bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of Pseudomonas aeruginosa fatty acid profiles in biofilms and batch planktonic cultures
Authors: Chao Jerry , Wolfaardt Gideon M. , Arts Michael T. 
Published: December 2010

The fatty acid composition of Pseudomonas aeruginosa PAO1 was compared between biofilm and batch planktonic cultures. Strain PAO1 biofilms were able to maintain a consistent fatty acid profile for up to 6 days, whereas strain PAO1 batch planktonic cultures showed a gradual loss of cis-monounsaturated fatty acids over 4 days. Biofilms exhibited a greater proportion of hydroxy fatty acids but a lower proportion of both cyclopropane fatty acids and saturated fatty acids (SAFAs). SAFAs with ≥16 carbons, in particular, decreased in biofilms when compared with that in batch planktonic cultures. A reduced proportion of SAFAs and a decline in overall fatty acid chain length indicate more fluidic biophysical properties for cell membranes of P. aeruginosa in biofilms. Separating the biofilms into 2 partitions and comparing their fatty acid compositions revealed additional trends that were not observed in the whole biofilm: the shear-nonremovable layer consistently showed greater proportions of hydroxy fatty acid than the bulk liquid + shear-removable portion of the biofilm. The shear-nonremovable portion demonstrated a relatively immediate decline in the proportion of monounsaturated fatty acids between days 2 and 4; which was offset by an increase in the proportion of cyclopropane fatty acids, specifically 19:0cyc(11,12). Simultaneously, the shear-removable portion of the biofilm showed an increase in the proportion of trans-monounsaturated fatty acids and cyclopropane fatty acids.
Differential forage use makes carrying capacity equivocal on ranges of Scandinavian moose (Alces alces)
Authors: Wam Hilde Karine , Hjeljord Olav , Solberg Erling Johan 
Published: December 2010

Availability of preferred forage is hypothesized to be positively related to demographic performance in selective ungulates. Comparing two regions with high density of moose ( Alces alces (L., 1758)) having contrasting demographic performance and different composition of available plant species, we show that such a positive relationship may not always apply. The high-performance region (HP) had an estimated 41% higher total availability of browse per capita than the low-performance region (LP), but the availability of preferred species did not differ between the two regions. Although birch (genus Betula L.) was the most abundant browse in both regions (comprising 66% and 50% of the shoot amount available per m2in HP and LP, respectively), it dominated the diet of moose only in HP (constituting, e.g., 69% of all trees browsed in summer compared with 22% in LP). Further research is needed to identify the cause of the seemingly suboptimal use of birch in LP. We also quantified factors that determine forage availability, of which recent logging clearly was the most important: it multiplied browse availability but also reduced coverage of bilberry ( Vaccinum myrtillus L.), an important forage plant. Our study shows that for selective ungulates, indices of carrying capacity based on forage availability may not apply uniformly across ranges.
Smart career advice; laptops as a classroom distraction
Authors: Rosenberger Jack , Robertson Judy 
Published: December 2010

http://cacm.acm.org/blogs/blog-cacm/94307

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Jack Rosenberger shares Patty Azzarello's life lessons about advancing in the workplace. Judy Robertson discusses students' in-class usage of laptops.
Engineering basic algorithms of an in-memory text search engine
Authors: Transier Frederik , Sanders Peter 
Published: December 2010

Inverted index data structures are the key to fast text search engines. We first investigate one of the predominant operation on inverted indexes, which asks for intersecting two sorted lists of document IDs of different lengths. We explore compression and performance of different inverted list data structures. In particular, we present
Lookup
, a new data structure that allows intersection in expected time linear in the smaller list.

