Finding the Center of Mass of a Soft Spring

This article shows how to use calculus to find the center of mass position of a soft cylindrical helical spring that is suspended vertically. The spring is non-uniformly stretched by the action of gravity. A general expression for the vertical position of the center of mass is obtained.Comment: LaTeX, 7 pages, 2 figures. Minor changes to agree with published versio

Comparative genomics-based investigation of resequencing targets in Vibrio fischeri: Focus on point miscalls and artefactual expansions

<p>Abstract</p> <p>Background</p> <p>Sequence closure often represents the end-point of a genome project, without a system in place for subsequent improvement and refinement. Building on the genome project of <it>Vibrio fischeri </it>ES114, we used a comparative approach to identify and investigate genes that had a high likelihood of sequence error.</p> <p>Results</p> <p>Comparison of the <it>V. fischeri </it>ES114 genome with that of conspecific strain MJ11 identified 82 target loci in ES114 as containing likely errors, and thus of high-priority for resequencing. Analysis of the targets identified 75 loci in which an error had occurred, resulting in the correction of 10,457 base pairs to generate the new ES114 genomic sequence. A majority of the inaccurate loci involved frameshift errors, correction of which fused adjacent ORFs. Although insertions/deletions are thought to be rare in microbial genome assemblies, fourteen of the loci contained extraneous sequence of over 300 bp, likely due to imperfect contig ends that were misassembled in tandem rather than as overlapping segments. Additionally we updated the entire genome annotation with 113 new features including previously uncalled protein-coding genes, regulatory RNA genes and operon leader peptides, and we analyzed the transcriptional apparatus encoded by ES114.</p> <p>Conclusion</p> <p>We demonstrate that errors in microbial genome sequences, thought to largely be confined to point mutations, may also consist of other prevalent large-scale rearrangements such as insertions. Ongoing genome quality control and annotation programs are necessary to accompany technological advancements in data generation. These updates further advance <it>V. fischeri </it>as an important model for understanding intercellular communication and colonization of animal tissue.</p

Spatiotemporal determinants of seasonal gleaning

1. Many coastal communities depend on ecosystems for goods and services that contribute to human well-being. As long-standing interactions between people and nature are modified by global environmental change, dynamic and diversified livelihood strategies that enable seasonal adaptation will be critical for vulnerable coastal communities. However, the success of such strategies depends on a range of poorly understood influences. 2. Gleaning, the hand-based collection of marine organisms from littoral habitats, provides an interesting case study of dynamic change in social-ecological interac- tions. It is an important coastal livelihood strategy, yet seasonal gleaning dynamics have not been empirically explored in contemporary communities. We examined seasonal gleaning in eight coastal communities on Atauro Island, Timor-Leste, using household surveys and satellite-derived maps of shallow-water benthic habitats. Our analysis explored the factors affecting household decisions to glean in each season, the relationship between gleaning and seafood consumption, and seasonal gleaning pressure on near-shore coastal resources. 3. Dynamic marine harvesting strategies differed among households and gleaning activity was seasonally heterogeneous. Not all gleaning households gleaned dur- ing the season characterised by rough sea conditions despite rough season glean- ing being associated with greater seafood consumption stability among seasons. Households also gleaned less regularly, and catches were smaller, in the rough season. 4. Differences in seasonal participation in gleaning were explained mostly by type and extent of shallow habitat proximate to a community. In the calm season, household gleaning was positively related to the total area of shallow habitat, and in the rough season the percentage of hard-bottom shallow habitat was also an important predictor of gleaning activity. 5.Our findings illustrate how changes in the biophysical environment mediate human–nature interactions at fine scales through time and space. Consequently, this research highlights the importance of context-specific perspectives for under- standing drivers and dynamics in fishing pressure on littoral ecosystems, access to ecosystem benefits and limits to adaptation. Factors influencing when livelihood activities are feasible and desirable are important for evaluating the social impacts of climate change, particularly in the context of rural communities in the Global South

Science and Film-making

The essay reviews the literature, mostly historical, on the relationship between science and film-making, with a focus on the science documentary. It then discusses the circumstances of the emergence of the wildlife making-of documentary genre. The thesis examined here is that since the early days of cinema, film-making has evolved from being subordinate to science, to being an equal partner in the production of knowledge, controlled by non-scientists

Variant O89 O-Antigen of E. coli Is Associated With Group 1 Capsule Loci and Multidrug Resistance

<p>Bacterial surface polysaccharides play significant roles in fitness and virulence. In Gram-negative bacteria such as Escherichia coli, major surface polysaccharides are lipopolysaccharide (LPS) and capsule, representing O- and K-antigens, respectively. There are multiple combinations of O:K types, many of which are well-characterized and can be related to ecotype or pathotype. In this investigation, we have identified a novel O:K permutation resulting through a process of major genome reorganization in a clade of E. coli. A multidrug-resistant, extended-spectrum β-lactamase (ESBL)-producing strain – E. coli 26561 – represented a prototype of strains combining a locus variant of O89 and group 1 capsular polysaccharide. Specifically, the variant O89 locus in this strain was truncated at gnd, flanked by insertion sequences and located between nfsB and ybdK and we apply the term O89m for this variant. The prototype lacked colanic acid and O-antigen loci between yegH and hisI with this tandem polysaccharide locus being replaced with a group 1 capsule (G1C) which, rather than being a recognized E. coli capsule type, this locus matched to Klebsiella K10 capsule type. A genomic survey identified more than 200 E. coli strains which possessed the O89m locus variant with one of a variety of G1C types. Isolates from our collection with the combination of O89m and G1C all displayed a mucoid phenotype and E. coli 26561 was unusual in exhibiting a mucoviscous phenotype more recognized as a characteristic among Klebsiella strains. Despite the locus truncation and novel location, all O89m:G1C strains examined showed a ladder pattern typifying smooth LPS and also showed high molecular weight, alcian blue-staining polysaccharide in cellular and/or extra-cellular fractions. Expression of both O-antigen and capsule biosynthesis loci were confirmed in prototype strain 26561 through quantitative proteome analysis. Further in silico exploration of more than 200 E. coli strains possessing the O89m:G1C combination identified a very high prevalence of multidrug resistance (MDR) – 85% possessed resistance to three or more antibiotic classes and a high proportion (58%) of these carried ESBL and/or carbapenemase. The increasing isolation of O89m:G1C isolates from extra-intestinal infection sites suggests that these represents an emergent clade of invasive, MDR E. coli.</p

