed in transgenic pigs, and its expression intensity was associated with transgene copy number but not related to its promoter DNA methylation level. To the best of our knowledge, this is first study that fully described the growth and reproduction performance, transgene insertion, expression, and transmission profiles in transgenic pigs produced by piggyBac system. It not only demonstrates that piggyBac transposition-mediated gene transfer is an effective and favorable approach for pig transgenesis, but also provides scientific information for understanding the transgene insertion, expression and transmission patterns in transgenic animals produced by piggyBac transposition. PMID:27565868

  15. Analysis of environmental factors influencing salinity patterns, oyster growth, and mortality in lower Breton Sound Estuary, Louisiana using 20 years of data

    USGS Publications Warehouse

    LaPeyre, Megan K.; Geaghan, James; Decossas, Gary A.; La Peyre, Jerome F.

    2016-01-01

    Freshwater inflow characteristics define estuarine functioning by delivering nutrients, sediments, and freshwater, which affect biological resources and ultimately system production. Using 20 years of water quality, weather, and oyster growth and mortality data from Breton Sound Estuary (BSE), Louisiana, we examined the relationship of riverine, weather, and tidal influence on estuarine salinity, and the relationship of salinity to oyster growth and mortality. Mississippi River discharge was found to be the most important factor determining salinity patterns over oyster grounds within lower portions of BSE, with increased river flow associated with lowered salinities, while easterly winds associated with increased salinity were less influential. These patterns were consistent throughout the year. Salinity and temperature (season) were found to critically control oyster growth and mortality, suggesting that seasonal changes to river discharge affecting water quality over the oyster grounds have profound impacts on oyster populations. The management of oyster reefs in estuaries (such as BSE) requires an understanding of how estuarine hydrodynamics and salinity are influenced by forcing factors such as winds, river flow, and by the volume, timing, and location of controlled releases of riverine water.

  16. ZnO nanowire array growth on precisely controlled patterns of inkjet-printed zinc acetate at low-temperatures.

    PubMed

    Tsangarides, Constantinos P; Ma, Hanbin; Nathan, Arokia

    2016-06-01

    ZnO nanowires have been fabricated through the hydrothermal method on inkjet-printed patterns of zinc acetate dihydrate. The silicon substrate used was heated accordingly during the printing period in order to maintain good spatial uniformity of the zinc acetate nanoparticles, responsible for the pattern morphology. Printing more than one pass of precursor ink leads to an increase in seed layer thickness that subsequently alters the density and dimensions of nanowires. It has been demonstrated that with the right inkjet-printing parameters and substrate temperature, ZnO nanowires can be effortlessly fabricated in accordance with the desired pattern variations under low temperature and mild conditions that ensures promising applications in optoelectronic devices. PMID:27223061

  17. Preliminary comparison of the Essie and PubMed search engines for answering clinical questions using MD on Tap, a PDA-based program for accessing biomedical literature.

    PubMed

    Sutton, Victoria R; Hauser, Susan E

    2005-01-01

    MD on Tap, a PDA application that searches and retrieves biomedical literature, is specifically designed for use by mobile healthcare professionals. With the goal of improving the usability of the application, a preliminary comparison was made of two search engines (PubMed and Essie) to determine which provided most efficient path to the desired clinically-relevant information. PMID:16779415

  18. Preliminary comparison of the Essie and PubMed search engines for answering clinical questions using MD on Tap, a PDA-based program for accessing biomedical literature

    PubMed Central

    Sutton, Victoria R.; Hauser, Susan E.

    2005-01-01

    MD on Tap, a PDA application that searches and retrieves biomedical literature, is specifically designed for use by mobile healthcare professionals. With the goal of improving the usability of the application, a preliminary comparison was made of two search engines (PubMed and Essie) to determine which provided most efficient path to the desired clinically-relevant information. PMID:16779415

  19. Selective Growth of CdTe on Nano-patterned CdS via Close-Space Sublimation

    NASA Astrophysics Data System (ADS)

    Aguirre, Brandon A.; Zubia, David; Ordonez, Rafael; Anwar, Farhana; Prieto, Heber; Sanchez, Carlos A.; Salazar, Maria T.; Pimentel, Alejandro. A.; Michael, Joseph R.; Zhou, Xiaowang; Mcclure, John C.; Nielson, Gregory N.; Cruz-Campa, Jose L.