Based on this result, we present the algorithmic core of a full text data base that allows fast Boolean queries, phrase queries, and document reporting using less space than the input text. The system uses a carefully choreographed combination of classical data compression techniques and inverted-index-based search data structures. Our experiments show that inverted indexes are preferable over purely suffix-array-based techniques for in-memory (English) text search engines.
A similar system is now running in practice in each core of the distributed data base engine TREX of SAP.
Extraction, characterization and utility of prototypical communication groups in the blogosphere
Authors: Choudhury Munmun De , Sundaram Hari , John Ajita , Seligmann Doree Duncan 
Published: December 2010

This article analyzes communication within a set of individuals to extract the representative prototypical groups and provides a novel framework to establish the utility of such groups. Corporations may want to identify representative groups (which are indicative of the overall communication set) because it is easier to track the prototypical groups rather than the entire set. This can be useful for advertising, identifying “hot” spots of resource consumption as well as in mining representative moods or temperature of a community. Our framework has three parts: extraction, characterization, and utility of prototypical groups. First, we extract groups by developing features representing communication dynamics of the individuals. Second, to characterize the overall communication set, we identify a subset of groups within the community as the prototypical groups. Third, we justify the utility of these prototypical groups by using them as predictors of related external phenomena; specifically, stock market movement of technology companies and political polls of Presidential candidates in the 2008 U.S. elections.
We have conducted extensive experiments on two popular blogs, Engadget and Huffington Post. We observe that the prototypical groups can predict stock market movement/political polls satisfactorily with mean error rate of 20.32%. Further, our method outperforms baseline methods based on alternative group extraction and prototypical group identification methods. We evaluate the quality of the extracted groups based on their conductance and coverage measures and develop metrics: predictivity and resilience to evaluate their ability to predict a related external time-series variable (stock market movement/political polls). This implies that communication dynamics of individuals are essential in extracting groups in a community, and the prototypical groups extracted by our method are meaningful in characterizing the overall communication sets.
Therapeutic Antibody Targeting of CD47 Eliminates Human Acute Lymphoblastic Leukemia
Authors: Chao Mark P. , Alizadeh Ash A. , Tang Chad , Jan Max , Weissman-Tsukamoto Rachel , Zhao Feifei , Park Christopher Y. , Weissman Irving L. , Majeti Ravindra 
Published: December 2010

AbstractAcute lymphoblastic leukemia (ALL) is the most common pediatric malignancy and constitutes 15% of adult leukemias. Although overall prognosis for pediatric ALL is favorable, high-risk pediatric patients and most adult patients have significantly worse outcomes. Multiagent chemotherapy is standard of care for both pediatric and adult ALL, but is associated with systemic toxicity and long-term side effects and is relatively ineffective against certain ALL subtypes. Recent efforts have focused on the development of targeted therapies for ALL including monoclonal antibodies. Here, we report the identification of CD47, a protein that inhibits phagocytosis, as an antibody target in standard and high-risk ALL. CD47 was found to be more highly expressed on a subset of human ALL patient samples compared with normal cell counterparts and to be an independent predictor of survival and disease refractoriness in several ALL patient cohorts. In addition, a blocking monoclonal antibody against CD47 enabled phagocytosis of ALL cells by macrophages in vitro and inhibited tumor engraftment in vivo. Significantly, anti-CD47 antibody eliminated ALL in the peripheral blood, bone marrow, spleen, and liver of mice engrafted with primary human ALL. These data provide preclinical support for the development of an anti-CD47 antibody therapy for treatment of human ALL. Cancer Res; 71(4); 1374–84. ©2010 AACR.
Serum Soluble Mesothelin Concentrations in Malignant Pleural Mesothelioma: Relationship to Tumor Volume, Clinical Stage and Changes in Tumor Burden
Authors: Creaney Jenette , Francis Roslyn J. , Dick Ian M. , Musk Arthur W. , Robinson Bruce W. S. , Byrne Michael J. , Nowak Anna K. 
Published: December 2010

