A statistical study of variation in the catch of plankton nets

Staternent of the Problern.----In a previous communication, Winsor and Walford (1936) analyzed the results of repeated vertical hauls of different types of plankton nets, making use of data available in the literature. They concluded that the observed results could be accounted for reasonably well on the assumptions that (a) the organisms were randomly distributed in the medium and (b) that the volume of medium effectively sampled varied from haul to haul. From this result it follows that as the total catch is increased (as by increasing the net size) the reliability of a population estimate is ultimately limited by variation in volume sampled; and that where such conditions hold, it is useless to attempt greater accuracy by increasing either the total catch or the fraction counted much beyond the point where 100 organisms of the kind in question are counted

The Tumor Suppressor HHEX Inhibits Axon Growth when Prematurely Expressed in Developing Central Nervous System Neurons

Neurons in the embryonic and peripheral nervoussystem respond to injury by activating transcriptional programs supportive of axon growth, ultimately resulting in functional recovery. In contrast, neurons in the adult central nervous system (CNS) possess a limited capacity to regenerate axons after injury, fundamentally constraining repair. Activating pro-regenerative gene expression in CNS neurons is a promising therapeutic approach, but progress is hampered by incomplete knowledge of the relevant transcription factors. An emerging hypothesis is that factors implicated in cellular growth and motility outside the nervous system may also control axon growth in neurons. We therefore tested sixty-nine transcription factors, previously identified as possessing tumor suppressive or oncogenic properties in non-neuronal cells, in assays of neurite outgrowth. This screen identified YAP1 and E2F1 as enhancers of neurite outgrowth, and PITX1, RBM14, ZBTB16, and HHEX as inhibitors. Follow-up experiments are focused on the tumor suppressor HHEX, one of the strongest growth inhibitors. HHEX is widely expressed in adult CNS neurons, including corticospinal tract neurons after spinal injury, but is present only in trace amounts in immature cortical neurons and adult peripheral neurons. HHEX overexpression in early postnatal cortical neurons reduced both initial axonogenesis and the rate of axon elongation, and domain deletion analysis strongly implicated transcriptional repression as the underlying mechanism. These findings suggest a role for HHEX in restricting axon growth in the developing CNS, and substantiate the hypothesis that previously identified oncogenes and tumor suppressors can play conserved roles in axon extension

The St. Lawrence polynya and the Bering shelf circulation : new observations and a model comparison

Author Posting. © American Geophysical Union, 2006. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 111 (2006): C09023, doi:10.1029/2005JC003268.Using 14 year-long instrumented moorings deployed south of St. Lawrence Island, along with oceanographic drifters, we investigate the circulation over the central Bering shelf and the role of polynyas in forming and disseminating saline waters over the shelf. We focus also on evaluating the Gawarkiewicz and Chapman [1995] model of eddy production within coastal polynyas. Principal results include: 1) The northern central shelf near-surface waters exhibit westward flow carrying low-salinity waters from the Alaskan coast in fall and early winter, with consequences for water mass formation and biological production. 2) Within the St. Lawrence polynya, the freshening effect of winter advection is about half as large as the salting effect of surface brine flux resulting from freezing. 3) Brine production over the Bering shelf occurs primarily offshore, rather than within coastal polynyas, even though ice production per unit area is much larger within the polynyas. 4) We find little evidence for the geostrophic flow adjustment predicted by recent polynya models. 5) In contrast to the theoretical prediction that dense water from the polynya is carried offshore by eddies, we find negligible cross-shelf eddy density fluxes within and surrounding the polynya and very low levels of eddy energy that decreased from fall to winter, even though dense water accumulated within the polynya and large cross-shore density gradients developed. 6) It is possible that dense polynya water was advected downstream of our array before appreciable eddy fluxes materialized.This work was supported by National Science Foundation grant OCE9730697 to the University of Alaska and grant OCE9730823 to the University of Washington. S. M. acknowledges the support of the National Science Foundation under OCE9811097 and of NASA under grant NNG04GM69G. The University of Hamburg contributions were funded by the Bundesminister für Bildung und Wissenschaft. Funding for the drifter deployment was made possible by the North Pacific Research Board, grant NPMRI T2130. Manuscript preparation was additionally supported by Office of Naval Research grants N00014-99-1-0345 and N00014-02-1-0305 to the University of Washington

Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes

Pseudomonas is a metabolically-diverse genus of bacteria known for its flexibility and leading free living to pathogenic lifestyles in a wide range of hosts. The Pseudomonas Genome Database (http://www.pseudomonas.com) integrates completely-sequenced Pseudomonas genome sequences and their annotations with genome-scale, high-precision computational predictions and manually curated annotation updates. The latest release implements an ability to view sequence polymorphisms in P. aeruginosa PAO1 versus other reference strains, incomplete genomes and single gene sequences. This aids analysis of phenotypic variation between closely related isolates and strains, as well as wider population genomics and evolutionary studies. The wide range of tools for comparing Pseudomonas annotations and sequences now includes a strain-specific access point for viewing high precision computational predictions including updated, more accurate, protein subcellular localization and genomic island predictions. Views link to genome-scale experimental data as well as comparative genomics analyses that incorporate robust genera-geared methods for predicting and clustering orthologs. These analyses can be exploited for identifying putative essential and core Pseudomonas genes or identifying large-scale evolutionary events. The Pseudomonas Genome Database aims to provide a continually updated, high quality source of genome annotations, specifically tailored for Pseudomonas researchers, but using an approach that may be implemented for other genera-level research communities

Pseudomonas Genome Database: facilitating user-friendly, comprehensive comparisons of microbial genomes