    2014-07-01

    Selective-area deposition of CdTe on CdS via close-space sublimation is used to study the effect of window size (2 μm and 300 nm) on grain growth. The basic fabrication procedures for each of the layers (CdS, SiO2, and CdTe) and for achieving selective-area growth are presented. Selective-area growth of both micro- and nano-scale CdTe islands on CdS substrates using close-spaced sublimation is demonstrated. Scanning electron microscopy and electron backscatter diffraction microstructure analysis show that the micro-scale CdTe islands remain polycrystalline. However, when the island size is reduced to 300 nm, single crystal CdTe can be achieved within the windows. The CdTe grains were most often in the (101) orientation for both the micro- and nano-sized CdTe islands.

  20. Effect of differential subsidence in growth-faulted regions on E-log patterns and preservation potential

    SciTech Connect

    Edwards, M.B.

    1985-02-01

    Detailed electric log correlation, supplemented by cores, in the Eocene Wilcox Group and the Oligocene Frio Formation of the Texas Gulf basin contradicts a commonly held notion that changes in log character across growth faults exclusively reflect changes in environment. An invariable consequence of growth faulting is thickening of a depositional unit in the downthrown block, reflecting a greater subsidence rate. The growth ratio (downthrown or upthrown) varies from just over 1:1 to as much as 10:1. Analysis and mapping of log character indicate that the basic unit of both deposition and physical correlation is regressive coarsening-upward sequences. In Wilcox deltas, prodelta shales pass up into delta-front sandstones while in Frio barrier-bar or standplains, shelf and lower-shoreface deposits pass up into upper-shoreface sandstones. Regressive packages grade downdip in environment from delta plain and bay or lagoon to offshore marine. Growth faults had no significant surface expression and did not separate contrasting environments. A marked change in log character (e.g., from smooth to serrated) across a growth fault in a regressive shoreface sequence appears to indicate that the subsidence rate of the downthrown block exceeded a threshold value, enabling preservation of low-energy muddy layers and possibly episodic waning-flow storm deposits that were largely destroyed by fair-weather wave reworking on the upthrown block. This concept has implications both to regional stratigraphy and reservoir properties. Correlative units can abruptly change log character across growth faults, impeding correlation. Sandstones in the downthrown block may contain shale barriers to vertical fluid flow if the threshold subsidence rate was exceeded.

  1. Growth Patterns of Clostridium difficile - Correlations with Strains, Binary Toxin and Disease Severity: A Prospective Cohort Study.

    PubMed

    Tschudin-Sutter, Sarah; Braissant, Olivier; Erb, Stefan; Stranden, Anne; Bonkat, Gernot; Frei, Reno; Widmer, Andreas F

    2016-01-01

    A broad spectrum of symptoms has been associated with C. difficile infection (CDI). Several studies indicate that toxin-production correlates with growth rates of C. difficile. This study aimed to correlate growth rates of C. difficile with disease severity and strain characteristics. From 01/2003 to 10/2011, strains from a prospective cohort of all inpatients with CDI at the University Hospital Basel, Switzerland were analyzed regarding binary toxin, presence of the tcdC deletion and ribotype. Isothermal microcalorimetry was performed to determine growth rates, quantified by the Gompertz function. Ordered logistic regression models were used to correlate disease severity with strain features and clinical characteristics. Among 199 patients, 31 (16%) were infected with binary toxin-producing strains, of which the tcdC gene-deletion nt117 was detected in 9 (4%). Disease severity was classified as mild in 130 patients (65.3%), as severe in 59 patients (29.7%) and as severe/complicated in 10 patients (5.0%). Growth rates were inversely associated with disease severity in univariable (OR 0.514, 95%CI 0.29-0.91, p = 0.023) and multivariable analyses (OR 0.51, 95%CI 0.26-0.97, p = 0.040). While none of the strain characteristics such as presence of the tcdC gene deletion or binary toxin predicted CDI severity, growth rates were inversely correlated with disease severity. Further investigations are needed to analyze growth-regulators and respective correlations with the level of toxin production in C. difficile, which may be important determinants of disease severity. PMID:27598309