Abstract
Purpose: To examine the clinical utility of soluble mesothelin in patients with malignant pleural mesothelioma.
Experimental Design: A total of 97 patients (female: 11; male: 86) were prospectively enrolled, longitudinal serum samples collected, and mesothelin concentrations determined. Baseline mesothelin levels were analyzed relative to tumor stage, presence of metastatic disease, the positron emission tomography (PET) parameters maximum standardized uptake value, tumor volume, total glycolytic volume, and survival. Changes in mesothelin level were correlated to objective response to chemotherapy, as assessed radiologically and by PET imaging, and with patient survival.
Results: Baseline mesothelin levels greater than 5 nmol/L were a significant negative prognostic indicator (HR = 2.25; 95% CI, 1.20–4.21) and correlated with tumor stage and volume. In 55 patients who received chemotherapy, change in mesothelin correlated with radiological response (χ2 = 11.32; P = 0.023) and change in metabolically active tumor volume (r = 0.58; P &lt; 0.01). Median survival for patients with a reduction in mesothelin following chemotherapy (19 months) was significantly longer than for patients with increased mesothelin (5 months; P &lt; 0.001).
Conclusion: These findings show the potential value of changes in mesothelin levels for prognostication and monitoring of treatment response in mesothelioma. Clin Cancer Res; 17(5); 1181–9. ©2010 AACR.
A Macroeconomic Structure of Employment: Rural-Urban Conflict in a Kaleckian Framework
Authors: Chakrabarti Saumya 
Published: December 2010

Faced with the phenomenon of “jobless growth” and to contain the vast “surplus population” the governments of the developing world have taken up measures to manage poverty and social security outside the sphere of accumulation-led growth in the “urban-modern” sector especially through “rural” employment generation. Many researchers criticize such policies, as government expenditure supporting accumulation and growth of the urban sector is thought to be competitive with government financed rural employment creation. However, my assertion is that there is no demand-driven trade-off between these urban and rural employment generations. In fact, I propose a supply-side trade-off. The generic “food-supply-constraint” creates this rural-urban conflict. To investigate this phenomenon, first a Kaleckian macroeconomic framework is constructed, with which I examine the role of the government and that of the “food sector” in supporting accumulation in the modern sector and thereby generating urban employment. Subsequently, the issue of rural employment creation with the help of food surplus and through direct government intervention is considered. Finally, we arrive at the issue of the rural-urban conflict: the conflict between the effects of government involvement in accumulation-led urban employment generation and of direct government intervention through “development management” administrating rural employment. However, I also propose a policy that could minimize such a contradiction. JEL classifications: O11, O18, O20, Q18
Casino Capitalism with Derivatives: Fragility and Instability in Contemporary Finance
Authors: McKenzie Rex A. 
Published: December 2010

This is a theoretical article exploring the relationship between financial fragility, derivative trading, and financial crisis. It synthesizes the work of Hyman Minsky (1977, 1985), Jan Toporowski (2001), and Dick Bryan and Michael Rafferty (2006). The decade immediately after 1971 is presented as a key period with key events that shaped a Wall Street revolution that now drives world capitalism. Balance sheet computations of expected profitability emerge as the main driver of a contemporary capitalism that is inherently more competitive than before. Debt, credit, and liquidity, therefore, play crucial parts in a world system where banks and corporations have been joined by new rentier institutions in riskier speculative business activities that now characterize the system. The conclusions are largely Keynesian “. . . when the capital development of a country becomes a by-product of the activities of a casino, the job is likely to be ill-done.” JEL classifications: G12, P1
A functional magnetic resonance proof of concept pilot trial of cognitive rehabilitation in multiple sclerosis
Authors: Sastre-Garriga J , Alonso J , Renom M , Arévalo MJ , González I , Galán I , Montalban X , Rovira A 
Published: December 2010

Background: Cognitive impairment is frequent in multiple sclerosis (MS) and lacks effective treatment. Cognitive rehabilitation is widely applied in neurorehabilitation settings. Functional magnetic resonance imaging (fMRI) may help in investigating changes in brain activity and provide a tool to assess the efficacy of rehabilitation. Aim: To investigate the effect on brain activity as measured by fMRI of a cognitive rehabilitation programme in patients with MS and cognitive impairment. Method: Fifteen patients with MS and cognitive impairment and five healthy subjects were recruited. Neuropsychological assessments were performed in patients with MS at study entry and after rehabilitation to assess cognitive changes. fMRI scans were performed at week −5 (baseline), week 0 (immediately before rehabilitation) and week 5 (immediately after rehabilitation). The fMRI paradigm was the Paced Auditory Serial Addition Test (PASAT). The cognitive rehabilitation programme was composed of 15 computer-aided drill and practice sessions and five non-computer-aided cognitive stimulation group sessions (over 5 weeks). Strict guidelines ensured comparability of all rehabilitation interventions. Results: Patients had increased brain fMRI activity after rehabilitation in several cerebellar areas when compared with healthy subjects. After rehabilitation, patients had significantly improved their performance on the backward version of the Digit Span Test ( p = 0.007) and on a composite score of neuropsychological outcomes ( p = 0.009). Conclusion: The results of the present study indicate that this cognitive rehabilitation programme increases brain activity in the cerebellum of cognitively impaired patients with MS. The role of fMRI in the assessment of neurorehabilitation schemes warrants further investigation.
CD4+T-bet+, CD4+pSTAT3+ and CD8+T-bet+ T cells accumulate in peripheral blood during NZB treatment
Authors: Frisullo Giovanni , Iorio Raffaele , Plantone Domenico , Marti Alessandro , Nociti Viviana , Patanella Agata Katia , Batocchi Anna Paola 
Published: December 2010