Pseudomonas aeruginosa is a well-studied opportunistic pathogen that is particularly known for its intrinsic antimicrobial resistance, diverse metabolic capacity, and its ability to cause life threatening infections in cystic fibrosis patients. The Pseudomonas Genome Database (http://www.pseudomonas.com) was originally developed as a resource for peer-reviewed, continually updated annotation for the Pseudomonas aeruginosa PAO1 reference strain genome. In order to facilitate cross-strain and cross-species genome comparisons with other Pseudomonas species of importance, we have now expanded the database capabilities to include all Pseudomonas species, and have developed or incorporated methods to facilitate high quality comparative genomics. The database contains robust assessment of orthologs, a novel ortholog clustering method, and incorporates five views of the data at the sequence and annotation levels (Gbrowse, Mauve and custom views) to facilitate genome comparisons. A choice of simple and more flexible user-friendly Boolean search features allows researchers to search and compare annotations or sequences within or between genomes. Other features include more accurate protein subcellular localization predictions and a user-friendly, Boolean searchable log file of updates for the reference strain PAO1. This database aims to continue to provide a high quality, annotated genome resource for the research community and is available under an open source license

Pressure Induced Topological Phase Transitions in Membranes

Some highly unusual features of a lipid-water liquid crystal are revealed by high pressure x-ray diffraction, light scattering and dilatometric studies of the lamellar (bilayer $L_{\alpha}$) to nonlamellar inverse hexagonal ($H_{II}$) phase transition. (i) The size of the unit cell of the $H_{II}$ phase increases with increasing pressure. (ii) The transition volume, $\Delta V_{bh}$, decreases and appears to vanish as the pressure is increased. (iii) The intensity of scattered light increases as $\Delta V_{bh}$ decreases. Data are presented which suggest that this increase is due to the formation of an intermediate cubic phase, as predicted by recent theoretical suggestions of the underlying universal phase sequence.Comment: 12 pages, typed using REVTEX 2.

Solid stress facilitates spheroid formation: potential involvement of hyaluronan

When neoplastic cells grow in confined spaces in vivo, they exert a finite force on the surrounding tissue resulting in the generation of solid stress. By growing multicellular spheroids in agarose gels of defined mechanical properties, we have recently shown that solid stress inhibits the growth of spheroids and that this growth-inhibiting stress ranges from 45 to 120 mmHg. Here we show that solid stress facilitates the formation of spheroids in the highly metastatic Dunning R3327 rat prostate carcinoma AT3.1 cells, which predominantly do not grow as spheroids in free suspension. The maximum size and the growth rate of the resulting spheroids decreased with increasing stress. Relieving solid stress by enzymatic digestion of gels resulted in gradual loss of spheroidal morphology in 8 days. In contrast, the low metastatic variant AT2.1 cells, which grow as spheroids in free suspension as well as in the gels, maintained their spheroidal morphology even after stress removal. Histological examination revealed that most cells in AT2.1 spheroids are in close apposition whereas a regular matrix separates the cells in the AT3.1 gel spheroids. Staining with the hyaluronan binding protein revealed that the matrix between AT3.1 cells in agarose contained hyaluronan, while AT3.1 cells had negligible or no hyaluronan when grown in free suspension. Hyaluronan was found to be present in both free suspensions and agarose gel spheroids of AT2.1. We suggest that cell–cell adhesion may be adequate for spheroid formation, whereas solid stress may be required to form spheroids when cell–matrix adhesion is predominant. These findings have significant implications for tumour growth, invasion and metastasis

Взаємозв’язок великих кондратьєвських циклів розвитку економіки і системних світових конфліктів

Однією з найважливіших проблем, що постала перед сучасною наукою у зв’язку із стрімким розгортанням глобальної економічної кризи, загостренням світових конфліктів, є вироблення науково обґрунтованих «метричних» експрес прогнозів розвитку суспільства на ближчу і далеку перспективу

Development of an inflammatory bowel disease (IBD) Patient‐Reported Experience Measure (PREM): A patient‐led consensus work and ‘think aloud’ study for a quality improvement programme

Background Patient-Reported Experience Measures (PREMs) are key in improving healthcare quality, but no PREM exists for inflammatory bowel disease (IBD). This study aimed to co-produce a PREM with IBD service users for IBD service evaluation and quality improvement programme. Methods A pool of 75 items was drawn from published survey instruments covering interactions with services and aspects of living with IBD. In Stage 1, during two workshops, eight expert service users reduced candidate items through a ranked-choice voting exercise and suggested further items. During Stage 2, 18 previously uninvolved people with IBD assessed the face and content validity of the candidate items in ‘Think Aloud’ interviews. During two final workshops (Stage 3), the expert service users removed, modified and added items based on the interview findings to produce a final version of the PREM. Results Stage 1 generated a draft working PREM mapped to the following four domains: Patient-Centred Care; Quality; Accessibility; Communication and Involvement. The PREM included a set of nine items created by the expert group which shifted the emphasis from ‘self-management’ to ‘living with IBD’. Stage 2 interviews showed that comprehension of the PREM was very good, although there were concerns about the wording, IBD-relevance and ambiguity of some items. During the final two workshops in Stage 3, the expert service users removed 7 items, modified 15 items and added seven new ones based on the interview findings, resulting in a 38-item PREM. Conclusions This study demonstrates how extensive service user involvement can inform PREM development. Patient or Public Contribution Patients were involved as active members of the research team and as research participants to co-produce and validate a PREM for IBD services. In Stage 1, eight expert service users (‘the expert group’) reduced candidate items for the PREM through a voting exercise and suggested new items. During Stage 2, 18 previously uninvolved people with IBD (the ‘think aloud’ participants) assessed the validity of the candidate items in ‘Think Aloud’ interviews as research participants. In Stage 3, the expert group removed, changed and added items based on the interview findings to produce a final version of the 38-item PREM. This study shows how service user involvement can meaningfully inform PREM development