  2. Physiological controls of large‐scale patterning in planarian regeneration: a molecular and computational perspective on growth and form

    PubMed Central

    Durant, Fallon; Lobo, Daniel; Hammelman, Jennifer

    2016-01-01

    Abstract Planaria are complex metazoans that repair damage to their bodies and cease remodeling when a correct anatomy has been achieved. This model system offers a unique opportunity to understand how large‐scale anatomical homeostasis emerges from the activities of individual cells. Much progress has been made on the molecular genetics of stem cell activity in planaria. However, recent data also indicate that the global pattern is regulated by physiological circuits composed of ionic and neurotransmitter signaling. Here, we overview the multi‐scale problem of understanding pattern regulation in planaria, with specific focus on bioelectric signaling via ion channels and gap junctions (electrical synapses), and computational efforts to extract explanatory models from functional and molecular data on regeneration. We present a perspective that interprets results in this fascinating field using concepts from dynamical systems theory and computational neuroscience. Serving as a tractable nexus between genetic, physiological, and computational approaches to pattern regulation, planarian pattern homeostasis harbors many deep insights for regenerative medicine, evolutionary biology, and engineering. PMID:27499881

  3. A Facile Route for Patterned Growth of Metal-Insulator Carbon Lateral Junction through One-Pot Synthesis.

    PubMed

    Park, Beomjin; Park, Jaesung; Son, Jin Gyeong; Kim, Yong-Jin; Yu, Seong Uk; Park, Hyo Ju; Chae, Dong-Hun; Byun, Jinseok; Jeon, Gumhye; Huh, Sung; Lee, Seoung-Ki; Mishchenko, Artem; Hyun, Seung; Lee, Tae Geol; Han, Sang Woo; Ahn, Jong-Hyun; Lee, Zonghoon; Hwang, Chanyong; Novoselov, Konstantin S; Kim, Kwang S; Hong, Byung Hee; Kim, Jin Kon

    2015-08-25

    Precise graphene patterning is of critical importance for tailor-made and sophisticated two-dimensional nanoelectronic and optical devices. However, graphene-based heterostructures have been grown by delicate multistep chemical vapor deposition methods, limiting preparation of versatile heterostructures. Here, we report one-pot synthesis of graphene/amorphous carbon (a-C) heterostructures from a solid source of polystyrene via selective photo-cross-linking process. Graphene is successfully grown from neat polystyrene regions, while patterned cross-linked polystyrene regions turn into a-C because of a large difference in their thermal stability. Since the electrical resistance of a-C is at least 2 orders of magnitude higher than that for graphene, the charge transport in graphene/a-C heterostructure occurs through the graphene region. Measurement of the quantum Hall effect in graphene/a-C lateral heterostructures clearly confirms the reliable quality of graphene and well-defined graphene/a-C interface. The direct synthesis of patterned graphene from polymer pattern could be further exploited to prepare versatile heterostructures. PMID:26144549

  4. Physiological controls of large-scale patterning in planarian regeneration: a molecular and computational perspective on growth and form.