Circulating T cells and monocytes expressing T-bet, pSTAT1 and pSTAT3 increase in relapsing–remitting multiple sclerosis (RRMS) during relapse. Natalizumab (NZB) is an effective drug in RRMS, but exacerbation of the disease after its discontinuation has been described in some patients. The aim of this research was to study the effect of NZB treatment on circulating lymphomonocyte subpopulations expressing T-bet, pSTAT1, pSTAT3 and CD4+CD25+Foxp3+ regulatory T cells. Flow cytometry was used to evaluate the percentages of circulating CD4+ and CD8+ T cells, CD14+ monocytes and B cells expressing T-bet, pSTAT1, and pSTAT3, and CD4+CD25+Foxp3+ regulatory T cells from RRMS patients before and after 6–12 NZB infusions. In NZB-treated RRMS patients, the percentages of CD4+pSTAT1+ and CD8+pSTAT1+ T cells, CD14+pSTAT1+ monocytes, CD4+T-bet+, CD8+T-bet+ and CD4+pSTAT3+ T cells and CD14+pSTAT3+ monocytes increased after 12 drug infusions and were similar to those observed in untreated relapsing RRMS patients. Otherwise in vitro NZB exposure of peripheral blood mononuclear cells from untreated RRMS patients and controls had no effect. It was concluded that NZB treatment determines an accumulation of CD4+pSTAT1+, CD8+pSTAT1+, CD4+T-bet+, CD8+T-bet+ and CD4+STAT3+ T cells in peripheral blood that may account for the exacerbation of the disease observed in some patients after the discontinuation of the drug.
HIF1α synergizes with glucocorticoids to promote BFU-E progenitor self-renewal
Authors: Flygare Johan , Estrada Violeta Rayon , Shin Chanseok , Gupta Sumeet , Lodish Harvey F. 
Published: December 2010

AbstractWith the aim of finding small molecules that stimulate erythropoiesis earlier than erythropoietin and that enhance erythroid colony-forming unit (CFU-E) production, we studied the mechanism by which glucocorticoids increase CFU-E formation. Using erythroid burst-forming unit (BFU-E) and CFU-E progenitors purified by a new technique, we demonstrate that glucocorticoids stimulate the earliest (BFU-E) progenitors to undergo limited self-renewal, which increases formation of CFU-E cells > 20-fold. Interestingly, glucocorticoids induce expression of genes in BFU-E cells that contain promoter regions highly enriched for hypoxia-induced factor 1α (HIF1α) binding sites. This suggests activation of HIF1α may enhance or replace the effect of glucocorticoids on BFU-E self-renewal. Indeed, HIF1α activation by a prolyl hydroxylase inhibitor (PHI) synergizes with glucocorticoids and enhances production of CFU-Es 170-fold. Because PHIs are able to increase erythroblast production at very low concentrations of glucocorticoids, PHI-induced stimulation of BFU-E progenitors thus represents a conceptually new therapeutic window for treating erythropoietin-resistant anemia.
Caenorhabditis elegans chromosome arms are anchored to the nuclear membrane via discontinuous association with LEM-2
Authors: Ikegami Kohta , Egelhofer Thea A , Strome Susan , Lieb Jason D 
Published: December 2010

Abstract
Background
Although Caenorhabditis elegans was the first multicellular organism with a completely sequenced genome, how this genome is arranged within the nucleus is not known.