High-Dose Carmustine, Etoposide, and Cyclophosphamide Followed by Allogeneic Hematopoietic Cell Transplantation for Non-Hodgkin Lymphoma

AbstractAllogeneic hematopoietic cell transplantation (HCT) has been shown to be curative in a group of patients with aggressive non-Hodgkin lymphoma (NHL). A previous study has demonstrated equivalent outcomes with a conditioning regimen based on total body irradiation and another not based on total body irradiation with preparative therapy using cyclophosphamide, carmustine, and etoposide (CBV) in autologous HCT. We investigated the safety and efficacy of using CBV in an allogeneic setting. Patients were required to have relapsed or be at high risk for subsequent relapse of NHL. All patients had a fully HLA-matched sibling donor. Patients received carmustine (15 mg/kg), etoposide (60 mg/kg), and cyclophosphamide (100 mg/kg) on days −6, −4, and −2, respectively, followed by allogeneic HCT. All patients were treated with cyclosporine and methylprednisolone as prophylaxis for graft-versus-host disease (GVHD). Thirty-one patients (median age, 46 years) who were felt to be inappropriate candidates for autologous transplantation were enrolled. Each subject had a median of 3 previous chemotherapy regimens. All patients engrafted. Fifteen of 31 patients are alive. Median follow-up time was 11.5 months (range, .4-126). There were 8 deaths due to relapse. Nonrelapse mortality (n = 8) included infection (n = 3), GVHD (n = 2), diffuse alveolar hemorrhage (n = 1), veno-occlusive disease in the setting of concurrent acute GVHD of the liver (n = 1), and leukoencephalopathy (n = 1). Probabilities of event-free survival and overall survival were, respectively, 44% (95% confidence interval, 26%-62%) and 51% (33%-69%) at 1 year and 44% (26%-62%) and 47% (29%-65%) at 5 years. Probability of relapse was 33% (15%-51%) at 1 year and 5 years. Probability of nonrelapse mortality was 31% (13%-49%) at 1 year and 5 years. Incidences were 29% for acute GVHD and 39% for chronic GVHD. None of the 12 patients who developed chronic GVHD has disease recurrence. Patients who had required >3 previous chemotherapy regimens before HCT had an increased probability of relapse. CBV is an effective preparative regimen for patients with aggressive NHL who undergo allogeneic HCT

WormBase 2007

WormBase (www.wormbase.org) is the major publicly available database of information about Caenorhabditis elegans, an important system for basic biological and biomedical research. Derived from the initial ACeDB database of C. elegans genetic and sequence information, WormBase now includes the genomic, anatomical and functional information about C. elegans, other Caenorhabditis species and other nematodes. As such, it is a crucial resource not only for C. elegans biologists but the larger biomedical and bioinformatics communities. Coverage of core areas of C. elegans biology will allow the biomedical community to make full use of the results of intensive molecular genetic analysis and functional genomic studies of this organism. Improved search and display tools, wider cross-species comparisons and extended ontologies are some of the features that will help scientists extend their research and take advantage of other nematode species genome sequences

Calling time on Oronsay: revising settlement models around the mesolithic–neolithic transition in Western Scotland, new evidence from Port Lobh, Colonsay

For over 120 years, the shell middens of western Scotland and the series of open-air sites on Oronsay have been the focus of debate in European Mesolithic studies. This paper challenges the significance of Oronsay in light of results from the geophysical survey and test-excavation of a new limpet and periwinkle shell midden dated to the late 5th or start of the 4th millennium cal BC at Port Lobh, Colonsay that offers fresh evidence to re-evaluate critically the role of Oronsay and coastal resources in island settlement models ahead of the Mesolithic–Neolithic transition. Test excavations recovered a marine molluscan assemblage dominated by limpet and periwinkle shells together with crab, sea urchin, a fishbone assemblage composed mainly of Gadidae, some identifiable bird and mammal bone, carbonised macroplant remains, and pumice as well as a bipolar lithic assemblage and coarse stone implements. Novel seasonality studies of saithe otolith thin-sections suggest wintertime tidal fishing practices. At least two activity events may be discerned, dating from the late 5th millennium cal BC. The midden could represent a small number of rapidly deposited assemblages or maybe the result of stocastic events within a more extended timeframe. We argue that alternative research questions are needed to advance long-standing debates about seasonal inter island mobility versus island sedentism that look beyond Oronsay to better understand later Mesolithic occupation patterns and the formation and date of Oronsay middens. We propose alternative methodological strategies to aid identification of contemporaneous sites using geophysical techniques and lithic technological signatures