    PubMed

    Durant, Fallon; Lobo, Daniel; Hammelman, Jennifer; Levin, Michael

    2016-04-01

    Planaria are complex metazoans that repair damage to their bodies and cease remodeling when a correct anatomy has been achieved. This model system offers a unique opportunity to understand how large-scale anatomical homeostasis emerges from the activities of individual cells. Much progress has been made on the molecular genetics of stem cell activity in planaria. However, recent data also indicate that the global pattern is regulated by physiological circuits composed of ionic and neurotransmitter signaling. Here, we overview the multi-scale problem of understanding pattern regulation in planaria, with specific focus on bioelectric signaling via ion channels and gap junctions (electrical synapses), and computational efforts to extract explanatory models from functional and molecular data on regeneration. We present a perspective that interprets results in this fascinating field using concepts from dynamical systems theory and computational neuroscience. Serving as a tractable nexus between genetic, physiological, and computational approaches to pattern regulation, planarian pattern homeostasis harbors many deep insights for regenerative medicine, evolutionary biology, and engineering. PMID:27499881

  5. Sensitivity of growth and biomass allocation patterns to increasing nitrogen: a comparison between ephemerals and annuals in the Gurbantunggut Desert, north-western China

    PubMed Central

    Zhou, Xiaobing; Zhang, Yuanming; Niklas, Karl J.

    2014-01-01

    Background and Aims Biomass accumulation and allocation patterns are critical to quantifying ecosystem dynamics. However, these patterns differ among species, and they can change in response to nutrient availability even among genetically related individuals. In order to understand this complexity further, this study examined three ephemeral species (with very short vegetative growth periods) and three annual species (with significantly longer vegetative growth periods) in the Gurbantunggut Desert, north-western China, to determine their responses to different nitrogen (N) supplements under natural conditions. Methods Nitrogen was added to the soil at rates of 0, 0·5, 1·0, 3·0, 6·0 and 24·0 g N m−2 year−1. Plants were sampled at various intervals to measure relative growth rate and shoot and root dry mass. Key Results Compared with annuals, ephemerals grew more rapidly, increased shoot and root biomass with increasing N application rates and significantly decreased root/shoot ratios. Nevertheless, changes in the biomass allocation of some species (i.e. Erodium oxyrrhynchum) in response to the N treatment were largely a consequence of changes in overall plant size, which was inconsistent with an optimal partitioning model. An isometric log shoot vs. log root scaling relationship for the final biomass harvest was observed for each species and all annuals, while pooled data of three ephemerals showed an allometric scaling relationship. Conclusions These results indicate that ephemerals and annuals differ observably in their biomass allocation patterns in response to soil N supplements, although an isometric log shoot vs. log root scaling relationship was maintained across all species. These findings highlight that different life history strategies behave differently in response to N application even when interspecific scaling relationships remain nearly isometric. PMID:24287812

  6. Effect of insect growth regulators on protein pattern of dermatophagoides farinae and its validity on inducing human alleregens.

    PubMed

    Mazyad, Said A M; Mohammad, Khairy A

    2006-12-01

    Two insect growth regulators, Methorprene and Hydroprene were evaluated as growth hormones on the common house dust mite; Dermatophagoides farinae. The adults and immature stages were treated with 4 concentrations of each regulator as contact and as diet. The data were recorded 30 & 90 days post-exposure. Both compounds significantly suppressed population growth, as compared to > or = 5% acetone controls. Methoprene was more effective than Hydroprene when given in diet by corporation bioassays but, slightly more effective for the 1st 30 days of the contact assays. A second set of contact and diet-incorporation assays was done using a 75% of Methoprene and Hydroprene to determine efficacy on D. farinae population dynamics, at weekly intervals for 13 weeks. The average number of the mites in the untreated control population was increased by more than 10 times than the original ones. On the other hand, the number of treated mites was not significantly increased. This was similar for both the contact and the diet-incorporation bioassays, although the average number of mites/container was significantly higher when the treatment was incorporated in the house dust mite diet than when applied directly as contact. Consequently, the insect growth regulators minimized the allergic efficacy of D. farinae in experimental exposed mice. PMID:17153716

  7. Seasonal patterns in above ground growth and nut abortion in young eastern black walnut trees in Midwestern United States

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Eastern black walnut (EBW) is an excellent choice for agroforestry practices in the eastern United States because of its value for nuts and timber. There appears to be competing sinks for photosynthate in young trees early in the growing season; however growth data to support such a hypothesis are l...