Results
We determined the genomic regions associated with the nuclear transmembrane protein LEM-2 in mixed-stage C. elegans embryos via chromatin immunoprecipitation. Large regions of several megabases on the arms of each autosome were associated with LEM-2. The center of each autosome was mostly free of such interactions, suggesting that they are largely looped out from the nuclear membrane. Only the left end of the X chromosome was associated with the nuclear membrane. At a finer scale, the large membrane-associated domains consisted of smaller subdomains of LEM-2 associations. These subdomains were characterized by high repeat density, low gene density, high levels of H3K27 trimethylation, and silent genes. The subdomains were punctuated by gaps harboring highly active genes. A chromosome arm translocated to a chromosome center retained its association with LEM-2, although there was a slight decrease in association near the fusion point.

Conclusions
Local DNA or chromatin properties are the main determinant of interaction with the nuclear membrane, with position along the chromosome making a minor contribution. Genes in small gaps between LEM-2 associated regions tend to be highly expressed, suggesting that these small gaps are especially amenable to highly efficient transcription. Although our data are derived from an amalgamation of cell types in mixed-stage embryos, the results suggest a model for the spatial arrangement of C. elegans chromosomes within the nucleus.
Molecular population genetics and selection in the glycolytic pathway
Authors: Eanes Walter F. 
Published: December 2010

SummaryIn this review, I discuss the evidence for differential natural selection acting across enzymes in the glycolytic pathway in Drosophila. Across the genome, genes evolve at very different rates and possess markedly varying levels of molecular polymorphism, codon bias and expression variation. Discovering the underlying causes of this variation has been a challenge in evolutionary biology. It has been proposed that both the intrinsic properties of enzymes and their pathway position have direct effects on their molecular evolution, and with the genomic era the study of adaptation has been taken to the level of pathways and networks of genes and their products. Of special interest have been the energy-producing pathways. Using both population genetic and experimental approaches, our laboratory has been engaged in a study of molecular variation across the glycolytic pathway in Drosophila melanogaster and its close relatives. We have observed a pervasive pattern in which genes at the top of the pathway, especially around the intersection at glucose 6-phosphate, show evidence for both contemporary selection, in the form of latitudinal allele clines, and inter-specific selection, in the form of elevated levels of amino acid substitutions between species. To further explore this question, future work will require corroboration in other species, expansion into tangential pathways, and experimental work to better characterize metabolic control through the pathway and to examine the pleiotropic effects of these genes on other traits and fitness components.
The making of a photosynthetic animal
Authors: Rumpho Mary E. , Pelletreau Karen N. , Moustafa Ahmed , Bhattacharya Debashish 
Published: December 2010

SummarySymbiotic animals containing green photobionts challenge the common perception that only plants are capable of capturing the sun's rays and converting them into biological energy through photoautotrophic CO2 fixation (photosynthesis). ‘Solar-powered’ sacoglossan molluscs, or sea slugs, have taken this type of symbiotic association one step further by solely harboring the photosynthetic organelle, the plastid (=chloroplast). One such sea slug, Elysia chlorotica, lives as a ‘plant’ when provided with only light and air as a result of acquiring plastids during feeding on its algal prey Vaucheria litorea. The captured plastids (kleptoplasts) are retained intracellularly in cells lining the digestive diverticula of the sea slug, a phenomenon sometimes referred to as kleptoplasty. Photosynthesis by the plastids provides E. chlorotica with energy and fixed carbon for its entire lifespan of ∼10 months. The plastids are not transmitted vertically (i.e. are absent in eggs) and do not undergo division in the sea slug. However, de novo protein synthesis continues, including plastid- and nuclear-encoded plastid-targeted proteins, despite the apparent absence of algal nuclei. Here we discuss current data and provide hypotheses to explain how long-term photosynthetic activity is maintained by the kleptoplasts. This fascinating ‘green animal’ provides a unique model to study the evolution of photosynthesis in a multicellular heterotrophic organism.