  8. PATTERNS OF NITROGEN AND CARBON STABLE ISOTOPE RATIOS IN MACROFUNGI, PLANTS AND SOILS IN TWO OLD-GROWTH CONIFER FORESTS

    EPA Science Inventory

    Natural abundance stable isotope ratios represent a potentially valuable tool for studying fungal ecology. We measured 15N and 13C in ectomycorrhizal and saprotrophic macrofungi from two old-growth conifer forests, and in plants, woody debris, and soils. Fungi, plants, and so...

  9. Patterns of U.S. Economic Growth. 1980 Projections of Final Demand, Interindustry Relationships, Output, Productivity, and Employment.

    ERIC Educational Resources Information Center

    Bureau of Labor Statistics (DOL), Washington, DC.

    This report projects employment by industry for 1980, in order to provide a framework for an occupational outlook program. Included are detailed projections of the labor force, aggregate and industry demand, output, employment, and occupational projections. A 4.3 percent growth rate is projected for gross national product, reflecting an increased…

  10. Cluster analyses of 20th century growth patterns in high elevation Great Basin bristlecone pine in the Snake Mountain Range, Nevada, USA

    NASA Astrophysics Data System (ADS)

    Tran, T. J.; Bruening, J. M.; Bunn, A. G.; Salzer, M. W.; Weiss, S. B.

    2015-12-01

    Great Basin bristlecone pine (Pinus longaeva) is a useful climate proxy because of the species' long lifespan (up to 5000 years) and the climatic sensitivity of its annually-resolved rings. Past studies have shown that growth of individual trees can be limited by temperature, soil moisture, or a combination of the two depending on biophysical setting at the scale of tens of meters. We extend recent research suggesting that trees vary in their growth response depending on their position on the landscape to analyze how growth patterns vary over time. We used hierarchical cluster analysis to examine the growth of 52 bristlecone pine trees near the treeline of Mount Washington, Nevada, USA. We classified growth of individual trees over the instrumental climate record into one of two possible scenarios: trees belonging to a temperature-sensitive cluster and trees belonging to a precipitation-sensitive cluster. The number of trees in the precipitation-sensitive cluster outnumbered the number of trees in the temperature-sensitive cluster, with trees in colder locations belonging to the temperature-sensitive cluster. When we separated the temporal range into two sections (1895-1949 and 1950-2002) spanning the length of the instrumental climate record, we found that most of the 52 trees remained loyal to their cluster membership (e.g., trees in the temperature-sensitive cluster in 1895-1949 were also in the temperature sensitive cluster in 1950-2002), though not without exception. Of those trees that do not remain consistent in cluster membership, the majority changed from temperature-sensitive to precipitation-sensitive as time progressed. This could signal a switch from temperature limitation to water limitation with warming climate. We speculate that topographic complexity in high mountain environments like Mount Washington might allow for climate refugia where growth response could remain constant over the Holocene.

  11. Does the silver moss Bryum argenteum exhibit sex-specific patterns in vegetative growth rate, asexual fitness or prezygotic reproductive investment?

    PubMed Central

    Horsley, Kimberly; Stark, Lloyd R.; McLetchie, D. Nicholas

    2011-01-01

    Background and Aims Expected life history trade-offs associated with sex differences in reproductive investment are often undetected in seed plants, with the difficulty arising from logistical issues of conducting controlled experiments. By controlling genotype, age and resource status of individuals, a bryophyte was assessed for sex-specific and location-specific patterns of vegetative, asexual and sexual growth/reproduction across a regional scale. Methods Twelve genotypes (six male, six female) of the dioecious bryophyte Bryum argenteum were subcultured to remove environmental effects, regenerated asexually to replicate each genotype 16 times, and grown over a period of 92 d. Plants were assessed for growth rates, asexual and sexual reproductive traits, and allocation to above- and below-ground regenerative biomass. Key Results The degree of sexual versus asexual reproductive investment appears to be under genetic control, with three distinct ecotypes found in this study. Protonemal growth rate was positively correlated with asexual reproduction and sexual reproduction, whereas asexual reproduction was negatively correlated (appeared to trade-off) with vegetative growth (shoot production). No sex-specific trade-offs were detected. Female sex-expressing shoots were longer than males, but the sexes did not differ in growth traits, asexual traits, sexual induction times, or above- and below-ground biomass. Males, however, had much higher rates of inflorescence production than females, which translated into a significantly higher (24x) prezygotic investment for males relative to females. Conclusions Evidence for three distinct ecotypes is presented for a bryophyte based on regeneration traits. Prior to zygote production, the sexes of this bryophyte did not differ in vegetative growth traits but significantly differed in reproductive investment, with the latter differences potentially implicated in the strongly biased female sex ratio. The disparity between males and

  12. A rodent model of low- to moderate-dose ethanol consumption during pregnancy: patterns of ethanol consumption and effects on fetal and offspring growth.

    PubMed

    Probyn, Megan E; Zanini, Simone; Ward, Leigh C; Bertram, John F; Moritz, Karen M

    2012-01-01

    It is unknown whether low to moderate maternal alcohol consumption adversely affects postnatal health. The aim of the present study was to develop a rodent model of low-moderate-dose prenatal ethanol (EtOH) exposure. Sprague-Dawley rats were fed a liquid diet with or without 6% v/v EtOH throughout gestation and the pattern of dietary consumption determined. Fetal bodyweights and hepatic alcohol-metabolising gene expression were measured on embryonic Day (E) 20 and offspring growth studied until 1 year. At E8 the plasma EtOH concentration was 0.03%. There was little difference in dietary consumption between the two treatment groups. At E20, EtOH-exposed fetuses were significantly lighter than controls and had significantly decreased ADH4 and increased CYP2E1 gene expression. Offspring killed on postnatal Day (PN) 30 did not exhibit any growth deficits. Longitudinal repeated measures of offspring growth demonstrated slower growth in males from EtOH-fed dams between 7 and 12 months of age; a cohort of male pups killed at 8 months of age had a reduced crown-rump length and kidney weight. In conclusion, a liquid diet of 6% v/v EtOH fed to pregnant dams throughout gestation caused a 3-8% reduction in fetal growth and brain sparing, with growth differences observed in male offspring later in life. This model will be useful for future studies on the effects of low-moderate EtOH on the developmental origins of health and disease. PMID:22781937

  13. Pattern and dynamics of biomass stock in old growth forests: The role of habitat and tree size

    NASA Astrophysics Data System (ADS)

    Yuan, Zuoqiang; Gazol, Antonio; Wang, Xugao; Lin, Fei; Ye, Ji; Zhang, Zhaochen; Suo, YanYan; Kuang, Xu; Wang, Yunyun; Jia, Shihong; Hao, Zhanqing

    2016-08-01

    Forest ecosystems play a fundamental role in the global carbon cycle. However, how stand-level changes in tree age and structure influence biomass stock and dynamics in old-growth forests is a question that remains unclear. In this study, we quantified the aboveground biomass (AGB) standing stock, the coarse woody productivity (CWP), and the change in biomass over ten years (2004-2014) in a 25 ha unmanaged broad-leaved Korean pine mixed forest in northeastern China. In addition, we quantified how AGB stock and change (tree growth, recruitment and mortality) estimations are influenced by the variation in habitat heterogeneity, tree size structure and subplot size. Our analysis indicated that Changbai forest had AGB of 265.4 Mg ha-1 in 2004, and gained1.36 Mg ha-1 y-1 between 2004 and 2014. Despite recruitment having better performance in nutrient rich habitat, we found that there is a directional tree growth trend independent of habitat heterogeneity for available nutrients in this old growth forest. The observed increases in AGB stock (∼70%) are mainly attributed to the growth of intermed